Dr H Rogier van Doorn

Research Area: Microbiology
Scientific Themes: Tropical Medicine & Global Health and Immunology & Infectious Disease
Keywords: Hand Foot and Mouth Disease, Enteroviruses, Virus discovery, Encephalitis and Outbreak Research
Web Links:

The Oxford University Clinical Research Unit-Vietnam (OUCRU) was established in Ho Chi Minh City in 1991. It is hosted by the Hospital for Tropical Diseases (HTD), originally founded in 1862. HTD is the referral hospital for infectious diseases for all of southern Viet Nam. 

Our strategic aim is to have a positive and significant impact on global health and, in particular, the prevention, diagnosis and treatment of infectious diseases. This is being achieved via an integrated long-term research programme, contributions to training, the scientific literature, national and international meetings and membership of national and international committees. OUCRU is one of five Wellcome Programmes.

The Oxford University Clinical Research Unit, Hanoi (OUCRU) was established in 2006 and is hosted by the National Hospital of Tropical Diseases (NHTD). NHTD is a tertiary care centre for infectious diseases in northern Viet Nam and unlike most hospitals is a specialist hospital under the direct supervision of the Ministry of Health. OUCRU’s research programme puts clinical and public health research at the centre of its integrated clinical science programme.

In addition to NHTD, OUCRU Hanoi works closely with many hospitals across northern Viet Nam and, in particular with the National Institute for Hygiene and Epidemiology. OUCRU Hanoi has state-of-the-art diagnostic and research capabilities which improve the prevention, diagnosis and treatment of major infectious diseases. 

The research programme at OUCRU Hanoi focuses on clinical and epidemiological aspects of respiratory infections (both bacterial and viral), antimicrobial resistance, zoonosis (including Streptococcus suis) and dengue. Furthermore, OUCRU Hanoi is studying zoonotic infections in collaboration with Hanoi Medical University as part of the VIZIONS project. Through NHTD OUCRU Hanoi has also been involved in consultations with the Ministry of Health on antibiotic treatment guidelines, management of avian influenza and Streptococcus suis, and other public health issues.

The importance of OUCRU Hanoi in Viet Nam

OUCRU Hanoi is close to all the key national institutes in Vietnam (see partners/collaborators) and the Ministry of Health. These relations ensure that OUCRU research findings also find their way into policies. Our research in the area of antibiotic resistance supported the development of a National Action Plan on Antibiotic Resistance that was signed by the Minister of Health mid 2013.

Our research locations

OUCRU Hanoi is based at the National Hospital of Tropical Diseases and we also have research offices and laboratory capacity at the National Institute of Hygiene and Epidemiology (NIHE), National Hospital of Paediatrics and Hanoi Medical University (HMU). With NIHE we now conduct influenza household transmission studies for over 8 years in Ha Nam. With HMU we conduct community based studies in Ba Vi and Dong Da.

OUCRU Ha Noi Ph D / D Phil STUDENTS

  • Huong Vu Thi Lan, Public Health Masters. Huong works on the burden of Streptococcus suis infections in Vietnam and risky food behaviour.
  • Do thi Thuy Nga, Pharmacist. Nga works on strategies to reduce antibiotic use in Vietnam.
  • Vu Dinh Phu, clinician and head of ICU NHTD. Dr Phu works on hospital acquired infections on ICUs in Vietnam
  • Tran Thi Sinh, Microbiologist at NHP. Sinh works on improving laboratory diagnosis of pediatric tuberculosis.
  • Nguyen thi Diep, Veterinarian at National Center for Veterinary Diagnosis. Diep works on poultry antibody landscapes of avian influenza.

Our collaborations/partnerships

  • National Hospital of Tropical Diseases
  • National Institute of Hygiene and Epidemiology
  • Hanoi Medical University
  • National Hospital of Pediatrics
  • National Center for Veterinary Diagnosis
  • National Lung hospital

Key milestones

We recently completed a national program (VINARES) to assess hospital acquired infections, antibiotic use and antibiotic resistance in 16 hospitals across Vietnam. We had a closing meeting in October 2013 with 120 international participants in Hanoi.

OUCRU Ha Noi has brought together NICE International and the Vietnamese Ministry of Health to establish a working process to design and implement evidence-based guidelines for AMR

OUCRU Ha Noi has obtained funding from the Fleming Fund UK and a mandate from the Vietnamese Ministry of Health to establish a National Reference Laboratory and Surveillance Network for Antimicrobial Resistance with the National Hospital of Tropical Disease

We are running one of the longest influenza household cohorts worldwide in Ha Nam, Vietnam. This cohort has been ongoing for over 8 years leading to new knowledge in the area of influenza transmission and immunology.

Name Department Institution Country
Professor Laurent Kaiser University of Geneva Switzerland
Professor Menno de Jong Academic Medical Centre, University of Amsterdam Netherlands
Professor Bryan Grenfell University of Princeton United States
Professor Edward Holmes University of Sydney Australia
Paul Kellam Wellcome Trust Sanger Institute United Kingdom
Phu VD, Nadjm B, Duy NHA, Co DX, Mai NTH, Trinh DT, Campbell J, Khiem DP, Quang TN, Loan HT et al. 2017. Ventilator-associated respiratory infection in a resource-restricted setting: impact and etiology. J Intensive Care, 5 pp. 69. | Show Abstract | Read more

Background: Ventilator-associated respiratory infection (VARI) is a significant problem in resource-restricted intensive care units (ICUs), but differences in casemix and etiology means VARI in resource-restricted ICUs may be different from that found in resource-rich units. Data from these settings are vital to plan preventative interventions and assess their cost-effectiveness, but few are available. Methods: We conducted a prospective observational study in four Vietnamese ICUs to assess the incidence and impact of VARI. Patients ≥ 16 years old and expected to be mechanically ventilated > 48 h were enrolled in the study and followed daily for 28 days following ICU admission. Results: Four hundred fifty eligible patients were enrolled over 24 months, and after exclusions, 374 patients' data were analyzed. A total of 92/374 cases of VARI (21.7/1000 ventilator days) were diagnosed; 37 (9.9%) of these met ventilator-associated pneumonia (VAP) criteria (8.7/1000 ventilator days). Patients with any VARI, VAP, or VARI without VAP experienced increased hospital and ICU stay, ICU cost, and antibiotic use (p < 0.01 for all). This was also true for all VARI (p < 0.01 for all) with/without tetanus. There was no increased risk of in-hospital death in patients with VARI compared to those without (VAP HR 1.58, 95% CI 0.75-3.33, p = 0.23; VARI without VAP HR 0.40, 95% CI 0.14-1.17, p = 0.09). In patients with positive endotracheal aspirate cultures, most VARI was caused by Gram-negative organisms; the most frequent were Acinetobacter baumannii (32/73, 43.8%) Klebsiella pneumoniae (26/73, 35.6%), and Pseudomonas aeruginosa (24/73, 32.9%). 40/68 (58.8%) patients with positive cultures for these had carbapenem-resistant isolates. Patients with carbapenem-resistant VARI had significantly greater ICU costs than patients with carbapenem-susceptible isolates (6053 USD (IQR 3806-7824) vs 3131 USD (IQR 2108-7551), p = 0.04) and after correction for adequacy of initial antibiotics and APACHE II score, showed a trend towards increased risk of in-hospital death (HR 2.82, 95% CI 0.75-6.75, p = 0.15). Conclusions: VARI in a resource-restricted setting has limited impact on mortality, but shows significant association with increased patient costs, length of stay, and antibiotic use, particularly when caused by carbapenem-resistant bacteria. Evidence-based interventions to reduce VARI in these settings are urgently needed.

Turner P, Suy K, Tan LV, Sar P, Miliya T, Hong NTT, Hang VTT, Ny NTH, Soeng S, Day NPJ et al. 2017. The aetiologies of central nervous system infections in hospitalised Cambodian children. BMC Infect Dis, 17 (1), pp. 806. | Show Abstract | Read more

BACKGROUND: Central nervous system (CNS) infections are an important cause of childhood morbidity and mortality. The aetiologies of these potentially vaccine-preventable infections have not been well established in Cambodia. METHODS: We did a one year prospective study of children hospitalised with suspected CNS infection at Angkor Hospital for Children, Siem Reap. Cerebrospinal fluid specimens (CSF) samples underwent culture, multiplex PCR and serological analysis to identify a range of bacterial and viral pathogens. Viral metagenomics was performed on a subset of pathogen negative specimens. RESULTS: Between 1st October 2014 and 30th September 2015, 284 analysable patients were enrolled. The median patient age was 2.6 years; 62.0% were aged <5 years. CSF white blood cell count was ≥10 cells/μL in 116/272 (42.6%) cases. CNS infection was microbiologically confirmed in 55 children (19.3%). Enteroviruses (21/55), Japanese encephalitis virus (17/55), and Streptococcus pneumoniae (7/55) accounted for 45 (81.8%) of all pathogens identified. Of the pathogens detected, 74.5% (41/55) were viruses and 23.6% (13/55) were bacteria. The majority of patients were treated with ceftriaxone empirically. The case fatality rate was 2.5%. CONCLUSIONS: Enteroviruses, JEV and S. pneumoniae are the most frequently detected causes of CNS infection in hospitalised Cambodian children.

van Doorn HR. 2017. Emerging infectious diseases Medicine, 45 (12), pp. 798-801. | Show Abstract | Read more

© 2017 The spectrum of human pathogens and the infectious diseases they cause is continuously changing through evolution, selection and changes in the way human populations interact with their environment and each other. New human pathogens often emerge or re-emerge from an animal reservoir, emphasizing the central role that non-human reservoirs play in human infectious diseases. Pathogens can also re-emerge with new characteristics, such as multidrug resistance, or in different places, such as Ebola virus in West Africa in 2013 and Zika virus in Brazil in 2015, to cause new epidemics. Most human pathogens have a history of evolution in which they first emerge and cause epidemics, become unstably adapted, re-emerge periodically and then – without intervention – eventually become endemic, with the potential for future outbreaks.

Kinh NV, Wertheim HFL, Thwaites GE, Khue LN, Thai CH, Khoa NT, Thi Bich Ha N, Trung NV, Crook D, van Doorn HR. 2017. Developing an antimicrobial resistance reference laboratory and surveillance programme in Vietnam. Lancet Glob Health, 5 (12), pp. e1186-e1187. | Read more

Diep NTN, Thai PQ, Trang NNM, Jäger J, Fox A, Horby P, Phuong HVM, Anh DD, Mai LETQ, VAN Doorn HR, Nadjm B. 2017. Strongyloides stercoralis seroprevalence in Vietnam. Epidemiol Infect, 145 (15), pp. 3214-3218. | Show Abstract | Read more

Strongyloidiasis is a neglected tropical disease caused by the roundworm Strongyloides stercoralis affecting 30-100 million people worldwide. Many Southeast-Asian countries report a high prevalence of S. stercoralis infection, but there are little data from Vietnam. Here, we evaluated the seroprevalence of S. stercoralis related to geography, sex and age in Vietnam through serological testing of anonymized sera. Sera (n = 1710, 1340 adults and 270 children) from an anonymized age-stratified serum bank from four regions in Vietnam between 2012 and 2013 were tested using a commercial Strongyloides ratti immunoglobulin G ELISA. Seroreactivity was found in 29·1% (390/1340) of adults and 5·5% (15/270) of children. Male adults were more frequently seroreactive than females (33·3% vs. 24·9%, P = 0·001). The rural central highlands had the highest seroprevalence (42·4% of adults). Seroreactivity in the other regions was 29·9% (Hue) and 26·0% and 18·2% in the large urban centres of Hanoi and Ho Chi Minh City, respectively. We conclude that seroprevalence of S. stercoralis was high in the Vietnamese adult population, especially in rural areas.

Huong VTL, Long HB, Kinh NV, Ngan TTD, Dung VTV, Nadjm B, van Doorn HR, Hoa NT, Horby P, Wertheim HFL. 2017. Long-term outcomes of patients with Streptococcus suis infection in Viet Nam: A case-control study. J Infect, | Show Abstract | Read more

OBJECTIVES: Streptococcus suis is a zoonotic cause of severe meningitis and sepsis in humans. We aimed to assess the long-term outcomes in patients who survived S. suis infection, in particular the progress and impact of vestibulocochlear sequelae. METHODS: This case-control study evaluated outcomes of S. suis infection at discharge and 3 and 9 months post-discharge for 47 prospectively enrolled cases and at 11-34 months for 31 retrospectively enrolled cases. Outcomes in patients were compared to 270 controls matched for age, sex and residency. RESULTS: The prevalence ratio (PR) of moderate-to-complete hearing loss was 5.0(95%CI 3.6-7.1) in cases at discharge, 3.7(2.5-5.4) at 3 months, 3.2(2.2-4.7) at 9 months, and 3.1(2.1-4.4) in retrospective cases compared to controls. Hearing improvement occurred mostly within the first 3 months with a change in hearing level of 11.1%(95%CI 7.0-15.1%) compared to discharge. The PR of vestibular dysfunction was 2.4(95%CI 1.7-3.3) at discharge, 2.2(1.4-3.1) at 3 months, 1.8(1.1-2.5) at 9 months, and 1.8(1.1-2.6) for retrospective cases compared to controls. Cases also indicated more problems with mobility, self-care and usual activities. CONCLUSIONS: Both hearing and vestibular impairment were common and persist in cases. Appropriate patient management strategies are needed to reduce the incidence and impact of these sequelae.

Do LAH, Pellet J, van Doorn HR, Tran AT, Nguyen BH, Tran TTL, Tran QH, Vo QB, Tran Dac NA, Trinh HN et al. 2017. Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection. J Infect Dis, 217 (1), pp. 134-146. | Show Abstract | Read more

Background: Most insights into the cascade of immune events after acute respiratory syncytial virus (RSV) infection have been obtained from animal experiments or in vitro models. Methods: In this study, we investigated host gene expression profiles in nasopharyngeal (NP) swabs and whole blood samples during natural RSV and rhinovirus (hRV) infection (acute versus early recovery phase) in 83 hospitalized patients <2 years old with lower respiratory tract infections. Results: Respiratory syncytial virus infection induced strong and persistent innate immune responses including interferon signaling and pathways related to chemokine/cytokine signaling in both compartments. Interferon-α/β, NOTCH1 signaling pathways and potential biomarkers HIST1H4E, IL7R, ISG15 in NP samples, or BCL6, HIST2H2AC, CCNA1 in blood are leading pathways and hub genes that were associated with both RSV load and severity. The observed RSV-induced gene expression patterns did not differ significantly in NP swab and blood specimens. In contrast, hRV infection did not as strongly induce expression of innate immunity pathways, and significant differences were observed between NP swab and blood specimens. Conclusions: We conclude that RSV induced strong and persistent innate immune responses and that RSV severity may be related to development of T follicular helper cells and antiviral inflammatory sequelae derived from high activation of BCL6.

Thao NTT, Donato C, Trang VTH, Kien NT, Trang PMMT, Khanh TQ, Nguyet DT, Sessions OM, Cuong HQ, Lan PT et al. 2017. Evolution and Spatiotemporal Dynamics of Enterovirus A71 Subgenogroups in Vietnam. J Infect Dis, 216 (11), pp. 1371-1379. | Show Abstract | Read more

Background: Enterovirus A71 (EV-A71) is the major cause of severe hand, foot, and mouth disease and viral encephalitis in children across the Asia-Pacific region, including in Vietnam, which has experienced a high burden of disease in recent years. Multiple subgenogroups (C1, C4, C5, and B5) concurrently circulate in the region with a large variation in epidemic severity. The relative differences in their evolution and epidemiology were examined within Vietnam and globally. Methods: A total of 752 VP1 gene sequences were analyzed (413 generated in this study combined with 339 obtained from GenBank), collected from patients in 36 provinces in Vietnam during 2003-2013, along with epidemiological metadata. Globally representative VP1 gene datasets of subgenogroups were used to coestimate time-resolved phylogenies and relative genetic diversity to infer virus origins and regional transmission network. Results: Despite frequent virus migration between countries, the highest genetic diversity of individual subgenogroups was maintained independently for several years in specific Asian countries representing genogroup-specific sources of EV-A71 diversity. Conclusion: This study highlights a persistent transmission network of EV-A71, with specific Asian countries seeding other countries in the region and beyond, emphasizing the need for improved EV-A71 surveillance and detailed genetic and antigenic characterization.

Hoa LNM, Tuan NA, My PH, Huong TTK, Chi NTY, Hau Thu TT, Carrique-Mas J, Duong MT, Tho ND, Hoang ND et al. 2017. Assessing evidence for avian-to-human transmission of influenza A/H9N2 virus in rural farming communities in northern Vietnam. J Gen Virol, 98 (8), pp. 2011-2016. | Show Abstract | Read more

Rural farming communities in northern Vietnam do not routinely practice vaccination for influenza A viruses (IAV) for either humans or poultry, which enables us to study transmission intensity via seroepidemiology. Using samples from a longitudinal cohort of farming households, we determined the number of symptomatic and asymptomatic human infections for seasonal IAV and avian A/H9 over 2 years. As expected, we detected virologically confirmed acute cases of seasonal IAV in humans, as well as large numbers of subclinical seroconversions to A/H1pdm [55/265 (21 %)], A/H3 [95/265 (36 %)] and A/H9 [24/265 (9 %)]. Five of the A/H9 human seroconverters likely represented true infections rather than heterosubtypic immunity, because the individuals seroconverted solely to A/H9. Among co-located poultry, we found significantly higher seroprevalance for A/H5 compared to A/H9 in both chickens and ducks [for northern study sites overall, 337/1105 (30.5 %) seropositive for A/H5 and 123/1105 (11.1 %) seropositive for A/H9].

Dat VQ, Vu HN, Nguyen The H, Nguyen HT, Hoang LB, Vu Tien Viet D, Bui CL, Van Nguyen K, Nguyen TV, Trinh DT et al. 2017. Bacterial bloodstream infections in a tertiary infectious diseases hospital in Northern Vietnam: aetiology, drug resistance, and treatment outcome. BMC Infect Dis, 17 (1), pp. 493. | Show Abstract | Read more

BACKGROUND: Bloodstream infections (BSIs) are associated with high morbidity and mortality worldwide. However their aetiology, antimicrobial susceptibilities and associated outcomes differ between developed and developing countries. Systematic data from Vietnam are scarce. Here we present aetiologic data on BSI in adults admitted to a large tertiary referral hospital for infectious diseases in Hanoi, Vietnam. METHODS: A retrospective study was conducted at the National Hospital for Tropical Diseases between January 2011 and December 2013. Cases of BSI were determined from records in the microbiology department. Case records were obtained where possible and clinical findings, treatment and outcome were recorded. BSI were classified as community acquired if the blood sample was drawn ≤48 h after hospitalization or hospital acquired if >48 h. RESULTS: A total of 738 patients with BSI were included for microbiological analysis. The predominant pathogens were: Klebsiella pneumoniae (17.5%), Escherichia coli (17.3%), Staphylococcus aureus (14.9%), Stenotrophomonas maltophilia (9.6%) and Streptococcus suis (7.6%). The overall proportion of extended spectrum beta-lactamase (ESBL) production among Enterobacteriaceae was 25.1% (67/267 isolates) and of methicillin-resistance in S. aureus (MRSA) 37% (40/108). Clinical data was retrieved for 477 (64.6%) patients; median age was 48 years (IQR 36-60) with 27.7% female. The overall case fatality rate was 28.9% and the highest case fatality was associated with Enterobacteriaceae BSI (34.7%) which accounted for 61.6% of all BSI fatalities. CONCLUSIONS: Enterobacteriaceae (predominantly K. pneumoniae and E. coli) are the most common cause of both community and hospital acquired bloodstream infections in a tertiary referral clinic in northern Vietnam.

Ny NTH, Anh NT, Hang VTT, Nguyet LA, Thanh TT, Ha DQ, Minh NNQ, Ha DLA, McBride A, Tuan HM et al. 2017. Enterovirus D68 in Viet Nam (2009-2015). Wellcome Open Res, 2 pp. 41. | Show Abstract | Read more

BACKGROUND: Since 1962, enterovirus D68 (EV-D68) has been implicated in multiple outbreaks and sporadic cases of respiratory infection worldwide, but especially in the USA and Europe with an increasing frequency between 2010 and 2014. We describe the detection, associated clinical features and molecular characterization of EV-D68 in central and southern Viet Nam between 2009 and 2015. METHODS: Enterovirus/rhinovirus PCR positive respiratory or CSF samples taken from children and adults with respiratory/central nervous system infections in Viet Nam were tested by an EV-D68 specific PCR. The included samples were derived from 3 different observational studies conducted at referral hospitals across central and southern Viet Nam between 2009 and 2015. Whole-genome sequencing was carried out using a MiSeq based approach. Phylogenetic reconstruction and estimation of evolutionary rate and recombination were carried out in BEAST and Recombination Detection Program, respectively. RESULTS: EV-D68 was detected in 21/625 (3.4%) enterovirus/rhinovirus PCR positive respiratory samples but in none of the 15 CSF. All the EV-D68 patients were young children (age range: 11.8 - 24.5 months) and had moderate respiratory infections. Phylogenetic analysis suggested that the Vietnamese sequences clustered with those from Asian countries, of which 9 fell in the B1 clade, and the remaining sequence was identified within the A2 clade. One intra sub-clade recombination event was detected, representing the second reported recombination within EV-D68. The evolutionary rate of EV-D68 was estimated to be 5.12E -3 substitutions/site/year. Phylogenetic analysis indicated that the virus was imported into Viet Nam in 2008. CONCLUSIONS: We have demonstrated for the first time EV-D68 has been circulating at low levels in Viet Nam since 2008, associated with moderate acute respiratory infection in children. EV-D68 in Viet Nam is most closely related to Asian viruses, and clusters separately from recent US and European viruses that were suggested to be associated with acute flaccid paralysis.

Trung NV, Hoi LT, Thuong NTH, Toan TK, Huong TTK, Hoa TM, Fox A, Kinh NV, van Doorn HR, Wertheim HFL et al. 2017. Seroprevalence of Scrub Typhus, Typhus, and Spotted Fever Among Rural and Urban Populations of Northern Vietnam. Am J Trop Med Hyg, 96 (5), pp. 1084-1087. | Show Abstract | Read more

AbstractRickettsial infections are recognized as important causes of fever throughout southeast Asia. Herein, we determined the seroprevalence to rickettsioses within rural and urban populations of northern Vietnam. Prevalence of individuals with evidence of prior rickettsial infections (IgG positive) was surprisingly low, with 9.14% (83/908) testing positive to the three major rickettsial serogroups thought to circulate in the region. Prevalence of typhus group rickettsiae (TG)-specific antibodies (6.5%, 58/908) was significantly greater than scrub typhus group orientiae (STG)- or spotted fever group rickettsiae (SFG)-specific antibodies (P < 0.05). The majority of TG seropositives were observed among urban rather than rural residents (P < 0.05). In contrast, overall antibody prevalence to STG and SFG were both very low (1.1%, 10/908 for STG; 1.7%, 15/908 for SFG), with no significant differences between rural and urban residents. These results provide data on baseline population characteristics that may help inform development of Rickettsia serological testing criteria in future clinical studies.

Anh NT, Thanh TT, Van HMT, Ngoc NM, Nhu LNT, Thanh LTM, Qui PT, Khanh TH, Nhan LNT, Viet HL et al. 2017. A52 Development and evaluation of a viral-specific random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot, and mouth disease pathogens. Virus Evol, 3 (Suppl 1), | Read more

Sudarmono P, Aman AT, Arif M, Syarif AK, Kosasih H, Karyana M, Chotpitayasunondh T, Vandepitte WP, Boonyasiri A, Lapphra K et al. 2017. Causes and outcomes of sepsis in southeast Asia: a multinational multicentre cross-sectional study LANCET GLOBAL HEALTH, 5 (2), pp. E157-E167.

Tran DN, Tran HH, Matsui M, Suzuki M, Suzuki S, Shibayama K, Pham TD, Van Phuong TT, Dang DA, Trinh HS et al. 2017. Emergence of New Delhi metallo-beta-lactamase 1 and other carbapenemase-producing Acinetobacter calcoaceticus-baumannii complex among patients in hospitals in Ha Noi, Viet Nam. Eur J Clin Microbiol Infect Dis, 36 (2), pp. 219-225. | Show Abstract | Read more

Acinetobacter baumannii is an important cause of multidrug-resistant hospital acquired infections in the world. Here, we investigate the presence of NDM-1 and other carbapenemases among carbapenem-resistant A. baumannii isolated between August 2010 and December 2014 from three large hospitals in Hanoi, Vietnam. We identified 23/582 isolates (4 %) (11 from hospital A, five from hospital B, and seven from hospital C) that were NDM-1 positive, and among them 18 carried additional carbapenemase genes, including seven isolates carrying NDM-1, IMP-1, and OXA-58 with high MICs for carbapenems. Genotyping indicated that NDM-1 carrying A. baumannii have expanded clonally in these hospitals. Five new STs (ST1135, ST1136, ST1137, ST1138, and ST1139) were identified. One isolate carried NDM-1 on a plasmid belonging to the N-repA replicon type; no NDM-1-positive plasmids were identified in the other isolates. We have shown the extent of the carbapenem resistance and the local clonal spread of A. baumannii carrying NDM-1 in these hospitals; coexistence of NDM-1 and IMP-1 is reported for the first time from Vietnam here, and this will further seriously limit future therapeutic options.

Thi Ty Hang V, Thi Han Ny N, My Phuc T, Thi Thanh Tam P, Thao Huong D, Dang Trung Nghia H, Tran Anh Vu N, Thi Hong Phuong P, Van Xang N, Dong N et al. 2017. Evaluation of the Luminex xTAG Respiratory Viral Panel FAST v2 assay for detection of multiple respiratory viral pathogens in nasal and throat swabs in Vietnam Wellcome Open Research, 2 pp. 80-80. | Read more

Thanh TT, Van HMT, Hong NTT, Nhu LNT, Anh NT, Tuan HM, Hien HV, Tuong NM, Kien TT, Khanh TH et al. 2016. The first genome sequences of human bocaviruses from Vietnam. Wellcome Open Res, 1 pp. 16. | Show Abstract | Read more

As part of an ongoing effort to generate complete genome sequences of hand, foot and mouth disease-causing enteroviruses directly from clinical specimens, two complete coding sequences and two partial genomic sequences of human bocavirus 1 (n=3) and 2 (n=1) were co-amplified and sequenced, representing the first genome sequences of human bocaviruses from Vietnam. The sequences may aid future study aiming at understanding the evolution of the pathogen.

Li R, van Doorn HR, Wertheim HFL, Khue LN, Ha NTB, Dat VQ, Hanh CT, Nga DTT, Trang NNM, Nadjm B et al. 2016. Combating antimicrobial resistance: quality standards for prescribing for respiratory infections in Vietnam. Lancet Glob Health, 4 (11), pp. e789. | Read more

Maude RR, Ghose A, Samad R, de Jong HK, Fukushima M, Wijedoru L, Hassan MU, Hossain MA, Karim MR, Sayeed AA et al. 2016. A prospective study of the importance of enteric fever as a cause of non-malarial febrile illness in patients admitted to Chittagong Medical College Hospital, Bangladesh. BMC Infect Dis, 16 (1), pp. 567. | Show Abstract | Read more

BACKGROUND: Fever is a common cause of hospital admission in Bangladesh but causative agents, other than malaria, are not routinely investigated. Enteric fever is thought to be common. METHODS: Adults and children admitted to Chittagong Medical College Hospital with a temperature of ≥38.0 °C were investigated using a blood smear for malaria, a blood culture, real-time PCR to detect Salmonella Typhi, S. Paratyphi A and other pathogens in blood and CSF and an NS1 antigen dengue ELISA. RESULTS: We enrolled 300 febrile patients with a negative malaria smear between January and June 2012: 156 children (aged ≤15 years) and 144 adults with a median (interquartile range) age of 13 (5-31) years and median (IQR) illness duration before admission of five (2-8) days. Clinical enteric fever was diagnosed in 52 patients (17.3 %), lower respiratory tract infection in 48 (16.0 %), non-specific febrile illness in 48 (16.0 %), a CNS infection in 37 patients (12.3 %), urinary sepsis in 23 patients (7.7 %), an upper respiratory tract infection in 21 patients (7.0 %), and diarrhea or dysentery in 21 patients (7.0 %). Malaria was still suspected in seven patients despite a negative microscopy test. S. Typhi was detected in blood by culture or PCR in 34 (11.3 %) of patients. Of note Rickettsia typhi and Orientia tsutsugamushi were detected by PCR in two and one patient respectively. Twenty-nine (9 %) patients died during their hospital admission (15/160 (9.4 %) of children and 14/144 (9.7 %) adults). Two of 52 (3.8 %) patients with enteric fever, 5/48 (10.4 %) patients with lower respiratory tract infections, and 12/37 (32.4 %) patients with CNS infection died. CONCLUSION: Enteric fever was confirmed in 11.3 % of patients admitted to this hospital in Bangladesh with non-malaria fever. Lower respiratory tract and CNS infections were also common. CNS infections in this location merit more detailed study due to the high mortality.

Do NTT, Ta NTD, Tran NTH, Than HM, Vu BTN, Hoang LB, van Doorn HR, Vu DTV, Cals JWL, Chandna A et al. 2016. Point-of-care C-reactive protein testing to reduce inappropriate use of antibiotics for non-severe acute respiratory infections in Vietnamese primary health care: a randomised controlled trial. Lancet Glob Health, 4 (9), pp. e633-e641. | Show Abstract | Read more

BACKGROUND: Inappropriate antibiotic use for acute respiratory tract infections is common in primary health care, but distinguishing serious from self-limiting infections is difficult, particularly in low-resource settings. We assessed whether C-reactive protein point-of-care testing can safely reduce antibiotic use in patients with non-severe acute respiratory tract infections in Vietnam. METHOD: We did a multicentre open-label randomised controlled trial in ten primary health-care centres in northern Vietnam. Patients aged 1-65 years with at least one focal and one systemic symptom of acute respiratory tract infection were assigned 1:1 to receive either C-reactive protein point-of-care testing or routine care, following which antibiotic prescribing decisions were made. Patients with severe acute respiratory tract infection were excluded. Enrolled patients were reassessed on day 3, 4, or 5, and on day 14 a structured telephone interview was done blind to the intervention. Randomised assignments were concealed from prescribers and patients but not masked as the test result was used to assist treatment decisions. The primary outcome was antibiotic use within 14 days of follow-up. All analyses were prespecified in the protocol and the statistical analysis plan. All analyses were done on the intention-to-treat population and the analysis of the primary endpoint was repeated in the per-protocol population. This trial is registered under number NCT01918579. FINDINGS: Between March 17, 2014, and July 3, 2015, 2037 patients (1028 children and 1009 adults) were enrolled and randomised. One adult patient withdrew immediately after randomisation. 1017 patients were assigned to receive C-reactive protein point-of-care testing, and 1019 patients were assigned to receive routine care. 115 patients in the C-reactive protein point-of-care group and 72 patients in the routine care group were excluded in the intention-to-treat analysis due to missing primary endpoint. The number of patients who used antibiotics within 14 days was 581 (64%) of 902 patients in the C-reactive protein group versus 738 (78%) of 947 patients in the control group (odds ratio [OR] 0·49, 95% CI 0·40-0·61; p<0·0001). Highly significant differences were seen in both children and adults, with substantial heterogeneity of the intervention effect across the 10 sites (I(2)=84%, 95% CI 66-96). 140 patients in the C-reactive protein group and 137 patients in the routine care group missed the urine test on day 3, 4, or 5. Antibiotic activity in urine on day 3, 4, or 5 was found in 267 (30%) of 877 patients in the C-reactive protein group versus 314 (36%) of 882 patients in the routine treatment group (OR 0·78, 95% CI 0·63-0·95; p=0·015). Time to resolution of symptoms was similar in both groups. Adverse events were rare, with no deaths and a total of 14 hospital admissions (six in the C-reactive protein group and eight in the control group). INTERPRETATION: C-reactive protein point-of-care testing reduced antibiotic use for non-severe acute respiratory tract infection without compromising patients' recovery in primary health care in Vietnam. Health-care providers might have become familiar with the clinical picture of low C-reactive protein, leading to reduction in antibiotic prescribing in both groups, but this would have led to a reduction in observed effect, rather than overestimation. Qualitative analysis is needed to address differences in context in order to implement this strategy to improve rational antibiotic use for patients with acute respiratory infection in low-income and middle-income countries. FUNDING: Wellcome Trust, UK, and Global Antibiotic Resistance Partnership, USA.

Nguyen DNT, Mai LQ, Bryant JE, Hang NLK, Hoa LNM, Nadjm B, Thai PQ, Duong TN, Anh DD, Horby P et al. 2016. Epidemiology and etiology of influenza-like-illness in households in Vietnam; it's not all about the kids! J Clin Virol, 82 pp. 126-132. | Show Abstract | Read more

BACKGROUND: Household studies provide opportunities to understand influenza-like-illness (ILI) transmission, but data from (sub)tropical developing countries are scarce. OBJECTIVE: To determine the viral etiology and epidemiology of ILI in households. STUDY DESIGN: ILI was detected by active case finding amongst a cohort of 263 northern Vietnam households between 2008 and 2013. Health workers collected nose and throat swabs for virus detection by multiplex real-time RT-PCR. RESULTS: ILI was detected at least once in 219 (23.7%) of 945 household members. 271 (62.3%) of 435 nose/throat swabs were positive for at least one of the 15 viruses tested. Six viruses predominated amongst positive swabs: Rhinovirus (28%), Influenza virus (17%), Coronavirus (8%), Enterovirus (5%), Respiratory syncytial virus (3%), Metapneumovirus virus (2.5%) and Parainfluenza virus 3 (1.8%). There was no clear seasonality, but 78% of episodes occurred in Winter/Spring for Influenza compared to 32% for Rhinovirus. Participants, on average, suffered 0.49 ILI, and 0.29 virus-positive ILI episodes, with no significant effects of gender, age, or household size. In contrast to US and Australian community studies, the frequency of ILI decreased as the number of household members aged below 5 years increased (p=0.006). CONCLUSION: The findings indicate the need for tailored ILI control strategies, and for better understanding of how local childcare practices and seasonality may influence transmission and the role of children.

Nguyen AT, Tran TT, Hoang VMT, Nghiem NM, Le NNT, Le TTM, Phan QT, Truong KH, Le NNT, Ho VL et al. 2016. Development and evaluation of a non-ribosomal random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot and mouth disease pathogens. Virol J, 13 (1), pp. 125. | Show Abstract | Read more

BACKGROUND: Hand, foot and mouth disease (HFMD) has become a major public health problem across the Asia-Pacific region, and is commonly caused by enterovirus A71 (EV-A71) and coxsackievirus A6 (CV-A6), CV-A10 and CV-A16. Generating pathogen whole-genome sequences is essential for understanding their evolutionary biology. The frequent replacements among EV serotypes and a limited numbers of available whole-genome sequences hinder the development of overlapping PCRs for whole-genome sequencing. We developed and evaluated a non-ribosomal random PCR (rPCR) and next-generation sequencing based assay for sequence-independent whole-genome amplification and sequencing of HFMD pathogens. A total of 16 EV-A71/CV-A6/CV-A10/CV-A16 PCR positive rectal/throat swabs (Cp values: 20.9-33.3) were used for assay evaluation. RESULTS: Our assay evidently outperformed the conventional rPCR in terms of the total number of EV-A71 reads and the percentage of EV-A71 reads: 2.6 % (1275/50,000 reads) vs. 0.1 % (31/50,000) and 6 % (3008/50,000) vs. 0.9 % (433/50,000) for two samples with Cp values of 30 and 26, respectively. Additionally the assay could generate genome sequences with the percentages of coverage of 94-100 % of 4 different enterovirus serotypes in 73 % of the tested samples, representing the first whole-genome sequences of CV-A6/10/16 from Vietnam, and could assign correctly serotyping results in 100 % of 24 tested specimens. In all but three the obtained consensuses of two replicates from the same sample were 100 % identical, suggesting that our assay is highly reproducible. CONCLUSIONS: In conclusion, we have successfully developed a non-ribosomal rPCR and next-generation sequencing based assay for sensitive detection and direct whole-genome sequencing of HFMD pathogens from clinical samples.

Hoang VMT, Nguyen TA, Tran TT, Ha MT, Do V, Ho V, Nguyen TH, Huu KT, Le N, Vinh CNV et al. 2016. Clinical features and virology of hand foot mouth disease in Southern Vietnam, July 2013 March 2015 INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 45 pp. 20-20. | Read more

Siegrist C, Kaiser L, Tapparel C, van Doorn HR. 2016. Clinical features, cytokine profiles and immune response in children with severe hand foot and mouth disease in Vietnam INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 45 pp. 192-193. | Read more

Nguyen AT, Nghiem N, Tran T, Hoang V, Le N, Phan Q, Le N, Ho V, Do V, Ha T et al. 2016. Development and evaluation of a vral-specific random PCR and next-generation sequencing based assay for detection and sequencing of hand, foot, and mouth disease pathogens INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 45 pp. 187-187. | Read more

Takahashi S, Liao Q, Van Boeckel TP, Xing W, Sun J, Hsiao VY, Metcalf CJE, Chang Z, Liu F, Zhang J et al. 2016. Hand, Foot, and Mouth Disease in China: Modeling Epidemic Dynamics of Enterovirus Serotypes and Implications for Vaccination. PLoS Med, 13 (2), pp. e1001958. | Show Abstract | Read more

BACKGROUND: Hand, foot, and mouth disease (HFMD) is a common childhood illness caused by serotypes of the Enterovirus A species in the genus Enterovirus of the Picornaviridae family. The disease has had a substantial burden throughout East and Southeast Asia over the past 15 y. China reported 9 million cases of HFMD between 2008 and 2013, with the two serotypes Enterovirus A71 (EV-A71) and Coxsackievirus A16 (CV-A16) being responsible for the majority of these cases. Three recent phase 3 clinical trials showed that inactivated monovalent EV-A71 vaccines manufactured in China were highly efficacious against HFMD associated with EV-A71, but offered no protection against HFMD caused by CV-A16. To better inform vaccination policy, we used mathematical models to evaluate the effect of prospective vaccination against EV-A71-associated HFMD and the potential risk of serotype replacement by CV-A16. We also extended the model to address the co-circulation, and implications for vaccination, of additional non-EV-A71, non-CV-A16 serotypes of enterovirus. METHODS AND FINDINGS: Weekly reports of HFMD incidence from 31 provinces in Mainland China from 1 January 2009 to 31 December 2013 were used to fit multi-serotype time series susceptible-infected-recovered (TSIR) epidemic models. We obtained good model fit for the two-serotype TSIR with cross-protection, capturing the seasonality and geographic heterogeneity of province-level transmission, with strong correlation between the observed and simulated epidemic series. The national estimate of the basic reproduction number, R0, weighted by provincial population size, was 26.63 for EV-A71 (interquartile range [IQR]: 23.14, 30.40) and 27.13 for CV-A16 (IQR: 23.15, 31.34), with considerable variation between provinces (however, predictions about the overall impact of vaccination were robust to this variation). EV-A71 incidence was projected to decrease monotonically with higher coverage rates of EV-A71 vaccination. Across provinces, CV-A16 incidence in the post-EV-A71-vaccination period remained either comparable to or only slightly increased from levels prior to vaccination. The duration and strength of cross-protection following infection with EV-A71 or CV-A16 was estimated to be 9.95 wk (95% confidence interval [CI]: 3.31, 23.40) in 68% of the population (95% CI: 37%, 96%). Our predictions are limited by the necessarily short and under-sampled time series and the possible circulation of unidentified serotypes, but, nonetheless, sensitivity analyses indicate that our results are robust in predicting that the vaccine should drastically reduce incidence of EV-A71 without a substantial competitive release of CV-A16. CONCLUSIONS: The ability of our models to capture the observed epidemic cycles suggests that herd immunity is driving the epidemic dynamics caused by the multiple serotypes of enterovirus. Our results predict that the EV-A71 and CV-A16 serotypes provide a temporary immunizing effect against each other. Achieving high coverage rates of EV-A71 vaccination would be necessary to eliminate the ongoing transmission of EV-A71, but serotype replacement by CV-A16 following EV-A71 vaccination is likely to be transient and minor compared to the corresponding reduction in the burden of EV-A71-associated HFMD. Therefore, a mass EV-A71 vaccination program of infants and young children should provide significant benefits in terms of a reduction in overall HFMD burden.

Cuong NV, Truc VNT, Nhung NT, Thanh TT, Chieu TTB, Hieu TQ, Men NT, Mai HH, Chi HT, Boni MF et al. 2016. Highly Pathogenic Avian Influenza Virus A/H5N1 Infection in Vaccinated Meat Duck Flocks in the Mekong Delta of Vietnam. Transbound Emerg Dis, 63 (2), pp. 127-135. | Show Abstract | Read more

We investigated episodes of suspected highly pathogenic avian influenza (HPAI)-like illness among 12 meat duck flocks in two districts in Tien Giang province (Mekong Delta, Vietnam) in November 2013. In total, duck samples from 8 of 12 farms tested positive for HPAI virus subtype A/haemagglutinin 5 and neuraminidase 1 (H5N1) by real-time RT-PCR. Sequencing results confirmed clade of 2.3.2.1.c as the cause of the outbreaks. Most (7/8) laboratory-confirmed positive flocks had been vaccinated with inactivated HPAI H5N1 clade 2.3.4 vaccines <6 days prior to onset of clinical signs. A review of vaccination data in relation to estimated production in the area suggested that vaccination efforts were biased towards larger flocks and that vaccination coverage was low [21.2% ducks vaccinated with two shots (range by district 7.4-34.9%)]. The low-coverage data, the experimental evidence of lack of cross-protection conferred by the currently used vaccines based on clade 2.3.4 together with the short lifespan of meat duck flocks (60-70 days), suggest that vaccination is not likely to be effective as a tool for control of H5N1 infection in meat duck flocks in the area.

Oude Munnink BB, Phan MVT, van der Hoek L, Kellam P, Cotten M. 2016. Genome Sequences of a Novel Vietnamese Bat Bunyavirus Genome Announcements, 4 (6), pp. e01366-16-e01366-16. | Show Abstract | Read more

© 2016 Oude Munnink et al. To document the viral zoonotic risks in Vietnam, fecal samples were systematically collected from a number of mammals in southern Vietnam and subjected to agnostic deep sequencing. We describe here novel Vietnamese bunyavirus sequences detected in bat feces. The complete L and S segments from 14 viruses were determined.

Oude Munnink BB, Phan MVT, Kellam P, Cotten M. 2016. Complete Genome Characterization of Two Wild-Type Measles Viruses from Vietnamese Infants during the 2014 Outbreak Genome Announcements, 4 (2), pp. e00250-16-e00250-16. | Show Abstract | Read more

© 2016 Oude Munnink et al. A large measles virus outbreak occurred across Vietnam in 2014. We identified and obtained complete measles virus genomes in stool samples collected from two diarrheal pediatric patients in Dong Thap Province. These are the first complete genome sequences of circulating measles viruses in Vietnam during the 2014 measles outbreak.

Do LAH, Bryant JE, Tran AT, Nguyen BH, Tran TTL, Tran QH, Vo QB, Tran Dac NA, Trinh HN, Nguyen TTH et al. 2016. Respiratory Syncytial Virus and Other Viral Infections among Children under Two Years Old in Southern Vietnam 2009-2010: Clinical Characteristics and Disease Severity. PLoS One, 11 (8), pp. e0160606. | Show Abstract | Read more

BACKGROUND: Despite a high burden of respiratory syncytial virus (RSV) infections among children, data on demographic and clinical characteristics of RSV are scarce in low and middle income countries. This study aims to describe the viral etiologies, the demographic, epidemiological, and clinical characteristics of children under two years of age who were hospitalized with a lower respiratory tract infections (LRTI), focusing on RSV (prevalence, seasonality, subgroups, viral load) and its association with disease severity. METHODS: A prospective study among children under two years of age, hospitalized with LRTI was conducted in two referral pediatric hospitals in Ho Chi Minh City, Vietnam, from May 2009 to December 2010. Socio-demographic, clinical data and nasopharyngeal swabs were collected on enrolment and discharge. Multiplex real-time RT-PCR (13 viruses) and quantitative RSV RT-PCR were used to identify viral pathogens, RSV load and subgroups. RESULTS: Among 632 cases, 48% were RSV positive. RSV infections occurred at younger age than three other leading viral infections i.e rhinovirus (RV), metapneumovirus (MPV), parainfluenza virus (PIV-3) and were significantly more frequent in the first 6 months of life. Clinical severity score of RSV infection was significantly higher than PIV-3 but not for RV or MPV. In multivariate analysis, RV infection was significantly associated with severity while RSV infection was not. Among RSV infections, neither viral load nor viral co-infections were significantly associated with severity. Young age and having fever at admission were significantly associated with both RSV and LRTI severity. A shift in RSV subgroup predominance was observed during two consecutive rainy seasons but was not associated with severity. CONCLUSION: We report etiologies, the epidemiological and clinical characteristics of LRTI among hospitalized children under two years of age and risk factors of RSV and LRTI severity.

Do LAH, Wilm A, Van Doorn HR, Lam HM, Sim S, Sukumaran R, Tran AT, Nguyen BH, Tran TTL, Tran QH et al. 2015. Direct whole-genome deep-sequencing of human respiratory syncytial virus A and B from Vietnamese children identifies distinct patterns of inter- and intra-host evolution. J Gen Virol, 96 (12), pp. 3470-3483. | Show Abstract | Read more

Human respiratory syncytial virus (RSV) is the major cause of lower respiratory tract infections in children ,2 years of age. Little is known about RSV intra-host genetic diversity over the course of infection or about the immune pressures that drive RSV molecular evolution. We performed whole-genome deep-sequencing on 53 RSV-positive samples (37 RSV subgroup A and 16 RSV subgroup B) collected from the upper airways of hospitalized children in southern Vietnam over two consecutive seasons. RSV A NA1 and RSV B BA9 were the predominant genotypes found in our samples, consistent with other reports on global RSV circulation during the same period. For both RSV A and B, the M gene was the most conserved, confirming its potential as a target for novel therapeutics. The G gene was the most variable and was the only gene under detectable positive selection. Further, positively selected sites inG were found in close proximity to and in some cases overlapped with predicted glycosylation motifs, suggesting that selection on amino acid glycosylation may drive viral genetic diversity. We further identified hotspots and coldspots of intra-host genetic diversity in the RSV genome, some of which may highlight previously unknown regions of functional importance.

Rabaa MA, Tue NT, Phuc TM, Carrique-Mas J, Saylors K, Cotten M, Bryant JE, Nghia HDT, Cuong NV, Pham HA et al. 2015. The Vietnam Initiative on Zoonotic Infections (VIZIONS): A Strategic Approach to Studying Emerging Zoonotic Infectious Diseases. Ecohealth, 12 (4), pp. 726-735. | Show Abstract | Read more

The effect of newly emerging or re-emerging infectious diseases of zoonotic origin in human populations can be potentially catastrophic, and large-scale investigations of such diseases are highly challenging. The monitoring of emergence events is subject to ascertainment bias, whether at the level of species discovery, emerging disease events, or disease outbreaks in human populations. Disease surveillance is generally performed post hoc, driven by a response to recent events and by the availability of detection and identification technologies. Additionally, the inventory of pathogens that exist in mammalian and other reservoirs is incomplete, and identifying those with the potential to cause disease in humans is rarely possible in advance. A major step in understanding the burden and diversity of zoonotic infections, the local behavioral and demographic risks of infection, and the risk of emergence of these pathogens in human populations is to establish surveillance networks in populations that maintain regular contact with diverse animal populations, and to simultaneously characterize pathogen diversity in human and animal populations. Vietnam has been an epicenter of disease emergence over the last decade, and practices at the human/animal interface may facilitate the likelihood of spillover of zoonotic pathogens into humans. To tackle the scientific issues surrounding the origins and emergence of zoonotic infections in Vietnam, we have established The Vietnam Initiative on Zoonotic Infections (VIZIONS). This countrywide project, in which several international institutions collaborate with Vietnamese organizations, is combining clinical data, epidemiology, high-throughput sequencing, and social sciences to address relevant one-health questions. Here, we describe the primary aims of the project, the infrastructure established to address our scientific questions, and the current status of the project. Our principal objective is to develop an integrated approach to the surveillance of pathogens circulating in both human and animal populations and assess how frequently they are exchanged. This infrastructure will facilitate systematic investigations of pathogen ecology and evolution, enhance understanding of viral cross-species transmission events, and identify relevant risk factors and drivers of zoonotic disease emergence.

Geoghegan JL, Tan LV, Kühnert D, Halpin RA, Lin X, Simenauer A, Akopov A, Das SR, Stockwell TB, Shrivastava S et al. 2015. Phylodynamics of Enterovirus A71-Associated Hand, Foot, and Mouth Disease in Viet Nam. J Virol, 89 (17), pp. 8871-8879. | Show Abstract | Read more

UNLABELLED: Enterovirus A71 (EV-A71) is a major cause of hand, foot, and mouth disease (HFMD) and is particularly prevalent in parts of Southeast Asia, affecting thousands of children and infants each year. Revealing the evolutionary and epidemiological dynamics of EV-A71 through time and space is central to understanding its outbreak potential. We generated the full genome sequences of 200 EV-A71 strains sampled from various locations in Viet Nam between 2011 and 2013 and used these sequence data to determine the evolutionary history and phylodynamics of EV-A71 in Viet Nam, providing estimates of the effective reproduction number (Re) of the infection through time. In addition, we described the phylogeography of EV-A71 throughout Southeast Asia, documenting patterns of viral gene flow. Accordingly, our analysis reveals that a rapid genogroup switch from C4 to B5 likely took place during 2012 in Viet Nam. We show that the Re of subgenogroup C4 decreased during the time frame of sampling, whereas that of B5 increased and remained >1 at the end of 2013, corresponding to a rise in B5 prevalence. Our study reveals that the subgenogroup B5 virus that emerged into Viet Nam is closely related to variants that were responsible for large epidemics in Malaysia and Taiwan and therefore extends our knowledge regarding its associated area of endemicity. Subgenogroup B5 evidently has the potential to cause more widespread outbreaks across Southeast Asia. IMPORTANCE: EV-A71 is one of many viruses that cause HFMD, a common syndrome that largely affects infants and children. HFMD usually causes only mild illness with no long-term consequences. Occasionally, however, severe infection may arise, especially in very young children, causing neurological complications and even death. EV-A71 is highly contagious and is associated with the most severe HFMD cases, with large and frequent epidemics of the virus recorded worldwide. Although major advances have been made in the development of a potential EV-A71 vaccine, there is no current prevention and little is known about the patterns and dynamics of EV-A71 spread. In this study, we utilize full-length genome sequence data obtained from HFMD patients in Viet Nam, a geographical region where the disease has been endemic since 2003, to characterize the phylodynamics of this important emerging virus.

Wertheim HFL, Nadjm B, Thomas S, Agustiningsih A, Malik S, Diep NNT, Vu TVD, Kinh NV, Chau NVV, Liem NT et al. 2015. Viral and atypical bacterial aetiologies of infection in hospitalised patients admitted with clinical suspicion of influenza in Thailand, Vietnam and Indonesia. Influenza Other Respir Viruses, 9 (6), pp. 315-322. | Show Abstract | Read more

BACKGROUND: Influenza constitutes a leading cause of morbidity and mortality worldwide. There is limited information about the etiology of infection presenting clinically as influenza in hospitalized adults and children in Southeast Asia. Such data are important for future management of respiratory infections. OBJECTIVES: To describe the etiology of infection presenting clinically as influenza in those hospitalized in Southeast Asia METHODS: Respiratory specimens archived from July 2008 to June 2009 from patients hospitalised with suspected influenza from (Indonesia, Thailand and Vietnam were tested for respiratory viruses and atypical bacteria by polymerase chain reaction. RESULTS: A total of 1222 patients' samples were tested. 776/1222 (63.5%) patients were under the age of 5. Viruses detected included rhinoviruses in 229/1222 patients (18.7%), bocaviruses in 200/1222 (16.4%), respiratory syncytial viruses in 144 (11.8%), parainfluenzaviruses in 140 (11.5%; PIV1: 32; PIV2: 12; PIV3: 71;PIV4: 25), adenovirus in 102 (8.4%), influenza viruses in 93 (7.6%; influenza A: 77; influenza B: 16), coronaviruses in 23 (1.8%; OC43: 14; E229: 9). Bacterial pathogens were: Mycoplasma pneumoniae (n=33, 2.7%), Chlamydophila psittaci (n=2), C. pneumoniae (n=1), Bordetella pertussis (n=1), and Legionella pneumophila (n=2). Overall in-hospital case fatality rate was 29/1222 (2.4%). CONCLUSION: Respiratory viruses were the most commonly detected pathogens in patients hospitalized with a clinical suspicion of influenza. Rhinovirus was the most frequently detected virus, and M. pneumoniae the most common atypical bacterium. The low number of detected influenza viruses demonstrate a low benefit for empirical oseltamivir therapy, unless during an influenza outbreak. This article is protected by copyright. All rights reserved.

Cleton NB, Godeke G-J, Reimerink J, Beersma MF, Doorn HRV, Franco L, Goeijenbier M, Jimenez-Clavero MA, Johnson BW, Niedrig M et al. 2015. Spot the difference-development of a syndrome based protein microarray for specific serological detection of multiple flavivirus infections in travelers. PLoS Negl Trop Dis, 9 (3), pp. e0003580. | Show Abstract | Read more

BACKGROUND: The family Flaviviridae, genus Flavivirus, holds many of the world's most prevalent arboviral diseases that are also considered the most important travel related arboviral infections. In most cases, flavivirus diagnosis in travelers is primarily based on serology as viremia is often low and typically has already been reduced to undetectable levels when symptoms set in and patients seek medical attention. Serological differentiation between flaviviruses and the false-positive results caused by vaccination and cross-reactivity among the different species, are problematic for surveillance and diagnostics of flaviviruses. Their partially overlapping geographic distribution and symptoms, combined with increase in travel, and preexisting antibodies due to flavivirus vaccinations, expand the need for rapid and reliable multiplex diagnostic tests to supplement currently used methods. GOAL: We describe the development of a multiplex serological protein microarray using recombinant NS1 proteins for detection of medically important viruses within the genus Flavivirus. Sera from clinical flavivirus patients were used for primary development of the protein microarray. RESULTS: Results show a high IgG and IgM sensitivity and specificity for individual NS1 antigens, and limited cross reactivity, even within serocomplexes. In addition, the serology based on this array allows for discrimination between infection and vaccination response for JEV vaccine, and no cross-reactivity with TBEV and YFV vaccine induced antibodies when testing for antibodies to other flaviviruses. CONCLUSION: Based on these data, multiplex NS1-based protein microarray is a promising tool for surveillance and diagnosis of flaviviruses.

Tuan TA, Thanh TT, Hai NTT, Tinh LBB, Kim LTN, Do LAH, Chinh B'Krong NTT, Tham NT, Hang VTT, Merson L et al. 2015. Characterization of hospital and community-acquired respiratory syncytial virus in children with severe lower respiratory tract infections in Ho Chi Minh City, Vietnam, 2010. Influenza Other Respir Viruses, 9 (3), pp. 110-119. | Show Abstract | Read more

BACKGROUND: Human respiratory syncytial virus (RSV) is an important community and nosocomial pathogen in developed countries but data regarding the importance of RSV in developing countries are relatively scarce. METHODS: During a 1-year surveillance study in 2010, we took serial samples from children admitted to the Emergency Unit of the Respiratory Ward of Children's Hospital 1 in Ho Chi Minh City, Vietnam. RSV was detected within 72 hours of admission to the ward in 26% (376/1439; RSV A: n = 320; RSV B: n = 54; and RSV A and B: n = 2). Among those negative in the first 72 hours after admission, 6.6% (25/377) acquired nosocomial RSV infection during hospitalization (RSV A: n = 22; and RSV B: n = 3). RESULTS: Children with nosocomial RSV infection were younger (P = 0.001) and had a longer duration of hospitalization (P < 0.001). The rate of incomplete recovery among children with nosocomial RSV infection was significantly higher than among those without (P < 0.001). Phylogenetic analysis of partial G gene sequences obtained from 79% (316/401) of positive specimens revealed the co-circulation of multiple genotypes with RSV A NA1 being predominant (A NA1: n = 275; A GA5: n = 5; B BA3: n = 3; B BA9: n = 26; and B BA10: n = 7). The RSV A GA5 and RSV B BA3 genotypes have not been reported from Vietnam, previously. CONCLUSION: Besides emphasizing the importance of RSV as a cause of respiratory infection leading to hospitalization in young children and as a nosocomial pathogen, data from this study extend our knowledge on the genetic diversity of RSV circulating in Vietnam.

Tan LV, Tuyen NTK, Thanh TT, Ngan TT, Van HMT, Sabanathan S, Van TTM, Thanh LTM, Nguyet LA, Geoghegan JL et al. 2015. A generic assay for whole-genome amplification and deep sequencing of enterovirus A71. J Virol Methods, 215-216 pp. 30-36. | Show Abstract | Read more

Enterovirus A71 (EV-A71) has emerged as the most important cause of large outbreaks of severe and sometimes fatal hand, foot and mouth disease (HFMD) across the Asia-Pacific region. EV-A71 outbreaks have been associated with (sub)genogroup switches, sometimes accompanied by recombination events. Understanding EV-A71 population dynamics is therefore essential for understanding this emerging infection, and may provide pivotal information for vaccine development. Despite the public health burden of EV-A71, relatively few EV-A71 complete-genome sequences are available for analysis and from limited geographical localities. The availability of an efficient procedure for whole-genome sequencing would stimulate effort to generate more viral sequence data. Herein, we report for the first time the development of a next-generation sequencing based protocol for whole-genome sequencing of EV-A71 directly from clinical specimens. We were able to sequence viruses of subgenogroup C4 and B5, while RNA from culture materials of diverse EV-A71 subgenogroups belonging to both genogroup B and C was successfully amplified. The nature of intra-host genetic diversity was explored in 22 clinical samples, revealing 107 positions carrying minor variants (ranging from 0 to 15 variants per sample). Our analysis of EV-A71 strains sampled in 2013 showed that they all belonged to subgenogroup B5, representing the first report of this subgenogroup in Vietnam. In conclusion, we have successfully developed a high-throughput next-generation sequencing-based assay for whole-genome sequencing of EV-A71 from clinical samples.

Anders KL, Nguyen HL, Nguyen NM, Van Thuy NT, Hong Van NT, Hieu NT, Hong Tham NT, Thanh Ha PT, Lien LB, Vinh Chau NV et al. 2015. Epidemiology and virology of acute respiratory infections during the first year of life: a birth cohort study in Vietnam. Pediatr Infect Dis J, 34 (4), pp. 361-370. | Show Abstract | Read more

BACKGROUND: Understanding viral etiology and age-specific incidence of acute respiratory infections in infants can help identify risk groups and inform vaccine delivery, but community-based data is lacking from tropical settings. METHODS: One thousand four hundred and seventy-eight infants in urban Ho Chi Minh City and 981 infants in a semi-rural district in southern Vietnam were enrolled at birth and followed to 1 year of age. Acute respiratory infection (ARI) episodes were identified through clinic-based illness surveillance, hospital admissions and self-reports. Nasopharyngeal swabs were collected from infants with respiratory symptoms and tested for 14 respiratory pathogens using multiplex reverse transcription-polymerase chain reaction. RESULTS: Estimated incidence of ARI was 542 and 2691 per 1000 infant-years, and hospitalization rates for ARI were 81 and 138 per 1000 infant-years, in urban and semi-rural cohorts, respectively, from clinic- and hospital-based surveillance. However self-reported ARI episodes were just 1.5-fold higher in the semi-rural versus urban cohort, indicating that part of the urban-rural difference was explained by under-ascertainment in the urban cohort. Incidence was higher in infants ≥6 months of age than <6 months, but this was pathogen-specific. One or more viruses were detected in 53% (urban) and 64% (semi-rural) of samples from outpatients with ARI and in 78% and 66% of samples from hospitalized ARI patients, respectively. The most frequently detected viruses were rhinovirus, respiratory syncytial virus, influenza virus A and bocavirus. ARI-associated hospitalizations were associated with longer stays and more frequent ICU admission than other infections. CONCLUSIONS: ARI is a significant cause of morbidity in Vietnamese infants and influenza virus A is an under-appreciated cause of vaccine-preventable disease and hospitalizations in this tropical setting. Public health strategies to reduce infant ARI incidence and hospitalization rates are needed.

Le T, Cash-Goldwasser S, Tho PV, Lan NPH, Campbell JI, van Doorn HR, Lam NT, Trung NV, Trinh DT, Van Kinh N, Wertheim HFL. 2015. Diagnosing Rhodococcus equi infections in a setting where tuberculosis is highly endemic: a double challenge. J Clin Microbiol, 53 (4), pp. 1431-1433. | Show Abstract | Read more

Rhodococcus equi infection is increasing in regions with high HIV prevalence worldwide. The microbiological features and clinical mimicry of tuberculosis infection pose diagnostic challenges in high-tuberculosis-incidence settings. We present two HIV-associated cases of R. equi infection from Vietnam and discuss the unique diagnostic challenges in such settings.

Chea S, Cheng Y-B, Chokephaibulkit K, Chotpitayasunondh T, Rogier van Doorn H, Hafy Z, Kawichai S, Liu C-C, Nam NT, Ooi MH et al. 2015. Workshop on use of intravenous immunoglobulin in hand, foot and mouth disease in Southeast Asia. Emerg Infect Dis, 21 (1), | Show Abstract | Read more

The South East Asia Infectious Disease Clinical Research Network convened subject matter experts at a workshop to make consensus recommendations for study design of a clinical trial for use of intravenous immunoglobulin (IVIg) in severe hand, foot and mouth disease (HFMD). HFMD is a highly contagious emerging infection among children in the region, a small proportion of whom develop neurologic and cardiopulmonary complications with high case-fatality rates. The use of IVIg for treatment of severe disease is widespread and a part of local, national, and international guidelines, but no clinical evidence warrants the use of this drug, which is expensive and has potentially serious side effects. During a 2-day workshop in March 2014, a group of HFMD experts reviewed the current evidence related to use of IVIg in HFMD and discussed potential study design, feasibility, inclusion and exclusion criteria, sample size, primary and secondary endpoints, and subsidiary studies for a randomized, placebo-controlled trial.

Thanh TT, Anh NT, Tham NT, Van HMT, Sabanathan S, Qui PT, Ngan TT, Van TTM, Nguyet LA, Ny NTH et al. 2015. Validation and utilization of an internally controlled multiplex Real-time RT-PCR assay for simultaneous detection of enteroviruses and enterovirus A71 associated with hand foot and mouth disease. Virol J, 12 (1), pp. 85. | Show Abstract | Read more

BACKGROUND: Hand foot and mouth disease (HFMD) is a disease of public health importance across the Asia-Pacific region. The disease is caused by enteroviruses (EVs), in particular enterovirus A71 (EV-A71). In EV-A71-associated HFMD, the infection is sometimes associated with severe manifestations including neurological involvement and fatal outcome. The availability of a robust diagnostic assay to distinguish EV-A71 from other EVs is important for patient management and outbreak response. METHODS: We developed and validated an internally controlled one-step single-tube real-time RT-PCR in terms of sensitivity, linearity, precision, and specificity for simultaneous detection of EVs and EV-A71. Subsequently, the assay was then applied on throat and rectal swabs sampled from 434 HFMD patients. RESULTS: The assay was evaluated using both plasmid DNA and viral RNA and has shown to be reproducible with a maximum assay variation of 4.41 % and sensitive with a limit of detection less than 10 copies of target template per reaction, while cross-reactivity with other EV serotypes was not observed. When compared against a published VP1 nested RT-PCR using 112 diagnostic throat and rectal swabs from 112 children with a clinical diagnosis of HFMD during 2014, the multiplex assay had a higher sensitivity and 100 % concordance with sequencing results which showed EVs in 77/112 (68.8 %) and EV-A71 in 7/112 (6.3 %). When applied to clinical diagnostics for 322 children, the assay detected EVs in throat swabs of 257/322 (79.8 %) of which EV-A71 was detected in 36/322 (11.2 %) children. The detection rate increased to 93.5 % (301/322) and 13.4 % (43/322) for EVs and EV-A71, respectively, when rectal swabs from 65 throat-negative children were further analyzed. CONCLUSION: We have successfully developed and validated a sensitive internally controlled multiplex assay for rapid detection of EVs and EV-A71, which is useful for clinical management and outbreak control of HFMD.

Cui B, Zhang D, Pan H, Zhang F, Farrar J, Law F, van Doorn HR, Wu B, Ba-Thein W. 2015. Viral aetiology of acute respiratory infections among children and associated meteorological factors in southern China. BMC Infect Dis, 15 (1), pp. 124. | Show Abstract | Read more

BACKGROUND: Acute respiratory infections (ARIs) are common in children and mostly caused by viruses, but the significance of the detection of multiple viruses in ARIs is unclear. This study investigated 14 respiratory viruses in ARIs among children and associated meteorological factors in Shantou, southern China. METHODS: Paired nasal/throat-flocked swabs collected from 1,074 children with ARIs, who visited outpatient walk-in clinics in a tertiary hospital between December 2010 and November 2011, were examined for fourteen respiratory viruses--influenza viruses (FluA, FluB), respiratory syncytial viruses (RSV A and B), human coronaviruses (hCoV: 229E, OC43, HKU1, NL63), human metapneumoviruses (hMPV A and B), parainfluenza viruses (PIV1-4), human rhinoviruses (HRV A, B, C), enteroviruses (EV), adenoviruses (ADV), human bocavirus (hBoV), and human parechoviruses (hPeV)--by multiplex real-time PCR. RESULTS: We identified at least one virus in 82.3% (884/1,074) and multiple viruses in 38.6% (415/1,074) of patients. EV and HRV were the most frequently detected single viruses (42.3%, 374/884 and 39.9%, 353/884 respectively) and co-detected pair (23.1%, 96/415). Overlapping seasonal trends of viruses were recorded over the year, with dual peaks for EV and single peaks for the others. By logistic regression analysis, EV was positively associated with the average temperature and humidity, hCoV, and PIV4, but negatively with HRV, PIV3, and hBoV. HRV was inversely associated with EV and PIV3. CONCLUSIONS: This study reports high viral detection and co-detection rates in pediatric ARI cases mainly due to EV and HRV. Many viruses circulated throughout the year with similar seasonal trends in association with temperature, humidity, and wind velocity. Statistically significant associations were present among the viruses. Understanding the polyviral etiology and viral interactions in the cases with multiple viruses warrants further studies.

Lan NPH, Kolader M-E, Van Dung N, Campbell JI, Tham NT, Chau NVV, van Doorn HR, Le DH. 2014. Mycobacterium fortuitum skin infections after subcutaneous injections with Vietnamese traditional medicine: a case report. BMC Infect Dis, 14 (1), pp. 550. | Show Abstract | Read more

BACKGROUND: Iatrogenic skin and soft tissue infections by rapidly growing mycobacteria are described with increasing frequency, especially among immunocompromised patients. CASE PRESENTATION: Here, we present an immunocompetent patient with extensive Mycobacterium fortuitum skin and soft tissue infections after subcutaneous injections to relieve joint pains by a Vietnamese traditional medicine practitioner. Moreover, we present dilemmas faced in less resourceful settings, influencing patient management. CONCLUSION: This case illustrates the pathogenic potential of rapid growing mycobacteria in medical or non-medical skin penetrating procedures, their world-wide distribution and demonstrates the dilemmas faced in settings with fewer resources.

Tan LV, Thai LH, Phu NH, Nghia HDT, Chuong LV, Sinh DX, Phong ND, Mai NTH, Man DNH, Hien VM et al. 2014. Viral aetiology of central nervous system infections in adults admitted to a tertiary referral hospital in southern Vietnam over 12 years. PLoS Negl Trop Dis, 8 (8), pp. e3127. | Show Abstract | Read more

BACKGROUND: Central nervous system (CNS) infections are important diseases in both children and adults worldwide. The spectrum of infections is broad, encompassing bacterial/aseptic meningitis and encephalitis. Viruses are regarded as the most common causes of encephalitis and aseptic meningitis. Better understanding of the viral causes of the diseases is of public health importance, in order to better inform immunization policy, and may influence clinical management. METHODOLOGY/PRINCIPAL FINDINGS: Study was conducted at the Hospital for Tropical Diseases in Ho Chi Minh City, a primary, secondary, and tertiary referral hospital for all southern provinces of Vietnam. Between December 1996 and May 2008, patients with CNS infections of presumed viral origin were enrolled. Laboratory diagnostics consisted of molecular and serological tests targeted at 14 meningitis/encephalitis-associated viruses. Of 291 enrolled patients, fatal outcome and neurological sequelae were recorded in 10% (28/291) and 27% (78/291), respectively. Mortality was especially high (9/19, 47%) amongst those with confirmed herpes simplex encephalitis which is attributed to the limited availability of intravenous acyclovir/valacyclovir. Japanese encephalitis virus, dengue virus, herpes simplex virus, and enteroviruses were the most common viruses detected, responsible for 36 (12%), 19 (6.5%), 19 (6.5%) and 8 (2.7%) respectively, followed by rubella virus (6, 2%), varicella zoster virus (5, 1.7%), mumps virus (2, 0.7%), cytomegalovirus (1, 0.3%), and rabies virus (1, 0.3%). CONCLUSIONS/SIGNIFICANCE: Viral infections of the CNS in adults in Vietnam are associated with high morbidity and mortality. Despite extensive laboratory testing, 68% of the patients remain undiagnosed. Together with our previous reports, the data confirm that Japanese encephalitis virus, dengue virus, herpes simplex virus, and enteroviruses are the leading identified causes of CNS viral infections in Vietnam, suggest that the majority of morbidity/mortality amongst patients with a confirmed/probable diagnosis is preventable by adequate vaccination/treatment, and are therefore of public health significance.

Peto L, Nadjm B, Horby P, Ngan TTD, van Doorn R, Van Kinh N, Wertheim HFL. 2014. The bacterial aetiology of adult community-acquired pneumonia in Asia: a systematic review. Trans R Soc Trop Med Hyg, 108 (6), pp. 326-337. | Show Abstract | Read more

BACKGROUND: Community-acquired pneumonia (CAP) is a major cause of adult mortality in Asia. Appropriate empirical treatment depends on knowledge of the pathogens commonly responsible. However, assessing the aetiological significance of identified organisms is often difficult, particularly with sputum isolates that might represent contamination with oropharyngeal flora. METHODS: A systematic review of all adult CAP aetiology studies from Asia, excluding the Middle East, published in English between 1 January 1990 and 1 March 2012 was conducted. Forty-eight studies reporting on 10 423 patients were included, representing data from China, India, Indonesia, Japan, Malaysia, The Philippines, Singapore, South Korea, Taiwan, Thailand and Vietnam. Data from large parts of Asia were unavailable and there was substantial heterogeneity in methodology. RESULTS: As in western studies, Streptococcus pneumoniae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella spp. and Haemophilus influenzae were all significant pathogens. However, compared with western studies, S. pneumoniae was of less relative importance. Gram-negative bacilli and Mycobacterium tuberculosis were more important, and in northeast Thailand Burkholderia pseudomallei was a major pathogen. CONCLUSION: These data have major implications for diagnostic strategies and empirical treatment. Narrow-spectrum antibiotics targeting S. pneumoniae may be inappropriate in many Asian settings, and agents active against TB may lead to partial response and delayed TB diagnosis.

Sabanathan S, Tan LV, Thwaites L, Wills B, Qui PT, Rogier van Doorn H. 2014. Enterovirus 71 related severe hand, foot and mouth disease outbreaks in South-East Asia: current situation and ongoing challenges. J Epidemiol Community Health, 68 (6), pp. 500-502. | Read more

Schultsz C, Lan NPH, Van Dung N, Visser C, Anh TTN, Bay PVB, Hong TTK, Brinke P, Hendriks W, Osinga T et al. 2014. Network building and knowledge exchange with telemicrobiology. Lancet Glob Health, 2 (2), pp. e78. | Read more

Cited:

23

Scopus

Sabanathan S, Van Tan L, Thwaites L, Wills B, Qui PT, Van Doorn HR. 2014. Enterovirus 71 related severe hand, foot and mouth disease outbreaks in South-East Asia: Current situation and ongoing challenges Journal of Epidemiology and Community Health, 68 (6), pp. 500-502. | Read more

Hoang LT, Tolfvenstam T, Ooi EE, Khor CC, Naim ANM, Ho EXP, Ong SH, Wertheim HF, Fox A, Van Vinh Nguyen C et al. 2014. Patient-based transcriptome-wide analysis identify interferon and ubiquination pathways as potential predictors of influenza A disease severity. PLoS One, 9 (11), pp. e111640. | Show Abstract | Read more

BACKGROUND: The influenza A virus is an RNA virus that is responsible for seasonal epidemics worldwide with up to five million cases of severe illness and 500,000 deaths annually according to the World Health Organization estimates. The factors associated with severe diseases are not well defined, but more severe disease is more often seen among persons aged >65 years, infants, pregnant women, and individuals of any age with underlying health conditions. METHODOLOGY/PRINCIPAL FINDINGS: Using gene expression microarrays, the transcriptomic profiles of influenza-infected patients with severe (N = 11), moderate (N = 40) and mild (N = 83) symptoms were compared with the febrile patients of unknown etiology (N = 73). We found that influenza-infected patients, regardless of their clinical outcomes, had a stronger induction of antiviral and cytokine responses and a stronger attenuation of NK and T cell responses in comparison with those with unknown etiology. More importantly, we found that both interferon and ubiquitination signaling were strongly attenuated in patients with the most severe outcomes in comparison with those with moderate and mild outcomes, suggesting the protective roles of these pathways in disease pathogenesis. CONCLUSION/SIGNIFICANCES: The attenuation of interferon and ubiquitination pathways may associate with the clinical outcomes of influenza patients.

Khauv P, Turner P, Soeng C, Soeng S, Moore CE, Bousfield R, Stoesser N, Emary K, Thanh DP, Baker S et al. 2014. Ophthalmic infections in children presenting to Angkor Hospital for Children, Siem Reap, Cambodia. BMC Res Notes, 7 (1), pp. 784. | Show Abstract | Read more

BACKGROUND: Ophthalmic infections cause significant morbidity in Cambodian children but aetiologic data are scarce. We investigated the causes of acute eye infections in 54 children presenting to the ophthalmology clinic at Angkor Hospital for Children, Siem Reap between March and October 2012. FINDINGS: The median age at presentation was 3.6 years (range 6 days - 16.0 years). Forty two patients (77.8%) were classified as having an external eye infection, ten (18.5%) as ophthalmia neonatorum, and two (3.7%) as intra-ocular infection. Organisms were identified in all ophthalmia neonatorum patients and 85.7% of patients with an external eye infection. Pathogens were not detected in either of the intra-ocular infection patients. Most commonly isolated bacteria were Staphylococcus aureus (23 isolates), coagulase-negative staphylococci (13), coliforms (7), Haemophilus influenzae/parainfluenzae (6), Streptococcus pneumoniae (4), and Neisseria gonorrhoeae (2). Chlamydia trachomatis DNA was detected in 60% of swabs taken from ophthalmia neonatorum cases. CONCLUSIONS: This small study demonstrates the wide range of pathogens associated with common eye infections in Cambodian children. The inclusion of molecular assays improved the spectrum of detectable pathogens, most notably in neonates.

van Doorn HR. 2014. Emerging infectious diseases. Medicine (Abingdon), 42 (1), pp. 60-63. | Show Abstract | Read more

The spectrum of human pathogens and the infectious diseases they cause is continuously changing through evolution and changes in the way human populations interact with their environment and each other. New human pathogens most often emerge from an animal reservoir, emphasizing the central role that non-human reservoirs play in human infectious diseases. Pathogens may also re-emerge with new characteristics, such as multidrug-resistance, or in different places, such as West Nile virus in the USA in 1999, to cause new epidemics. Most human pathogens have a history of evolution in which they first emerge and cause epidemics, become unstably adapted, re-emerge periodically, and eventually become endemic with the potential for future outbreaks.

Le VT, de Jong MD, Nguyen VK, Nguyen VT, Taylor W, Wertheim HFL, van der Ende A, van der Hoek L, Canuti M, Crusat M et al. 2014. Limited geographic distribution of the novel cyclovirus CyCV-VN. Sci Rep, 4 (1), pp. 3967. | Show Abstract | Read more

A novel cyclovirus, CyCV-VN, was recently identified in cerebrospinal fluid (CSF) from patients with central nervous system (CNS) infections in central and southern Vietnam. To explore the geographic distribution of this novel virus, more than 600 CSF specimens from patients with suspected CNS infections in northern Vietnam, Cambodia, Nepal and The Netherlands were screened for the presence of CyCV-VN but all were negative. Sequence comparison and phylogenetic analysis between CyCV-VN and another novel cyclovirus recently identified in CSF from Malawian patients indicated that these represent distinct cycloviral species, albeit phylogenetically closely related. The data suggest that CyCV-VN has a limited geographic distribution within southern and central Vietnam. Further research is needed to determine the global distribution and diversity of cycloviruses and importantly their possible association with human disease.

Crusat M, Liu J, Palma AS, Childs RA, Liu Y, Wharton SA, Lin YP, Coombs PJ, Martin SR, Matrosovich M et al. 2013. Changes in the hemagglutinin of H5N1 viruses during human infection - Influence on receptor binding Virology, 447 (1-2), pp. 326-337. | Show Abstract | Read more

As avian influenza A(H5N1) viruses continue to circulate in Asia and Africa, global concerns of an imminent pandemic persist. Recent experimental studies suggest that efficient transmission between humans of current H5N1 viruses only requires a few genetic changes. An essential step is alteration of the virus hemagglutinin from preferential binding to avian receptors for the recognition of human receptors present in the upper airway. We have identified receptor-binding changes which emerged during H5N1 infection of humans, due to single amino acid substitutions, Ala134Val and Ile151Phe, in the hemagglutinin. Detailed biological, receptor-binding, and structural analyses revealed reduced binding of the mutated viruses to avian-like receptors, but without commensurate increased binding to the human-like receptors investigated, possibly reflecting a receptor-binding phenotype intermediate in adaptation to more human-like characteristics. These observations emphasize that evolution in nature of avian H5N1 viruses to efficient binding of human receptors is a complex multistep process. © 2013 The Authros.

Le MQ, Horby P, Fox A, Nguyen HT, Le Nguyen HK, Hoang PMV, Nguyen KC, de Jong MD, Jeeninga RE, Rogier van Doorn H et al. 2013. Subclinical avian influenza A(H5N1) virus infection in human, Vietnam. Emerg Infect Dis, 19 (10), pp. 1674-1677. | Show Abstract | Read more

Laboratory-confirmed cases of subclinical infection with avian influenza A(H5N1) virus in humans are rare, and the true number of these cases is unknown. We describe the identification of a laboratory-confirmed subclinical case in a woman during an influenza A(H5N1) contact investigation in northern Vietnam.

Crusat M, Liu J, Palma AS, Childs RA, Liu Y, Wharton SA, Lin YP, Coombs PJ, Martin SR, Matrosovich M et al. 2013. Changes in the hemagglutinin of H5N1 viruses during human infection--influence on receptor binding. Virology, 447 (1-2), pp. 326-337. | Show Abstract | Read more

As avian influenza A(H5N1) viruses continue to circulate in Asia and Africa, global concerns of an imminent pandemic persist. Recent experimental studies suggest that efficient transmission between humans of current H5N1 viruses only requires a few genetic changes. An essential step is alteration of the virus hemagglutinin from preferential binding to avian receptors for the recognition of human receptors present in the upper airway. We have identified receptor-binding changes which emerged during H5N1 infection of humans, due to single amino acid substitutions, Ala134Val and Ile151Phe, in the hemagglutinin. Detailed biological, receptor-binding, and structural analyses revealed reduced binding of the mutated viruses to avian-like receptors, but without commensurate increased binding to the human-like receptors investigated, possibly reflecting a receptor-binding phenotype intermediate in adaptation to more human-like characteristics. These observations emphasize that evolution in nature of avian H5N1 viruses to efficient binding of human receptors is a complex multistep process.

Giri A, Arjyal A, Koirala S, Karkey A, Dongol S, Thapa SD, Shilpakar O, Shrestha R, van Tan L, Thi Thuy Chinh BN et al. 2013. Aetiologies of central nervous system infections in adults in Kathmandu, Nepal: a prospective hospital-based study. Sci Rep, 3 (1), pp. 2382. | Show Abstract | Read more

We conducted a prospective hospital based study from February 2009-April 2011 to identify the possible pathogens of central nervous system (CNS) infections in adults admitted to a tertiary referral hospital (Patan Hospital) in Kathmandu, Nepal. The pathogens of CNS infections were confirmed in cerebrospinal fluid (CSF) using molecular diagnostics, culture (bacteria) and serology. 87 patients were recruited for the study and the etiological diagnosis was established in 38% (n = 33). The bacterial pathogens identified were Neisseria meningitidis (n = 6); Streptococcus pneumoniae (n = 5) and Staphylococcus aureus (n = 2) in 13/87(14%). Enteroviruses were found in 12/87 (13%); Herpes Simplex virus (HSV) in 2/87(2%). IgM against Japanese encephalitis virus (JEV) was detected in the CSF of 11/73 (15%) tested samples. This is the first prospective molecular and serology based CSF analysis in adults with CNS infections in Kathmandu, Nepal. JEV and enteroviruses were the most commonly detected pathogens in this setting.

South East Asia Infectious Disease Clinical Research Network. 2013. Effect of double dose oseltamivir on clinical and virological outcomes in children and adults admitted to hospital with severe influenza: double blind randomised controlled trial. BMJ, 346 (may30 2), pp. f3039. | Show Abstract | Read more

OBJECTIVE: To investigate the validity of recommendations in treatment guidelines to use higher than approved doses of oseltamivir in patients with severe influenza. DESIGN: Double blind randomised trial. SETTING: Thirteen hospitals in Indonesia, Singapore, Thailand, and Vietnam. PARTICIPANTS: Patients aged ≥ 1 year admitted to hospital with confirmed severe influenza. INTERVENTIONS: Oral oseltamivir at double dose (150 mg twice a day/paediatric equivalent) versus standard dose (75 mg twice a day/paediatric equivalent). MAIN OUTCOME MEASURE: Viral status according to reverse transcriptase polymerase chain reaction (RT-PCR) for influenza RNA in nasal and throat swabs on day five. RESULTS: Of 326 patients (including 246 (75.5%) children aged <15), 165 and 161 were randomised to double or standard dose oseltamivir, respectively. Of these, 260 (79.8%) were infected with influenza virus A (133 (40.8%) with A/H3N2, 72 (22.1%) with A/H1N1-pdm09, 38 (11.7%) with seasonal A/H1N1, 17 (5.2%) with A/H5N1) and 53 (16.2%) with influenza virus B. A further 3.9% (13) were false positive by rapid antigen test (negative by RT-PCR and no rise in convalescent haemagglutination inhibition titers). Similar proportions of patients were negative for RT-PCR on day five of treatment: 115/159 (72.3%, 95% confidence interval 64.9% to 78.7%) double dose recipients versus 105/154 (68.2%, 60.5% to 75.0%) standard dose recipients; difference 4.2% (-5.9 to 14.2); P=0.42. No differences were found in clearance of virus in subgroup analyses by virus type/subtype, age, and duration of illness before randomisation. Mortality was similar: 12/165 (7.3%, 4.2% to 12.3%) in double dose recipients versus 9/161 (5.6%, 3.0% to 10.3%) in standard dose recipients. No differences were found between double and standard dose arms in median days on supplemental oxygen (3 (interquartile range 2-5) v 3.5 (2-7)), in intensive care (4.5 (3-6) v 5 (2-11), and on mechanical ventilation (2.5 (1-16) v 8 (1-16)), respectively. No important differences in tolerability were found. CONCLUSIONS: There were no virological or clinical advantages with double dose oseltamivir compared with standard dose in patients with severe influenza admitted to hospital. REGISTRATION: Clinical Trials NCT00298233.

Kolader M-E, Vinh H, Ngoc Tuyet PT, Thompson C, Wolbers M, Merson L, Campbell JI, Ngoc Dung TT, Manh Tuan H, Vinh Chau NV et al. 2013. An oral preparation of Lactobacillus acidophilus for the treatment of uncomplicated acute watery diarrhoea in Vietnamese children: study protocol for a multicentre, randomised, placebo-controlled trial. Trials, 14 (1), pp. 27. | Show Abstract | Read more

BACKGROUND: Diarrhoeal disease is a major global health problem, particularly affecting children under the age of 5 years. Besides oral rehydration solution, probiotics are also commonly prescribed to children with acute watery diarrhoea in some settings. Results from randomised clinical trials (RCTs) in which investigators studied the effect of probiotics on diarrhoeal symptoms have largely shown a positive effect; yet, the overall quality of the data is limited. In Vietnam, probiotics are the most frequently prescribed treatment for children hospitalised with acute watery diarrhoea, but there is little justification for this treatment in this location. We have designed a RCT to test the hypothesis that an oral preparation of Lactobacillus acidophilus is superior to placebo in the treatment of acute watery diarrhoea in Vietnamese children. METHODS: This RCT was designed to study the effect of treatment with L. acidophilus (4 × 109 colony-forming units/day) for 5 days for acute watery diarrhoea against a placebo in 300 children ages 9 to 60 months admitted to hospitals in Vietnam. Clinical and laboratory data plus samples will be collected on admission, daily during hospitalisation, at discharge, and at follow-up visits for a subset of participants. The primary end point will be defined as the time from the first dose of study medication to the start of the first 24-hour period without diarrhoea as assessed by the on-duty nurse. Secondary endpoints include the time to cessation of diarrhoea as recorded by parents or guardians in an hourly checklist, stool frequency over the first 3 days, treatment failure, rotavirus and norovirus viral loads, and adverse events. DISCUSSION: The existing evidence for the use of probiotics in treating acute watery diarrhoea seems to favour their use. However, the size of the effect varies across publications. An array of different probiotic organisms, doses, treatment durations, study populations, designs, settings, and aetiologies have been described. In this trial, we will investigate whether probiotics are beneficial as an adjuvant treatment for children with acute watery diarrhoea in Vietnam, with the aim of guiding clinical practice through improved regional evidence. TRIAL REGISTRATION: Current Controlled Trials ISRCTN88101063.

Tan LV, van Doorn HR, Nghia HDT, Chau TTH, Tu LTP, de Vries M, Canuti M, Deijs M, Jebbink MF, Baker S et al. 2013. Identification of a new cyclovirus in cerebrospinal fluid of patients with acute central nervous system infections. MBio, 4 (3), pp. e00231-e00213. | Show Abstract | Read more

Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology remains unknown in a large proportion of cases. We identified and characterized the full genome of a novel cyclovirus (tentatively named cyclovirus-Vietnam [CyCV-VN]) in cerebrospinal fluid (CSF) specimens of two Vietnamese patients with CNS infections of unknown etiology. CyCV-VN was subsequently detected in 4% of 642 CSF specimens from Vietnamese patients with suspected CNS infections and none of 122 CSFs from patients with noninfectious neurological disorders. Detection rates were similar in patients with CNS infections of unknown etiology and those in whom other pathogens were detected. A similar detection rate in feces from healthy children suggested food-borne or orofecal transmission routes, while high detection rates in feces from pigs and poultry (average, 58%) suggested the existence of animal reservoirs for such transmission. Further research is needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus.

Chheng K, Carter MJ, Emary K, Chanpheaktra N, Moore CE, Stoesser N, Putchhat H, Sona S, Reaksmey S, Kitsutani P et al. 2013. A prospective study of the causes of febrile illness requiring hospitalization in children in Cambodia. PLoS One, 8 (4), pp. e60634. | Show Abstract | Read more

BACKGROUND: Febrile illnesses are pre-eminent contributors to morbidity and mortality among children in South-East Asia but the causes are poorly understood. We determined the causes of fever in children hospitalised in Siem Reap province, Cambodia. METHODS AND FINDINGS: A one-year prospective study of febrile children admitted to Angkor Hospital for Children, Siem Reap. Demographic, clinical, laboratory and outcome data were comprehensively analysed. Between October 12(th) 2009 and October 12(th) 2010 there were 1225 episodes of febrile illness in 1180 children. Median (IQR) age was 2.0 (0.8-6.4) years, with 850 (69%) episodes in children <5 years. Common microbiological diagnoses were dengue virus (16.2%), scrub typhus (7.8%), and Japanese encephalitis virus (5.8%). 76 (6.3%) episodes had culture-proven bloodstream infection, including Salmonella enterica serovar Typhi (22 isolates, 1.8%), Streptococcus pneumoniae (13, 1.1%), Escherichia coli (8, 0.7%), Haemophilus influenzae (7, 0.6%), Staphylococcus aureus (6, 0.5%) and Burkholderia pseudomallei (6, 0.5%). There were 69 deaths (5.6%), including those due to clinically diagnosed pneumonia (19), dengue virus (5), and melioidosis (4). 10 of 69 (14.5%) deaths were associated with culture-proven bloodstream infection in logistic regression analyses (odds ratio for mortality 3.4, 95% CI 1.6-6.9). Antimicrobial resistance was prevalent, particularly in S. enterica Typhi, (where 90% of isolates were resistant to ciprofloxacin, and 86% were multi-drug resistant). Comorbid undernutrition was present in 44% of episodes and a major risk factor for acute mortality (OR 2.1, 95% CI 1.1-4.2), as were HIV infection and cardiac disease. CONCLUSION: We identified a microbiological cause of fever in almost 50% of episodes in this large study of community-acquired febrile illness in hospitalized children in Cambodia. The range of pathogens, antimicrobial susceptibility, and co-morbidities associated with mortality described will be of use in the development of rational guidelines for infectious disease treatment and control in Cambodia and South-East Asia.

Boni MF, Nguyen TD, de Jong MD, van Doorn HR. 2013. Virulence attenuation during an influenza A/H5N1 pandemic. Philos Trans R Soc Lond B Biol Sci, 368 (1614), pp. 20120207. | Show Abstract | Read more

More than 15 years after the first human cases of influenza A/H5N1 in Hong Kong, the world remains at risk for an H5N1 pandemic. Preparedness activities have focused on antiviral stockpiling and distribution, development of a human H5N1 vaccine, operationalizing screening and social distancing policies, and other non-pharmaceutical interventions. The planning of these interventions has been done in an attempt to lessen the cumulative mortality resulting from a hypothetical H5N1 pandemic. In this theoretical study, we consider the natural limitations on an H5N1 pandemic's mortality imposed by the virus' epidemiological-evolutionary constraints. Evolutionary theory dictates that pathogens should evolve to be relatively benign, depending on the magnitude of the correlation between a pathogen's virulence and its transmissibility. Because the case fatality of H5N1 infections in humans is currently 60 per cent, it is doubtful that the current viruses are close to their evolutionary optimum for transmission among humans. To describe the dynamics of virulence evolution during an H5N1 pandemic, we build a mathematical model based on the patterns of clinical progression in past H5N1 cases. Using both a deterministic model and a stochastic individual-based simulation, we describe (i) the drivers of evolutionary dynamics during an H5N1 pandemic, (ii) the range of case fatalities for which H5N1 viruses can successfully cause outbreaks in humans, and (iii) the effects of different kinds of social distancing on virulence evolution. We discuss two main epidemiological-evolutionary features of this system (i) the delaying or slowing of an epidemic which results in a majority of hosts experiencing an attenuated virulence phenotype and (ii) the strong evolutionary pressure for lower virulence experienced by the virus during a period of intense social distancing.

Dieu Ngan TT, Thomas S, Larsson M, Horby P, Diep NN, Dat VQ, Trung NV, Ha NH, Rogier van Doorn H, Van Kinh N, Wertheim HFL. 2013. First report of human psittacosis in Vietnam. J Infect, 66 (5), pp. 461-464. | Read more

Khanh TH, Sabanathan S, Thanh TT, Thoa LPK, Thuong TC, Hang VTT, Farrar J, Hien TT, Chau NVV, van Doorn HR. 2012. Enterovirus 71-associated hand, foot, and mouth disease, Southern Vietnam, 2011. Emerg Infect Dis, 18 (12), pp. 2002-2005. | Show Abstract | Read more

We prospectively studied 3,791 children hospitalized during 2011 during a large outbreak of enterovirus 71-associated hand, foot, and mouth disease in Vietnam. Formal assessment of public health interventions, use of intravenous immunoglobulin and other therapies, and factors predisposing for progression of disease is needed to improve clinical management.

Tham NT, Hang VTT, Khanh TH, Viet DC, Hien TT, Farrar J, Chau NVV, van Doorn HR. 2012. Comparison of the Roche RealTime ready Influenza A/H1N1 Detection Set with CDC A/H1N1pdm09 RT-PCR on samples from three hospitals in Ho Chi Minh City, Vietnam. Diagn Microbiol Infect Dis, 74 (2), pp. 131-136. | Show Abstract | Read more

Real-time polymerase chain reaction (PCR) can be considered the gold standard for detection of influenza viruses due to its high sensitivity and specificity. Roche has developed the RealTime ready Influenza A/H1N1 Detection Set, consisting of a generic influenza virus A PCR targeting the M2 gene (M2 PCR) and a specific PCR targeting the hemagglutinin (HA) of A/H1N1-pdm09 (HA PCR, 2009 H1N1), with the intention to make a reliable, rapid, and simple test to detect and quantify 2009 H1N1 in clinical samples. We evaluated this kit against the US Centers for Disease Control and Prevention (USCDC)/World Health Organization real-time PCR for influenza virus using 419 nose and throat swabs from 210 patients collected in 3 large hospitals in Ho Chi Minh City, Vietnam. In the per-patient analysis, when compared to CDC PCR, the sensitivity and specificity of the M2 PCR were 85.8% and 97.6%, respectively; the sensitivity and specificity of HA PCR were 88.2% and 100%, respectively. In the per-sample analysis, the sensitivity and specificity in nose swabs were higher than those in throat swabs for both M2 and HA PCRs. The viral loads as determined with the M2 and HA PCRs correlated well with the Ct values of the CDC PCR. Compared with the CDC PCR, the kit has a reasonable sensitivity and very good specificity for the detection and quantification of influenza A virus and A/H1N1-pdm09. However, given the current status of 2009 H1N1, a kit that can detect all circulating seasonal influenza viruses would be preferable.

Khanh TH, Sabanathan S, Thoa LPK, Thuong TC, Farrar J, Hien TT, van Doorn HR. 2012. A large epidemic of enterovirus 71 associated hand, foot and mouth disease in southern Vietnam, 2011 INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES, 16 pp. E274-E274. | Read more

Thao VP, Le T, Török EM, Yen NTB, Chau TTH, Jurriaans S, van Doorn HR, de Jong MD, Farrar JJ, Dunstan SJ. 2012. HIV-1 drug resistance in antiretroviral-naive individuals with HIV-1-associated tuberculous meningitis initiating antiretroviral therapy in Vietnam. Antivir Ther, 17 (5), pp. 905-913. | Show Abstract | Read more

BACKGROUND: Access to antiretroviral therapy (ART) for HIV-infected individuals in Vietnam is rapidly expanding, but there are limited data on HIV drug resistance (HIVDR) to guide ART strategies. METHODS: We retrospectively conducted HIVDR testing in 220 ART-naive individuals recruited to a randomized controlled trial of immediate versus deferred ART in individuals with HIV-associated tuberculous meningitis in Ho Chi Minh City (HCMC) from 2005-2008. HIVDR mutations were identified by population sequencing of the HIV pol gene and were defined based on 2009 WHO surveillance drug resistance mutations (SDRMs). RESULTS: We successfully sequenced 219/220 plasma samples of subjects prior to ART; 218 were subtype CRF01_AE and 1 was subtype B. SDRMs were identified in 14/219 (6.4%) subjects; 8/14 were resistant to nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs; T69D, L74V, V75M, M184V/I and K219R), 5/14 to non-nucleoside reverse transcriptase inhibitors (NNRTIs; K103N, V106M, Y181C, Y188C and G190A), 1/14 to both NRTIs and NNRTIs (D67N and Y181C) and none to protease inhibitors. After 6 months of ART, eight subjects developed protocol-defined virological failure. HIVDR mutations were identified in 5/8 subjects. All five had mutations with high-level resistance to NNRTIs and three had mutations with high-level resistance to NRTIs. Due to a high early mortality rate (58%), the effect of pre-existing HIVDR mutations on treatment outcome could not be accurately assessed. CONCLUSIONS: The prevalence of WHO SDRMs in ART-naive individuals with HIV-associated tuberculous meningitis in HCMC from 2005-2008 is 6.4%. The SDRMs identified conferred resistance to NRTIs and/or NNRTIs, reflecting the standard first-line ART regimens in Vietnam.

van Doorn HR, Kinh NV, Tuan HM, Tuan TA, Minh NNQ, Bryant JE, Hang VTT, Uyen LTT, Thinh LQ, Anh TTN et al. 2012. Clinical validation of a point-of-care multiplexed in vitro immunoassay using monoclonal antibodies (the MSD influenza test) in four hospitals in Vietnam. J Clin Microbiol, 50 (5), pp. 1621-1625. | Show Abstract | Read more

Point-of-care (POC) diagnostic tests for influenza can considerably shorten the time to clinical decision making. An investigational POC test based on a multiplexed immunoassay was developed by Meso Scale Diagnostics, LLC (MSD), with the objective to make a more sensitive rapid test that can also subtype influenza A viruses (1977 H1, H3, and H5). Between February and November 2010, we conducted a prospective multicenter study at four hospitals in Vietnam and compared the performance of this test to that of the WHO/CDC real-time reverse transcriptase PCR (RT-PCR) on nasal and throat swab specimens from patients presenting with influenza-like illness. Five hundred sixty-three adults and children with a median age of 25 months were enrolled. Sensitivity and specificity of the test with combined results from nasal and throat swab samples were 74.0% (131/177) and 99.7% (351/352), respectively, compared to RT-PCR. The POC test was as sensitive for influenza virus B as for influenza virus A (74.4% [64/86] versus 73.6% [67/91]). The positivity rate was associated with lower cycle threshold values (a marker for higher viral loads), sample type (73.6% for nasal swab versus 52.4% for throat swab), and younger age. A total of 210 (18.7%) out of 1,126 MSD tests failed, and for 34 (6%) of patients, both test samples failed (these were excluded from the performance analysis). Subtyping could be assessed only for influenza virus A/H3N2, as 1977 H1N1 was not circulating at the time and no H5N1-infected patients were enrolled, and was successful only in 9/54 patients infected with H3 influenza virus who had a positive POC test result for influenza virus A. This novel POC test provided highly sensitive detection of influenza viruses A and B compared to the reported sensitivities of other rapid tests. However, 18.7% of tests failed for technical reasons and subtyping for H3 was poor. Drawbacks to the technology include the requirement for a dedicated reader instrument and the need for continual updating of subtyping antibodies within the test array.

Tham NT, Hang VTT, Khanh TH, Viet DC, Hien TT, Farrar J, Chau NVV, van Doorn HR. 2012. Comparison of the Roche RealTime ready Influenza A/H1N1 Detection Set with CDC A/H1N1pdm09 RT-PCR on samples from three hospitals in Ho Chi Minh City, Vietnam Diagnostic Microbiology and Infectious Disease, 74 (2), pp. 131-136. | Show Abstract | Read more

Real-time polymerase chain reaction (PCR) can be considered the gold standard for detection of influenza viruses due to its high sensitivity and specificity. Roche has developed the RealTime ready Influe nza A/H1N1 Detection Set, consisting of a generic influenza virus A PCR targeting the M2 gene (M2 PCR) and a specific PCR targeting the hemagglutinin (HA) of A/H1N1-pdm09 (HA PCR, 2009 H1N1), with the intention to make a reliable, rapid, and simple test to detect and quantify 2009 H1N1 in clinical samples. We evaluated this kit against the US Centers for Disease Control and Prevention (USCDC)/World Health Organization real-time PCR for influenza virus using 419 nose and throat swabs from 210 patients collected in 3 large hospitals in Ho Chi Minh City, Vietnam. In the per-patient analysis, when compared to CDC PCR, the sensitivity and specificity of the M2 PCR were 85.8% and 97.6%, respectively; the sensitivity and specificity of HA PCR were 88.2% and 100%, respectively. In the per-sample analysis, the sensitivity and specificity in nose swabs were higher than those in throat swabs for both M2 and HA PCRs. The viral loads as determined with the M2 and HA PCRs correlated well with the Ct values of the CDC PCR. Compared with the CDC PCR, the kit has a reasonable sensitivity and very good specificity for the detection and quantification of influenza A virus and A/H1N1-pdm09. However, given the current status of 2009 H1N1, a kit that can detect all circulating seasonal influenza viruses would be preferable. © 2012 Elsevier Inc.

Do LAH, van Doorn HR, Bryant JE, Nghiem MN, Nguyen Van VC, Vo CK, Nguyen MD, Tran TH, Farrar J, De Jong MD. 2012. A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus Journal of Virological Methods, 179 (1), pp. 250-255. | Show Abstract | Read more

Improved diagnostic tools for rapid detection, quantitation, and subgrouping of human respiratory syncytial virus (RSV) are needed to aid the development and evaluation of novel intervention strategies. A quantitative real-time RT-PCR using specific locked nucleic acid (LNA) probes was developed to identify RSV and to distinguish RSV subgroups A and B (RSV LNA assay). RSV subgroup diversity and the relationship between viral load and disease severity in confirmed RSV infections were also explored. 264 archived respiratory specimens from pediatric patients were tested in parallel using the commercial multiplex Seeplex™ RV detection kit (Seegene) and the novel RSV LNA assay. The LNA assay demonstrated a significantly higher sensitivity than Seeplex, improving overall detection rates from 24% (64/264) to 32% (84/264). Detection limits of 9.0×10 1 and 6.0×10 2 copies/mL were observed for RSV A and B, respectively. RSV A was detected in 53/84 (63%) cases, and 31/84 (37%) were positive for RSV B. This novel method offers a rapid, quantitative, highly specific and sensitive approach to laboratory diagnosis of RSV. © 2011 Elsevier B.V.

Thao VP, Le T, Toeroek EM, Yen NTB, Chau TTH, Jurriaans S, van Doorn HR, de Jong MD, Farrar JJ, Dunstan SJ. 2012. HIV-1 drug resistance in antiretroviral-naive individuals with HIV-1-associated tuberculous meningitis initiating antiretroviral therapy in Vietnam (vol 17, pg 905, 2012) ANTIVIRAL THERAPY, 17 (5), pp. 937-937. | Read more

Vien LTM, Minh NNQ, Thuong TC, Khuong HD, Nga TVT, Thompson C, Campbell JI, de Jong M, Farrar JJ, Schultsz C et al. 2012. The co-selection of fluoroquinolone resistance genes in the gut flora of Vietnamese children. PLoS One, 7 (8), pp. e42919. | Show Abstract | Read more

Antimicrobial consumption is one of the major contributing factors facilitating the development and maintenance of bacteria exhibiting antimicrobial resistance. Plasmid-mediated quinolone resistance (PMQR) genes, such as the qnr family, can be horizontally transferred and contribute to reduced susceptibility to fluoroquinolones. We performed an observational study, investigating the copy number of PMQR after antimicrobial therapy. We enrolled 300 children resident in Ho Chi Minh City receiving antimicrobial therapy for acute respiratory tract infections (ARIs). Rectal swabs were taken on enrollment and seven days subsequently, counts for Enterobacteriaceae were performed and qnrA, qnrB and qnrS were quantified by using real-time PCR on metagenomic stool DNA. On enrollment, we found no association between age, gender or location of the participants and the prevalence of qnrA, qnrB or qnrS. Yet, all three loci demonstrated a proportional increase in the number of samples testing positive between day 0 and day 7. Furthermore, qnrB demonstrated a significant increase in copy number between paired samples (p<0.001; Wilcoxon rank-sum), associated with non-fluoroquinolone combination antimicrobial therapy. To our knowledge, this is the first study describing an association between the use of non-fluoroquinolone antimicrobials and the increasing relative prevalence and quantity of qnr genes. Our work outlines a potential mechanism for the selection and maintenance of PMQR genes and predicts a strong effect of co-selection of these resistance determinants through the use of unrelated and potentially unnecessary antimicrobial regimes.

Ho Dang Trung N, Le Thi Phuong T, Wolbers M, Nguyen Van Minh H, Nguyen Thanh V, Van MP, Thieu NTV, Van TL, Song DT, Thi PL et al. 2012. Aetiologies of central nervous system infection in Viet Nam: a prospective provincial hospital-based descriptive surveillance study. PLoS One, 7 (5), pp. e37825. | Show Abstract | Read more

BACKGROUND: Infectious diseases of the central nervous system (CNS) remain common and life-threatening, especially in developing countries. Knowledge of the aetiological agents responsible for these infections is essential to guide empiric therapy and develop a rational public health policy. To date most data has come from patients admitted to tertiary referral hospitals in Asia and there is limited aetiological data at the provincial hospital level where most patients are seen. METHODS: We conducted a prospective Provincial Hospital-based descriptive surveillance study in adults and children at thirteen hospitals in central and southern Viet Nam between August 2007-April 2010. The pathogens of CNS infection were confirmed in CSF and blood samples by using classical microbiology, molecular diagnostics and serology. RESULTS: We recruited 1241 patients with clinically suspected infection of the CNS. An aetiological agent was identified in 640/1241 (52%) of the patients. The most common pathogens were Streptococcus suis serotype 2 in patients older than 14 years of age (147/617, 24%) and Japanese encephalitis virus in patients less than 14 years old (142/624, 23%). Mycobacterium tuberculosis was confirmed in 34/617 (6%) adult patients and 11/624 (2%) paediatric patients. The acute case fatality rate (CFR) during hospital admission was 73/617 (12%) in adults and to 42/624 (7%) in children. CONCLUSIONS: Zoonotic bacterial and viral pathogens are the most common causes of CNS infection in adults and children in Viet Nam.

Fox A, Le NMH, Horby P, van Doorn HR, Nguyen VT, Nguyen HH, Nguyen TC, Vu DP, Nguyen MH, Diep NTN et al. 2012. Severe pandemic H1N1 2009 infection is associated with transient NK and T deficiency and aberrant CD8 responses. PLoS One, 7 (2), pp. e31535. | Show Abstract | Read more

BACKGROUND: It is unclear why the severity of influenza varies in healthy adults or why the burden of severe influenza shifts to young adults when pandemic strains emerge. One possibility is that cross-protective T cell responses wane in this age group in the absence of recent infection. We therefore compared the acute cellular immune response in previously healthy adults with severe versus mild pandemic H1N1 infection. METHODS AND PRINCIPAL FINDINGS: 49 previously healthy adults admitted to the National Hospital of Tropical Diseases, Viet Nam with RT-PCR-confirmed 2009 H1N1 infection were prospectively enrolled. 39 recovered quickly whereas 10 developed severe symptoms requiring supplemental oxygen and prolonged hospitalization. Peripheral blood lymphocyte subset counts and activation (HLADR, CD38) and differentiation (CD27, CD28) marker expression were determined on days 0, 2, 5, 10, 14 and 28 by flow cytometry. NK, CD4 and CD8 lymphopenia developed in 100%, 90% and 60% of severe cases versus 13% (p<0.001), 28%, (p = 0.001) and 18% (p = 0.014) of mild cases. CD4 and NK counts normalized following recovery. B cell counts were not significantly associated with severity. CD8 activation peaked 6-8 days after mild influenza onset, when 13% (6-22%) were HLADR+CD38+, and was accompanied by a significant loss of resting/CD27+CD28+ cells without accumulation of CD27+CD28- or CD27-CD28- cells. In severe influenza CD8 activation peaked more than 9 days post-onset, and/or was excessive (30-90% HLADR+CD38+) in association with accumulation of CD27+CD28- cells and maintenance of CD8 counts. CONCLUSION: Severe influenza is associated with transient T and NK cell deficiency. CD8 phenotype changes during mild influenza are consistent with a rapidly resolving memory response whereas in severe influenza activation is either delayed or excessive, and partially differentiated cells accumulate within blood indicating that recruitment of effector cells to the lung could be impaired.

Do LAH, van Doorn HR, Bryant JE, Nghiem MN, Nguyen Van VC, Vo CK, Nguyen MD, Tran TH, Farrar J, de Jong MD. 2012. A sensitive real-time PCR for detection and subgrouping of human respiratory syncytial virus. J Virol Methods, 179 (1), pp. 250-255. | Show Abstract | Read more

Improved diagnostic tools for rapid detection, quantitation, and subgrouping of human respiratory syncytial virus (RSV) are needed to aid the development and evaluation of novel intervention strategies. A quantitative real-time RT-PCR using specific locked nucleic acid (LNA) probes was developed to identify RSV and to distinguish RSV subgroups A and B (RSV LNA assay). RSV subgroup diversity and the relationship between viral load and disease severity in confirmed RSV infections were also explored. 264 archived respiratory specimens from pediatric patients were tested in parallel using the commercial multiplex Seeplex™ RV detection kit (Seegene) and the novel RSV LNA assay. The LNA assay demonstrated a significantly higher sensitivity than Seeplex, improving overall detection rates from 24% (64/264) to 32% (84/264). Detection limits of 9.0×10(1) and 6.0×10(2)copies/mL were observed for RSV A and B, respectively. RSV A was detected in 53/84 (63%) cases, and 31/84 (37%) were positive for RSV B. This novel method offers a rapid, quantitative, highly specific and sensitive approach to laboratory diagnosis of RSV.

Thai KTD, Henn MR, Zody MC, Tricou V, Nguyet NM, Charlebois P, Lennon NJ, Green L, de Vries PJ, Hien TT et al. 2012. High-resolution analysis of intrahost genetic diversity in dengue virus serotype 1 infection identifies mixed infections. J Virol, 86 (2), pp. 835-843. | Show Abstract | Read more

Little is known about the rate at which genetic variation is generated within intrahost populations of dengue virus (DENV) and what implications this diversity has for dengue pathogenesis, disease severity, and host immunity. Previous studies of intrahost DENV variation have used a low frequency of sampling and/or experimental methods that do not fully account for errors generated through amplification and sequencing of viral RNAs. We investigated the extent and pattern of genetic diversity in sequence data in domain III (DIII) of the envelope (E) gene in serial plasma samples (n = 49) taken from 17 patients infected with DENV type 1 (DENV-1), totaling some 8,458 clones. Statistically rigorous approaches were employed to account for artifactual variants resulting from amplification and sequencing, which we suggest have played a major role in previous studies of intrahost genetic variation. Accordingly, nucleotide sequence diversities of viral populations were very low, with conservative estimates of the average levels of genetic diversity ranging from 0 to 0.0013. Despite such sequence conservation, we observed clear evidence for mixed infection, with the presence of multiple phylogenetically distinct lineages present within the same host, while the presence of stop codon mutations in some samples suggests the action of complementation. In contrast to some previous studies we observed no relationship between the extent and pattern of DENV-1 genetic diversity and disease severity, immune status, or level of viremia.

Long NT, Thanh TT, van Doorn HR, Vu PP, Dung PT, Dung TTK, Tien TN, Thao DTT, Hung P, Quang NV et al. 2011. Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010. Transbound Emerg Dis, 58 (6), pp. 537-543. | Show Abstract | Read more

We report 15 new avian influenza virus A/H5N1 haemagglutinin (HA) sequences sampled from visibly sick domestic poultry in southern Vietnam, between 1 January 2010 and 6 March 2010. These HA sequences form a new sub-clade of the clade 1 H5N1 viruses that have been circulating in Vietnam since 2003/2004. The viruses are characterized by a change from isoleucine to valine at position 514 (I514V) and are 1.8% divergent at the nucleotide level from HA sequences sampled in Vietnam in 2007. Five new amino acid changes were observed at previously identified antigenic sites, and three were located within structural elements of the receptor-binding domain. One new mutation removed a potential N-linked glycosylation site, and a methionine insertion was observed in one virus at the polybasic cleavage site. Five of these viruses were sampled from farms where poultry were vaccinated against H5N1, but there was no association between observed amino acid changes and flock vaccination status. Despite the current lack of evidence for antigenic drift or immune escape in Vietnamese H5N1 viruses, continued surveillance remains a high priority.

Pouplin T, Pouplin JN, Van Toi P, Lindegardh N, Rogier van Doorn H, Hien TT, Farrar J, Török ME, Chau TTH. 2011. Valacyclovir for herpes simplex encephalitis. Antimicrob Agents Chemother, 55 (7), pp. 3624-3626. | Show Abstract | Read more

The recommended treatment for herpes simplex encephalitis (HSE) remains intravenous acyclovir. In resource-poor countries, however, intravenous formulations are usually unavailable or unaffordable. We report the penetration of acyclovir into the cerebrospinal fluid (CSF) in patients with HSE, treated with the oral prodrug valacyclovir at 1,000 mg three times daily. The oral therapy achieved adequate acyclovir concentrations in the CSF and may be an acceptable early treatment for suspected HSE in resource-limited settings.

Long NT, Thanh TT, van Doorn HR, Vu PP, Dung PT, Dung TTK, Tien TN, Thao DTT, Hung P, Quang NV et al. 2011. Recent avian influenza virus A/H5N1 evolution in vaccinated and unvaccinated poultry from farms in Southern Vietnam, January-March 2010 Transboundary and Emerging Diseases, 58 (6), pp. 537-543. | Show Abstract | Read more

We report 15 new avian influenza virus A/H5N1 haemagglutinin (HA) sequences sampled from visibly sick domestic poultry in southern Vietnam, between 1 January 2010 and 6 March 2010. These HA sequences form a new sub-clade of the clade 1 H5N1 viruses that have been circulating in Vietnam since 2003/2004. The viruses are characterized by a change from isoleucine to valine at position 514 (I514V) and are 1.8% divergent at the nucleotide level from HA sequences sampled in Vietnam in 2007. Five new amino acid changes were observed at previously identified antigenic sites, and three were located within structural elements of the receptor-binding domain. One new mutation removed a potential N-linked glycosylation site, and a methionine insertion was observed in one virus at the polybasic cleavage site. Five of these viruses were sampled from farms where poultry were vaccinated against H5N1, but there was no association between observed amino acid changes and flock vaccination status. Despite the current lack of evidence for antigenic drift or immune escape in Vietnamese H5N1 viruses, continued surveillance remains a high priority. © 2011 Blackwell Verlag GmbH.

Do AHL, van Doorn HR, Nghiem MN, Bryant JE, Hoang THT, Do QH, Van TL, Tran TT, Wills B, Nguyen VCV et al. 2011. Viral etiologies of acute respiratory infections among hospitalized Vietnamese children in Ho Chi Minh City, 2004-2008. PLoS One, 6 (3), pp. e18176. | Show Abstract | Read more

BACKGROUND: The dominant viral etiologies responsible for acute respiratory infections (ARIs) are poorly understood, particularly among hospitalized children in resource-limited tropical countries where morbidity and mortality caused by ARIs are highest. Improved etiological insight is needed to improve clinical management and prevention. OBJECTIVES: We conducted a three-year prospective descriptive study of severe respiratory illness among children from 2 months to 13 years of age within the largest referral hospital for infectious diseases in southern Vietnam. METHODS: Molecular detection for 15 viral species and subtypes was performed on three types of respiratory specimens (nose, throat swabs and nasopharyngeal aspirates) using a multiplex RT-PCR kit (Seeplex™ RV detection, Seegene) and additional monoplex real-time RT-PCRs. RESULTS: A total of 309 children were enrolled from November 2004 to January 2008. Viruses were identified in 72% (222/309) of cases, including respiratory syncytial virus (24%), influenza virus A and B (17%), human bocavirus (16%), enterovirus (9%), human coronavirus (8%), human metapneumovirus (7%), parainfluenza virus 1-3 (6%), adenovirus (5%), and human rhinovirus A (4%). Co-infections with multiple viruses were detected in 20% (62/309) of patients. When combined, diagnostic yields in nose and throat swabs were similar to nasopharyngeal aspirates. CONCLUSION: Similar to other parts in the world, RSV and influenza were the predominant viral pathogens detected in Vietnamese hospitalized children. Combined nasal and throat swabs are the specimens of choice for sensitive molecular detection of a broad panel of viral agents. Further research is required to better understand the clinical significance of single versus multiple viral coinfections and to address the role of bacterial (co-)infections involved in severe respiratory illness.

Tan LV, Van Doorn HR, Van der Hoek L, Minh Hien V, Jebbink MF, Quang Ha D, Farrar J, Van Vinh Chau N, de Jong MD. 2011. Random PCR and ultracentrifugation increases sensitivity and throughput of VIDISCA for screening of pathogens in clinical specimens. J Infect Dev Ctries, 5 (2), pp. 142-148. | Show Abstract

INTRODUCTION: Virus discovery based on cDNA-AFLP (VIDISCA) is a sequence-independent virus discovery method that was recently developed and successfully used to characterize unknown viruses in cell cultures. Its applicability, however, is limited by its low sensitivity. METHODOLOGY: We evaluated whether the introduction of prior amplification of target sequences by random PCR (rPCR) increases the sensitivity of this method to improve its use on clinical specimens. In addition, ultracentrifugation was added to the protocol to allow for pooling of multiple samples, thereby increasing analytical throughput of the VIDSCA. RESULTS: We showed that rPCR enhanced the sensitivity of VIDISCA by 100-fold for two out of four viruses in different clinical samples, and that the ultracentrifugation step allowed for analyzing samples of large volumes (4 ml) and simultaneous processing of multiple (~40) clinical specimens. CONCLUSIONS: We conclude that this modified VIDISCA protocol is a relatively easy method to use for screening of large numbers of clinical samples that are suspected to contain previously unrecognized pathogens, in settings where ultradeep sequencing platforms are not available.

Chau TTH, Campbell JI, Schultsz C, Chau NVV, Diep TS, Baker S, Chinh NT, Farrar JJ, van Doorn HR. 2010. Three adult cases of Listeria monocytogenes meningitis in Vietnam. PLoS Med, 7 (7), pp. e1000306. | Read more

Thai KTD, Cazelles B, Nguyen NV, Vo LT, Boni MF, Farrar J, Simmons CP, van Doorn HR, de Vries PJ. 2010. Dengue dynamics in Binh Thuan province, southern Vietnam: periodicity, synchronicity and climate variability. PLoS Negl Trop Dis, 4 (7), pp. e747. | Show Abstract | Read more

BACKGROUND: Dengue is a major global public health problem with increasing incidence and geographic spread. The epidemiology is complex with long inter-epidemic intervals and endemic with seasonal fluctuations. This study was initiated to investigate dengue transmission dynamics in Binh Thuan province, southern Vietnam. METHODOLOGY: Wavelet analyses were performed on time series of monthly notified dengue cases from January 1994 to June 2009 (i) to detect and quantify dengue periodicity, (ii) to describe synchrony patterns in both time and space, (iii) to investigate the spatio-temporal waves and (iv) to associate the relationship between dengue incidence and El Niño-Southern Oscillation (ENSO) indices in Binh Thuan province, southern Vietnam. PRINCIPAL FINDINGS: We demonstrate a continuous annual mode of oscillation and a multi-annual cycle of around 2-3-years was solely observed from 1996-2001. Synchrony in time and between districts was detected for both the annual and 2-3-year cycle. Phase differences used to describe the spatio-temporal patterns suggested that the seasonal wave of infection was either synchronous among all districts or moving away from Phan Thiet district. The 2-3-year periodic wave was moving towards, rather than away from Phan Thiet district. A strong non-stationary association between ENSO indices and climate variables with dengue incidence in the 2-3-year periodic band was found. CONCLUSIONS: A multi-annual mode of oscillation was observed and these 2-3-year waves of infection probably started outside Binh Thuan province. Associations with climatic variables were observed with dengue incidence. Here, we have provided insight in dengue population transmission dynamics over the past 14.5 years. Further studies on an extensive time series dataset are needed to test the hypothesis that epidemics emanate from larger cities in southern Vietnam.

Nguyen NTK, Ha V, Tran NVT, Stabler R, Pham DT, Le TMV, van Doorn HR, Cerdeño-Tárraga A, Thomson N, Campbell J et al. 2010. The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam. PLoS Negl Trop Dis, 4 (6), pp. e702. | Show Abstract | Read more

BACKGROUND: Plasmid mediated antimicrobial resistance in the Enterobacteriaceae is a global problem. The rise of CTX-M class extended spectrum beta lactamases (ESBLs) has been well documented in industrialized countries. Vietnam is representative of a typical transitional middle income country where the spectrum of infectious diseases combined with the spread of drug resistance is shifting and bringing new healthcare challenges. METHODOLOGY: We collected hospital admission data from the pediatric population attending the hospital for tropical diseases in Ho Chi Minh City with Shigella infections. Organisms were cultured from all enrolled patients and subjected to antimicrobial susceptibility testing. Those that were ESBL positive were subjected to further investigation. These investigations included PCR amplification for common ESBL genes, plasmid investigation, conjugation, microarray hybridization and DNA sequencing of a bla(CTX-M) encoding plasmid. PRINCIPAL FINDINGS: We show that two different bla(CTX-M) genes are circulating in this bacterial population in this location. Sequence of one of the ESBL plasmids shows that rather than the gene being integrated into a preexisting MDR plasmid, the bla(CTX-M) gene is located on relatively simple conjugative plasmid. The sequenced plasmid (pEG356) carried the bla(CTX-M-24) gene on an ISEcp1 element and demonstrated considerable sequence homology with other IncFI plasmids. SIGNIFICANCE: The rapid dissemination, spread of antimicrobial resistance and changing population of Shigella spp. concurrent with economic growth are pertinent to many other countries undergoing similar development. Third generation cephalosporins are commonly used empiric antibiotics in Ho Chi Minh City. We recommend that these agents should not be considered for therapy of dysentery in this setting.

van Dommelen L, Verbon A, van Doorn HR, Goossens VJ. 2010. Acute hepatitis B virus infection with simultaneous high HBsAg and high anti-HBs signals in a previously HBV vaccinated HIV-1 positive patient. J Clin Virol, 47 (3), pp. 293-296. | Show Abstract | Read more

We present a case of a clinical manifest hepatitis B virus infection and a potentially misleading HBV serological profile in an HIV-1 positive patient despite previous HBV vaccination. The patient presented with an acute hepatitis B and there was no indication of chronic HBV infection or the presence of a mutation in the 'a' determinant. Remarkably, simultaneously with high HBV surface antigen and HBV viral load, high anti-HBs antibodies were present. If, due to previous HBV vaccination only anti-HBs was tested in this patient, the result of the high anti-HBs antibodies could be very misleading and offering a false sense of security. Our findings contribute to the ongoing discussion on how to assess HBV specific immunological memory and determining the role of HBV booster vaccinations in immunocompromised individuals.

Thai KTD, Phuong HL, Thanh Nga TT, Giao PT, Hung LQ, Van Nam N, Binh TQ, Simmons C, Farrar J, Hien TT et al. 2010. Clinical, epidemiological and virological features of Dengue virus infections in Vietnamese patients presenting to primary care facilities with acute undifferentiated fever. J Infect, 60 (3), pp. 229-237. | Show Abstract | Read more

OBJECTIVES: To explore clinical and virological characteristics and describe the epidemiology of dengue in patients who presented with acute undifferentiated fever (AUF) at primary health centers (PHC) in Binh Thuan Province, Vietnam. METHODS: A prospective observational study was conducted from 2001 to 2006 to study the aetiology in AUF patients. Demographic and clinical information was obtained, and dengue polymerase chain reaction (RT-PCR) and serology were performed on a random selection of patients. RESULTS: Three hundred fifty-one serologically confirmed dengue patients including 68 primary and 283 secondary infections were included in this study. In 25% (86/351) dengue virus (DENV) was detected by RT-PCR among which 32 DENV-1, 16 DENV-2, 1 DENV-3 and 37 DENV-4 were identified. The predominant dengue serotype varied by year with seasonal fluctuation: DENV-4 in 2001-2002, DENV-1 and DENV-2 from 2003 to 2006. Primary dengue was more common in children. Higher viraemia levels (P=0.010) were found in primary infections compared to secondary infections. DENV-1 infected patients had higher viraemia levels than DENV-2 (P=0.003) and DENV-4 (P<0.001) infected patients. Clinical symptoms were often seen in adults. Few differences in clinical symptoms were found between primary and secondary infection and no significant differences in clinical symptoms between the serotypes were observed. CONCLUSIONS: Our data provide insight in the epidemiology, clinical profile and virological features of mild symptomatic dengue patients who presented to PHC with AUF in Vietnam.

Le QM, Wertheim HFL, Tran ND, van Doorn HR, Nguyen TH, Horby P, Vietnam H1N1 Investigation Team. 2010. A community cluster of oseltamivir-resistant cases of 2009 H1N1 influenza. N Engl J Med, 362 (1), pp. 86-87. | Read more

Le VT, Phan TQ, Do QH, Nguyen BH, Lam QB, Bach VC, Truong HK, Tran TH, Nguyen VVC, Tran TT et al. 2010. Viral etiology of encephalitis in children in southern Vietnam: results of a one-year prospective descriptive study. PLoS Negl Trop Dis, 4 (10), pp. e854. | Show Abstract | Read more

BACKGROUND: Acute encephalitis is an important and severe disease in children in Vietnam. However, little is known about the etiology while such knowledge is essential for optimal prevention and treatment. To identify viral causes of encephalitis, in 2004 we conducted a one-year descriptive study at Children's Hospital Number One, a referral hospital for children in southern Vietnam including Ho Chi Minh City. METHODOLOGY/PRINCIPAL FINDINGS: Children less than 16 years of age presenting with acute encephalitis of presumed viral etiology were enrolled. Diagnostic efforts included viral culture, serology and real time (RT)-PCRs. A confirmed or probable viral causative agent was established in 41% of 194 enrolled patients. The most commonly diagnosed causative agent was Japanese encephalitis virus (n = 50, 26%), followed by enteroviruses (n = 18, 9.3%), dengue virus (n = 9, 4.6%), herpes simplex virus (n = 1), cytomegalovirus (n = 1) and influenza A virus (n = 1). Fifty-seven (29%) children died acutely. Fatal outcome was independently associated with patient age and Glasgow Coma Scale (GCS) on admission. CONCLUSIONS/SIGNIFICANCE: Acute encephalitis in children in southern Vietnam is associated with high mortality. Although the etiology remains unknown in a majority of the patients, the result from the present study may be useful for future design of treatment and prevention strategies of the disease. The recognition of GCS and age as predictive factors may be helpful for clinicians in managing the patient.

Hien TT, Boni MF, Bryant JE, Ngan TT, Wolbers M, Nguyen TD, Truong NT, Dung NT, Ha DQ, Hien VM et al. 2010. Early pandemic influenza (2009 H1N1) in Ho Chi Minh City, Vietnam: a clinical virological and epidemiological analysis. PLoS Med, 7 (5), pp. e1000277. | Show Abstract | Read more

BACKGROUND: To date, little is known about the initial spread and response to the 2009 pandemic of novel influenza A ("2009 H1N1") in tropical countries. Here, we analyse the early progression of the epidemic from 26 May 2009 until the establishment of community transmission in the second half of July 2009 in Ho Chi Minh City (HCMC), Vietnam. In addition, we present detailed systematic viral clearance data on 292 isolated and treated patients and the first three cases of selection of resistant virus during treatment in Vietnam. METHODS AND FINDINGS: Data sources included all available health reports from the Ministry of Health and relevant health authorities as well as clinical and laboratory data from the first confirmed cases isolated at the Hospital for Tropical Diseases in HCMC. Extensive reverse transcription (RT)-PCR diagnostics on serial samples, viral culture, neuraminidase-inhibition testing, and sequencing were performed on a subset of 2009 H1N1 confirmed cases. Virological (PCR status, shedding) and epidemiological (incidence, isolation, discharge) data were combined to reconstruct the initial outbreak and the establishment of community transmission. From 27 April to 24 July 2009, approximately 760,000 passengers who entered HCMC on international flights were screened at the airport by a body temperature scan and symptom questionnaire. Approximately 0.15% of incoming passengers were intercepted, 200 of whom tested positive for 2009 H1N1 by RT-PCR. An additional 121 out of 169 nontravelers tested positive after self-reporting or contact tracing. These 321 patients spent 79% of their PCR-positive days in isolation; 60% of PCR-positive days were spent treated and in isolation. Influenza-like illness was noted in 61% of patients and no patients experienced pneumonia or severe outcomes. Viral clearance times were similar among patient groups with differing time intervals from illness onset to treatment, with estimated median clearance times between 2.6 and 2.8 d post-treatment for illness-to-treatment intervals of 1-4 d, and 2.0 d (95% confidence interval 1.5-2.5) when treatment was started on the first day of illness. CONCLUSIONS: The patients described here represent a cross-section of infected individuals that were identified by temperature screening and symptom questionnaires at the airport, as well as mildly symptomatic to moderately ill patients who self-reported to hospitals. Data are observational and, although they are suggestive, it is not possible to be certain whether the containment efforts delayed community transmission in Vietnam. Viral clearance data assessed by RT-PCR showed a rapid therapeutic response to oseltamivir.

Wertheim HFL, Puthavathana P, Nghiem NM, van Doorn HR, Nguyen TV, Pham HV, Subekti D, Harun S, Malik S, Robinson J et al. 2010. Laboratory capacity building in Asia for infectious disease research: experiences from the South East Asia Infectious Disease Clinical Research Network (SEAICRN). PLoS Med, 7 (4), pp. e1000231. | Show Abstract | Read more

Enhancing laboratory capacity is essential for generating reliable and accurate data from clinical research, especially in resource-constrained settings. Local well-trained laboratory experts and scientists are important to research, and must participate actively in scientific activities and continuing education programs. Improving laboratory capacity is more than supplying new equipment and reagents; it also includes a long-term commitment to staff training, quality control, and biosafety. Improved laboratory capacity optimizes responses to an epidemic or an outbreak of a novel virulent pathogens, and can support international agendas to reduce the impact of pandemic influenza viruses. © 2010 Wertheim et al.

Cited:

43

Scopus

Mai LQ, Wertheim HFL, Duong TN, van Doorn HR, Hien NT, Horby P. 2010. A Community Cluster of Oseltamivir-Resistant Cases of 2009 H1N1 Influenza New England Journal of Medicine, 362 (1), pp. 86-87. | Read more

Cited:

49

Scopus

Le VT, Phan TQ, Do QH, Nguyen BH, Lam QB, Bach VC, Truong HK, Tran TH, Nguyen VVC, Tran TT et al. 2010. Viral etiology of encephalitis in children in southern Vietnam: results of a one-year prospective descriptive study. PLoS neglected tropical diseases, 4 (10), | Show Abstract

Acute encephalitis is an important and severe disease in children in Vietnam. However, little is known about the etiology while such knowledge is essential for optimal prevention and treatment. To identify viral causes of encephalitis, in 2004 we conducted a one-year descriptive study at Children's Hospital Number One, a referral hospital for children in southern Vietnam including Ho Chi Minh City. Children less than 16 years of age presenting with acute encephalitis of presumed viral etiology were enrolled. Diagnostic efforts included viral culture, serology and real time (RT)-PCRs. A confirmed or probable viral causative agent was established in 41% of 194 enrolled patients. The most commonly diagnosed causative agent was Japanese encephalitis virus (n = 50, 26%), followed by enteroviruses (n = 18, 9.3%), dengue virus (n = 9, 4.6%), herpes simplex virus (n = 1), cytomegalovirus (n = 1) and influenza A virus (n = 1). Fifty-seven (29%) children died acutely. Fatal outcome was independently associated with patient age and Glasgow Coma Scale (GCS) on admission. Acute encephalitis in children in southern Vietnam is associated with high mortality. Although the etiology remains unknown in a majority of the patients, the result from the present study may be useful for future design of treatment and prevention strategies of the disease. The recognition of GCS and age as predictive factors may be helpful for clinicians in managing the patient.

Cited:

26

Scopus

Nguyen NTK, Ha V, Tran NVT, Stabler R, Pham DT, Le TMV, van Doorn HR, Cerdeño-Tárraga A, Thomson N, Campbell J et al. 2010. The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. Circulating in Southern Vietnam. PLoS neglected tropical diseases, 4 (6), | Show Abstract | Read more

BACKGROUND: Plasmid mediated antimicrobial resistance in the Enterobacteriaceae is a global problem. The rise of CTX-M class extended spectrum beta lactamases (ESBLs) has been well documented in industrialized countries. Vietnam is representative of a typical transitional middle income country where the spectrum of infectious diseases combined with the spread of drug resistance is shifting and bringing new healthcare challenges. METHODOLOGY: We collected hospital admission data from the pediatric population attending the hospital for tropical diseases in Ho Chi Minh City with Shigella infections. Organisms were cultured from all enrolled patients and subjected to antimicrobial susceptibility testing. Those that were ESBL positive were subjected to further investigation. These investigations included PCR amplification for common ESBL genes, plasmid investigation, conjugation, microarray hybridization and DNA sequencing of a bla(CTX-M) encoding plasmid. PRINCIPAL FINDINGS: We show that two different bla(CTX-M) genes are circulating in this bacterial population in this location. Sequence of one of the ESBL plasmids shows that rather than the gene being integrated into a preexisting MDR plasmid, the bla(CTX-M) gene is located on relatively simple conjugative plasmid. The sequenced plasmid (pEG356) carried the bla(CTX-M-24) gene on an ISEcp1 element and demonstrated considerable sequence homology with other IncFI plasmids. SIGNIFICANCE: The rapid dissemination, spread of antimicrobial resistance and changing population of Shigella spp. concurrent with economic growth are pertinent to many other countries undergoing similar development. Third generation cephalosporins are commonly used empiric antibiotics in Ho Chi Minh City. We recommend that these agents should not be considered for therapy of dysentery in this setting.

Cited:

39

Scopus

Boni MF, de Jong MD, van Doorn HR, Holmes EC. 2010. Guidelines for identifying homologous recombination events in influenza A virus PLoS ONE, 5 (5), | Show Abstract | Read more

The rapid evolution of influenza viruses occurs both clonally and non-clonally through a variety of genetic mechanisms and selection pressures. The non-clonal evolution of influenza viruses comprises relatively frequent reassortment among gene segments and a more rarely reported process of non-homologous RNA recombination. Homologous RNA recombination within segments has been proposed as a third such mechanism, but to date the evidence for the existence of this process among influenza viruses has been both weak and controversial. As homologous recombination has not yet been demonstrated in the laboratory, supporting evidence, if it exists, may come primarily from patterns of phylogenetic incongruence observed in gene sequence data. Here, we review the necessary criteria related to laboratory procedures and sample handling, bioinformatic analysis, and the known ecology and evolution of influenza viruses that need to be met in order to confirm that a homologous recombination event occurred in the history of a set of sequences. To determine if these criteria have an effect on recombination analysis, we gathered 8307 publicly available full-length sequences of influenza A segments and divided them into those that were sequenced via the National Institutes of Health Influenza Genome Sequencing Project (IGSP) and those that were not. As sample handling and sequencing are executed to a very high standard in the IGSP, these sequences should be less likely to be exposed to contamination by other samples or by laboratory strains, and thus should not exhibit laboratory-generated signals of homologous recombination. Our analysis shows that the IGSP data set contains only two phylogenetically-supported single recombinant sequences and no recombinant clades. In marked contrast, the non-IGSP data show a very large amount of potential recombination. We conclude that the presence of false positive signals in the non-IGSP data is more likely than false negatives in the IGSP data, and that given the evidence to date, homologous recombination seems to play little or no role in the evolution of influenza A viruses. © 2010 Boni et al.

Cited:

75

Scopus

Yu H, Liao Q, Yuan Y, Zhou L, Xiang N, Huai Y, Guo X, Zheng Y, Van Doorn HR, Farrar J et al. 2010. Effectiveness of oseltamivir on disease progression and viral RNA shedding in patients with mild pandemic 2009 influenza A H1N1: Opportunistic retrospective study of medical charts in China BMJ (Online), 341 (7775), pp. 714. | Show Abstract | Read more

Objective: To describe the clinical features and effectiveness of oseltamivir on disease progression and viral RNA shedding in patients with mild pandemic 2009 influenza A(H1N1) virus infection. Design: Opportunistic retrospective review of medical charts of patients with confirmed 2009 H1N1 identified through the national surveillance system in China from May to July 2009. Setting: Under coordination of the Ministry of Health, local health departments were asked to collect medical records of confirmed patients and send them to the Chinese Centre for Disease Control and Prevention on a voluntary basis as part of the public health response. Population: 1291 patients with confirmed 2009 H1N1 infection and available data for chart review. Main outcome measures: Demographic characteristics, comorbidities, symptoms and signs, laboratory tests, findings on chest radiography, antiviral treatment, duration of fever, and duration of viral RNA shedding. Results: The median age of 1291 patients was 20 years (interquartile range 12-26); 701 (54%) were male. The most common symptoms were fever (820, 64%), cough (864, 67%), sore throat (425, 33%), sputum (239, 19%), and rhinorrhoea (228, 18%). Of 920 patients who underwent chest radiography, 110 (12%) had abnormal findings consistent with pneumonia. Some 983 (76%) patients were treated with oseltamivir from a median of the third day of symptoms (2-4). No patients required admission to the intensive care unit or mechanical ventilation. 2009 H1N1 was shed from one day before onset of symptoms to up to eight days after onset in most (91%) patients, with a median of 5 (3-6) days of shedding after onset. Treatment with oseltamivir significantly protected against subsequent development of radiographically confirmed pneumonia (odds ratio 0.12, 95% confidence interval 0.08 to 0.18), and treatment started within two days of symptom onset reduced the duration of fever and viral RNA shedding. Conclusions: Chinese patients with 2009 H1N1 infection predominantly presented with features of uncomplicated, self limiting acute respiratory illness. 2009 H1N1 might be shed longer than seasonal influenza virus. Treatment with oseltamivir was associated with a significantly reduced development of radiographically confirmed pneumonia and a shorter duration of fever and viral RNA shedding. Though these patients benefited from treatment, the findings should be interpreted with caution as the study was retrospective and not all patients underwent chest radiography.

Thanh TT, Pawestri HA, Ngoc NM, Hien VM, Syahrial H, Trung NV, van Doorn RH, Wertheim HFL, Chau NVV, Ha do Q et al. 2010. A real-time RT-PCR for detection of clade 1 and 2 H5N1 influenza A virus using locked nucleic acid (LNA) TaqMan probes. Virol J, 7 (1), pp. 46. | Show Abstract | Read more

BACKGROUND: The emergence and co-circulation of two different clades (clade 1 and 2) of H5N1 influenza viruses in Vietnam necessitates the availability of a diagnostic assay that can detect both variants. RESULTS: We developed a single real-time RT-PCR assay for detection of both clades of H5N1 viruses, directly from clinical specimens, using locked nucleic acid TaqMan probes. Primers and probe used in this assay were designed based on a highly conserved region in the HA gene of H5N1 viruses. The analytical sensitivity of the assay was < 0.5 PFU and 10-100 ssDNA plasmid copies. A total of 106 clinical samples (58 from patients infected with clade 1, 2.1 or 2.3 H5N1 viruses and 48 from uninfected or seasonal influenza A virus-infected individuals) were tested by the assay. The assay showed 97% concordance with initial diagnostics for H5 influenza virus infection with a specificity of 100%. CONCLUSIONS: This assay is a useful tool for diagnosis of H5N1 virus infections in regions where different genetic clades are co-circulating.

Yu H, Liao Q, Yuan Y, Zhou L, Xiang N, Huai Y, Guo X, Zheng Y, van Doorn HR, Farrar J et al. 2010. Effectiveness of oseltamivir on disease progression and viral RNA shedding in patients with mild pandemic 2009 influenza A H1N1: opportunistic retrospective study of medical charts in China. BMJ, 341 (sep28 1), pp. c4779. | Show Abstract | Read more

OBJECTIVE: To describe the clinical features and effectiveness of oseltamivir on disease progression and viral RNA shedding in patients with mild pandemic 2009 influenza A(H1N1) virus infection. DESIGN: Opportunistic retrospective review of medical charts of patients with confirmed 2009 H1N1 identified through the national surveillance system in China from May to July 2009. SETTING: Under coordination of the Ministry of Health, local health departments were asked to collect medical records of confirmed patients and send them to the Chinese Centre for Disease Control and Prevention on a voluntary basis as part of the public health response. Population 1291 patients with confirmed 2009 H1N1 infection and available data for chart review. MAIN OUTCOME MEASURES: Demographic characteristics, comorbidities, symptoms and signs, laboratory tests, findings on chest radiography, antiviral treatment, duration of fever, and duration of viral RNA shedding. RESULTS: The median age of 1291 patients was 20 years (interquartile range 12-26); 701 (54%) were male. The most common symptoms were fever (820, 64%), cough (864, 67%), sore throat (425, 33%), sputum (239, 19%), and rhinorrhoea (228, 18%). Of 920 patients who underwent chest radiography, 110 (12%) had abnormal findings consistent with pneumonia. Some 983 (76%) patients were treated with oseltamivir from a median of the third day of symptoms (2-4). No patients required admission to the intensive care unit or mechanical ventilation. 2009 H1N1 was shed from one day before onset of symptoms to up to eight days after onset in most (91%) patients, with a median of 5 (3-6) days of shedding after onset. Treatment with oseltamivir significantly protected against subsequent development of radiographically confirmed pneumonia (odds ratio 0.12, 95% confidence interval 0.08 to 0.18), and treatment started within two days of symptom onset reduced the duration of fever and viral RNA shedding. CONCLUSIONS: Chinese patients with 2009 H1N1 infection predominantly presented with features of uncomplicated, self limiting acute respiratory illness. 2009 H1N1 might be shed longer than seasonal influenza virus. Treatment with oseltamivir was associated with a significantly reduced development of radiographically confirmed pneumonia and a shorter duration of fever and viral RNA shedding. Though these patients benefited from treatment, the findings should be interpreted with caution as the study was retrospective and not all patients underwent chest radiography.

Boni MF, de Jong MD, van Doorn HR, Holmes EC. 2010. Guidelines for identifying homologous recombination events in influenza A virus. PLoS One, 5 (5), pp. e10434. | Show Abstract | Read more

The rapid evolution of influenza viruses occurs both clonally and non-clonally through a variety of genetic mechanisms and selection pressures. The non-clonal evolution of influenza viruses comprises relatively frequent reassortment among gene segments and a more rarely reported process of non-homologous RNA recombination. Homologous RNA recombination within segments has been proposed as a third such mechanism, but to date the evidence for the existence of this process among influenza viruses has been both weak and controversial. As homologous recombination has not yet been demonstrated in the laboratory, supporting evidence, if it exists, may come primarily from patterns of phylogenetic incongruence observed in gene sequence data. Here, we review the necessary criteria related to laboratory procedures and sample handling, bioinformatic analysis, and the known ecology and evolution of influenza viruses that need to be met in order to confirm that a homologous recombination event occurred in the history of a set of sequences. To determine if these criteria have an effect on recombination analysis, we gathered 8307 publicly available full-length sequences of influenza A segments and divided them into those that were sequenced via the National Institutes of Health Influenza Genome Sequencing Project (IGSP) and those that were not. As sample handling and sequencing are executed to a very high standard in the IGSP, these sequences should be less likely to be exposed to contamination by other samples or by laboratory strains, and thus should not exhibit laboratory-generated signals of homologous recombination. Our analysis shows that the IGSP data set contains only two phylogenetically-supported single recombinant sequences and no recombinant clades. In marked contrast, the non-IGSP data show a very large amount of potential recombination. We conclude that the presence of false positive signals in the non-IGSP data is more likely than false negatives in the IGSP data, and that given the evidence to date, homologous recombination seems to play little or no role in the evolution of influenza A viruses.

Kremer K, van-der-Werf MJ, Au BKY, Anh DD, Kam KM, van-Doorn HR, Borgdorff MW, van-Soolingen D. 2009. Vaccine-induced immunity circumvented by typical Mycobacterium tuberculosis Beijing strains. Emerg Infect Dis, 15 (2), pp. 335-339. | Show Abstract | Read more

The frequency of typical and atypical Beijing strains of Mycobacterium tuberculosis was determined in the Netherlands; Vietnam; and Hong Kong Special Administrative Region, People's Republic of China. The strains' associations with drug resistance, M. bovis BCG vaccination, and patient characteristics were assessed. BCG vaccination may have positively selected the prevalent typical Beijing strains.

Schultsz C, Nguyen VD, Hai LT, Do QH, Peiris JSM, Lim W, Garcia J-M, Nguyen DT, Nguyen THL, Huynh HT et al. 2009. Prevalence of antibodies against avian influenza A (H5N1) virus among Cullers and poultry workers in Ho Chi Minh City, 2005. PLoS One, 4 (11), pp. e7948. | Show Abstract | Read more

BACKGROUND: Between 2003 and 2005, highly pathogenic avian influenza A (H5N1) viruses caused large scale outbreaks in poultry in the Ho Chi Minh City area in Vietnam. We studied the prevalence of antibodies against H5N1 in poultry workers and cullers who were active in the program in Ho Chi Minh City in 2004 and 2005. METHODOLOGY/PRINCIPAL FINDINGS: Single sera from 500 poultry workers and poultry cullers exposed to infected birds were tested for antibodies to avian influenza H5N1, using microneutralization assays and hemagglutination inhibition assay with horse blood. All sera tested negative using microneutralization tests. Three samples showed a 1ratio80 titer in the hemagglutination inhibition assay. CONCLUSIONS/SIGNIFICANCE: This study provides additional support for the low transmissibility of clade 1 H5N1 to humans, but limited transmission to highly exposed persons cannot be excluded given the presence of low antibody titers in some individuals.

van Doorn HR, An DD, de Jong MD, Lan NTN, Hoa DV, Quy HT, Chau NVV, Duy PM, Tho DQ, Chinh NT et al. 2008. Fluoroquinolone resistance detection in Mycobacterium tuberculosis with locked nucleic acid probe real-time PCR. Int J Tuberc Lung Dis, 12 (7), pp. 736-742. | Show Abstract

SETTING: Pham Ngoc Thach Hospital for Tuberculosis and Lung Diseases, Ho Chi Minh City, Vietnam. OBJECTIVE: Fluoroquinolones (FQs) are increasingly used in the treatment of tuberculosis (TB) and are the second-line drugs of choice for treatment of multidrug-resistant TB. We aimed to set up a polymerase chain reaction (PCR) based assay to detect the most common FQ-resistance-associated mutations in gyrase A (gyrA) of Mycobacterium tuberculosis. DESIGN: A total of 42 FQ-resistant and 40 FQ-susceptible isolates were collected in 2005-2006 and sequenced in gyrA. Using sequencing results as gold standard, a real-time PCR using three locked nucleic acid probes (LNA-PCR) was designed to detect mutations at positions 90, 91 and 94 (97% of gyrA FQ-resistance-associated mutations) and evaluated. RESULTS: Sequencing of 42 FQ-resistant isolates revealed no gyrA mutations in 10 isolates, 20 isolates had a single mutation and 12 isolates showed double peaks at resistance-associated alleles, suggesting a heterogeneous population. With LNA-PCR, all wild-type and 19/20 mutant isolates were correctly identified. Eleven of 12 heterogeneous isolates were correctly identified as resistant mutants. Overall, 71% ([19 + 11]/42) of phenotypically FQ-resistant isolates were detected. Specificity was 100% on 40 FQ-susceptible isolates. CONCLUSION: This assay provides a simple and rapid means to reliably detect FQ-resistance-associated gyrA mutations in M. tuberculosis.

Thanh TT, van Doorn HR, de Jong MD. 2008. Human H5N1 influenza: current insight into pathogenesis. Int J Biochem Cell Biol, 40 (12), pp. 2671-2674. | Show Abstract | Read more

Since their emergence as avian (1996) and zoonotic human pathogens (1997), H5N1 influenza viruses have become endemic among poultry in large parts of Asia, but outbreaks have also been seen in Africa and Europe. Transmission from animals to humans remains sporadic, but mortality of human infection is high (63%). To date, reported cases of human to human transmission have been rare. Patient and laboratory data suggest that highly efficient viral replication and the resulting intensified immune response of the human host are the determining factors in H5N1 pathogenesis and case fatality rate. Therefore, in the management of H5N1 disease (early) suppression of viral replication is key. The underlying biochemistry and cell biology of H5N1 pathogenesis and treatment are briefly discussed in this review.

van Kruijssen AM, Templeton KE, van der Plas RN, van Doorn HR, Claas ECJ, Sukhai RN, Kuijper EJ. 2007. Detection of respiratory pathogens by real-time PCR in children with clinical suspicion of pertussis. Eur J Pediatr, 166 (11), pp. 1189-1191. | Show Abstract | Read more

The use of a multiplex respiratory real-time PCR in patients clinically suspected of pertussis increases the number of pathogens detected.

van Doorn HR, Wentink-Bonnema E, Rentenaar RJ, van Gool T. 2007. Specific cross-reactivity in sera from cystic echinococcosis patients in an enzyme-linked immunoelectrotransfer blot for cysticercosis diagnostics. Trans R Soc Trop Med Hyg, 101 (9), pp. 948-950. | Show Abstract | Read more

A commercially available enzyme-linked immunoelectrotransfer blot originally intended for diagnosis of cysticercosis was evaluated for echinococcosis diagnosis, because a characteristic band pattern--different from the specific cysticercosis pattern--was observed in sera from patients with echinococcosis. This band pattern was observed in 29 (78%) of 37 parasitologically proven cystic echinococcosis patients. Specificity of these bands was 100% for echinococcosis, when tested with 75 control sera.

van Doorn HR, Hofwegen H, Koelewijn R, Gilis H, Wentink-Bonnema E, Pinelli E, van Genderen PJJ, Schipper HG, van Gool T. 2007. Reliable serodiagnosis of imported cystic echinococcosis with a commercial indirect hemagglutination assay. Diagn Microbiol Infect Dis, 57 (4), pp. 409-412. | Show Abstract | Read more

A commercially available indirect hemagglutination assay (IHA) (Echinococcosis Fumouze; Laboratoires Fumouze, Levallois-Perret, France) was evaluated using sera from 52 patients with proven cystic echinococcosis. The specificity was assessed using 247 sera from patients with various parasitic, bacterial, viral, and fungal infectious diseases; sera containing autoimmune antibodies; and sera from healthy blood donors. With a cutoff value for a positive result of 320 (as recommended by the manufacturer), the sensitivity and specificity were 88% and 98.4%; with a cutoff of 160, the sensitivity and specificity were 94% and 95.1%, respectively. The IHA is rapid, easy to perform, and is a very sensitive serodiagnostic test for cystic echinococcosis.

van Doorn HR, Koelewijn R, Hofwegen H, Gilis H, Wetsteyn JCFM, Wismans PJ, Sarfati C, Vervoort T, van Gool T. 2007. Use of enzyme-linked immunosorbent assay and dipstick assay for detection of Strongyloides stercoralis infection in humans. J Clin Microbiol, 45 (2), pp. 438-442. | Show Abstract | Read more

A homemade enzyme-linked immunosorbent assay (ELISA) (Academic Medical Center ELISA [AMC-ELISA]) and a dipstick assay for the detection of anti-Strongyloides stercoralis antibodies in serum were developed and evaluated together with two commercially available ELISAs (IVD-ELISA [IVD Research, Inc.] and Bordier-ELISA [Bordier Affinity Products SA]) for their use in the serodiagnosis of imported strongyloidiasis. Both commercially available ELISAs have not been evaluated previously. The sensitivities of the assays were evaluated using sera from 90 patients with parasitologically proven intestinal strongyloidiasis and from 9 patients with clinical larva currens. The sensitivities of the AMC-ELISA, dipstick assay, IVD-ELISA, and Bordier-ELISA were 93, 91, 89, and 83%, respectively, for intestinal strongyloidiasis. In all tests, eight of nine sera from patients with larva currens were positive. The specificity was assessed using a large serum bank of 220 sera from patients with various parasitic, bacterial, viral, and fungal infectious diseases; sera containing autoimmune antibodies; and sera from healthy blood donors. The specificities of AMC-ELISA, dipstick assay, IVD-ELISA, and Bordier-ELISA were 95.0, 97.7, 97.2, and 97.2%, respectively. Our data suggest that all four assays are sensitive and specific tests for the diagnosis of both intestinal and cutaneous strongyloidiasis.

Rentenaar RJ, van Doorn HR, Rijneveld AW. 2006. [Acute anaemia in a Vietnamese patient with alpha-thalassaemia and a parvovirus infection]. Ned Tijdschr Geneeskd, 150 (40), pp. 2223.

van Doorn HR, Bruijnesteijn van Coppenraet ES, Duim B, Vandenbroucke-Grauls CMJE, Weel JF, Dankert J, Kuijper EJ, de Jong MD. 2006. Silica-guanidinium thiocyanate-based nucleic acid isolation protocol does not improve sensitivity of two commercial tests for detection of Mycobacterium tuberculosis in respiratory samples. Eur J Clin Microbiol Infect Dis, 25 (10), pp. 673-675. | Read more

van Doorn HR, de Haas PEW, Kremer K, Vandenbroucke-Grauls CMJE, Borgdorff MW, van Soolingen D. 2006. Public health impact of isoniazid-resistant Mycobacterium tuberculosis strains with a mutation at amino-acid position 315 of katG: a decade of experience in The Netherlands. Clin Microbiol Infect, 12 (8), pp. 769-775. | Show Abstract | Read more

A previous limited study demonstrated that Mycobacterium tuberculosis isolates with a mutation at amino-acid position 315 of katG (Delta315) exhibited high-level resistance to isoniazid and were more frequently resistant to streptomycin. In the present study, isoniazid-resistant M. tuberculosis isolates from 8,332 patients in The Netherlands (1993-2002) were screened for the Delta315 mutation. Isoniazid resistance was found in 592 (7%) isolates, of which 323 (55%) carried Delta315. IS6110 restriction fragment length polymorphism analysis showed that Delta315 isolates occurred in clusters, suggesting recent transmission, at the same frequency as isoniazid-susceptible isolates. In contrast, other isoniazid-resistant isolates clustered significantly less frequently. Delta315 isolates were high-level isoniazid-resistant, streptomycin-resistant and multidrug-resistant significantly more often, and may have a greater impact on public health, than other isoniazid-resistant isolates.

van Doorn HR, Lo-A-Njoe SM, Ottenkamp J, Pajkrt D. 2006. Widened coronary arteries in a feverish child. Pediatr Cardiol, 27 (4), pp. 515-518. | Show Abstract | Read more

A 3-year-old girl with fever of unknown origin after a visit to Surinam was seen at our hospital. Signs and symptoms were indicative of either Kawasaki syndrome or an acute viral or (atypical) bacterial illness. No cardiac abnormalities were noted at echocardiography. She was treated with intravenous immunoglobulin and clarithromycin and made a quick recovery. Serologically, the diagnosis of murine typhus was made; a flea-borne rickettsiosis caused by Rickettsia typhi. A follow-up echocardiography 1 week later showed a dilated left coronary artery, which was normal again 4 weeks later. We suggest that this phenomenon was a manifestation of rickettsial vasculitis.

van Doorn HR, van Vugt M, Wetsteyn JCFM, van Gool T. 2005. [Infestation with the tapeworm Diphyllobothrium latum after eating raw fish]. Ned Tijdschr Geneeskd, 149 (44), pp. 2470-2472. | Show Abstract

A 31-year-old man with no relevant medical history encountered a white, ribbon-shaped object, 15 cm long and approximately 1 cm wide, in his faeces. It turned out to be Diphyllobothrium latum, a tapeworm that has fish as the intermediate host. The patient had eaten raw fish and shellfish during a holiday in Brazil 5 months before. He recovered after a single dose of praziquantel.

van Doorn HR, Hofwegen H, Koelewijn R, Gilis H, Peek R, Wetsteyn JCFM, van Genderen PJJ, Vervoort T, van Gool T. 2005. Use of rapid dipstick and latex agglutination tests and enzyme-linked immunosorbent assay for serodiagnosis of amebic liver abscess, amebic Colitis, and Entamoeba histolytica Cyst Passage. J Clin Microbiol, 43 (9), pp. 4801-4806. | Show Abstract | Read more

A homemade enzyme-linked immunosorbent assay (ELISA) and a dipstick assay (Dipstick) for the detection of anti-Entamoeba histolytica antibodies in serum were developed and evaluated together with a commercially available latex agglutination test (LAT; Laboratoires Fumouze) for their use in serodiagnosis of amebiasis. The sensitivity of these assays was evaluated with sera from 27 patients with radiologically proven, cellulose acetate precipitation (CAP) test-positive amebic liver abscess, 7 patients with parasitologically and PCR-proven amebic colitis, and 11 patients with parasitologically and PCR-proven E. histolytica cyst passage. The sensitivities of the ELISA, Dipstick, and LAT were all 93.3% (42/45). With a combination of Dipstick and LAT, all abscess and colitis patients had at least one positive result. The specificity was assessed with 238 sera from patients with various parasitic, bacterial, viral, and fungal infectious diseases, sera containing autoimmune antibodies, and sera from healthy blood donors. The specificities of the ELISA, Dipstick, and LAT were 97.1%, 98.1%, and 99.5%, respectively. Of 61 sera from patients with PCR-proven E. dispar infection, 60 (98.4%) were negative in both Dipstick and LAT and 59 (96.7%) were negative in ELISA. Our data suggest that all three assays are sensitive serological tests. The rapid LAT and Dipstick provide fast results and can easily be applied in routine laboratories in order to facilitate the diagnosis of amebiasis.

van Doorn HR, Claas ECJ, Templeton KE, van der Zanden AGM, te Koppele Vije A, de Jong MD, Dankert J, Kuijper EJ. 2003. Detection of a point mutation associated with high-level isoniazid resistance in Mycobacterium tuberculosis by using real-time PCR technology with 3'-minor groove binder-DNA probes. J Clin Microbiol, 41 (10), pp. 4630-4635. | Show Abstract | Read more

Tuberculosis remains one of the leading infectious causes of death worldwide. The emergence of drug-resistant strains of Mycobacterium tuberculosis is a serious public health threat. Resistance to isoniazid (INH) is the most prevalent form of resistance in M. tuberculosis and is mainly caused by mutations in the catalase peroxidase gene (katG). Among high-level INH-resistant isolates (MIC > or = 2), 89% are associated with a mutation at codon 315 of katG. There is a need to develop rapid diagnostic tests to permit appropriate antibiotic treatment and to improve clinical management. Therefore, a single-tube real-time PCR, using a novel kind of probe (3'-minor groove binder-DNA probe), was developed to detect either the wild-type or the mutant codon directly in Ziehl-Neelsen-positive sputum samples. The detection limit of the assay for purified DNA was 5 fg per well (one mycobacterial genome), and with spiked sputum samples, it was 20 copies per well, corresponding to 10(3) mycobacteria per ml of sputum. Sputum samples from 20 patients living in Kazakhstan or Moldova and infected with monodrug- or multidrug-resistant M. tuberculosis and 20 sputum samples from patients infected with INH-susceptible M. tuberculosis were tested. The sensitivities and specificities of the probes were 70 and 94% for the wild-type probe and 82 and 100% for the mutant probe. Binding to either probe was nonambiguous. This real-time PCR allows the rapid identification of a mutant katG allele and can easily be implemented in a clinical microbiology laboratory.

van Doorn HR, Kuijper EJ, van der Ende A, Welten AG, van Soolingen D, de Haas PE, Dankert J. 2001. The susceptibility of Mycobacterium tuberculosis to isoniazid and the Arg-->Leu mutation at codon 463 of katG are not associated. J Clin Microbiol, 39 (4), pp. 1591-1594. | Show Abstract | Read more

A mutation (CCG-->CTG [Arg-->Leu]) in codon 463 of katG (catalase peroxidase) of Mycobacterium tuberculosis has been found in isoniazid (INH)-resistant strains. A PCR restriction endonuclease analysis to detect this mutation was applied to 395 M. tuberculosis isolates from patients in The Netherlands. The proportion of isolates with a detectable mutation was 32% (32 out of 100) and 29% (85 out of 295) among INH-susceptible isolates and INH-resistant or -intermediate isolates, respectively. Sequencing of five INH-susceptible isolates with such mutations showed that all five had the Arg463Leu mutation. We conclude that the Arg463Leu mutation of katG of M. tuberculosis is not a reliable indicator of INH resistance.

van Soolingen D, de Haas PE, van Doorn HR, Kuijper E, Rinder H, Borgdorff MW. 2000. Mutations at amino acid position 315 of the katG gene are associated with high-level resistance to isoniazid, other drug resistance, and successful transmission of Mycobacterium tuberculosis in the Netherlands. J Infect Dis, 182 (6), pp. 1788-1790. | Show Abstract | Read more

The prevalence of mutations at amino acid (aa) position 315 in the katG gene of isoniazid (INH)-resistant Mycobacterium tuberculosis isolates in The Netherlands and the mutation's association with the level of INH resistance, multidrug resistance, and transmission were determined. Of 4288 M. tuberculosis isolates with available laboratory results, 295 (7%) exhibited INH resistance. Of 148 aa 315 mutants, 89% had MICs of 5-10 microg/mL, whereas 75% of the other 130 INH-resistant strains had MICs of 0.5-1 microg/mL. Of the aa 315 mutants, 33% exhibited monodrug resistance, compared with 69% of other INH-resistant strains (P<.0001). Multidrug resistance was found among 14% of the aa 315 mutants and 7% of the other INH-resistant strains (P>.05). The probability of being in an IS6110 DNA restriction fragment length polymorphism cluster was similar for aa 315 mutants and INH-susceptible strains, but the probability was reduced in other INH-resistant strains. Thus, aa 315 mutants lead to secondary cases of tuberculosis as often as INH-susceptible strains do.

Schuurman J, Van Ree R, Perdok GJ, Van Doorn HR, Tan KY, Aalberse RC. 1999. Normal human immunoglobulin G4 is bispecific: it has two different antigen-combining sites. Immunology, 97 (4), pp. 693-698. | Show Abstract | Read more

Unlike other immunoglobulin G (IgG) subclasses, IgG4 antibodies in plasma have been reported to be functionally monovalent. In this paper we show that the apparent monovalency of circulating IgG4 is caused by asymmetry of plasma IgG4. A large fraction of plasma IgG4 molecules have two different antigen-binding sites, resulting in bispecificity. Sera from patients with IgG4 antibodies to both house dust mite and grass pollen induced cross-linking of Sepharose-bound grass pollen antigen to radiolabelled house dust mite allergen Der p I. This bispecific binding activity was not observed in sera with IgG4 antibodies to either grass pollen or house dust mite exclusively. Depletion of IgG4 antibodies resulted in disappearance of the bispecific activity. By size exclusion chromatography we excluded the possibility that bispecific activity was caused by aggregation of IgG4 antibodies. These results indicate that circulating (polyclonal) IgG4 antibodies have two different antigen-binding sites and therefore are functionally monovalent antibodies.

South East Asia Infectious Disease Clinical Research Network. 2013. Effect of double dose oseltamivir on clinical and virological outcomes in children and adults admitted to hospital with severe influenza: double blind randomised controlled trial. BMJ, 346 (may30 2), pp. f3039. | Show Abstract | Read more

OBJECTIVE: To investigate the validity of recommendations in treatment guidelines to use higher than approved doses of oseltamivir in patients with severe influenza. DESIGN: Double blind randomised trial. SETTING: Thirteen hospitals in Indonesia, Singapore, Thailand, and Vietnam. PARTICIPANTS: Patients aged ≥ 1 year admitted to hospital with confirmed severe influenza. INTERVENTIONS: Oral oseltamivir at double dose (150 mg twice a day/paediatric equivalent) versus standard dose (75 mg twice a day/paediatric equivalent). MAIN OUTCOME MEASURE: Viral status according to reverse transcriptase polymerase chain reaction (RT-PCR) for influenza RNA in nasal and throat swabs on day five. RESULTS: Of 326 patients (including 246 (75.5%) children aged <15), 165 and 161 were randomised to double or standard dose oseltamivir, respectively. Of these, 260 (79.8%) were infected with influenza virus A (133 (40.8%) with A/H3N2, 72 (22.1%) with A/H1N1-pdm09, 38 (11.7%) with seasonal A/H1N1, 17 (5.2%) with A/H5N1) and 53 (16.2%) with influenza virus B. A further 3.9% (13) were false positive by rapid antigen test (negative by RT-PCR and no rise in convalescent haemagglutination inhibition titers). Similar proportions of patients were negative for RT-PCR on day five of treatment: 115/159 (72.3%, 95% confidence interval 64.9% to 78.7%) double dose recipients versus 105/154 (68.2%, 60.5% to 75.0%) standard dose recipients; difference 4.2% (-5.9 to 14.2); P=0.42. No differences were found in clearance of virus in subgroup analyses by virus type/subtype, age, and duration of illness before randomisation. Mortality was similar: 12/165 (7.3%, 4.2% to 12.3%) in double dose recipients versus 9/161 (5.6%, 3.0% to 10.3%) in standard dose recipients. No differences were found between double and standard dose arms in median days on supplemental oxygen (3 (interquartile range 2-5) v 3.5 (2-7)), in intensive care (4.5 (3-6) v 5 (2-11), and on mechanical ventilation (2.5 (1-16) v 8 (1-16)), respectively. No important differences in tolerability were found. CONCLUSIONS: There were no virological or clinical advantages with double dose oseltamivir compared with standard dose in patients with severe influenza admitted to hospital. REGISTRATION: Clinical Trials NCT00298233.

Tan LV, van Doorn HR, Nghia HDT, Chau TTH, Tu LTP, de Vries M, Canuti M, Deijs M, Jebbink MF, Baker S et al. 2013. Identification of a new cyclovirus in cerebrospinal fluid of patients with acute central nervous system infections. MBio, 4 (3), pp. e00231-e00213. | Show Abstract | Read more

Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology remains unknown in a large proportion of cases. We identified and characterized the full genome of a novel cyclovirus (tentatively named cyclovirus-Vietnam [CyCV-VN]) in cerebrospinal fluid (CSF) specimens of two Vietnamese patients with CNS infections of unknown etiology. CyCV-VN was subsequently detected in 4% of 642 CSF specimens from Vietnamese patients with suspected CNS infections and none of 122 CSFs from patients with noninfectious neurological disorders. Detection rates were similar in patients with CNS infections of unknown etiology and those in whom other pathogens were detected. A similar detection rate in feces from healthy children suggested food-borne or orofecal transmission routes, while high detection rates in feces from pigs and poultry (average, 58%) suggested the existence of animal reservoirs for such transmission. Further research is needed to address the epidemiology and pathogenicity of this novel, potentially zoonotic virus.

Boni MF, Nguyen TD, de Jong MD, van Doorn HR. 2013. Virulence attenuation during an influenza A/H5N1 pandemic. Philos Trans R Soc Lond B Biol Sci, 368 (1614), pp. 20120207. | Show Abstract | Read more

More than 15 years after the first human cases of influenza A/H5N1 in Hong Kong, the world remains at risk for an H5N1 pandemic. Preparedness activities have focused on antiviral stockpiling and distribution, development of a human H5N1 vaccine, operationalizing screening and social distancing policies, and other non-pharmaceutical interventions. The planning of these interventions has been done in an attempt to lessen the cumulative mortality resulting from a hypothetical H5N1 pandemic. In this theoretical study, we consider the natural limitations on an H5N1 pandemic's mortality imposed by the virus' epidemiological-evolutionary constraints. Evolutionary theory dictates that pathogens should evolve to be relatively benign, depending on the magnitude of the correlation between a pathogen's virulence and its transmissibility. Because the case fatality of H5N1 infections in humans is currently 60 per cent, it is doubtful that the current viruses are close to their evolutionary optimum for transmission among humans. To describe the dynamics of virulence evolution during an H5N1 pandemic, we build a mathematical model based on the patterns of clinical progression in past H5N1 cases. Using both a deterministic model and a stochastic individual-based simulation, we describe (i) the drivers of evolutionary dynamics during an H5N1 pandemic, (ii) the range of case fatalities for which H5N1 viruses can successfully cause outbreaks in humans, and (iii) the effects of different kinds of social distancing on virulence evolution. We discuss two main epidemiological-evolutionary features of this system (i) the delaying or slowing of an epidemic which results in a majority of hosts experiencing an attenuated virulence phenotype and (ii) the strong evolutionary pressure for lower virulence experienced by the virus during a period of intense social distancing.

Do AHL, van Doorn HR, Nghiem MN, Bryant JE, Hoang THT, Do QH, Van TL, Tran TT, Wills B, Nguyen VCV et al. 2011. Viral etiologies of acute respiratory infections among hospitalized Vietnamese children in Ho Chi Minh City, 2004-2008. PLoS One, 6 (3), pp. e18176. | Show Abstract | Read more

BACKGROUND: The dominant viral etiologies responsible for acute respiratory infections (ARIs) are poorly understood, particularly among hospitalized children in resource-limited tropical countries where morbidity and mortality caused by ARIs are highest. Improved etiological insight is needed to improve clinical management and prevention. OBJECTIVES: We conducted a three-year prospective descriptive study of severe respiratory illness among children from 2 months to 13 years of age within the largest referral hospital for infectious diseases in southern Vietnam. METHODS: Molecular detection for 15 viral species and subtypes was performed on three types of respiratory specimens (nose, throat swabs and nasopharyngeal aspirates) using a multiplex RT-PCR kit (Seeplex™ RV detection, Seegene) and additional monoplex real-time RT-PCRs. RESULTS: A total of 309 children were enrolled from November 2004 to January 2008. Viruses were identified in 72% (222/309) of cases, including respiratory syncytial virus (24%), influenza virus A and B (17%), human bocavirus (16%), enterovirus (9%), human coronavirus (8%), human metapneumovirus (7%), parainfluenza virus 1-3 (6%), adenovirus (5%), and human rhinovirus A (4%). Co-infections with multiple viruses were detected in 20% (62/309) of patients. When combined, diagnostic yields in nose and throat swabs were similar to nasopharyngeal aspirates. CONCLUSION: Similar to other parts in the world, RSV and influenza were the predominant viral pathogens detected in Vietnamese hospitalized children. Combined nasal and throat swabs are the specimens of choice for sensitive molecular detection of a broad panel of viral agents. Further research is required to better understand the clinical significance of single versus multiple viral coinfections and to address the role of bacterial (co-)infections involved in severe respiratory illness.

Le QM, Wertheim HFL, Tran ND, van Doorn HR, Nguyen TH, Horby P, Vietnam H1N1 Investigation Team. 2010. A community cluster of oseltamivir-resistant cases of 2009 H1N1 influenza. N Engl J Med, 362 (1), pp. 86-87. | Read more

Le VT, Phan TQ, Do QH, Nguyen BH, Lam QB, Bach VC, Truong HK, Tran TH, Nguyen VVC, Tran TT et al. 2010. Viral etiology of encephalitis in children in southern Vietnam: results of a one-year prospective descriptive study. PLoS Negl Trop Dis, 4 (10), pp. e854. | Show Abstract | Read more

BACKGROUND: Acute encephalitis is an important and severe disease in children in Vietnam. However, little is known about the etiology while such knowledge is essential for optimal prevention and treatment. To identify viral causes of encephalitis, in 2004 we conducted a one-year descriptive study at Children's Hospital Number One, a referral hospital for children in southern Vietnam including Ho Chi Minh City. METHODOLOGY/PRINCIPAL FINDINGS: Children less than 16 years of age presenting with acute encephalitis of presumed viral etiology were enrolled. Diagnostic efforts included viral culture, serology and real time (RT)-PCRs. A confirmed or probable viral causative agent was established in 41% of 194 enrolled patients. The most commonly diagnosed causative agent was Japanese encephalitis virus (n = 50, 26%), followed by enteroviruses (n = 18, 9.3%), dengue virus (n = 9, 4.6%), herpes simplex virus (n = 1), cytomegalovirus (n = 1) and influenza A virus (n = 1). Fifty-seven (29%) children died acutely. Fatal outcome was independently associated with patient age and Glasgow Coma Scale (GCS) on admission. CONCLUSIONS/SIGNIFICANCE: Acute encephalitis in children in southern Vietnam is associated with high mortality. Although the etiology remains unknown in a majority of the patients, the result from the present study may be useful for future design of treatment and prevention strategies of the disease. The recognition of GCS and age as predictive factors may be helpful for clinicians in managing the patient.

Hien TT, Boni MF, Bryant JE, Ngan TT, Wolbers M, Nguyen TD, Truong NT, Dung NT, Ha DQ, Hien VM et al. 2010. Early pandemic influenza (2009 H1N1) in Ho Chi Minh City, Vietnam: a clinical virological and epidemiological analysis. PLoS Med, 7 (5), pp. e1000277. | Show Abstract | Read more

BACKGROUND: To date, little is known about the initial spread and response to the 2009 pandemic of novel influenza A ("2009 H1N1") in tropical countries. Here, we analyse the early progression of the epidemic from 26 May 2009 until the establishment of community transmission in the second half of July 2009 in Ho Chi Minh City (HCMC), Vietnam. In addition, we present detailed systematic viral clearance data on 292 isolated and treated patients and the first three cases of selection of resistant virus during treatment in Vietnam. METHODS AND FINDINGS: Data sources included all available health reports from the Ministry of Health and relevant health authorities as well as clinical and laboratory data from the first confirmed cases isolated at the Hospital for Tropical Diseases in HCMC. Extensive reverse transcription (RT)-PCR diagnostics on serial samples, viral culture, neuraminidase-inhibition testing, and sequencing were performed on a subset of 2009 H1N1 confirmed cases. Virological (PCR status, shedding) and epidemiological (incidence, isolation, discharge) data were combined to reconstruct the initial outbreak and the establishment of community transmission. From 27 April to 24 July 2009, approximately 760,000 passengers who entered HCMC on international flights were screened at the airport by a body temperature scan and symptom questionnaire. Approximately 0.15% of incoming passengers were intercepted, 200 of whom tested positive for 2009 H1N1 by RT-PCR. An additional 121 out of 169 nontravelers tested positive after self-reporting or contact tracing. These 321 patients spent 79% of their PCR-positive days in isolation; 60% of PCR-positive days were spent treated and in isolation. Influenza-like illness was noted in 61% of patients and no patients experienced pneumonia or severe outcomes. Viral clearance times were similar among patient groups with differing time intervals from illness onset to treatment, with estimated median clearance times between 2.6 and 2.8 d post-treatment for illness-to-treatment intervals of 1-4 d, and 2.0 d (95% confidence interval 1.5-2.5) when treatment was started on the first day of illness. CONCLUSIONS: The patients described here represent a cross-section of infected individuals that were identified by temperature screening and symptom questionnaires at the airport, as well as mildly symptomatic to moderately ill patients who self-reported to hospitals. Data are observational and, although they are suggestive, it is not possible to be certain whether the containment efforts delayed community transmission in Vietnam. Viral clearance data assessed by RT-PCR showed a rapid therapeutic response to oseltamivir.

Boni MF, de Jong MD, van Doorn HR, Holmes EC. 2010. Guidelines for identifying homologous recombination events in influenza A virus. PLoS One, 5 (5), pp. e10434. | Show Abstract | Read more

The rapid evolution of influenza viruses occurs both clonally and non-clonally through a variety of genetic mechanisms and selection pressures. The non-clonal evolution of influenza viruses comprises relatively frequent reassortment among gene segments and a more rarely reported process of non-homologous RNA recombination. Homologous RNA recombination within segments has been proposed as a third such mechanism, but to date the evidence for the existence of this process among influenza viruses has been both weak and controversial. As homologous recombination has not yet been demonstrated in the laboratory, supporting evidence, if it exists, may come primarily from patterns of phylogenetic incongruence observed in gene sequence data. Here, we review the necessary criteria related to laboratory procedures and sample handling, bioinformatic analysis, and the known ecology and evolution of influenza viruses that need to be met in order to confirm that a homologous recombination event occurred in the history of a set of sequences. To determine if these criteria have an effect on recombination analysis, we gathered 8307 publicly available full-length sequences of influenza A segments and divided them into those that were sequenced via the National Institutes of Health Influenza Genome Sequencing Project (IGSP) and those that were not. As sample handling and sequencing are executed to a very high standard in the IGSP, these sequences should be less likely to be exposed to contamination by other samples or by laboratory strains, and thus should not exhibit laboratory-generated signals of homologous recombination. Our analysis shows that the IGSP data set contains only two phylogenetically-supported single recombinant sequences and no recombinant clades. In marked contrast, the non-IGSP data show a very large amount of potential recombination. We conclude that the presence of false positive signals in the non-IGSP data is more likely than false negatives in the IGSP data, and that given the evidence to date, homologous recombination seems to play little or no role in the evolution of influenza A viruses.

822