Professor Maciej Boni

Research Area: Bioinformatics & Stats (inc. Modelling and Computational Biology)
Technology Exchange: Bioinformatics and Computational biology
Scientific Themes: Tropical Medicine & Global Health
Keywords: influenza, malaria, dengue, drug resistance, recombination, mathematical modeling and economic epidemiology
Web Links:
Map showing phylogenetically-inferred global migration routes for H3N2 influenza viruses between 2001-2008.  Published in 2013 as Le et al in Emerging Infectious Diseases.  Thicker lines show stronger migratory connections between regions.  Red lines show connections between Vietnam and other countries.

Map showing phylogenetically-inferred global migration routes for H3N2 influenza viruses between 200 ...

Human antibody titers to avian influenza viruses in southern Vietnam, showing the H5, H7, and H9 subtypes.  Titers are broken down by age group, and show that some older individuals show high titers to certain avian influenza viruses.  However, it cannot be ruled out that these laboratory-measured antibody reactions are not high-concentrations human influenza antibodies  that show some binding to avian influenza antigens.  This was originally published in the Journal of Infectious Diseases (Boni et al, 2013).

Human antibody titers to avian influenza viruses in southern Vietnam, showing the H5, H7, and H9 sub ...

My lab's research centers on

  • human influenza epidemiology and evolution - we run a range of field and clinical studies centered on questions in tropical influenza epidemiology, and we use methods in computational epidemiology to analyze data coming our of these studies.  Our group works at the interface of field studies, theoretical epidemiology, and statistical fitting of epidemiological models to field data.
  • evaluating population-level malaria treatment strategies with individual-based microsimulation models
  • phylogenetic analysis of avian influenza evolution in southern Vietnam
  • economic epidemiology of avian influenza
  • evaluating population-level efficacy of a potential dengue vaccine with mathematical models

Broad interests include: seroepidemiology, participatory epidemiology, evolutionary epidemiology, economic epidemiology, evaluation of treatment strategies, drug-resistance evolution, immune-escape evolution, niche construction.

Name Department Institution Country
Professor Marion Koopmans Dutch Institute for Public Health and the Environment (RIVM) Netherlands
Professor Neil M Ferguson OBE FMedSci Imperial College London United Kingdom
Dr Le Thi Quynh Mai National Institutes for Hygiene and Epidemiology (NIHE) Vietnam
Dr Pham Quang Thai National Institutes for Hygiene and Epidemiology (NIHE) Vietnam

Rasmussen DA, Boni MF, Koelle K. 2014. Reconciling phylodynamics with epidemiology: the case of dengue virus in southern Vietnam. Mol Biol Evol, 31 (2), pp. 258-271. Read abstract | Read more

Coalescent methods are widely used to infer the demographic history of populations from gene genealogies. These approaches-often referred to as phylodynamic methods-have proven especially useful for reconstructing the dynamics of rapidly evolving viral pathogens. Yet, population dynamics inferred from viral genealogies often differ widely from those observed from other sources of epidemiological data, such as hospitalization records. We demonstrate how a modeling framework that allows for the direct fitting of mechanistic epidemiological models to genealogies can be used to test different hypotheses about what ecological factors cause phylodynamic inferences to differ from observed dynamics. We use this framework to test different hypotheses about why dengue serotype 1 (DENV-1) population dynamics in southern Vietnam inferred using existing phylodynamic methods differ from hospitalization data. Specifically, we consider how factors such as seasonality, vector dynamics, and spatial structure can affect inferences drawn from genealogies. The coalescent models we derive to take into account vector dynamics and spatial structure reveal that these ecological complexities can substantially affect coalescent rates among lineages. We show that incorporating these additional ecological complexities into coalescent models can also greatly improve estimates of historical population dynamics and lead to new insights into the factors shaping viral genealogies. Hide abstract

Le MQ, Lam HM, Cuong VD, Lam TT, Halpin RA, Wentworth DE, Hien NT, Thanh LET, Phuong HV, Horby P, Boni MF. 2013. Migration and persistence of human influenza A viruses, Vietnam, 2001-2008. Emerg Infect Dis, 19 (11), pp. 1756-1765. Read abstract | Read more

Understanding global influenza migration and persistence is crucial for vaccine strain selection. Using 240 new human influenza A virus whole genomes collected in Vietnam during 2001-2008, we looked for persistence patterns and migratory connections between Vietnam and other countries. We found that viruses in Vietnam migrate to and from China, Hong Kong, Taiwan, Cambodia, Japan, South Korea, and the United States. We attempted to reduce geographic bias by generating phylogenies subsampled at the year and country levels. However, migration events in these phylogenies were still driven by the presence or absence of sequence data, indicating that an epidemiologic study design that controls for prevalence is required for robust migration analysis. With whole-genome data, most migration events are not detectable from the phylogeny of the hemagglutinin segment alone, although general migratory relationships between Vietnam and other countries are visible in the hemagglutinin phylogeny. It is possible that virus lineages in Vietnam persisted for >1 year. Hide abstract

Boni MF, Galvani AP, Wickelgren AL, Malani A. 2013. Economic epidemiology of avian influenza on smallholder poultry farms. Theor Popul Biol, 90 pp. 135-144. Read abstract | Read more

Highly pathogenic avian influenza (HPAI) is often controlled through culling of poultry. Compensating farmers for culled chickens or ducks facilitates effective culling and control of HPAI. However, ensuing price shifts can create incentives that alter the disease dynamics of HPAI. Farmers control certain aspects of the dynamics by setting a farm size, implementing infection control measures, and determining the age at which poultry are sent to market. Their decisions can be influenced by the market price of poultry which can, in turn, be set by policy makers during an HPAI outbreak. Here, we integrate these economic considerations into an epidemiological model in which epidemiological parameters are determined by an outside agent (the farmer) to maximize profit from poultry sales. Our model exhibits a diversity of behaviors which are sensitive to (i) the ability to identify infected poultry, (ii) the average price of infected poultry, (iii) the basic reproductive number of avian influenza, (iv) the effect of culling on the market price of poultry, (v) the effect of market price on farm size, and (vi) the effect of poultry density on disease transmission. We find that under certain market and epidemiological conditions, culling can increase farm size and the total number of HPAI infections. Our model helps to inform the optimization of public health outcomes that best weigh the balance between public health risk and beneficial economic outcomes for farmers. Hide abstract

Boni MF, Chau NV, Dong N, Todd S, Nhat NT, de Bruin E, van Beek J, Hien NT, Simmons CP, Farrar J, Koopmans M. 2013. Population-level antibody estimates to novel influenza A/H7N9. J Infect Dis, 208 (4), pp. 554-558. Read abstract | Read more

There are no contemporary data available describing human immunity to novel influenza A/H7N9. Using 1723 prospectively collected serum samples in southern Vietnam, we tested for antibodies to 5 avian influenza virus antigens, using a protein microarray. General-population antibody titers against subtype H7 virus are higher than antibody titers against subtype H5 and lower than titers against H9. The highest titers were observed for human influenza virus subtypes. Titers to avian influenza virus antigens increased with age and with geometric mean antibody titer to human influenza virus antigens. There were no titer differences between the urban and the rural location in our study. Hide abstract

Baker S, Duy PT, Nga TV, Dung TT, Phat VV, Chau TT, Turner AK, Farrar J, Boni MF. 2013. Fitness benefits in fluoroquinolone-resistant Salmonella Typhi in the absence of antimicrobial pressure. Elife, 2 pp. e01229. Read abstract | Read more

Fluoroquinolones (FQ) are the recommended antimicrobial treatment for typhoid, a severe systemic infection caused by the bacterium Salmonella enterica serovar Typhi. FQ-resistance mutations in S. Typhi have become common, hindering treatment and control efforts. Using in vitro competition experiments, we assayed the fitness of eleven isogenic S. Typhi strains with resistance mutations in the FQ target genes, gyrA and parC. In the absence of antimicrobial pressure, 6 out of 11 mutants carried a selective advantage over the antimicrobial-sensitive parent strain, indicating that FQ resistance in S. Typhi is not typically associated with fitness costs. Double-mutants exhibited higher than expected fitness as a result of synergistic epistasis, signifying that epistasis may be a critical factor in the evolution and molecular epidemiology of S. Typhi. Our findings have important implications for the management of drug-resistant S. Typhi, suggesting that FQ-resistant strains would be naturally maintained even if fluoroquinolone use were reduced. DOI: Hide abstract

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. Read 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. Hide abstract

Hien TT, Boni MF, Bryant JE, Ngan TT, Wolbers M, Nguyen TD, Truong NT, Dung NT 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. Read 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. Hide abstract

Boni MF, Smith DL, Laxminarayan R. 2008. Benefits of using multiple first-line therapies against malaria. Proc Natl Acad Sci U S A, 105 (37), pp. 14216-14221. Read abstract | Read more

Despite the availability of many drugs and therapies to treat malaria, many countries' national policies recommend using a single first-line therapy for most clinical malaria cases. To assess whether this is the best strategy for the population as a whole, we designed an evolutionary-epidemiological modeling framework for malaria and compared the benefits of different treatment strategies in the context of resistance evolution. Our results show that the population-wide use of multiple first-line therapies (MFT) against malaria yields a better clinical outcome than using a single therapy or a cycling strategy where therapies are rotated, either on a fixed cycling schedule or when resistance levels or treatment failure become too high. MFT strategies also delay the emergence and slow the fixation of resistant strains (phenotypes), and they allow a larger fraction of the population to be treated without trading off future treatment of cases that may be untreatable because of high resistance levels. Earlier papers have noted that cycling strategies have the disadvantage of creating a less temporally variable environment than MFT strategies, making resistance evolution easier for the parasite. Here, we illustrate a second feature of parasite ecology that impairs the performance of cycling policies, namely, that cycling policies degrade the mean fitness of the parasite population more quickly than MFT policies, making it easier for new resistant types to invade and spread. The clinical benefits of using multiple first-line therapies against malaria suggest that MFT policies should play a key role in malaria elimination and control programs. Hide abstract

Boni MF, Posada D, Feldman MW. 2007. An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics, 176 (2), pp. 1035-1047. Read abstract | Read more

Statistical tests for detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern or a signal that would be unlikely to appear under clonal reproduction. Dozens of such tests have been described, but many are hampered by long running times, confounding of selection and recombination, and/or inability to isolate the mosaic-producing event. We introduce a test that is exact, nonparametric, rapidly computable, free of the infinite-sites assumption, able to distinguish between recombination and variation in mutation/fixation rates, and able to identify the breakpoints and sequences involved in the mosaic-producing event. Our test considers three sequences at a time: two parent sequences that may have recombined, with one or two breakpoints, to form the third sequence (the child sequence). Excess similarity of the child sequence to a candidate recombinant of the parents is a sign of recombination; we take the maximum value of this excess similarity as our test statistic Delta(m,n,b). We present a method for rapidly calculating the distribution of Delta(m,n,b) and demonstrate that it has comparable power to and a much improved running time over previous methods, especially in detecting recombination in large data sets. Hide abstract

Peak CM, Thuan PD, Britton A, Nguyen TD, Wolbers M, Thanh NV, Buckee CO, Boni MF. 2015. Measuring the association between artemisinin-based case management and malaria incidence in southern Vietnam, 1991-2010. Am J Trop Med Hyg, 92 (4), pp. 811-817. Read abstract | Read more

In addition to being effective, fast-acting, and well tolerated, artemisinin-based combination therapies (ACTs) are able to kill certain transmission stages of the malaria parasite. However, the population-level impacts of ACTs on reducing malaria transmission have been difficult to assess. In this study on the history of malaria control in Vietnam, we assemble annual reporting on malaria case counts, coverage with insecticide-treated nets (ITN) and indoor residual spraying (IRS), and drug purchases by provincial malaria control programs from 1991 to 2010 in Vietnam's 20 southern provinces. We observe a significant negative association between artemisinin use and malaria incidence, with a 10% absolute increase in the purchase proportion of artemisinin-containing regimens being associated with a 29.1% (95% confidence interval: 14.8-41.0%) reduction in slide-confirmed malaria incidence, after accounting for changes in urbanization, ITN/IRS coverage, and two indicators of health system capacity. One budget-related indicator of health system capacity was found to have a smaller association with malaria incidence, and no other significant factors were found. Our findings suggest that including an artemisinin component in malaria drug regimens was strongly associated with reduced malaria incidence in southern Vietnam, whereas changes in urbanization and coverage with ITN or IRS were not. Hide abstract