Dr 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:

Research centers on

  • human influenza epidemiology and evolution
  • bioinformatic analysis of avian influenza evolution in southern Vietnam
  • economic epidemiology of avian influenza
  • evaluating population-level malaria treatment strategies with mathematical models
  • evaluating population-level efficacy of a potential dengue vaccine with mathematical models

Interests in theory of ecology and evolution include: evolutionary epidemiology, economic epidemiology, niche construction, drug-resistance evolution, immune-escape evolution.

Name Department Institution Country
Prof Marion Koopmans Dutch Institute for Public Health and the Environment (RIVM) Netherlands
Prof 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

Long NT, Thanh TT, van Doorn HR, Vu PP, Dung PT, Dung TT, Tien TN, Thao DT 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. Read 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. Hide abstract

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. Read 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. 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

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. Hide abstract

Boni MF, Manh BH, Thai PQ, Farrar J, Hien TT, Hien NT, Van Kinh N, Horby P. 2009. Modelling the progression of pandemic influenza A (H1N1) in Vietnam and the opportunities for reassortment with other influenza viruses. BMC Med, 7 (1), pp. 43. Read abstract | Read more

A novel variant of influenza A (H1N1) is causing a pandemic and, although the illness is usually mild, there are concerns that its virulence could change through reassortment with other influenza viruses. This is of greater concern in parts of Southeast Asia, where the population density is high, influenza is less seasonal, human-animal contact is common and avian influenza is still endemic. Hide abstract

Boni MF, Buckee CO, White NJ. 2008. Mathematical models for a new era of malaria eradication. PLoS Med, 5 (11), pp. e231. | Read more

Boni MF, Zhou Y, Taubenberger JK, Holmes EC. 2008. Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus Journal of Virology, 82 (10), pp. 4807-4811. | Read more

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. 2008. Vaccination and antigenic drift in influenza Vaccine, 26 pp. C8-C14. | Read more

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

Boni MF, Gog JR, Andreasen V, Feldman MW. 2006. Epidemic dynamics and antigenic evolution in a single season of influenza A. Proceedings. Biological sciences / The Royal Society, 273 (1592), pp. 1307-1316. Read abstract | Read more

We use a mathematical model to study the evolution of influenza A during the epidemic dynamics of a single season. Classifying strains by their distance from the epidemic-originating strain, we show that neutral mutation yields a constant rate of antigenic evolution, even in the presence of epidemic dynamics. We introduce host immunity and viral immune escape to construct a non-neutral model. Our population dynamics can then be framed naturally in the context of population genetics, and we show that departure from neutrality is governed by the covariance between a strain's fitness and its distance from the original epidemic strain. We quantify the amount of antigenic evolution that takes place in excess of what is expected under neutrality and find that this excess amount is largest under strong host immunity and long epidemics. Hide abstract

Boni MF, Gog JR, Andreasen V, Christiansen FB. 2004. Influenza drift and epidemic size: the race between generating and escaping immunity. Theor Popul Biol, 65 (2), pp. 179-191. Read abstract | Read more

Influenza in humans is characterised by strongly annual dynamics and antigenic evolution leading to partial escape from prior host immunity. The variability of new epidemic strains depends on the amount of virus currently circulating. In this paper, the amount of antigenic variation produced each year is dependent on the epidemic size. Our model reduces to a one-dimensional map and a full mathematical analysis is presented. This simple system suggests some basic principles which may be more generally applicable. In particular, for diseases with antigenic drift, vaccination may be doubly beneficial. Not only does it protect the population through classical herd immunity, but the overall case reduction reduces the chance of new variants being produced; hence, subsequent epidemics may be milder as a result of this positive feedback. Also, a disease with a high innate rate of antigenic variation will always be able to invade a susceptible population, whereas a disease with less potential for variation may require several introduction events to become endemic. Hide abstract

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