Biology subjects

Boni, M. F.

Publications and source records attributed to Boni, M. F..

6 recordsLinked to original sources

bioRxiv2018

Game theory of vaccination and depopulation for managing avian influenza on poultry farms

Highly pathogenic avian influenza is endemic in domestic poultry populations in East and South Asia and is a major threat to human health, animal health, and the poultry production industry. The behavioral response of farmers to the disease and its epidemiological effects are still poorly understood. We considered a symmetric game in a region with widespread smallholder poultry production, where the players are broiler poultry farmers and between-farm disease transmission is both environmental (local) and mediated by the trade of infected birds. Three types of farmer behaviors were modelled: vaccination, depopulation, and cessation of poultry farming. We found that the transmission level of avian influenza through trade networks had strong qualitative effects on the systems epidemiological-economic equilibria. In the case of low trade-based transmission, when the monetary cost of infection is sufficiently high, depopulation behavior persists and maintains a disease-free equilibrium. In the case of high trade-based transmission, depopulation behavior has perverse epidemiological effects - as it accelerates the spread of disease via poultry traders - but has a high enough payoff to farmers that it persists at the systems game theoretic equilibrium. In this situation, state interventions should focus on making effective vaccination technologies available at a low price rather than penalizing infected farms. Our results emphasize the need in endemic countries to further investigate the commercial circuits through which birds from infected farms are traded.

epidemiology↗

bioRxiv2018

Demographic features and mortality risks in smallholder poultry farms of the Mekong river delta region

This study describes the demographic structure and dynamics of small scale poultry farms of the Mekong river delta region, one of the worlds highest-risk regions for avian influenza outbreaks. Fifty farms were monitored over a 20-month period, with farm sizes, species, age, arrival/departure of poultry, and farm management practices recorded monthly. The history of poultry flocks in the sampled farms was recovered using a flock-matching algorithm. Median flock population sizes were 16 for chickens (IQR: 10 - 40), 32 for ducks (IQR: 18 - 101) and 11 for Muscovy ducks (IQR: 7 - 18); farm size distributions for the three species were heavily right-skewed. There was substantial flock overlap on almost all farms, with only one farm practicing an all-in-all-out management system. The rate of interspecific contacts was high, with two out of three farms housing at least two bird species. Among poultry species, demographic dynamics varied. Muscovy ducks were kept for long periods, in small numbers and outdoors, while chickens and ducks were farmed in larger numbers, indoors or in pens, with more rapid flock turnover. Most chicks were sold young to be fattened on other farms, and broiler and layer ducks had a short production period and higher degree of specialization. The rate of mortality due to disease did not differ much among species, with birds being less likely to die from disease at older ages, but frequency of disease symptoms differed by species. Time series of disease-associated mortality and population size were correlated for Muscovy ducks (Kendalls coefficient {tau} = 0.49, p value < 0.01).\n\nImpacts O_LIThe structure and dynamics of poultry populations kept in small scale farms in the Mekong river delta were accurately described.\nC_LIO_LIPoultry farms mix poultry of different species, ages, and production types, with multiple overlapping flocks present on a farm at all times. This promotes the persistence of pathogens.\nC_LIO_LIThe three main farmed poultry species of poultry (chickens, ducks and Muscovy ducks) are managed differently and have different demographic characteristics.\nC_LI

epidemiology↗

bioRxiv2017

MULTILOCUS SEQUENCE TYPING REVEALS A UNIQUE CO-DOMINANT POPULATION STRUCTURE OF CRYPTOCOCCUS NEOFORMANS VAR. GRUBII IN VIETNAM

Cryptococcosis is amongst the most important invasive fungal infections globally, with cryptococcal meningitis causing an estimated 180,000 deaths each year in HIV infected patients alone. Patients with other forms of immunosuppression are also at risk, and disease is increasingly recognized in apparently immunocompetent individuals. Cryptococcus neoformans var. grubii (serotype A, molecular type VNI) has a global distribution and is responsible for the majority of cases. Here, we used the consensus ISHAM Multilocus Sequence Typing (MLST) for C. neoformans to define the population structure of clinical isolates of Cryptococcus neoformans var. grubii from Vietnam (n=136) and Laos (n=81). We placed these isolates into the global context using published MLST data from 8 other countries (total N = 669). We observed a phylo-geographical relationship in which Laos was similar to its Southeast Asian neighbor Thailand in being dominated (83%) by Sequence Type (ST) 4 and its Single Locus Variant ST6. On the other hand, Vietnam was uniquely intermediate between Southeast Asia and East Asia having both ST4/ST6 (35%) and ST5 (48%) which causes the majority of cases in East Asia. Analysis of genetic distance (Fst) between different populations of Cryptococcus neoformans var. grubii supported the intermediate nature of the population from Vietnam. A strong association between ST5 and infection in apparently immunocompetent, HIV-uninfected patients was observed in Vietnam (OR: 7.97, [95%CI: 3.18-19.97], p < 0.0001). Our study emphasizes that Vietnam, with its intermediate Cryptococcus neoformans var. grubii population structure, provides the strongest epidemiological evidence of the relationship between ST5 and infection of HIV-uninfected patients. Human population genetic distances within the region suggest these differences in CNVG population across Southeast Asia are driven by ecological factors rather than host factors.\n\nAuthor summaryCryptococcus neoformans is a yeast that causes meningitis in people, usually with damaged immune systems. There are >180,000 deaths in HIV-infected patients each year, most occurring where there are the highest HIV/AIDS disease burdens. Vietnam and Laos have contributed significantly to clinical trials aiming to improve the treatment of cryptococcal meningitis, but the relationship of isolates from these countries to the global population is not yet described. Here, we address this knowledge gap by using Multilocus Sequence Typing to study the population of Cryptococcus neoformans var. grubii (CNVG) in Laos and Vietnam, with the specific aim of incorporating these populations into the wider global context. We found that, in most countries, a single lineage (family) of strains was responsible for most disease. The Vietnamese CNVG population was unusual in that 2 main lineages circulated at the same time. The Vietnamese CNVG population occupies a middle ground between Thailand/Laos in the west and China in the east. The differences in population structure moving from West to East are probably due to ecological differences. Disease in HIV uninfected patients was almost always due to members of a single family of strains (ST5).

molecular biology↗

bioRxiv2017

The decline of malaria in Vietnam, 1991-2014

A central component of malaria control initiatives throughout the world is the use of artemisinin-based combination therapies (ACTs) for treatment of uncomplicated P. falciparium malaria. Despite the well-documented clinical efficacy of ACTs, the population-level effects of ACT case management on malaria transmission have not been studied thoroughly until recently. An ideal case study for the population-level effects of artemisinin use can be found in Vietnam, where a major increase of malaria cases in the 1980s was followed by the gradual adoption of artemisinin-based clinical case management. We assembled annual data from Vietnams National Institutes for Malariology, Parasitology, and Entomology showing the degree to which artemisinin therapies were adopted in different provinces, the effort placed on vector control, and the funding available to provincial malaria control programs, from 1991 to 2014. Data on urbanization were also collected for this period. We found that a 10% increase in the artemisinin proportion of treatments procured by a provincial control program corresponded to a 32.8% (95% CI: 27.7 - 37.5%) decline in estimated malaria cases; the association persisted and the effect size was nearly unchanged if confirmed cases or suspected cases were used. There was no consistent effect of vector control on malaria cases in Vietnam as a whole, nor was any effect found when the data were broken up regionally. The association between urbanization and malaria was generally negative and sometimes statistically significant. This was most pronounced in the central region of Vietnam, where a 10% increase in urbanization corresponded to a 43.3% (95% CI: 21.6 - 58.9%) decrease in suspected malaria incidence; this association was not statistically significant if confirmed cases or estimated cases were used. The decline of malaria in Vietnam from 1991 to 2014 can largely be attributed to the rapid adoption of artemisinin-based drugs. Recent analyses of aggregated data from Africa have shown that insecticide-treated nets have had the greatest effect on lowering malaria prevalence over the past fifteen years, suggesting that the success of different types of malaria interventions is region specific. Continuing global efforts on malaria elimination should focus on both vector control measures and increased access to artemisinin-combination therapies.

epidemiology↗

bioRxiv2017

Non-annual seasonality of influenza-like illness in a tropical urban setting

In temperate countries, influenza and other viral respiratory diseases often have distinct seasonal peaks occurring during colder, wintertime months. However, little is known about the dynamics of influenza and viral respiratory disease dynamics in the tropics, despite high morbidity and a clear epidemiological link between tropical and temperate countries. In temperate countries, the dynamics of influenza and other respiratory diseases are often analyzed using syndromic surveillance data describing influenza-like illness (ILI) as ILI is highly correlated with virological surveillance for influenza. To obtain a detailed picture of respiratory disease incidence patterns in a large tropical city, we established an mHealth study in community outpatient clinics in Ho Chi Minh City, Vietnam (11N latitude). From August 2009 through December 2015, clinics reported daily case numbers of ILI using standard mobile-phone SMS messaging. A subset of these clinics performed molecular diagnostics for influenza A and B viruses. Unlike the annual patterns seen in temperate countries, ILI activity in Ho Chi Minh City exhibited strong non-annual periodicity and was not correlated with PCR-confirmed influenza. The dominant periodicity in the data was approximately 200 days. This was confirmed by a time series decomposition, a step-wise regression analysis on annual and non-annual covariates, and a forecasting exercise showing that forecasting was 30% to 40% more accurate when a 200-day non-annual cycle was included in the forecast. This suggests, for the first-time, that a non-annual cycle may be an essential driver of ILI dynamics in the tropics. This raises new questions about the seasonality and drivers of respiratory disease transmission in tropical countries.

epidemiology↗

bioRxiv2016

Structure of general-population antibody titer distributions to influenza A virus

Seroepidemiological studies aim to understand population-level exposure and immunity to infectious diseases. Results from serological assays are normally presented as binary outcomes describing the presence or absence of pathogen-specific antibody, despite the fact that many assays measure continuous quantities. A populations natural distribution of antibody titers to an endemic infectious disease may in fact include information on multiple serological states - e.g. naivete, recent infection, non-recent infection - depending on the disease in question and the acquisition and waning patterns of host immunity. In this study, we investigate a collection of 20,152 general-population serum samples from southern Vietnam collected between 2009 and 2013 from which we report antibody titers to the influenza virus HA1 protein using a continuous titer measurement from a protein microarray assay. We describe the distributions of antibody titers to subtypes 2009 H1N1 and H3N2. Using a model selection approach to fit mixture distributions, we show that 2009 H1N1 antibody titers fall into four titer subgroups and that H3N2 titers fall into three subgroups. For H1N1, our interpretation is that the two highest-titer subgroups correspond to recent infection and historical infection, which is consistent with 2009 pandemic attack rates. For H3N2, observations censored at the highest titer dilutions make similar interpretations difficult to validate.

epidemiology↗