Maciej F. Boni
A5056799272- Malaria Research and Control
- Mosquito-borne diseases and control
- Influenza Virus Research Studies
- COVID-19 epidemiological studies
- Animal Disease Management and Epidemiology
- SARS-CoV-2 and COVID-19 Research
- Evolution and Genetic Dynamics
- Viral Infections and Vectors
- Viral gastroenteritis research and epidemiology
- Respiratory viral infections research
- Animal Virus Infections Studies
- Computational Drug Discovery Methods
- Vaccine Coverage and Hesitancy
- Viral Infections and Outbreaks Research
- Parasites and Host Interactions
- Salmonella and Campylobacter epidemiology
- COVID-19 Pandemic Impacts
- Mathematical and Theoretical Epidemiology and Ecology Models
- Livestock and Poultry Management
- Tuberculosis Research and Epidemiology
- Vibrio bacteria research studies
- Virology and Viral Diseases
- Fungal Infections and Studies
- CRISPR and Genetic Engineering
- Dengue and Mosquito Control Research
Temple College
2024
Temple University
2020-2024
Center for Disease Dynamics, Economics & Policy
2013-2024
Pennsylvania State University
2017-2024
Oxford University Clinical Research Unit
2014-2024
Nuffield Orthopaedic Centre
2013-2024
University of Oxford
2015-2024
Angkor Hospital for Children
2013-2024
University of Siena
2024
Erasmus University Rotterdam
2024
Abstract The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. first was associated with a mix of lineages, while the second and third waves were driven Beta (B.1.351) Delta (B.1.617.2) variants, respectively 1–3 . In November 2021, genomic surveillance teams South Botswana detected new variant rapid resurgence infections Gauteng province, Africa. Within days genome being uploaded, it designated concern (Omicron, B.1.1.529) World Health Organization and,...
Statistical tests for detecting mosaic structure or recombination among nucleotide sequences usually rely on identifying a pattern signal that would be unlikely to appear under clonal reproduction. Dozens of such have been described, but many are hampered by long running times, confounding selection and recombination, and/or inability isolate the mosaic-producing event. We introduce test is exact, nonparametric, rapidly computable, free infinite-sites assumption, able distinguish between...
Significance Dengue virus has rapidly spread into new human populations due to travel and changing suitability for the mosquito vector, causing severe febrile illness significant mortality. Accurate predictive models identifying vulnerability dengue outbreaks are necessary epidemic preparedness containment of virus. Here we show that an epidemiological model transmission in travelers, based on mobility data from ∼40 million mobile phone subscribers climatic information, predicts geographic...
Norovirus (NoV) is the leading cause of viral gastroenteritis globally. Since 1996, NoV variants a single genetic lineage, GII.4, have been associated with at least six pandemics acute and caused between 62 80% all outbreaks. The emergence these novel GII.4 has attributed to rapid evolution antigenic variation in response herd immunity; however, contribution recombination as mechanism facilitating increasingly evident. In this study, we sought examine role that intragenotype played variants....
Virus host shifts are generally associated with novel adaptations to exploit the cells of new species optimally. Surprisingly, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has apparently required little no significant adaptation humans since start Disease 2019 (COVID-19) pandemic and October 2020. Here we assess types natural selection taking place in Sarbecoviruses horseshoe bats versus early SARS-CoV-2 evolution humans. While there is moderate evidence diversifying positive...
Identifying recombinant sequences in an era of large genomic databases is challenging as it requires efficient algorithm to identify candidate recombinants and parents, well appropriate statistical methods correct for the number comparisons performed. In 2007, a computation was introduced exact nonparametric mosaicism statistic that gave high-precision P values putative recombinants. This meant multiple-comparisons corrected also had high precision, which crucial when performing millions or...
MalariaGEN is a data-sharing network that enables groups around the world to work together on genomic epidemiology of malaria. Here we describe new release curated genome variation data 7,000 Plasmodium falciparum samples from partner studies in 28 malaria-endemic countries. High-quality genotype calls 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using standardised analysis pipeline. Copy number variants associated with drug resistance structural cause...
Defining acceptable performance characteristics for SARS-CoV-2 serological tests requires factoring in how the results will be used.
Among the 30 nonsynonymous nucleotide substitutions in Omicron S-gene are 13 that have only rarely been seen other SARS-CoV-2 sequences. These mutations cluster within three functionally important regions of at sites will likely impact (1) interactions between subunits Spike trimer and predisposition to shift from down up configurations, (2) with ACE2 receptors, (3) priming for membrane fusion. We show here that, based on both rarity these intrapatient sequencing reads patterns selection...
<ns3:p>We describe the MalariaGEN Pf7 data resource, seventh release of <ns3:italic>Plasmodium falciparum</ns3:italic> genome variation from network. It comprises over 20,000 samples 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented. For first time we include dried blood spot sequenced after selective whole amplification, necessitating new methods to genotype copy number variations. We identify a large newly emerging...
The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. first was associated with a mix of lineages, while the second and third waves were driven Beta (B.1.351) Delta (B.1.617.2) variants, respectively1–3. In November 2021, genomic surveillance teams South Botswana detected new variant rapid resurgence infections Gauteng province, Africa. Within days genome being uploaded, it designated concern (Omicron, B.1.1.529) World Health Organization and, within...
Abstract Increasing levels of artemisinin and partner drug resistance threaten malaria control elimination globally. Triple artemisinin-based combination therapies (TACTs) which combine derivatives with two drugs are efficacious well tolerated in clinical trials, including areas multidrug-resistant malaria. Whether early TACT adoption could delay the emergence spread antimalarial is a question vital importance. Using independent individual-based models Plasmodium falciparum epidemiology...
Despite the availability of many drugs and therapies to treat malaria, countries' national policies recommend using a single first-line therapy for most clinical malaria cases. To assess whether this is best strategy population as whole, we designed an evolutionary-epidemiological modeling framework compared benefits different treatment strategies in context resistance evolution. Our results show that population-wide use multiple (MFT) against yields better outcome than or cycling where are...
By 2009, there were worrying signs from western Cambodia that parasitological responses to artesunate-containing treatment regimens for uncomplicated Plasmodium falciparum malaria slower than elsewhere which suggested the emergence of artemisinin resistance. Vietnam shares a long land border with large number migrants crossing it on daily basis. Therefore, is an urgent need investigate whether any evidence change in response derivatives Vietnam. From August 2010 May 2011, randomized...
Typhoid is a systemic infection caused by Salmonella Typhi and Paratyphi A, human-restricted bacteria that are transmitted faeco-orally. S . A clonal, their limited genetic diversity has precluded the identification of long-term transmission networks in areas with high disease burden. To improve our understanding typhoid we have taken novel approach, performing longitudinal spatial case–control study for Nepal, combining single-nucleotide polymorphism genotyping case localization via global...
Acute central nervous system (CNS) infections cause substantial morbidity and mortality, but the etiology remains unknown in a large proportion of cases. We identified characterized full genome novel cyclovirus (tentatively named cyclovirus-Vietnam [CyCV-VN]) cerebrospinal fluid (CSF) specimens two Vietnamese patients with CNS etiology. CyCV-VN was subsequently detected 4% 642 CSF from suspected none 122 CSFs noninfectious neurological disorders. Detection rates were similar those whom other...
Fluoroquinolones (FQ) are the recommended antimicrobial treatment for typhoid, a severe systemic infection caused by bacterium Salmonella enterica serovar Typhi. FQ-resistance mutations in S. Typhi have become common, hindering and control efforts. Using vitro competition experiments, we assayed fitness of eleven isogenic strains with resistance FQ target genes, gyrA parC. In absence pressure, 6 out 11 mutants carried selective advantage over antimicrobial-sensitive parent strain, indicating...