A5009528251- Viral gastroenteritis research and epidemiology
- SARS-CoV-2 and COVID-19 Research
- Animal Virus Infections Studies
- Respiratory viral infections research
- COVID-19 epidemiological studies
- Bacteriophages and microbial interactions
- Viral Infections and Outbreaks Research
- Viral Infections and Vectors
- Congenital Diaphragmatic Hernia Studies
- Machine Learning and Algorithms
- Virology and Viral Diseases
- Viral Infections and Immunology Research
- Tracheal and airway disorders
- Animal Disease Management and Epidemiology
- Statistical Methods and Inference
- Plant Virus Research Studies
- Hepatitis Viruses Studies and Epidemiology
- Advanced Bandit Algorithms Research
- COVID-19 Clinical Research Studies
- Virus-based gene therapy research
- SARS-CoV-2 detection and testing
- Genomics and Phylogenetic Studies
- Salmonella and Campylobacter epidemiology
- Child Nutrition and Water Access
- Zoonotic diseases and public health
Uganda Virus Research Institute
2020-2024
Duy Tan University
2024
Arizona State University
2024
Medical Research Council
2020-2023
MRC University of Glasgow Centre for Virus Research
2020-2023
University of Massachusetts Amherst
2019-2023
University of York
2023
Amherst College
2023
London School of Hygiene & Tropical Medicine
2023
Wellcome Sanger Institute
2014-2022
The COVID-19 pandemic has been characterised by sequential variant-specific waves shaped viral, individual human and population factors. SARS-CoV-2 variants are defined their unique combinations of mutations there a clear adaptation to more efficient infection since the emergence this new coronavirus in late 2019. Here, we use machine learning models identify shared signatures, i.e., common underlying mutational processes link these subset that define concern (VOCs). First, examined global...
Significance Shigella sonnei is a globally emerging agent of bacterial dysentery. Here, we use genomics to examine the microevolution S. in Vietnam. We show that was introduced into Vietnam early 1980s, where it continued evolve, spreading geographically establish localized founder populations. The population Ho Chi Minh City has undergone several clonal replacement events, during which small number microevolutionary changes have risen dominance. These changes, induced by horizontal gene...
To end the largest known outbreak of Ebola virus disease (EVD) in West Africa and to prevent new transmissions, rapid epidemiological tracing cases contacts was required. The ability quickly identify unknown sources chains transmission is key ending EVD epidemic even greater importance context recent reports (EBOV) persistence survivors. Phylogenetic analysis complete EBOV genomes can provide important information on source any infection. A local deep sequencing facility established at...
Abstract Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with population of approximately 40 million people. We 322 full genomes 39,424 reported infections, thus representing 0.8% the cases. Phylogenetic analyses these sequences revealed emergence lineage A.23.1 A.23. Lineage represented 88% observed December 2020, then 100% 2021. The was also 26 other countries. Although precise changes differ those first three...
During the course of SARS-CoV-2 pandemic, viral variants have emerged that often contain notable mutations in spike gene. Mutations encode changes S1/S2 (furin) activation site been considered especially impactful.
Abstract Background Shigellosis remains considerable public health problem in some developing countries. The nature of Shigellae suggests that they are highly adaptable when placed under selective pressure a human population. This is demonstrated by variation and fluctuations serotypes antimicrobial resistance profile organisms circulating differing setting endemic locations. Antimicrobial the genus Shigella constant threat, with reports Asia being resistant to multiple antimicrobials new...
ABSTRACT Norovirus is a highly transmissible infectious agent that causes epidemic gastroenteritis in susceptible children and adults. infections can be severe initiated from an exceptionally small number of viral particles. Detailed genome sequence data are useful for tracking norovirus transmission evolution. To address this need, we have developed whole-genome deep-sequencing method generates entire sequences amounts clinical specimens. This novel approach employs algorithm reverse...
We performed a prospective multicenter study to address the lack of data on etiology, clinical and demographic features hospitalized pediatric diarrhea in Ho Chi Minh City (HCMC), Vietnam. Over 2,000 (1,419 symptomatic 609 non-diarrheal control) children were enrolled three hospitals over 1-year period 2009–2010. Aiming detect panel pathogens, we identified known diarrheal pathogen stool samples from 1,067/1,419 (75.2%) with 81/609 (13.3%) without diarrhea. Rotavirus predominated (664/1,419;...
Abstract The Coronaviridae family of viruses encompasses a group pathogens with zoonotic potential as observed from previous outbreaks the severe acute respiratory syndrome coronavirus and Middle East coronavirus. Accordingly, it seems important to identify document coronaviruses in animal reservoirs, many which are uncharacterized potentially missed by more standard diagnostic assays. A combination sensitive deep sequencing technology computational algorithms is essential for virus...
Abstract The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection unusual emergence spread should therefore include such cities as part risk-based surveillance. A catch-all metagenomic sequencing approach urban sewage could potentially provide an unbiased insight into dynamics viral pathogens circulating in community irrespective access to care, potential which already has been proven...
Introductory paragraph SARS-CoV-2 genomic surveillance in Uganda provides an opportunity to provide a focused description of the virus evolution small landlocked East African country. Here we show recent shift local epidemic with newly emerging lineage A.23 evolving into A.23.1 which is now dominating cases and has spread 26 other countries. Although precise changes as it adapted are different from variants concern (VOC), shows convergence on similar set proteins. The spike protein coding...
The African continent like all other parts of the world with high infection/low vaccination rates can, and will, be a source novel SARS-CoV-2 variants. A.23 viral lineage, characterized by three spike mutations F157L, V367F Q613H, was first identified in COVID-19 cases from Ugandan prison July 2020, then general population additional (R102I, L141F, E484K P681R) to comprise lineage A.23.1 September this virus being designated variant interest (VOI) Africa subsequent spread 26 countries. P681R...
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve and infect individuals. exterior surface of the SARS-CoV-2 virion is dominated by spike protein, current work examined protein biochemical features that have changed during 3 years in which has infected humans. Our analysis identified a striking change charge, from −8.3 original Lineage A B viruses −1.26 most Omicron viruses. We conclude addition immune selection pressure, evolution also altered viral...
Enteric fever, caused by Salmonella enterica serovars Typhi and Paratyphi A (S. S. A) remains a major public health problem in many settings. The disease is limited to locations with poor sanitation which facilitates the transmission of infecting organisms. Efficacious inexpensive vaccines are available for Typhi, yet not commonly deployed control disease. Lack vaccination due partly uncertainty burden arising from paucity epidemiological information key locations. We have collected analyzed...
Coordinated and synchronous surveillance for zoonotic viruses in both human clinical cases animal reservoirs provides an opportunity to identify interspecies virus movement. Rotavirus (RV) is important cause of viral gastroenteritis humans animals. In this study, we document the RV diversity within co-located animals sampled from Mekong delta region Vietnam using a primer-independent, agnostic, deep sequencing approach. A total 296 stool samples (146 diarrhoeal patients 150 pigs living same...
This study aimed to optimize a method identify human enteric viruses in sewage and stool samples using random primed next-generation sequencing. We tested three methods, two employed virus enrichment based on the binding properties of viral capsid pig-mucin capture or by selecting RNA prior library preparation through SureSelect target enrichment. The third was non-specific biophysical precipitation with polyethylene glycol. Full genomes number common including norovirus, rotavirus,...
Abstract A novel protein translocation system, the type-6 secretion system (T6SS), may play a role in virulence of Campylobacter jejuni. We investigated 181 C. jejuni isolates from humans, chickens, and environmental sources Vietnam, Thailand, Pakistan, United Kingdom for T6SS. The marker was most prevalent human chicken Vietnam.
It is predicted that the integration of climate-based early warning systems into existing action plans will facilitate timely provision interventions to diarrheal disease epidemics in resource-poor settings. Diarrhea remains a considerable public health problem Ho Chi Minh City (HCMC), Vietnam and we aimed quantify variation impact environmental conditions on risk across city. Using all inpatient admissions data from three large hospitals within HCMC, developed mixed effects regression model...
Abstract We established rapid local viral sequencing to document the genomic diversity of severe acute respiratory syndrome coronavirus 2 entering Uganda. Virus lineages closely followed travel origins infected persons. Our sequence data provide an important baseline for tracking any further transmission virus throughout country and region.
Between November 2023 and March 2024, coastal Kenya experienced a new wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections detected through our continued genomic surveillance. Herein, we report the clinical epidemiology SARS-CoV-2 from 179 individuals (total 185 positive samples) residing in Kilifi Health Demographic Surveillance (KHDSS) area (~900 km2). Sixteen lineages within three sub-variants (XBB.2.3-like (58.4%), JN.1-like (40.5%) XBB.1-like (1.1%)) were...
Rotavirus (RoV) and Norovirus (NoV) are the main causes of viral gastroenteritis. Currently, there is no validated multiplex real-time PCR that can detect quantify RoV NoV simultaneously. The aim study was to develop, validate, internally control a one-step RT in stool samples. sensitivity assessed by comparing amplification against current gold standard, enzyme immunoassay (EIA), on samples from 94 individuals with diarrhea without diarrhea. detected 10% more positive than EIA stools...
Group A rotaviruses (ARoVs) are a common cause of severe diarrhea among children worldwide and the approximately 45% pediatric hospitalizations for acute in Vietnam. ARoVs known to significant economic losses livestock producers by reducing growth performance production efficiencies, however little is about implications asymptomatic endemic circulation ARoV. We aimed determine prevalence predominant circulating genotypes on pig farms southern province found overall animal-level farm-level...