A5070664967- Viral gastroenteritis research and epidemiology
- Hepatitis Viruses Studies and Epidemiology
- Animal Virus Infections Studies
- SARS-CoV-2 and COVID-19 Research
- Viral Infections and Outbreaks Research
- Viral Infections and Immunology Research
- Respiratory viral infections research
- SARS-CoV-2 detection and testing
- COVID-19 diagnosis using AI
- Biomedical Text Mining and Ontologies
- COVID-19 epidemiological studies
- Bacteriophages and microbial interactions
- Biotechnology and Related Fields
- IoT Networks and Protocols
- Genetics, Bioinformatics, and Biomedical Research
- RNA and protein synthesis mechanisms
- Metabolism and Genetic Disorders
- Vaccine Coverage and Hesitancy
- Influenza Virus Research Studies
- Congenital Anomalies and Fetal Surgery
- Genomics and Rare Diseases
University of Bern
2024
Kenya Medical Research Institute
2018-2023
Pwani University
2018-2023
Wellcome Trust
2018-2019
Abstract Background Rotavirus remains a leading cause of pediatric diarrheal illness and death worldwide. Data on rotavirus vaccine effectiveness in sub-Saharan Africa are limited. Kenya introduced monovalent (RV1) July 2014. We assessed RV1 against rotavirus-associated hospitalization Kenyan children. Methods Between 2014 December 2017, we conducted surveillance for acute gastroenteritis (AGE) 3 hospitals. From children age-eligible ≥1 dose, with stool tested confirmed vaccination history...
Abstract High-throughput sequencing techniques and sequence analysis have enabled the taxonomic classification of pathogens present in clinical samples. Sequencing provides an unbiased identification systematic this is generally achieved by comparing novel sequences to pre-existing annotated reference databases. However, approach limited large-scale databases which require considerable computational resources skills compare against. Alternative robust methods such as machine learning are...
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...
Abstract Background Kenya introduced the monovalent G1P [8] Rotarix® vaccine into infant immunization schedule in July 2014. We examined trends rotavirus group A (RVA) genotype distribution pre- (January 2010–June 2014) and post- (July 2014–December 2018) RVA introduction. Methods Stool samples were collected from children aged < 13 years four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic Nairobi, Lwak Mission Siaya Referral Hospital (children 5 only). Samples...
Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use vaccines in more than 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged less 13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected 55 (22.2%). Of these, VP7 (G) VP4 (P) segments were...
Abstract The emergence and establishment of SARS-CoV-2 variants concern presented a major global public health crisis across the world. There were six waves cases in Kenya that corresponded with introduction eventual dominance SARS-COV-2 concern, excepting first 2 both wild-type virus. We estimate more than 1000 introductions occurred two-year epidemic period (March 2020 – September 2022) total 930 associated namely Beta (n=78), Alpha(n=108), Delta(n=239) Omicron (n=505). A 29 A.23.1 variant...
Abstract The introduction of rotavirus vaccines into the national immunization programme in many countries has led to a decline childhood diarrhoea disease burden. Coincidentally, incidence some group A (RVA) genotypes increased, which may result from non-vaccine-type replacement. Here, we investigate evolutionary genomics G2P[4] shown an increase that introduced monovalent Rotarix® vaccine. We examined sixty-three RVA strains sampled children (aged below 13 years) admitted Kilifi County...
<ns4:p><ns4:bold>Background: </ns4:bold>Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014. Long-term surveillance data is important prior to wide-scale use assess impact on disease and investigate occurrence of heterotypic strains arising through immune selection. This report presents baseline RVA genotype circulation patterns intra-genotype genetic diversity over a 7-year period pre-vaccine era Kilifi, Kenya, from 2002 2004 2010...
<ns4:p><ns4:bold>Background: </ns4:bold>Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014. Long-term surveillance data is important prior to wide-scale use assess impact on disease and investigate occurrence of heterotypic strains arising through immune selection. This report presents baseline RVA genotype circulation patterns intra-genotype genetic diversity over a 7-year period pre-vaccine era Kilifi, Kenya, from 2002 2004 2010...
A multi-pronged approach to combating the COVID-19 pandemic in Kenya resulted formation of multidisciplinary research initiatives including genomic sequencing, syndromic surveillance, sero-surveillance, vaccination, and mathematical modelling. These generated an overwhelming amount data that posed a challenge researchers public health officials, effectively manage, analyse promptly interpret for immediate response. As result, there was demand platform collate integrate these datasets with...
<title>Abstract</title> Whole genome sequencing (WGS) is crucial for studying influenza A virus (IAV) genomic diversity in various host species to mitigate its impact on human and animal health. While the multisegment RT-PCR (mRT-PCR) efficiently amplifies all segments a single reaction, sensitivity larger suboptimal. To improve WGS sensitivity, we optimized mRT-PCR protocol by adjusting RT PCR cycling conditions, achieving 1000-fold increase sensitivity. Additionally, developed...
Abstract Background Rotavirus vaccines are moderately protective against illness in high mortality settings compared with low settings. Vaccine effectiveness (VE) evaluations may clarify our understanding of these disparities, but estimates among key subpopulations and rare outcomes not available many analyses due to sample size. We combined 25 datasets from test-negative design case-control 24 countries that enrolled children medically-attended diarrhea, laboratory-confirmed rotavirus stool...
The recombinant FY.4 SARS-CoV-2 variant was first reported in Kenya March 2023 and the dominant circulating between April July 2023. characterised by two important mutations: Y451H receptor binding domain of spike protein P42L open reading frame 3a. Using phylogenetics phylodynamic approaches, we investigated emergence spread rest world. Our findings suggest circulated early before export to North America Europe. Early circulation predominantly observed coastal part country estimated time...
Background: Random priming coupled with next-generation sequencing provides pathogen full genome sequences and information on mixed infections that can be present in clinical samples. These methods have rarely been implemented studying rotavirus epidemiology, despite its immense diversity segmented genome. The agnostic method was characterizing the epidemiology of group A (RVA) detected Kilifi County, Kenya, using data. Methods & Materials: RNA from 95 stool samples were extracted, reverse...
Globally, rotavirus group A (RVA) remains a major cause of severe childhood diarrhea, despite the use vaccines in &amp;gt; 100 countries. RVA sequencing for local outbreaks facilitates investigation into strain composition, origins, spread, and vaccine failure. In 2018, we collected 248 stool samples from children aged &amp;lt;13 years admitted with diarrheal illness to Kilifi County Hospital, coastal Kenya. Antigen screening detected 55 (22.2%). Of these, VP7 (G) VP4 (P) segments...
<ns4:p><ns4:bold>Background: </ns4:bold>The emergence of the Omicron variant concern in late 2021 led to a resurgence SARS-CoV-2 infections globally. By September 2022, Seychelles had experienced two major surges driven by variant. Here, we examine genomic epidemiology between November and 2022.</ns4:p><ns4:p> </ns4:p><ns4:p> <ns4:bold>Methods:</ns4:bold> We analysed 618 genomes identified 2022 infer virus introductions local transmission patterns using phylogenetics ancestral state...
Abstract We report a newly emerged SARS-CoV-2 Omicron lineage, named FY.4, that has two unique mutations; spike:Y451H and ORF3a:P42L. FY.4 emergence coincided with increased cases in coastal Kenya, April-May 2023. demonstrate the value of continued genomic surveillance post-acute pandemic era understanding new COVID-19 outbreaks.
Abstract Background: Kenya introduced the monovalent G1P[8] Rotarix® vaccine into infant immunization schedule in July 2014. We examined trends rotavirus group A (RVA) genotype distribution pre- (January 2010 - June 2014) and post- (July 2014-December 2018) RVA introduction.Methods: Stool samples were collected from children aged <13 years four surveillance sites across Kenya: Kilifi County Hospital, Tabitha Clinic, Lwak Mission Siaya Referral Hospital (children <5 only). Samples...