The Library
Genomic epidemiology of Human Adenovirus F40 and F41 in Coastal Kenya : a retrospective hospital-based surveillance study (2013-2022)
Tools
Lambisia, Arnold W., Makori, Timothy O., Mutunga, Martin, Cheruiyot, Robinson, Murunga, Nickson, Quick, Joshua, Githinji, George, Nokes, D. James, Houldcroft, Charlotte J. and Agoti, Charles N. (2023) Genomic epidemiology of Human Adenovirus F40 and F41 in Coastal Kenya : a retrospective hospital-based surveillance study (2013-2022). Virus Evolution . vead023. doi:10.1093/ve/vead023 ISSN 2057-1577.
|
PDF
WRAP-genomic-epidemiology-Human-Adenovirus-F40-F41-Coastal-Kenya-retrospective-hospital-based-surveillance-study-(2013-2022).pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons: Attribution-Noncommercial 4.0. Download (924Kb) | Preview |
Official URL: https://doi.org/10.1093/ve/vead023
Abstract
Human adenovirus species F (HAdV-F) is a leading cause of childhood diarrhoeal deaths. Genomic analysis would be key for understanding transmission dynamics, potential drivers of disease severity, transmission dynamics, and for vaccine development. However, currently there are limited HAdV-F genomic data globally. Here, we sequenced and analysed HAdV-F from stool samples collected in coastal Kenya between 2013 and 2022. The samples were collected at Kilifi County Hospital in coastal, Kenya, from children < 13 years of age who reported a history of ≥ 3 loose stools in the previous 24hrs. The genomes were analyzed together with data from the rest of the world by phylogenetic analysis and mutational profiling. Types and lineages were assigned based on phylogenetic clustering consistent with previously described criteria and nomenclature. Participant clinical and demographic data were linked to genotypic data. Of 91 cases identified using real-time PCR, 88 near-complete genomes were assembled, and these classified into HAdV-F40 (n=41) and F41 (n=47). These types cocirculated throughout the study period. Three and four distinct lineages were observed for HAdV-F40 (Lineage 1-3) and F41 (Lineage 1, 2A, 3A, 3C and 3D). Types F40 and F41 coinfections were observed in five samples, and F41 and B7 in one sample. Two children with F40 and 41 coinfections were also infected with rotavirus and had moderate and severe disease as defined using the Vesikari Scoring System, respectively. Intratypic recombination was found in 4 HAdV-F40 sequences occurring between lineages 1 and 3. None of the HAdV-F41 cases had jaundice. This study provides evidence of extensive genetic diversity, coinfections, and recombination within HAdV-F40 in a rural coastal Kenya that will inform public health policy, vaccine development that includes the locally circulating lineages, and molecular diagnostic assay development. We recommend future comprehensive studies elucidating on HAdV-F genetic diversity and immunity for rational vaccine development.
Item Type: | Journal Article | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Subjects: | Q Science > QR Microbiology | ||||||||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||||||||||||
SWORD Depositor: | Library Publications Router | ||||||||||||||||||
Library of Congress Subject Headings (LCSH): | Adenoviruses , Adenoviruses -- Epidemiology -- Kenya | ||||||||||||||||||
Journal or Publication Title: | Virus Evolution | ||||||||||||||||||
Publisher: | Oxford University Press | ||||||||||||||||||
ISSN: | 2057-1577 | ||||||||||||||||||
Official Date: | 24 March 2023 | ||||||||||||||||||
Dates: |
|
||||||||||||||||||
Article Number: | vead023 | ||||||||||||||||||
DOI: | 10.1093/ve/vead023 | ||||||||||||||||||
Status: | Peer Reviewed | ||||||||||||||||||
Publication Status: | Published | ||||||||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||||||||
Date of first compliant deposit: | 20 June 2023 | ||||||||||||||||||
Date of first compliant Open Access: | 21 June 2023 | ||||||||||||||||||
RIOXX Funder/Project Grant: |
|
Request changes or add full text files to a record
Repository staff actions (login required)
View Item |
Downloads
Downloads per month over past year