Household genomic epidemiology of SARS-CoV-2 in rural coastal Kenya
Journal of Public Health in Africa
; 13:33, 2022.
Article
in English
| EMBASE | ID: covidwho-2006775
ABSTRACT
Introduction/ Background:
Household environments are characterized by frequent person-to-person contacts and potential transmission of respiratory infections. We used whole genome sequencing to describe the molecular epidemiology of SARS-CoV-2 in households in rural coastal Kenya.Methods:
We collected 1,802 nasopharyngeal/ oropharyngeal swabs from 137 households (502 participants) in Kilifi County between 10th December 2020 and 14th September 2021. These households were selected because a member had been confirmed to have SAR-CoV-2 infection by routine health service testing, or because a member was a close contact of a confirmed case. RT- PCR positive samples with a cycle threshold of < 30.0 were targeted for genome sequencing. Phylogenetic relationships were inferred using maximum likelihood methods and the number of independent introductions into the households inferred using both pairwise nucleotide differences and ancestral state reconstruction approaches.Results:
A total of 332 samples from 155 participants in 71 households tested SARS-CoV-2 positive, 132 (39.7%) of which yielded genomes with >80% coverage (73 participants in 41 households). All recovered genomes were classified within lineages of known variants of concern Alpha (n=60), Beta (n=18) and Delta (n=54). Of the 41 households with sequence data recovered, 26 (63%) had one distinct introduction, 10 (24%) had two introductions, 4 (10%) had three introductions and 1 (3%) had four introductions. Among these sequenced households 31 within household transmission events and 16 interhousehold transmission events were identified from the genomic data. Impact Transmission of SARS-CoV-2 infection within and between households is common in rural Kenya, is often asymptomatic, and realistic measures to mitigate infection spread within households are needed to reduce the disease burden.Conclusion:
We found both frequent SARS-CoV-2 transmission within households and its multiple introductions into households. Genomic data adds value in estimating household attack rates by distinguishing single from multiple introductions to households.
nucleotide; adult; attack rate; conference abstract; controlled study; coronavirus disease 2019; disease burden; female; household; human; human tissue; Kenya; major clinical study; male; maximum likelihood method; molecular epidemiology; nonhuman; oropharyngeal swab; phylogeny; polymerase chain reaction; Severe acute respiratory syndrome coronavirus 2; variant of concern; whole genome sequencing
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Collection:
Databases of international organizations
Database:
EMBASE
Type of study:
Observational study
Language:
English
Journal:
Journal of Public Health in Africa
Year:
2022
Document Type:
Article
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