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Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya

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Githinji, George , de Laurent, Zaydah R. , Mohammed, Khadija Said , Omuovo, Donwilliams O. , Macharia, Peter M. , Morobe, John M. , Otieno, Edward , Kinyanjui, Samson M. , Agweyu, Ambrose, Maitha, Eric et al.
(2021) Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya. Nature Communications, 12 . 4809 . doi:10.1038/s41467-021-25137-x

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Official URL: https://doi.org/10.1038/s41467-021-25137-x

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Abstract

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Here, we generated 311 SARS-CoV-2 genomes from samples collected in coastal Kenya between 17th March and 31st July 2020. We estimated multiple independent SARS-CoV-2 introductions into the region were primarily of European origin, although introductions could have come through neighbouring countries. Lineage B.1 accounted for 74% of sequenced cases. Lineages A, B and B.4 were detected in screened individuals at the Kenya-Tanzania border or returning travellers. Though multiple lineages were introduced into coastal Kenya following the initial confirmed case, none showed extensive local expansion other than lineage B.1. International points of entry were important conduits of SARS-CoV-2 importations into coastal Kenya and early public health responses prevented established transmission of some lineages. Undetected introductions through points of entry including imports from elsewhere in the country gave rise to the local epidemic at the Kenyan coast.

Item Type: Journal Article
Subjects: R Medicine > RA Public aspects of medicine
Divisions: Faculty of Science > Life Sciences (2010- )
Library of Congress Subject Headings (LCSH): Epidemiology, SARS (Disease) -- coastal Kenya, COVID-19 (Disease), Virus diseases -- Transmission -- coastal Kenya, Phylogeny
Journal or Publication Title: Nature Communications
Publisher: Nature Publishing Group
ISSN: 2041-1723
Official Date: 10 August 2021
Dates:
DateEvent
10 August 2021Published
27 July 2021Accepted
Volume: 12
Article Number: 4809
DOI: 10.1038/s41467-021-25137-x
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Open Access
RIOXX Funder/Project Grant:
Project/Grant IDRIOXX Funder NameFunder ID
17/63/82[NIHR] National Institute for Health Researchhttp://dx.doi.org/10.13039/501100000272
16/136/33 [NIHR] National Institute for Health Researchhttp://dx.doi.org/10.13039/501100000272
102975Wellcome Trusthttp://dx.doi.org/10.13039/100010269
220985Wellcome Trusthttp://dx.doi.org/10.13039/100010269
107769/Z/10/Z]Wellcome Trusthttp://dx.doi.org/10.13039/100010269
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  • bioRxiv

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