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

George Githinji (), Zaydah R. Laurent, Khadija Said Mohammed, Donwilliams O. Omuoyo, Peter M. Macharia, John M. Morobe, Edward Otieno, Samson M. Kinyanjui, Ambrose Agweyu, Eric Maitha, Ben Kitole, Thani Suleiman, Mohamed Mwakinangu, John Nyambu, John Otieno, Barke Salim, Kadondi Kasera, John Kiiru, Rashid Aman, Edwine Barasa, George Warimwe, Philip Bejon, Benjamin Tsofa, Lynette Isabella Ochola-Oyier, D. James Nokes and Charles N. Agoti
Additional contact information
George Githinji: KEMRI-Wellcome Trust Research Programme
Zaydah R. Laurent: KEMRI-Wellcome Trust Research Programme
Khadija Said Mohammed: KEMRI-Wellcome Trust Research Programme
Donwilliams O. Omuoyo: KEMRI-Wellcome Trust Research Programme
Peter M. Macharia: KEMRI-Wellcome Trust Research Programme
John M. Morobe: KEMRI-Wellcome Trust Research Programme
Edward Otieno: KEMRI-Wellcome Trust Research Programme
Samson M. Kinyanjui: KEMRI-Wellcome Trust Research Programme
Ambrose Agweyu: KEMRI-Wellcome Trust Research Programme
Eric Maitha: Department of Health
Ben Kitole: Department of Health
Thani Suleiman: Department of Health
Mohamed Mwakinangu: Department of Health
John Nyambu: Department of Health
John Otieno: Department of Health
Barke Salim: Department of Health
Kadondi Kasera: Government of Kenya
John Kiiru: Government of Kenya
Rashid Aman: Government of Kenya
Edwine Barasa: University of Oxford
George Warimwe: KEMRI-Wellcome Trust Research Programme
Philip Bejon: KEMRI-Wellcome Trust Research Programme
Benjamin Tsofa: KEMRI-Wellcome Trust Research Programme
Lynette Isabella Ochola-Oyier: KEMRI-Wellcome Trust Research Programme
D. James Nokes: KEMRI-Wellcome Trust Research Programme
Charles N. Agoti: KEMRI-Wellcome Trust Research Programme

Nature Communications, 2021, vol. 12, issue 1, 1-10

Abstract: 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.

Date: 2021
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-021-25137-x Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-25137-x

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-021-25137-x

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().