The Library
Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves : a retrospective genomic study
Tools
Tools
Tools
(2022) Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves : a retrospective genomic study. eLife, 11 . e71703. doi:10.7554/eLife.71703 ISSN 2050-084X.
|
PDF
WRAP-Transmission-networks-SARS-CoV-2-Coastal-Kenya-two-waves-genomic-2022.pdf - Accepted Version - Requires a PDF viewer. Available under License Creative Commons Attribution 4.0. Download (11Mb) | Preview |
Official URL: http://doi.org/10.7554/eLife.71703
Abstract
Background: Detailed understanding on SARS-CoV-2 regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic.
Methods: Here, we analysed 1,139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction and virus dispersal between counties were estimated using discrete phylogeographic analysis.
Results: During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; nine of which occurred in both waves, and four seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1 and N.8). Most of the sequenced infections belonged to lineage B.1 (n=723, 63%) which predominated in both Wave 1 (73%, followed by lineages N.8 (6%) and B.1.1 (6%)) and Wave 2 (56%, followed by lineages B.1.549 (21%) and B.1.530 (5%). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many COVID-19 government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity.
Conclusions: Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission.
| Item Type: | Journal Article | ||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Subjects: | Q Science > QH Natural history R Medicine > RA Public aspects of medicine |
||||||||||||||||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||||||||||||
| Library of Congress Subject Headings (LCSH): | COVID-19 (Disease), COVID-19 (Disease) -- Transmission -- Kenya, COVID-19 (Disease) -- Epidemiology -- Kenya, Genomics -- Kenya | ||||||||||||||||||
| Journal or Publication Title: | eLife | ||||||||||||||||||
| Publisher: | eLife Sciences Publications Ltd. | ||||||||||||||||||
| ISSN: | 2050-084X | ||||||||||||||||||
| Official Date: | 14 June 2022 | ||||||||||||||||||
| Dates: |
|
||||||||||||||||||
| Volume: | 11 | ||||||||||||||||||
| Article Number: | e71703 | ||||||||||||||||||
| DOI: | 10.7554/eLife.71703 | ||||||||||||||||||
| Status: | Peer Reviewed | ||||||||||||||||||
| Publication Status: | Published | ||||||||||||||||||
| Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||||||||
| Copyright Holders: | © 2022, Agoti et al. | ||||||||||||||||||
| Date of first compliant deposit: | 16 June 2022 | ||||||||||||||||||
| Date of first compliant Open Access: | 17 June 2022 | ||||||||||||||||||
| RIOXX Funder/Project Grant: |
|
||||||||||||||||||
| Related URLs: |
Request changes or add full text files to a record
Repository staff actions (login required)
 |
View Item |
Downloads
Downloads per month over past year
