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


Nat Commun

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 17(th) March and 31(st) 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.

Githinji, G., de Laurent, Z. R., Mohammed, K. S., Omuoyo, D. O., Macharia, P. M., Morobe, J. M., Otieno, E., Kinyanjui, S. M., Agweyu, A., Maitha, E., Kitole, B., Suleiman, T., Mwakinangu, M., Nyambu, J., Otieno, J., Salim, B., Kasera, K., Kiiru, J., Aman, R., Barasa, E., Warimwe, G., Bejon, P., Tsofa, B., Ochola-Oyier, L. I., Nokes, D. J., Agoti, C. N.

Pages:4809, Volume:12, Edition:8/12/2021, Date,Aug-10


Notes:Githinji, George|de Laurent, Zaydah R|Mohammed, Khadija Said|Omuoyo, Donwilliams O|Macharia, Peter M|Morobe, John M|Otieno, Edward|Kinyanjui, Samson M|Agweyu, Ambrose|Maitha, Eric|Kitole, Ben|Suleiman, Thani|Mwakinangu, Mohamed|Nyambu, John|Otieno, John|Salim, Barke|Kasera, Kadondi|Kiiru, John|Aman, Rashid|Barasa, Edwine|Warimwe, George|Bejon, Philip|Tsofa, Benjamin|Ochola-Oyier, Lynette Isabella|Nokes, D James|Agoti, Charles N|eng|102975/WT_/Wellcome Trust/United Kingdom|107769/Z/10/Z/WT_/Wellcome Trust/United Kingdom|17/63/82/DH_/Department of Health/United Kingdom|EP-C-15-003/EPA/EPA/|WT_/Wellcome Trust/United Kingdom|220985/WT_/Wellcome Trust/United Kingdom|16/136/33/DH_/Department of Health/United Kingdom|Research Support, Non-U.S. Gov’t|England|2021/08/12 06:00|Nat Commun. 2021 Aug 10;12(1):4809. doi: 10.1038/s41467-021-25137-x.

ISBN: 2041-1723 (Electronic)|2041-1723 (Linking) Permanent ID: PMC8355311 Accession Number: 34376689

Author Address: KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.|Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya.|KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya.|Population Health Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya.|Nuffield Department of Medicine, University of Oxford, Oxford, UK.|Department of Health, Kilifi, Kenya.|Department of Health, Mombasa, Kenya.|Department of Health, Kwale, Kenya.|Department of Health, Taita Taveta, Kenya.|Department of Health, Lamu, Kenya.|Department of Health, Tana River, Kenya.|Ministry of Health, Government of Kenya, Nairobi, Kenya.|Health Economics Research Unit, KEMRI-Wellcome Trust Research Programme, Nairobi, Kenya.|School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK.|School of Public Health, Pwani University, Kilifi, Kenya.