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

Githinji, George and Laurent, Zaydah R. de and Mohammed, Khadija Said and Omuoyo, Donwilliams O. and Macharia, Peter M. and Morobe, John M. and Otieno, Edward and Kinyanjui, Samson M. and Agweyu, Ambrose and Maitha, Eric and Kitole, Ben and Suleiman, Thani and Mwakinangu, Mohamed and Nyambu, John and Otieno, John and Salim, Barke and Kasera, Kadondi and Kiiru, John and Aman, Rashid and Barasa, Edwine and Warimwe, George and Bejon, Philip and Tsofa, Benjamin and Ochola-Oyier, Lynette Isabella and Nokes, D. James and Agoti, Charles N. (2021) Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya. Nature Communications, 12 (1). ISSN 2041-1723

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 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.