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

George Githinji, Zaydah R de 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 BarasaGeorge Warimwe, Philip Bejon, Benjamin Tsofa, Lynette Isabella Ochola-Oyier, D James Nokes, Charles N Agoti

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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.

Original languageEnglish
Article number4809
JournalNature Communications
Issue number1
Publication statusPublished - 2021


  • Adolescent
  • Adult
  • Aged
  • Aged, 80 and over
  • COVID-19/diagnosis
  • Child
  • Child, Preschool
  • Female
  • Genetic Variation
  • Genome, Viral
  • Humans
  • Infant
  • Kenya/epidemiology
  • Male
  • Middle Aged
  • Pandemics
  • Phylogeny
  • Public Health
  • SARS-CoV-2/classification
  • Sequence Analysis
  • Tanzania
  • Travel
  • Young Adult


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