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

Our take —

This study, available as a preprint and thus not yet peer reviewed, of SARS-CoV-2 sequences collected at hospitals, ports of entry, and community testing events between March and June 2020 in coastal Kenya provides evidence for multiple introductions of the virus into Kenya, but finds that only a single lineage is present in community-transmitted cases. The study is limited by sample size and potential sequencing errors, but overall offers evidence that the interventions imposed in Kenya early in the outbreak, including testing and quarantining at ports of entry, limited new introductions of the virus from spreading throughout the local community. The interventions implemented in Kenya could be used to inform containment measures in other parts of the world.

Study design


Study population and setting

This study involves generation and analysis of 274 SARS-CoV-2 sequences collected in coastal Kenya between March 17 and June 24, 2020. These genomes come from four of six coastal communities, and were sampled from individuals arriving at ports of entry into Kenya, individuals presenting at major hospitals in this region, contacts of confirmed cases, and as part of a mass testing effort in the city of Mombasa. The 274 genomes were analyzed alongside 983 publicly-available genomes (collected from December 2019 to June 2020) from around the globe. The purpose of this study was to assess the effectiveness of early public health interventions in Kenya and to help design future COVID-19 control measures in Kenya and the surrounding region.

Summary of Main Findings

The authors generated 274 SARS-CoV-2 sequences collected in coastal Kenya. Phylogenetic analysis showed that these sequences belong to many different lineages, suggesting multiple introductions of the virus into the local population. The authors found that a majority of the sequences belong to the B.1 lineage, which is widespread in Europe and the United States. This lineage accounted for 82% of the sequenced samples and was found in individuals with no known travel or contacts, suggesting community transmission. While several other lineages were identified, these lineages were found in smaller numbers and in patients with known travel. This suggests there was limited community spread of these additional lineages. The limited detection of non-B.1 lineages outside of ports of entry suggests that the containment efforts and travel restrictions imposed in Kenya as early as March 2020 were effective.

Study Strengths

By focusing on samples collected at ports of entry, the authors of this study ensured that they could capture introductions that did not lead to sustained transmission within the surrounding communities. This sampling strategy allowed them to answer specific questions about the effectiveness of quarantine and containment measures.


The authors acknowledged that the sample size was small and that a limited number of samples came from counties outside Mombasa, Kenya. This could mean that they were simply not capturing community transmission of additional lineages that exist. Additionally, they performed a brief analysis of 19 patients who were placed in quarantine facilities and were tested more than once. In two cases, they found that samples from the same patient belonged to different viral clades – while the authors claim this is likely due to co-infections, this is not consistent with other literature. This observation calls into question the accuracy of their sequences. While the overall findings of the study likely still hold—that they found multiple lineages at ports of entry, but the B.1 lineage uniquely caused community transmission—any more detailed analyses of specific clades should be taken with some caution due to potential sequencing error. Finally, because of the low diversity of this virus, it is impossible to determine if the B.1 lineage circulating in the community is the result of a single or many introductions.

Value added

This paper finds evidence for multiple introductions of SARS-CoV-2 into coastal Kenya yet limited sustained transmission. This points to the effectiveness of the interventions imposed in this region, which focused on catching cases at ports of entry and avoiding community transmission. This strategy could be a model for other countries struggling to contain the virus.

This review was posted on: 20 November 2020