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

George Githinji,Ben Kitole,John Otieno,Edward Otieno,John Kiiru,Barke Salim,Samson Kinyanjui ,Thani Suleiman,John Nyambu,Mohamed Mwakinangu,Khadija Said Mohammed,Ambrose Agweyu,Edwine Barasa,D James Nokes,Kadondi Kasera,Donwilliams O Omuoyo,George M Warimwe ,Lynette Isabella Ochola‐Oyier ,Zaydah R De Laurent,Eric Maitha,Philip Bejon,John Mwita Morobe ,Peter M Macharia,Rashid Aman,Benjamin Tsofa,Charles N Agoti

doi:10.1038/s41467-021-25137-x

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 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.

Highlights

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission
The testing criteria were dependant on the guidelines provided by the Ministry of Health (MoH), and we split the period into four phases (Supplemetary Table 1) depending on the number of cases that were reported in the country
Between 12th March and 31st July 2020, Rapid Response Teams (RRTs) obtained samples from repatriated citizens including among individuals arriving at ports of entry, and from persons presenting at major hospitals with symptoms consistent with SARS-CoV-2 infection, contacts of confirmed cases and targeted testing of residents in Mombasa

Summary

Introduction

Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and the patterns of local and global transmission. Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2), the aetiological agent of coronavirus disease 2019 (COVID-19), was first reported and confirmed in Kenya on 13th March 20201 This was shortly after the World Health. Movement into or out of areas that were considered epidemic hotspots became restricted, and the government introduced strict quarantine procedures and isolation of infected individuals Despite these public health measures, the number of SARS-CoV-2 cases increased steadily across the country implying already established local transmission[3,4]. We sequenced and analysed 406 RT-PCR positive samples collected between March and 31st July 2020 at the Kenyan Coast from which we obtained 311 sequences suitable for phylogenetic analysis to provide the first large-scale genomic epidemiology study of SARS-CoV-2 from the region

Methods

Results

Conclusion