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

Results from the first major genomic epidemiology of SARS-CoV-2 infections in Kenya were published today in the esteemed Nature Communications (DOI:10.1038/s41467-021-25137-x) peer-reviewed journal. The work carried by a team of scientist at the KEMRI-Wellcome Trust Research Programme and the Ministry of Health, examined cases during the early phase of the epidemic (March – July 2020). Out of the 406 samples sequenced, 311 provided high quality genomes and using these data, the researchers provide evidence for at least 35-40 unique introductions of the virus in the coast region – specifically the epidemic that was largely observed in Mombasa County.

This work shows that Europe was a major source of introductions into Kenya, with the dominant lineage at the coast being B.1, the same lineage that was observed in Europe. We also saw introduction of at least 15 cases of lineage A (viruses from lineage A comprise the earliest lineages of SARS-CoV-2 and were the dominant virus exports from China) as evidence of introductions through ports of entry with neighbouring countries which however did not establish local transmissions. This could be due to effective control mechanisms or that they were outcompeted by B.1 lineages, which though plausible is unlikely. Introductions to coast Kenya could also have come from other regions such as Nairobi. Control efforts by the Ministry of Health at the time were aimed at limiting local transmission and reducing the number of global introductions.

Although this is likely to be an underestimate of the actual number of introductions, given that it was not possible to sequence each case and because samples characterised by low viral load mostly from asymptomatic individuals are difficult to sequence. Furthermore, given the early interventions, it was not possible to identify each positive case as the level of testing was also low and the research team could only access identified PCR diagnosed cases.

The slow take off, of the epidemic across other counties, as evidenced by fewer introductions in these counties, shows that effective and stringent measures curtailed a lot of the local transmissions and fresh introductions were averted. This is evident in that the first wave only observed in Mombasa and Nairobi, with Kilifi, Tana River, Lamu and Taita Taveta for example seeing only a small number of cases. In addition, Lamu county had an epidemic that was characterised by a South American lineage and comprised the first positive cases in late June 2020 and following easing of travel restrictions. Scientists observed that these early cases in Lamu are likely to have come from this single introduction.

Government efforts and MoH guidelines were important control measures and partly worked by reducing introduction of specific lineages (e.g. lineage A and other minor lineages) from taking hold and potentially slowed down the number of infections. Nonetheless a few asymptomatic cases were sufficient to seed the epidemic. This underlines the severe challenge to the strategy that aimed at preventing the introduction of virus as any cases that escaped the net had potential to establish community spread.

“Research continues to play a key role in the fight against COVID 19. We continue providing the MOH the most up to date sequencing information as part of our mandate in supporting the government make the best health decisions for Kenyans” says the Ag. DG KEMRI Prof Sam Kariuki.