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Europe was the origin of the dominant coronavirus strain in Kenya, a report has revealed.
The research conducted by Kemri-Wellcome Trust Research Programme in Kilifi shows that the dominant strain of the deadly virus in Kenya’s Coast was of European lineage, consistent with what has been reported in some parts of the world, including several African countries.
This specific strain (lineage B.1) of the coronavirus was first identified globally on February 15 and it accounted for 45 out of the 76 introductions in Kenya.
“Though multiple lineages were introduced in coastal Kenya within three months following the initial confirmed case, none showed extensive local expansion other than cases characterised by lineage B.1,” reads the report dated October 7.
In the findings, at least 274 SARS-Cov-2 samples were collected in Mombasa, Kwale, Taita Taveta and Kilifi counties, with European lineage accounting for 82.1 per cent of the cases.
Other lineages were detected from screened returning travellers at the Kenya-Tanzania border though they did not lead to established transmission.
Based on global data, European origin lineage comprised the majority of the large Italian and United Kingdom (UK) outbreaks, and was observed in several other European outbreaks and the rest of the world.
Kenya reported its first confirmed case of Covid-19 on March 13, just two days after the virus was declared a pandemic by the World Health Organisation (WHO).
By then, SARS-Cov-2 outbreaks had been confirmed in parts of Asia, Europe and North America following original emergence in Wuhan, China, in December 2019.
In the month of June, Kenya had reported 6,180 Covid-19 cases and 144 associated deaths.
Early public health response by the Government prevented many introductions, leading to established transmission.
Several public health measures were put in place to prevent spread and contamination of the virus, including closure of international borders, dusk-to-dawn curfew and closure of all learning institutions.
Religious meetings
Restaurants, bars and nightclubs and religious meetings were also banned.
However, despite measures put in place, Kemri notes that the European lineage virus continued to dominate the cases in the coastal region, including most recent samples sequenced from June.
In the report, Kemri states that international points of entry were important conduits of SARS-CoV-2 importations, but few undetected introductions were sufficient to give rise to an established epidemic.
Researchers note that based on self-reported history of travel, approximately 40 per cent of infected individuals had no history of travel outside their localities, giving evidence of an established local transmission.
A separate introduction of lineage A was observed from an individual who had travelled from Dubai. Lineage A, is characterised by the early Chinese sequences.
“However, following these introductions, there was no evidence of ongoing transmission from lineage A viruses,” adds the report.
“Given the dominance of B.1 lineage during the early phase of the epidemic, it is not surprising that many of the coastal sequences contained the spike D614G variant. This mutation arose early during the epidemic, and now dominates the majority of the cases across the globe.”
The researchers say government actions to enhance border control and screening, quarantine and isolation of cases were effective in mitigating transmission.
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