Kenya: Beta-like SARS-CoV-2 variant found >1 yr after disappearance

Africa, Beta, Coronavirus, Evolution, Genome, Health, Kenya, Mutation, Persistent Infection, Testing, Transmission

A preprint out today gives details of a Beta-like SARS-CoV-2 variant with additional mutations recently found in Kenya.

We report identification a Beta VOC-like sequence in coastal Kenya with 22 additional mutations some of which have been identified in other VOCs. This finding suggests that some of the previous SARS-CoV-2 VOCs that have been undetected for months may be still in circulation in communities albeit at low frequencies.

We observed a Beta-like sequence with additional six synonymous and 16 non-synonymous mutations within the ORF1ab, ORF3a, M, and S genes. The mutations were observed in the consensus genome from both the ONT and Illumina platforms. The additional mutations observed were predominantly seen within the Delta and Omicron VOC lineages and non-VOC lineages including B.1.1.456 and B.1.1.374. The additional alleles observed in the newly sequenced samples had sufficient read depth (>90%) compared to the Wuhan reference.

Preprint: Detection of a SARS-CoV-2 Beta-like Variant with Additional Mutations in Coastal Kenya after >1 Year of Disappearance 



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