| dc.description.abstract |
The rise of new SARS-CoV-2 mutations brought challenges and progress in
the global fight against COVID-19. Mutations in spike and accessory genes affect transmission,
vaccine efficacy, treatments, testing, and public health strategies. Monitoring emerging variants is
crucial to halt virus spread. Methods: 44 nasopharyngeal/oropharyngeal swabs from Kenyan
patients were sequenced with the Illumina platform. Galaxy's bioinformatic tools were used for
genomic analysis. SARS-CoV-2 genome classification was done using PANGOLIN and mutation
annotation with the COVID-19 Annotator tool. Results: The study showed 5 clades to be circulating
in the region. 38(86%) were BA.1.1; 2(5%) were BA.1.1.1; 1(2%) was BA.1; 1(2%) was BA.1.14 and
2(5%) were AY.46. These clades had a cumulative of 173 mutations among them with 50 novel
mutations. Forty-eight of these novel mutations occurred in a low frequency of 2.3% of the
sequences tested while the other two, S:R214R, and NSP2:A555A, were for 43.2% and 18.2% of the
cases respectively. Conclusions: The high-frequency novel mutations were synonymous mutations,
a phenomenon that was previously viewed as phenotypically silent but recent studies indicate they
can affect viral fitness with potential functional associations. These findings add to the
understanding of the SARS-CoV-2 virus future evolutionary and immunological dynamics in the
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