Mbogori, E.; Thiongo, K.; Deng, H. Y.; Gikunyu, C.; Cheriro, W.; Musyoki, S.; Biegon, R.; Matoke-Muhia, D.; Patel, K.; Liang, B.; Songok, E. Emerging Mutations of SARS-COV-2 in Kenya. Preprints2024, 2024050647. https://doi.org/10.20944/preprints202405.0647.v1
APA Style
Mbogori, E., Thiongo, K., Deng, H. Y., Gikunyu, C., Cheriro, W., Musyoki, S., Biegon, R., Matoke-Muhia, D., Patel, K., Liang, B., & Songok, E. (2024). Emerging Mutations of SARS-COV-2 in Kenya. Preprints. https://doi.org/10.20944/preprints202405.0647.v1
Chicago/Turabian Style
Mbogori, E., Binhua Liang and Elijah Songok. 2024 "Emerging Mutations of SARS-COV-2 in Kenya" Preprints. https://doi.org/10.20944/preprints202405.0647.v1
Abstract
Background: 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 region
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
