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Title: | Emerging Mutations of SARS-COV-2 in Kenya |
Authors: | Mbogori, Elius Thiongo, Kelvin Deng, Harrison Yunying Gikunyu, Caroline Cheriro, Winfrida Musyoki, Stanslaus Biegon, Richard Matoke-Muhia, Damaris Patel, Kirtika Liang, Binhua Songok, Elijah |
Keywords: | SARS-CoV-2 COVID-19 Spike protein Epistasis Reverse transcription Pathogenesis Vaccine efficacy Complementary DNA; Reverse transcription-polymerase chain reaction |
Issue Date: | 10-May-2024 |
Publisher: | Preprints.org |
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 region |
URI: | https://doi.org/10.20944/preprints202405.0647.v1 http://ir.mu.ac.ke:8080/jspui/handle/123456789/9246 |
Appears in Collections: | School of Medicine |
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