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Population genetics in the early emergence of the Omicron SARS-CoV-2 variant in the provinces of South Africa

View ORCID ProfileMaría Fernanda Contreras-González, View ORCID ProfileHugo G. Castelán-Sánchez, View ORCID ProfileErik Diaz-Valenzuela, View ORCID ProfileAngélica Cibrián-Jaramillo
doi: https://doi.org/10.1101/2023.02.09.527920
María Fernanda Contreras-González
1Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico
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  • ORCID record for María Fernanda Contreras-González
Hugo G. Castelán-Sánchez
2Programa Investigadoras e Investigadores por México, Grupo de Genómica y Dinámica Evolutiva de Microorganismos Emergentes. Consejo Nacional de Ciencia y Tecnología. Ciudad de México, México
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Erik Diaz-Valenzuela
1Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico
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Angélica Cibrián-Jaramillo
1Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Irapuato, Guanajuato, Mexico
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  • For correspondence: angelica.cibrian@gmail.com
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Abstract

Population genetic analyses of viral genome populations provide insight into the emergence and evolution of new variants of SARS-CoV-2. In this study, we use a population genetic approach to examine the evolution of the Omicron variant of SARS-CoV-2 in four provinces of South Africa (Eastern Cape, Gauteng, KwaZulu-Natal, and Mpumalanga) during the first months before emergence and after early spread. Our results show that Omicron polymorphisms increase sharply from September to November. We found differences between SARS-CoV-2 populations from Gauteng and Kwazulu-Natal and viruses from the Eastern Cape, where allele frequencies were higher, suggesting that natural selection may have contributed to the increase in frequency or that this was the site of origin. We found that the frequency of variants N501Y, T478K, and D614G increased in the spike in November compared with other mutations, some of which are also present in other animal hosts. Gauteng province was the most isolated, and most genetic variation was found within populations. Our population genomic approach is useful for small-scale genomic surveillance and identification of novel allele-level variants that can help us understand how SARS-CoV-2 will continue to adapt to humans and other hosts.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • María Fernanda Contreras-González maria.contreras{at}cinvestav.mx, Hugo G. Castelán-Sánchez hugo.castelan{at}conacyt.mx, Erik Díaz-Valenzuela erdiazval{at}gmail.com, Angelica Cibrian-Jaramillo angelica.cibrian{at}cinvestav.mx

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 10, 2023.
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Population genetics in the early emergence of the Omicron SARS-CoV-2 variant in the provinces of South Africa
María Fernanda Contreras-González, Hugo G. Castelán-Sánchez, Erik Diaz-Valenzuela, Angélica Cibrián-Jaramillo
bioRxiv 2023.02.09.527920; doi: https://doi.org/10.1101/2023.02.09.527920
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Population genetics in the early emergence of the Omicron SARS-CoV-2 variant in the provinces of South Africa
María Fernanda Contreras-González, Hugo G. Castelán-Sánchez, Erik Diaz-Valenzuela, Angélica Cibrián-Jaramillo
bioRxiv 2023.02.09.527920; doi: https://doi.org/10.1101/2023.02.09.527920

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