RT Journal Article
SR Electronic
T1 Population genetics in the early emergence of the Omicron SARS-CoV-2 variant in the provinces of South Africa
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.02.09.527920
DO 10.1101/2023.02.09.527920
A1 María Fernanda Contreras-González
A1 Hugo G. Castelán-Sánchez
A1 Erik Diaz-Valenzuela
A1 Angélica Cibrián-Jaramillo
YR 2023
UL http://biorxiv.org/content/early/2023/02/10/2023.02.09.527920.abstract
AB 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 StatementThe authors have declared no competing interest.