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

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.

Genome evolution and early introductions of the SARS-CoV-2 Omicron Variant in Mexico (preprint)

A new variant of SARS-CoV-2 Omicron (Pango lineage designation B.1.1.529), was first reported to the World Health Organization (WHO) by South African health authorities on November 24, 2021. The Omicron variant possesses numerous mutations associated with increased transmissibility and immune escape properties. In November 2021, Mexican authorities reported Omicrons presence in the country. In this study, we infer the first introductory events of Omicron and the impact that human mobility can have on the spread of the virus. We also evaluated the adaptive evolutionary processes in Mexican SARS-CoV-2 genomes during the first month of circulation of Omicron. We infer 173 introduction events of Omicron in Mexico in the first two months of detection; subsequently, of the introductions, there was an increase in the prevalence for January. This higher prevalence of the novel variant results in a peak of cases reported, on average, six weeks after a higher mobility trend was reported. The peak of cases reported is due to the BA.1.1 Omicron sub-lineage dominated, followed by BA.1 and BA.15 sub-lineages in the country from January to February 2022. Additionally, we identified the presence of diversifying natural selection in the genomes of Omicron and found mainly five non-synonymous mutations in the RDB domain of the Spike protein, all of them related to evasion of the immune response. In contrast, the other proteins in the genome are highly conserved--however, there are homoplasies mutations in non-structural proteins, indicating a parallel evolution.

Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico (preprint)

Up to November 2021, over 200 different SARS-CoV-2 lineages circulated in Mexico. To investigate lineage replacement dynamics, we applied a phylodynamic approach to explore the evolutionary trajectories of five dominant lineages that circulated during the first year of the local epidemic. For most lineages, peaks in sampling frequencies coincided with different epidemiological waves of infection in the country. Lineages B.1.1.222 and B.1.1.519 showed comparable dynamics, represented by clades likely originating in Mexico and persisting for over a year. Lineages B.1.1.7, P.1 and B.1.617.2 also displayed similar dynamics, characterized by multiple introduction events leading to a few successful extended local transmission chains that persisted for several months. We further explored viral movements across the country, applied within the largest clades identified (belonging to lineage B.1.617.2). Many clades were located within the south region of the country, suggesting that this area played a key role in the spread of SARS-CoV-2 in Mexico.