Insights from a 3-Year Genomic Evolution of SARS-CoV-2 Shows a Predominance of Variants from Developing Countries

Abstract Since the emergence of SARS-CoV-2, the virus has rapidly disseminated globally, with consequential genetic changes that have profoundly affected its pathogenicity, transmissibility, and immune evasion. Therefore, the pressing need to gain a comprehensive understanding of the genetic evolution and dissemination of this virus across diverse regions is paramount. In light of this, the present study aimed to investigate the spatial and temporal distribution of SARS-CoV-2 variants by leveraging genomic sequencing data. We analyzed a representative dataset of 14,759 genomic sequences of SARS-CoV-2 obtained from 142 countries, spanning the period from January 2020 to January 2023. The findings showed that the early spread of certain SARS-CoV-2 lineages was geographically limited. However, the subsequent lifting of quarantine and travel restrictions facilitated the homogenization of the virus' genetic diversity across diverse regions. Moreover, our temporal analysis demonstrated that the lifespan of SARS-CoV-2 variants has been significantly truncated over time, with dominant strains frequently being outcompeted by more adaptive variants. We further observed that a significant proportion of newly emerged SARS-CoV-2 variants were identified in developing countries, particularly in sub-Saharan Africa, South America, and South Asia. Lastly, our results underscore the impact of weakened health systems, a high prevalence of immunocompromised individuals, and delayed reporting of these variants on the spread and severity of the virus in these regions.