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

Abstract Introduction: In nearly 3 years of circulation among the human population, SARS-CoV-2 underwent a complex evolution, shaping its genetics and adaptation to humans. Our study highlights varying prevalence, distribution across regions, and pandemic timeline. Methodology: In this study we used a dataset of 14,759 SARS-CoV-2 genomes collected between December 2019 and January 2023 from 214 countries. The sequences were analyzed comparatively to explore how SARS-CoV-2 variant mutation patterns varied across time and geographic locations. Results: We identified a total of 801 lineages harboring 17,360 nucleic mutations, with an average annual evolution rate of 26.07 substitutions per sample. The lifespan of these variants significantly shortened over time, as dominant virus strains were successively replaced by more adapted variants. SARS-CoV-2 variants' lifespan notably decreased as the pandemic progressed. Dominant virus strains were replaced by more fit variants carrying mutations associated with neutralizing antibodies and potential immune escape. Importantly, we identified a significant proportion of new SARS-CoV-2 variants emerging from developing countries, particularly in sub-Saharan Africa, South America, and South Asia, in spite of the overall homogenization of the SARS-CoV-2 genomic landscape since January 2021. Conclusions: Our analysis underscores the dynamic evolution of SARS-CoV-2, with variants rapidly emerging, adapting, and spreading globally, particularly from specific geographic regions of the world which shaped the course of the pandemic.