Comprehensive genomic surveillance analysis of SARS-CoV-2: Global epidemic dynamics and geographic variability of variants

Abstract

Almost 4 years into the COVID-19 pandemic, the world has shifted into a phase characterized by the Omicron variant, which has maintained prevalence for over a year, giving rise to more than 3690 subvariants globally. To investigate the worldwide genomic surveillance of SARS-CoV-2, metadata from over 5.5 million high-quality genomes were analyzed. The results revealed significant geographic heterogeneity in the distribution of variants of concern/interest (VOC/VOI) across different continents, especially noticeable for the Epsilon and Iota VOIs. Moreover, the sequencing turnaround times exhibited notable geographic heterogeneity. These disparities in turnaround time and geographic coverage are critical for refining policies, guidelines, and mitigation strategies to effectively address the COVID-19 pandemic. In the context of the persistent COVID-19 pandemic and the global spread of various variants, understanding the mortality and transmissibility rates of SARS-CoV-2 is crucial. The mean mortality rate of SARS-CoV-2 stands at 2.62% (median: 2.17%; 95% confidence interval [CI]: 1.06 – 6.81%). Notably, the Omicron variant exhibits distinct transmissibility characteristics (mean: 13.22; median: 12.06; 95% CI: 6.02 – 20.59) compared to other SARS-CoV-2 variants (mean: 1.40; median: 1.12; 95% CI: 0.97 – 2.28). These data underscore the need for future genomic surveillance strategies, including strategic sampling, randomized baseline surveillance, and rapid reporting, to enhance global public health efforts. Such strategies are essential for monitoring and responding to the evolving landscape of the pandemic, as evidenced by the variability in mortality and transmission rates among different variants.