Genome surveillance of SARS-CoV-2 Omicron XBB subvariants in Wuhan in June 2023

The COVID-19 pandemic caused by SARS-CoV-2 has had a significant impact on global social and economic activities. The continuous emergence of new SARS-CoV-2 variants has made the global pandemic of COVID-19 difficult to predict. Therefore, it is of great significance to closely monitor the SARS-CoV-2 epidemic and understand the evolution and transmission characteristics of SARS-CoV-2. In this study, we examined 36 cases of SARS-CoV-2 infection in Wuhan in June 2023. Genomic surveillance revealed that this outbreak was caused by Omicron XBB variants, among which FY.3 and its descendants FY.3.1 and FY.3.2 dominated, and this trend was consistent with the prevalence of SARS-CoV-2 nationwide in June and July. Analysis of sequence variations within hosts and between populations suggested that the S and ORF8 genes had undergone positive selection, possibly due to their important role in host adaptation, suggesting that some of these variations might be harmful mutations that reduce vaccine effectiveness. These findings may provide insights that will aid in predicting the evolutionary direction of SARS-CoV-2 in terms of variant competition, informing the design of next-generation multivalent vaccines and therapeutic strategies targeting conserved or rapidly evolving regions such as the S and ORF8 genes and supporting the evaluation and adjustment of surveillance, prevention, and control strategies in the Wuhan region.