Evolution of a Distinct SARS-CoV-2 Lineage Identified during an Investigation of a Hospital Outbreak

The SARS-CoV-2 virus steadily evolves, and numerous antigenically distinct variants have emerged over the past three years. Tracking the evolution of the virus would help us understand the process that generates the diverse variants and predict the future evolutionary trajectory of SARS-CoV-2. Here, we report the evolutionary trajectory of a unique Omicron lineage identified during an outbreak investigation that occurred in a residence unit in the healthcare system. The new lineage had four distinct non-synonymous and two distinct synonymous mutations apart from its parental lineage. Since this lineage of virus was exclusively found during the outbreak, we were able to track the detailed evolutionary history of the entire lineage along the transmission path. Furthermore, we estimated the evolutionary rate of the SARS-CoV-2 Omicron variant from the analysis of the evolution of the lineage. This new Omicron sub-lineage acquired 3 mutations in a 12-day period, and the evolutionary rate was estimated as 3.05 × 10^{−3} subs/site/year. This study provides more insight into an ever-evolving virus.