Department of Research, Central Texas Veterans Health Care System, Temple, TX 76504, USA.
Department of Medicine, Central Texas Veterans Health Care System, Temple, TX 76504, USA.
Viruses. 2024 Feb 22;16(3):337. doi: 10.3390/v16030337.
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 subs/site/year. This study provides more insight into an ever-evolving virus.
新冠病毒持续进化，在过去三年中出现了许多抗原不同的变体。追踪病毒的进化将有助于我们了解产生多种变体的过程，并预测 SARS-CoV-2 的未来进化轨迹。在这里，我们报告了在医疗系统的居住单位爆发调查期间发现的一种独特的奥密克戎谱系的进化轨迹。除了与亲代谱系不同外，新谱系还有四个不同的非同义突变和两个不同的同义突变。由于这种病毒谱系仅在疫情爆发期间被发现，我们能够沿着传播途径追踪整个谱系的详细进化历史。此外，我们通过对谱系进化的分析估计了 SARS-CoV-2 奥密克戎变体的进化率。这个新的奥密克戎亚谱系在 12 天内获得了 3 个突变，进化率估计为 3.05×10 个亚单位/位点/年。本研究为不断进化的病毒提供了更多的了解。
