Scarpa Fabio, Locci Chiara, Azzena Ilenia, Casu Marco, Fiori Pier Luigi, Ciccozzi Alessandra, Giovanetti Marta, Quaranta Miriana, Ceccarelli Giancarlo, Pascarella Stefano, Ciccozzi Massimo, Sanna Daria
Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy.
Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy.
Microorganisms. 2023 Jul 17;11(7):1824. doi: 10.3390/microorganisms11071824.
Recombination events are very common and represent one of the primary drivers of RNA virus evolution. The XBF SARS-CoV-2 lineage is one of the most recently generated recombinants during the COVID-19 pandemic. It is a recombinant of BA.5.2.3 and BA.2.75.3, both descendants of lineages that caused many concerns (BA.5 and BA.2.75, respectively). Here, we performed a genomic survey focused on comparing the recombinant XBF with its parental lineages to provide a comprehensive assessment of the evolutionary potential, epidemiological trajectory, and potential risks. Genetic analyses indicated that although XBF initially showed the typical expansion depicted by a steep curve, causing several concerns, currently there is no indication of significant expansion potential or a contagion rate surpassing that of other currently active or previously prevalent lineages. BSP indicated that the peak has been reached around 19 October 2022 and then the genetic variability suffered slight oscillations until early 5 March 2023 when the population size reduced for the last time starting its last plateau that is still lasting. Structural analyses confirmed its reduced potential, also indicating that properties of NTDs and RBDs of XBF and its parental lineages present no significant difference. Of course, cautionary measures must still be taken and genome-based monitoring remains the best tool for detecting any important changes in viral genome composition.
重组事件非常普遍，是RNA病毒进化的主要驱动因素之一。XBF新冠病毒谱系是新冠疫情期间最新产生的重组毒株之一。它是BA.5.2.3和BA.2.75.3的重组体，而这两个谱系（分别为BA.5和BA.2.75）的后代曾引发诸多担忧。在此，我们开展了一项基因组调查，重点是将重组的XBF与其亲本谱系进行比较，以全面评估其进化潜力、流行病学轨迹和潜在风险。基因分析表明，尽管XBF最初呈现出典型的陡峭曲线式扩张，引发了一些担忧，但目前没有迹象表明其有显著的扩张潜力或传播率超过其他当前活跃或先前流行的谱系。贝叶斯天际线图分析表明，在2022年10月19日左右达到峰值，随后遗传变异性出现轻微波动，直到2023年3月5日早些时候种群规模最后一次下降，开始其仍在持续的最后一个平稳期。结构分析证实了其较低的潜力，还表明XBF及其亲本谱系的NTDs和RBDs特性没有显著差异。当然，仍必须采取预防措施，基于基因组的监测仍然是检测病毒基因组组成任何重要变化的最佳工具。
