Wang Liang, Didelot Xavier, Bi Yuhai, Gao George F
Institute of Microbiology, Chinese Academy of Sciences.
School of Life Sciences and Department of Statistics, University of Warwick.
Brief Bioinform. 2022 Mar 10;23(2). doi: 10.1093/bib/bbab594.
Since the start of the SARS-CoV-2 pandemic in late 2019, several variants of concern (VOC) have been reported to have increased transmissibility. In addition, despite the progress of vaccination against SARS-CoV-2 worldwide, all vaccines currently in used are known to protect only partially from infection and onward transmission. We combined phylogenetic analysis with Bayesian inference under an epidemiological model to infer the reproduction number (Rt) and also trace person-to-person transmission. We examined the impact of phylogenetic uncertainty and sampling bias on the estimation. Our result indicated that lineage B had a significantly higher transmissibility than lineage A and contributed to the global pandemic to a large extent. In addition, although the transmissibility of VOCs is higher than other exponentially growing lineages, this difference is not very high. The probability of detecting onward transmission from patients infected with SARS-CoV-2 VOCs who had received at least one dose of vaccine was approximate 1.06% (3/284), which was slightly lower but not statistically significantly different from a probability of 1.21% (10/828) for unvaccinated individuals. In addition to VOCs, exponentially growing lineages in each country should also be account for when tailoring prevention and control strategies. One dose of vaccination could not efficiently prevent the onward transmission of SARS-CoV-2 VOCs. Consequently, nonpharmaceutical interventions (such as wearing masks and social distancing) should still be implemented in each country during the vaccination period.
自2019年末新型冠状病毒肺炎疫情开始以来，据报道几种值得关注的变异株（VOC）的传播力有所增强。此外，尽管全球范围内针对新型冠状病毒的疫苗接种取得了进展，但目前所有正在使用的疫苗都仅能部分预防感染和后续传播。我们将系统发育分析与流行病学模型下的贝叶斯推断相结合，以推断再生数（Rt）并追踪人际传播。我们研究了系统发育不确定性和抽样偏差对估计的影响。我们的结果表明，B谱系的传播力明显高于A谱系，并在很大程度上促成了全球疫情。此外，尽管VOC的传播力高于其他呈指数增长的谱系，但这种差异并不是很大。在至少接种过一剂疫苗的感染新型冠状病毒VOC的患者中检测到后续传播的概率约为1.06%（3/284），略低于未接种疫苗个体的1.21%（10/828），但在统计学上无显著差异。除了VOC之外，在制定预防和控制策略时，还应考虑每个国家呈指数增长的谱系。一剂疫苗不能有效预防新型冠状病毒VOC的后续传播。因此，在疫苗接种期间，每个国家仍应实施非药物干预措施（如戴口罩和保持社交距离）。
