SARS-CoV-2 within-host evolution from RVTN

SARS-CoV-2 has undergone repeated and rapid evolution to circumvent host immunity. However, outside of prolonged infections in immunocompromised hosts, within-host positive selection has rarely been detected. The low diversity within-hosts and strong linkage among sites make accurately detecting positive selection difficult. Longitudinal sampling is a powerful method for detecting selection that has seldom been used for SARS-CoV-2. Here we combine longitudinal sampling with replicate sequencing to increase the accuracy of and lower the threshold for variant calling. We sequenced 577 specimens from 105 individuals from a household cohort during primarily the BA.1 wave. There was extremely low diversity and a low rate of divergence. Specimens had 0-12 intrahost single nucleotide variants (iSNV) at >0.5% frequency, and the majority of the iSNV were at frequencies <2%. Within-host dynamics were dominated by genetic drift and purifying selection. Positive selection was rare but highly concentrated in spike. Two individuals with BA.1 infections had S:371F, a lineage defining substitution for BA.2. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 14 loci with 7 in spike, including S:448 and S:339. We also detected significant genetic hitchhiking between of synonymous sites and nonsynonymous iSNV under selection. The detectable immune mediated selection detected may be caused by the relatively narrow antibody repertoire during this phase of the pandemic. As the virus and population immunity both evolves, understanding the corresponding shifts in within-processes shift will be important.

严重急性呼吸综合征冠状病毒2（SARS-CoV-2）会经历反复且快速的演化以逃逸宿主免疫。然而，除免疫功能低下宿主的长期感染案例外，学界极少能检测到宿主内正选择现象。宿主内较低的多样性水平与较强的位点间连锁效应，使得精准检出正选择极具难度。纵向采样是检测选择作用的有效手段，但在SARS-CoV-2研究中却鲜有应用。本研究将纵向采样与重复测序相结合，以提升变异检出（variant calling）的准确性并降低变异检出阈值。研究人员主要在BA.1毒株流行波期间，对某家庭队列中的105名个体采集了577份样本并完成测序。样本内多样性极低，演化分化速率也较慢。在频率高于0.5%的位点中，每份样本携带0~12个宿主内单核苷酸变异（intrahost single nucleotide variants，iSNV），且绝大多数iSNV的频率低于2%。宿主内演化动态主要由遗传漂变与纯化选择主导。正选择现象较为罕见，但高度集中于刺突蛋白（spike）区域。2名感染BA.1毒株的个体携带了S:371F突变——这是BA.2毒株的谱系标志性替换突变。赖特-费舍尔近似贝叶斯计算模型（Wright Fisher Approximate Bayesian Computational model）在14个位点中检出了正选择信号，其中7个位于刺突蛋白区域，包括S:448与S:339位点。本研究还检测到，受选择作用的非同义宿主内单核苷酸变异与同义位点间存在显著的遗传搭车效应。本次检测到的免疫介导选择作用，可能源于该大流行阶段人群相对有限的抗体库。随着病毒与人群免疫水平共同演化，解析宿主内演化过程的相应变化将至关重要。