Assessing within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat

The long-term evolution of viruses is ultimately due to viral mutants that arise within infected individuals and transmit to other individuals. We used deep sequencing to investigate the transmission of viral genetic variation among individuals during a SARS-CoV-2 outbreak that infected the vast majority of crew members on a fishing boat. We deep-sequenced nasal swabs to characterize the within-host viral population of infected crew members, using experimental duplicates and strict computational filters to ensure accurate variant calling. We find that within-host viral diversity is low in infected crew members. The mutations that did fix in some crew members during the outbreak are not observed at detectable frequencies in any of the sampled crew members in which they are not fixed, suggesting viral evolution involves occasional fixation of low-frequency mutations during transmission rather than persistent maintenance of within-host viral diversity. Overall, our results show that strong transmission bottlenecks dominate viral evolution even during a superspreading event with a very high attack rate.

病毒的长期演化归根结底源于感染个体内产生的病毒突变体，且此类突变体可传播至其他个体。我们借助深度测序（deep sequencing）技术，对某渔船暴发的严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）疫情展开研究，该疫情感染了船上绝大多数船员，旨在探究病毒遗传变异在个体间的传播规律。我们对采集的鼻咽拭子样本进行深度测序，以表征感染者体内的病毒种群特征；实验设置了实验重复，并采用严格的计算过滤流程以确保变异鉴定的准确性。我们发现，感染船员体内的病毒种群多样性水平较低。暴发期间在部分船员体内得以固定的突变，在未发生该突变固定的其余采样船员样本中，均未以可检测频率被观测到。这表明病毒演化涉及传播过程中低频突变的偶发固定，而非宿主体内病毒多样性的持续维持。总体而言，我们的研究结果显示，即便在攻击率极高的超级传播事件中，强烈的传播瓶颈仍主导着病毒的演化进程。