Alpert Tara, Vogels Chantal B F, Breban Mallery I, Petrone Mary E, Wyllie Anne L, Grubaugh Nathan D, Fauver Joseph R
Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College St, New Haven, CT 06510, USA.
Virus Evol. 2022 Jan 3;8(1):veab098. doi: 10.1093/ve/veab098. eCollection 2022.
Genomic sequencing is crucial to understanding the epidemiology and evolution of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Often, genomic studies rely on remnant diagnostic material, typically nasopharyngeal (NP) swabs, as input into whole-genome SARS-CoV-2 next-generation sequencing pipelines. Saliva has proven to be a safe and stable specimen for the detection of SARS-CoV-2 RNA via traditional diagnostic assays; however, saliva is not commonly used for SARS-CoV-2 sequencing. Using the ARTIC Network amplicon-generation approach with sequencing on the Oxford Nanopore MinION, we demonstrate that sequencing SARS-CoV-2 from saliva produces genomes comparable to those from NP swabs, and that RNA extraction is necessary to generate complete genomes from saliva. In this study, we show that saliva is a useful specimen type for genomic studies of SARS-CoV-2.
基因组测序对于了解严重急性呼吸综合征冠状病毒2（SARS-CoV-2）的流行病学和进化至关重要。通常，基因组研究依赖于残余的诊断材料，典型的是鼻咽（NP）拭子，作为全基因组SARS-CoV-2下一代测序流程的输入。唾液已被证明是通过传统诊断检测来检测SARS-CoV-2 RNA的一种安全且稳定的样本；然而，唾液并不常用于SARS-CoV-2测序。使用ARTIC网络扩增子生成方法并在牛津纳米孔MinION上进行测序，我们证明从唾液中对SARS-CoV-2进行测序所产生的基因组与从NP拭子中产生的基因组相当，并且从唾液中生成完整基因组需要进行RNA提取。在本研究中，我们表明唾液是用于SARS-CoV-2基因组研究的一种有用的样本类型。
