Analyzing the genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from clinical samples is crucial for understanding viral spread and evolution as well as for vaccine development. Existing RNA sequencing methods are demanding on user technique and time and, thus, not ideal for time-sensitive clinical samples; these methods are also not optimized for high performance on viral genomes. We developed a facile, practical, and robust approach for metagenomic and deep viral sequencing from clinical samples. We demonstrate the utility of our approach on pharyngeal, sputum, and stool samples collected from coronavirus disease 2019 (COVID-19) patients, successfully obtaining whole metatranscriptomes and complete high-depth, high-coverage SARS-CoV-2 genomes with high yield and robustness. With a shortened hands-on time from sample to virus-enriched sequencing-ready library, this rapid, versatile, and clinic-friendly approach will facilitate molecular epidemiology studies during current and future outbreaks.

分析临床样本中严重急性呼吸综合征冠状病毒 2 (SARS-CoV-2) 的基因组对于了解病毒传播和进化以及疫苗开发至关重要。现有的RNA测序方法对用户技术和时间要求较高，因此不适合时间敏感的临床样本；这些方法也没有针对病毒基因组的高性能进行优化。我们开发了一种简便、实用且稳健的方法，用于从临床样本中进行宏基因组和深度病毒测序。我们展示了我们的方法对从 2019 年冠状病毒病 (COVID-19) 患者收集的咽、痰和粪便样本的效用，成功获得了完整的宏转录组和完整的高深度、高覆盖率的 SARS-CoV-2 基因组，且产量高、产量高。鲁棒性。通过缩短从样本到富含病毒的测序库的实际操作时间，这种快速、多功能且适合临床的方法将促进当前和未来疫情期间的分子流行病学研究。