Department of Laboratory Medicine, University of Washington, Seattle, WA.
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA.
Clin Chem. 2020 Jul 1;66(7):966-972. doi: 10.1093/clinchem/hvaa106.
More than 2 months separated the initial description of SARS-CoV-2 and discovery of its widespread dissemination in the United States. Despite this lengthy interval, implementation of specific quantitative reverse transcription (qRT)-PCR-based SARS-CoV-2 tests in the US has been slow, and testing is still not widely available. Metagenomic sequencing offers the promise of unbiased detection of emerging pathogens, without requiring prior knowledge of the identity of the responsible agent or its genomic sequence.
To evaluate metagenomic approaches in the context of the current SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, WA were evaluated by metagenomic sequencing, with comparison to a 2019 reference genomic database created before the emergence of SARS-CoV-2.
Within 36 h our results showed clear identification of a novel human Betacoronavirus, closely related to known Betacoronaviruses of bats, in laboratory-proven cases of SARS-CoV-2. A subset of samples also showed superinfection or colonization with human parainfluenza virus 3 or Moraxella species, highlighting the need to test directly for SARS-CoV-2 as opposed to ruling out an infection using a viral respiratory panel. Samples negative for SARS-CoV-2 by RT-PCR were also negative by metagenomic analysis, and positive for Rhinovirus A and C. Unlike targeted SARS-CoV-2 qRT-PCR testing, metagenomic analysis of these SARS-CoV-2 negative samples identified candidate etiological agents for the patients' respiratory symptoms.
Taken together, these results demonstrate the value of metagenomic analysis in the monitoring and response to this and future viral pandemics.
从首次描述 SARS-CoV-2 到发现其在美国广泛传播，中间相隔了两个多月。尽管时间很长，但美国实施特定的基于定量逆转录聚合酶链反应（qRT）-PCR 的 SARS-CoV-2 检测的速度仍然很慢，检测仍然不是广泛可用的。宏基因组测序有望在无需事先了解负责病原体及其基因组序列的情况下，实现对新兴病原体的无偏检测。
为了在当前 SARS-CoV-2 流行的背景下评估宏基因组方法，对来自华盛顿州西雅图的实验室确诊的阳性和阴性样本进行了宏基因组测序，并与在 SARS-CoV-2 出现之前创建的 2019 年参考基因组数据库进行了比较。
在 36 小时内，我们的结果明确鉴定出一种新型人类贝塔冠状病毒，与已知的蝙蝠贝塔冠状病毒密切相关，在实验室确诊的 SARS-CoV-2 病例中。一部分样本还显示存在人副流感病毒 3 或莫拉氏菌属的混合感染或定植，这突出表明需要直接检测 SARS-CoV-2，而不是通过病毒呼吸道检测试剂盒来排除感染。通过 RT-PCR 检测为 SARS-CoV-2 阴性的样本也通过宏基因组分析呈阴性，而检测出鼻病毒 A 和 C 呈阳性。与靶向 SARS-CoV-2 qRT-PCR 检测不同，对这些 SARS-CoV-2 阴性样本进行的宏基因组分析确定了患者呼吸道症状的潜在病因。
综上所述，这些结果表明宏基因组分析在监测和应对此次以及未来的病毒大流行方面具有价值。
