Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants.
Genome Sequencing of Sewage Detects Regionally Prevalent SARS-CoV-2 Variants.
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DOI：
10.1128/mbio.02703-20
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发表时间：
2021-01-19
期刊：
影响因子：
6.4
通讯作者：
Nelson KL
中科院分区：
文献类型：
--
作者：
Crits-Christoph A;Kantor RS;Olm MR;Whitney ON;Al-Shayeb B;Lou YC;Flamholz A;Kennedy LC;Greenwald H;Hinkle A;Hetzel J;Spitzer S;Koble J;Tan A;Hyde F;Schroth G;Kuersten S;Banfield JF;Nelson KL
病毒基因组测序指导了我们对COVID-19大流行期间SARS-CoV-2的传播和遗传多样性程度的理解。SARS-CoV-2病毒基因组通常从个体患者的鼻咽拭子中测序，以跟踪病毒传播。病毒基因组测序指导了我们对COVID-19大流行期间SARS-CoV-2的传播和遗传多样性程度的了解。SARS-CoV-2病毒基因组通常从个体患者的鼻咽拭子中测序，以跟踪病毒传播。最近，城市污水的RT-qPCR已被用于量化全球几个地区的SARS-CoV-2丰度。然而，废水的元转录组测序可用于分析受感染社区的病毒遗传多样性。在这里，我们直接从旧金山弗朗西斯科湾区市政公用事业区收集的污水中测序RNA，以生成完整和接近完整的SARS-CoV-2基因组。在污水中检测到的SARS-CoV-2基因型与该地区的临床基因组相同。在宏基因组背景下使用单核苷酸变体调用管道，我们表征了废水中的次要SARS-CoV-2等位基因，并检测了在整个加州的临床基因组中也发现的病毒基因型。所观察到的废水变体更类似于当地加州患者来源的基因型，而不是来自美国或全球其他地区的基因型。在废水中检测到的其他变异体仅在加州以外采样的患者基因组中发现，这表明废水测序可以在当地临床测序检测到病毒谱系之前为最近引入的病毒谱系提供证据。这些结果表明，通过废水测序进行流行病学监测有助于在流行病背景下追踪确切的病毒株。
Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Viral genome sequencing has guided our understanding of the spread and extent of genetic diversity of SARS-CoV-2 during the COVID-19 pandemic. SARS-CoV-2 viral genomes are usually sequenced from nasopharyngeal swabs of individual patients to track viral spread. Recently, RT-qPCR of municipal wastewater has been used to quantify the abundance of SARS-CoV-2 in several regions globally. However, metatranscriptomic sequencing of wastewater can be used to profile the viral genetic diversity across infected communities. Here, we sequenced RNA directly from sewage collected by municipal utility districts in the San Francisco Bay Area to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in the sewage were identical to clinical genomes from the region. Using a pipeline for single nucleotide variant calling in a metagenomic context, we characterized minor SARS-CoV-2 alleles in the wastewater and detected viral genotypes which were also found within clinical genomes throughout California. Observed wastewater variants were more similar to local California patient-derived genotypes than they were to those from other regions within the United States or globally. Additional variants detected in wastewater have only been identified in genomes from patients sampled outside California, indicating that wastewater sequencing can provide evidence for recent introductions of viral lineages before they are detected by local clinical sequencing. These results demonstrate that epidemiological surveillance through wastewater sequencing can aid in tracking exact viral strains in an epidemic context.