Papoutsis Andreas, Borody Thomas, Dolai Siba, Daniels Jordan, Steinberg Skylar, Barrows Brad, Hazan Sabine
ProgenaBiome, Ventura, CA, United States.
Centre for Digestive Diseases, Sydney, Australia.
Gut Pathog. 2021 Jan 30;13(1):7. doi: 10.1186/s13099-021-00398-5.
SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment next-generation sequencing (NGS) from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients.
Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS.
These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal-oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication. Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1 ).
严重急性呼吸综合征冠状病毒2（SARS-CoV-2）不仅在呼吸道分泌物中被检测到，在粪便样本中也有发现。本研究旨在通过粪便样本的富集下一代测序（NGS）来鉴定SARS-CoV-2，并利用全基因组分析来表征COVID-19患者中SARS-CoV-2的突变变异。
研究参与者接受了通过全基因组富集NGS对粪便样本进行的SARS-CoV-2检测（n = 14），以及逆转录聚合酶链反应（RT-PCR）鼻咽拭子分析（n = 12）。粪便富集NGS检测SARS-CoV-2与RT-PCR鼻咽分析的一致性为100%。在4名患者中鉴定出独特的变异，在通过全基因组富集NGS检测到SARS-CoV-2的患者中共有33种不同的突变。
这些结果突出了SARS-CoV-2在粪便中的潜在生存能力、其持续的突变积累以及其在粪口传播中的可能作用。本研究还阐明了SARS-CoV-2富集NGS的优势，这可能是记录病毒完全清除的关键方法。试验注册ClinicalTrials.gov，NCT04359836，于2020年4月24日注册，https://clinicaltrials.gov/ct2/show/NCT04359836?term=NCT04359836&draw=2&rank=1 。
