Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing

被引:14
作者
Papoutsis, Andreas [1 ]
Borody, Thomas [2 ]
Dolai, Siba [2 ]
Daniels, Jordan [1 ]
Steinberg, Skylar [1 ]
Barrows, Brad [1 ]
Hazan, Sabine [1 ,3 ]
机构
[1] ProgenaBiome, Ventura, CA 93003 USA
[2] Ctr Digest Dis, Sydney, NSW, Australia
[3] Ventura Clin Trials, Ventura, CA USA
关键词
Coronavirus; SARS-CoV-2; COVID-19; NGS; Fecal-oral transmission; CORONAVIRUS;
D O I
10.1186/s13099-021-00398-5
中图分类号
R57 [消化系及腹部疾病];
学科分类号
摘要
Background 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. Results 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. Conclusion 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, ).
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页数:8
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