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

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Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing
Gut Pathogens ( IF 4.3 ) Pub Date : 2021-01-30 , DOI: 10.1186/s13099-021-00398-5
Andreas Papoutsis , Thomas Borody , Siba Dolai , Jordan Daniels , Skylar Steinberg , Brad Barrows , Sabine Hazan

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 ).

更新日期：2021-02-01

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