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Gut Pathogens

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01-12-2021 | Coronavirus | Research

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

Authors: Andreas Papoutsis, Thomas Borody, Siba Dolai, Jordan Daniels, Skylar Steinberg, Brad Barrows, Sabine Hazan

Published in: Gut Pathogens | Issue 1/2021

Abstract

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.

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Title: Detection of SARS-CoV-2 from patient fecal samples by whole genome sequencing
Authors: Andreas Papoutsis
Thomas Borody
Siba Dolai
Jordan Daniels
Skylar Steinberg
Brad Barrows
Sabine Hazan
Publication date: 01-12-2021
Publisher: BioMed Central
Keywords: Coronavirus
SARS-CoV-2
COVID-19
Published in: Gut Pathogens / Issue 1/2021
Electronic ISSN: 1757-4749
DOI: https://doi.org/10.1186/s13099-021-00398-5

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