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

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

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. Trial registration ClinicalTrials.gov, NCT04359836, Registered 24 April 2020, https://ichgcp.net/clinical-trials-registry/NCT04359836?term=NCT04359836&draw=2&rank=1 ).

Keywords: COVID-19; Coronavirus; Fecal–oral transmission; NGS; SARS-CoV-2.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Mapping outcomes of patient NGS data against the SARS-CoV-2 Wuhan-Hu-1 (MN90847.3) complete genome. The x-axis depicts the genomic coordinates and the y-axis represents the read depth at specific loci

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Source: PubMed

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