Detection of SARS-CoV-2 from Patient Fecal Samples by Whole Genome Sequencing

Background: SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections, by RT-PCR; thus herein, we sought to identify faecal SARS-CoV-2, and its variants, via next-generation sequencing (NGS).

Methods: Fecal samples from COVID patients were collected and whole genome analysis was used to detect and characterize SARS-CoV-2 mutational variations. Of note, NGS detects genomic RNA sequences, not infectious agents.

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 presence of SARS-CoV-2 in faeces, that is, the presence of SARS-CoV-2 genetic material, even in the lack of shedding in faeces. Further studies on virus viability in the stool are necessary as the role in fecal-oral transmission. These findings are exploratory as they are based on a small sample size.

Keywords: Coronavirus, SARS-CoV-2, COVID-19, NGS, fecal-oral transmission, stools