The Association Between Stool Shedding of SARS-Cov-2 Microbiome Diversity and Intestinal Inflammation

ABSTRACT

Introduction: The transmission of the etiologic virus of COVID-19 (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) is thought to occur mainly via respiratory droplets even though limited evidence has shown the virus can be found in feces and involve the gastrointestinal (GI) tract. The aim of this study was to assess if patients with COVID-19 present with fecal shedding of SARS-CoV-2, intestinal inflammation or changes in their microbiota. Method(s) This was a prospective cohort study that included outpatients that presented with symptoms of COVID-19 and were tested using a nasopharyngeal PCR test (NPT). Two cohorts were selected one with a (1) NPT and a control group with a (-) NPT. Stool and a clinical data were collected at baseline and then, days 14, 28 and 42. SARS-CoV-2 viral loads were measured in stool using PCR and stool microbiome was analyzed using 16S rRNA gene sequencing (V3/V4 region). Fecal calprotectin levels were also measured on each sample and used as a surrogate marker of intestinal inflammation. Result(s) 101 patients were recruited (410 total samples). Of those, 55 had a (1) COVID-19 NPT. Most patients with a (1) COVID-19 NPT PCR had a detectable fecal viral load (71%). Among these patients, 23 (55%) had detectable viral stool loads only at baseline, 12 through day 14, 6 through day 28 and 1 through day 42. One patient had a (-) NPT but detectable SARS-CoV-2 in the baseline stool sample. Subjects with (1) NPT presented more commonly with myalgias (p=0.02), dysgeusia (p=0.019) and anosmia (p=0.03) when compared to those with (-) NPT but there were no differences in any other symptoms including GI manifestations.Within the group with a (1) NPT, those patient with detectable SARS-CoV-2 in the stool were younger but no differences were seen in demographic, symptoms, or fecal calprotectin levels (Table). There was no correlation between fecal SARS-CoV-2 loads and fecal calprotectin levels (rho 0.007 [p=0.95]). Patients with a (1) NPT PCR had higher evenness when compared to those that tested (-) for a NPT PCR. However, no differences were seen in other alpha or beta diversity (Figures 1A and 1B, respectively). Conclusion(s) Even though intestinal viral shedding of SARS-CoV-2 in patients with COVID-19 is common, these patients do not present with evidence of inflammation of the GI tract, a significantly disrupted gut microbiome or a higher incidence of GI symptoms when compared to patients with respiratory symptoms and no COVID-19.