Thread by @jeremiahfaith1

1) Here are a few highlights from our recent preprint: SARS-CoV-2-specific IgA and limited inflammatory cytokines are present in the stool of select patients with acute COVID-19 medrxiv.org/content/10.110…

2) Summary: SARS-CoV-2 RNA is sometimes detected in COVID-19 feces (as in other studies). We found an antigen-specific immune response (fecal IgA) in a few people. Intestinal inflammatory response, as measured in stool, is muted compared to other body sites.

3) Assays: virus RNA qPCR, viral genome sequencing, antigen specific fecal IgA, fecal cytokines, fecal microbiome (16S+metagenomics). Detailed virus inactivation compatible methods and QC are provided.

4) Dataset/credits: stools from 44 symptomatic COVID-19 patients hospitalized between Apr15-May21 2020, several with longitudinal follow-up. This was a joint effort with the Mehandru lab and co-first authors @grahambiota @achenliaw Francesca Cossarini @a_livanos @MatthewSpindl10

5) Credits 2: special thanks to ISMMS microbiology/genomics collaborators who were totally generous with methods/resources despite extremely busy lives in the COVID-19 NYC peak including @FatimaAmanat
@florian_krammer @daisyhoagz @virusninja Ana Gonzalez-Reiche Harm van Bakel.

6) Focus: The study focused on patients with GI symptoms but also had those without.

7) RESULT - fecal SARS-CoV-2 RNA part 1: Detectable in only ~40% of individuals. Higher viral RNA in subset with diarrhea. Higher viral RNA in subset that did not survive.

8) RESULT - Viral genome: This is the first study I am aware of that sequenced the viral genome from feces (thanks Ana/Harm!). The 3 SARS-CoV-2 genomes were all in clade 20C (the most abundant clade in NYC). It does not appear virus in stool is enriched for a particular strain.

9) RESULT - Gut Inflammation: fecal cytokines and fecal calprotectin changes were largely mild. most were not associated with COVID-19, disease severity, or diarrhea. Most notable was a decrease in fecal IL-10 in COVID-19 stools. (Y-axis = pg cytokine/mg stool of)

10) RESULT - Antigen-specificity: With recombinant protein to assay SARS-CoV-2 specific antibodies (thanks Fatima/Florian!), serum and fecal IgA were correlated with far less signal in stool. Only a small subset of COVID-19 stools were above background of pre-COVID-19 controls.

11) SEE ALSO (GI focused looking at gut tissue) - Gastrointestinal involvement attenuates COVID-19 severity and mortality medrxiv.org/content/10.110…