Project Summary The COVID-19 pandemic currently has infected over 4 million people worldwide and led to over 300,000 deaths. These numbers continue to grow and with an anticipated resurgence in the fall and winter months. It is now clear that SARS-CoV-2 can enter the gastrointestinal (GI) tract, that it can bind to the ACE2 receptor abundantly expressed on intestinal epithelial cells, that it can be isolated live from stool, and that it sheds in the stool for several weeks after COVID-19 symptom onset. This information combined with the observations that GI manifestations of the disease, such as nausea and diarrhea, appear to be on the rise, place an urgent need for more clearly understanding the intestinal microenvironment in patients with COVID-19. This broad objective will not only allow for more tailored treatment for patients with GI manifestations currently diagnosed with COVID- 19, it will also help to understand whether a perturbed GI tract as a result of COVID-19 may lead to later GI pathology. Perhaps most importantly, this objective will help understand the factors that influence degree of SARS-CoV-2 GI persistence and shedding in stool, which directly relate to the potential of fecal-oral transmission. This proposal specifically addresses these objectives by examining whether the extensive antibiotics administered to COVID-19 patients are creating unintended effects on the GI tract that result in a favorable environment for SARS-CoV-2 infection and persistence in the gut. The principle of competitive exclusion has been demonstrated in the human GI tract in multiple publications using both oral and intravenous antibiotics, whereby the suppression of the total bacterial community and/or specific members, can result in increased colonization by fungi, viruses, and antibiotic-resistant bacteria. Among the many roles of the gut microbiota, one fundamental role is to provide colonization resistance against foreign invaders. We do not yet know how this microbial ecology plays out in the context of SARS-CoV-2. We hypothesize that antibiotic perturbation of the gut microbiota and its metabolome in COVID-19 patients results in increased load and persistence of SARS-CoV-2 in the intestines, and intestinal inflammation. We believe this may reflect disease stage/severity. As a result, we anticipate findings will be rapidly translated to govern clinical management of antimicrobials in patients as well as provide insight into pathways that influence transmission, development and resolution of COVID-19. Using biobanked specimens from COVID-19 patients that we have prospectively collected, we will test our hypotheses in the following specific aims: Aim 1. Determine the relationship between bacterial and fungal intestinal communities and SARS-CoV-2 viral load longitudinally in SARS-CoV-2 positive and negative patients, with and without exposure to different antibiotics, and Aim 2. Determine whether alterations to the gut microbiome is reflected in an altered metabolite and inflammatory profile.

Project Narrative The COVID-19 pandemic is a public health emergency that requires urgent discovery to understand the mechanisms that cause viral persistence in all body sites and therefore possible modes of transmission. This proposal aims to discover causes of viral persistence in the GI tract, and non-invasive biomarkers of potential intestinal damage.