Fig. 1.

INSTINCT (n = 45) and ISARIC4C (n = 43) study sample collection schedules and cohort demographics. (A) PCR-negative controls and ambulatory community COVID-19 cases were collected via INSTINCT. Serial faecal, blood and nasopharyngeal swabs were collected over 28 days. Moderate and severely ill COVID-19 cases were recruited via ISARIC4C. Faecal samples and nasopharyngeal swabs were collected at enrolment which occurred immediately following hospitalisation. ISARIC4C and INSTINCT sample collection schedules are aligned to show that comparisons are made between faecal samples collected at D0 and D7 respectively. (B) Table showing patient state and descriptor for each severity group. (C) Participant age and (D) Biological sex and (E) Bristol stool score stratified by symptom severity group. Colours represent Severity Groups. Results of Kruskal Wallis tests with Dunn’s multiple comparison tests are displayed *p < 0.05, **p < 0.01, ***p < 0.001. ECMO = extracorporeal membrane oxygenation.