Evaluating the microbial context of SARS-CoV-2 in patients and the hospital built environment

The ongoing transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prompts an urgent need to understand factors that promote or inhibit the spread of viral infections, especially in enclosed environments. We collected environmental and human specimens over time among confirmed patients with coronavirus disease 2019 (COVID-19) in spring 2020. Samples were collected from COVID-19 positive patients, multiple surfaces in their hospital rooms, and their health care providers before, during, and after admission. We screened for SARS-CoV-2 viral RNA using RT-qPCR and characterized the microbial communities through 16S rRNA gene amplicon sequencing. 16% of surfaces in rooms with COVID-19 patients were positive, with the highest prevalence rate coming from floors next to patient beds (36%). Patient nares and stool samples had higher viral load compared to forehead and surface samples. SARS-CoV-2 positive samples had higher phylogenetically-informed microbial alpha-diversity across all sample types. We identified a single amplicon sequence variant (ASV) from the genus Rothia that was highly predictive of SARS-CoV-2 in fecal, nares, and forehead samples, and found that it had higher prevalence in positive samples across all sample types, even when comparing to samples from sick patients in an intensive care unit prior to the COVID-19 outbreak. In surface samples, microbial composition was not driven by SARS-CoV-2 status, but higher microbial and human biomass was positively correlated with viral detection. These results suggest that microbial co-occurrences and biomass may contribute to persistence of the virus both in the host and hospital environment.