COVID-19 Surveillance through Wastewater Microbiome Analysis

Nasal swabs and saliva are conventional methods for detection of SARS-CoV-2, but the virus is also present in feces. Therefore, fecal material in wastewater samples could be used to track community dynamics of the virus. To do that, Brumfield et al. (2022) collected wastewater samples from manholes and then processed them for microbial genome sequencing and metatranscriptomic RNA sequencing. The CosmosID-HUB pipeline was used for microbiome profiling of viruses, bacteria, archaea, fungi, protozoa and antimicrobial resistance, and virulence factors in their genomes. SARS-CoV2 N protein copy number was calculated from the data and compared with epidemiological data. Using this method, the study identified that N protein copy number/mL followed the increased trend of COVID-19 cases in winter and a decrease in warmer months, but identified no significant associations. Regarding the microbiome, the study identified a strong positive correlation of SARS-CoV-2 RNA associated with Bifidobacterium, Leclercia, Pyramidobacter, Tannerella, Massilimaliae, and Erythrobacter relative abundance. The sole virus that correlated with SARS-CoV-2 was JC polyomavirus. Link to the paper.