Microbiome analysis for wastewater surveillance during COVID-19

COVID-19 is a contagious disease caused by a virus (SARS-CoV-2). With over 400 million cases reported globally since 2019 and continued emergence of new variants, COVID-19 is now reported as a pandemic. Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals. Wastewater samples can be used to test all individuals of a community contributing to the sewage collection system. Here, we profile community wastewater collected from a sewage collection system, detect presence of SARS-CoV-2, determine variants of SARS-CoV-2 that are present, and perform COVID-19 risk assessment of the study area. Using metagenomics analysis, we also detect other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Results show that by analyzing all microorganisms present in wastewater, pathogens circulating in a community can provide an early warning for contagious diseases.