Microbiome analysis for wastewater surveillance during COVID-19
Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage and its variations in a community. Composite wastewater samples (24 hr) were collected weekly from a manhole between December, 2020, and November, 2021 in Maryland, USA. RT-qPCR results showed concentrations of SARS-CoV-2 RNA recovered from wastewater samples reflected incidence of COVID-19 cases in the community serviced by the sewage collection system. When a spike in recovered SARS-CoV-2 RNA was detected in February, 2021, samples were selected for microbiome analysis (DNA metagenomics, RNA metatranscriptomics, and targeted SARS-CoV-2 genome sequencing). The increase in SARS-CoV-2 RNA observed in February, 2021, correlated with B.1.351 (Beta, V2), but other variants, predominantly B.1.1.7 (Alpha, V1), were also detected throughout the study. Microbiome analysis (DNA and RNA) provided important insight with respect to human health-related factors, including detection of pathogens and their virulence/antibiotic resistance genes. Specific microbial species comprising the wastewater microbiome correlated with incidence of SARS-CoV-2 RNA, suggesting potential association with SARS-CoV-2 infection. Climatic conditions, namely temperature, were related to incidence of COVID-19 and detection of SARS-CoV-2 in wastewater, having been monitored as part of an environmental risk assessment carried out in this study. In summary, the wastewater microbiome provides useful public health information, hence a valuable tool to proactively detect and characterize pathogenic agents circulating in a community. In effect, the metagenomics of wastewater can serve as an early warning system for communicable diseases.