NCM 2021: Detecting SARS-CoV-2 and other pathogens in aerosols at wastewater treatment plants

Hugh explained that wastewater is ‘a catalogue of pathogens present in human populations served by a given wastewater system’. The UC Davis wastewater treatment facility is ‘an interesting case’, as it receives wastewater from diverse sources, so it is quite biologically complex. In their research, Hugh’s team aimed to detect SARS-CoV-2 bioaerosols generated by primary wastewater aeration (now published in the Chemosphere journal). Hugh highlighted that there is a need for comprehensive monitoring for the potential appearance of new pathogens, to protect ourselves from pandemics that are ‘inevitably in our future’. To this end, they aimed to evaluate nucleic acid sequencing of the wastewater aerobiome for pathogen surveillance. The team collected aerosol samples, at a rate of 200 L/minute, for 24 hours a day over 4 consecutive days; the sample was split for RNA and DNA extraction, and DNA, direct RNA, and cDNA nanopore sequencing. A range of software tools were used for their analyses, including Shasta (assembly), minimap2 (alignment), Kraken2 (classification), and the ARTIC v3 and Midnight pipelines (SARS-CoV-2 genome analysis). Overall, ~92% of classified DNA reads were classed as bacteria, ~7.5% as human, ~0.3% as fungi, and ~0.1% as viral. Hugh concluded that SARS-CoV-2 nucleic acids were found in aerosols generated at wastewater treatment plants, and that their methods of air sampling and nucleic acid extraction provided intact genetic material at sufficient quantities for detailed sample analyses. Hugh closed with the question: can this approach be a surveillance method for agnostic detection of new pathogens?