The Promise and Pitfalls of Environmental DNA and RNA Approaches for the Monitoring of Human and Animal Pathogens from Aquatic Sources

Abstract

Novel forensics-inspired molecular approaches have revolutionized species detection in the wild and are particularly useful for tracing endangered or invasive species. These new environmental DNA or RNA (eDNA or eRNA)–based techniques are now being applied to human and animal pathogen surveillance, particularly in aquatic environments. They allow better disease monitoring (presence or absence and geographical spread) and understanding of pathogen occurrence and transmission, benefitting species conservation and, more recently, our understanding of the COVID-19 global human pandemic. In the present article, we summarize the benefits of eDNA-based monitoring, highlighted by two case studies: The first is a fibropapillomatosis tumor-associated herpesvirus (chelonid herpesvirus 5) driving a sea turtle panzootic, and the second relates to eRNA-based detection of the SARS-CoV-2 coronavirus driving the COVID-19 human pandemic. The limitations of eDNA- or eRNA-based approaches are also summarized, and future directions and recommendations of the field are discussed. Continuous eDNA- or eRNA-based monitoring programs can potentially improve human and animal health by predicting disease outbreaks in advance, facilitating proactive rather than reactive responses.

Detection and population genomics of sea turtle species via noninvasive environmental DNA analysis of nesting beach sand tracks and oceanic water

“…Environmental DNA‐based conservation approaches are redefining our ability to monitor and protect vulnerable species, and our study demonstrates the varied applications possible when such approaches are applied to the study and conservation of migratory species with complex life cycles, such as endangered sea turtles (Adams et al, 2019; Beng & Corlett, 2020; Farrell, Whitmore, et al, 2021; Farrell, Yetsko, et al, 2021; Lacoursiere‐Roussel et al, 2016, 2018). This study has demonstrated the utility of species‐specific C .…”

“…Furthermore, we revealed the ability to collect data for population genetics studies through shotgun sequencing or conventional PCR of eDNA extracted from sand crawl samples. These approaches open a variety of conservation and health applications for sea turtle eDNA, from surveying population range shifts, to simultaneous host and pathogen monitoring, to conducting noninvasive population genetics on nesting females and hatchlings (Farrell, Whitmore, et al, 2021; Farrell, Yetsko, et al, 2021; Yetsko et al, 2021). We previously successfully employed the C .…”

“…We previously successfully employed the C . mydas assay in a rehabilitation setting to correlate sea turtle viral shedding with fibropapillomatosis tumor burden and the shedding of host turtle eDNA in patient tanks (Farrell, Whitmore, et al, 2021; Yetsko et al, 2020). Here we applied the same C .…”

“…Environmental DNA has been successfully retrieved from water, permafrost, snow, air, soil, and sand (Barnes & Turner, 2016; Barnes et al, 2014; Davy et al, 2015; Kelly et al, 2014; Rees et al, 2014). These technological approaches will be a crucial future conservation tool for detecting and monitoring low‐density threatened turtle species (Beng & Corlett, 2020; Farrell et al, 2021 et al, 2021; Farrell, Yetsko, et al, 2021; Harper et al, 2020; Jerde et al, 2011; Veilleux et al, 2021; Yetsko et al, 2021).…”

An Efficient Tetraplex Surveillance Tool for Salmonid Pathogens

“…The baseline ddPCR tetraplex assay presented here can be repurposed and adjusted to advanced technologies, including new pathogens of interest or analytical methods, which will foster scientific research output and expand the molecular surveillance toolbox. For example, applying occupancy and co-occurrence modeling approaches on the detection signals of different pathogens enables detection probabilities even if all samples return negative ( Willoughby et al, 2016 ; Laurin et al, 2020 ) and provides a cost-efficient tool for aquaculture surveillance ( Farrell et al, 2021 ).…”