Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA

nature ecology & evolution Article https://doi.org/10.1038/s41559-023-02056-2 Inadvertent human genomic bycatch and intentional capture raise beneficial applications and ethical concerns with environmental DNA Received: 21 April 2022 Accepted: 29 March 2023 Liam Whitmore1,2,6, Mark McCauley 1,3,6, Jessica A. Farrell1,4,6, Maximilian R. Stammnitz 5, Samantha A. Koda 1, Narges Mashkour1, Victoria Summers1, Todd Osborne 1, Jenny Whilde1 & David J. Duffy 1,4 Published online: 15 May 2023 Check for updates The field of environmental DNA (eDNA) is advancing rapidly, yet human eDNA applications remain underutilized and underconsidered. Broader adoption of eDNA analysis will produce many well-recognized benefits for pathogen surveillance, biodiversity monitoring, endangered and invasive species detection, and population genetics. Here we show that deep-sequencing-based eDNA approaches capture genomic information from humans (Homo sapiens) just as readily as that from the intended target species. We term this phenomenon human genetic bycatch (HGB). Additionally, high-quality human eDNA could be intentionally recovered from environmental substrates (water, sand and air), holding promise for beneficial medical, forensic and environmental applications. However, this also raises ethical dilemmas, from consent, privacy and surveillance to data ownership, requiring further consideration and potentially novel regulation. We present evidence that human eDNA is readily detectable from ‘wildlife’ environmental samples as human genetic bycatch, demonstrate that identifiable human DNA can be intentionally recovered from human-focused environmental sampling and discuss the translational and ethical implications of such findings. The field of environmental DNA (eDNA) research has been rapidly expanding in recent years, resulting in unprecedented advances in a range of biological monitoring applications. Environmental DNA research provides a non-invasive and cost-effective approach for the study and management of wild populations and invasive species, by using a forensics approach to the extraction and identification of DNA fragments released as organisms travel through and interact with the environment1–7. Environmental DNA analysis is also being applied to issues of human and animal health—for example, in pathogen, parasite and pollen monitoring1,8–10. This includes the rapidly emerging field of human eDNA-based pathogen detection from human wastewater. Such approaches developed quickly during the early stages of the COVID-19 Whitney Laboratory for Marine Bioscience and Sea Turtle Hospital, University of Florida, St. Augustine, FL, USA. 2Department of Biological Sciences, School of Natural Sciences, Faculty of Science and Engineering, University of Limerick, Limerick, Ireland. 3Department of Chemistry, University of Florida, Gainesville, FL, USA. 4Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA. 5Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain. 6These authors contributed equally: Liam Whitmore, Mark McCauley, Jessica A. Farrell. e-mail: 1 Nature Ecology & Evolution | Volume 7 | June 2023 | 873–888 873 Article pandemic and have already been repurposed for other pathogens such as monkeypox, poliovirus and tuberculosis1,11–15. Environmental DNA has been successfully obtained from a range of sample types including air, soil, terrestrial and aquatic sediments, water (marine, freshwater and wastewater), permafrost, snow and ice cores10,16,17. Environmental DNA research has traditionally relied primarily on targeted methodologies, such as quantitative PCR (qPCR) and metabarcoding-based next-generation sequencing, and early applications focused on bacterial communities18. However, continued improvements in deep sequencing technology and novel bioinformatics refinements mean that untargeted shotgun-sequencing-based approaches are becoming feasible (Extended Data Fig. 1a), which more fully capture the true extent of genetic diversity within a sample1,8,19. Shotgun sequencing is set to become more labour- and cost-effective than qPCR or metabarcoding in the near future while providing the least biased biodiversity assessments, thus providing the broadest possible presence and abundance information across all taxa. We have recently shown that untargeted shotgun deep sequencing (the direct sequencing of total eDNA with no prior enrichment or selection) can provide both host and pathogen sequence data8,17, while also simultaneously capturing all other biodiversity within an environmental sample. Similar to biodiversity assessments, shotgun sequencing of wastewater samples could be applied to monitor all human pathogens simultaneously but would also probably capture a large volume of human genomic data. While there is a plethora of beneficial applications of eDNA, we postulate that an unintended negative consequence of eDNA approaches might be the capture of human genomic information (human genetic bycatch (HGB); Fig. 1a). Beneficial applications of human-focused eDNA sampling can also be envisaged. Currently, human DNA is rarely (if ever) the intended target of eDNA studies, leaving the field with a lack of specific human-related regulatory guidelines or ethical approvals. Current targeted qPCR and metabarcoding-based eDNA approaches do not recover any substantial human genomic information. However, as eDNA shifts towards shotgun sequencing, potentially large volumes of human eDNA will be retrieved, including sufficient data to identify and phenotype human individuals. Obtaining genetic data from identifiable persons requires informed consent20. Legal and ethical frameworks are common in studies involving humans and studies that generate patient data, albeit with continued debate regarding whether such policies are sufficiently rigorous in relation to informed consent, data ownership and data protection20–24. To ascertain whether human genomic DNA could be harvested from eDNA data, we aligned the sequencing data previously generated8,17 as part of our wildlife and pathogen eDNA projects against the human reference genome. Having demonstrated the occurrence of HGB, we next applied species-specific qPCR to quantify the level of human eDNA in environmental water samples from sites distant from and close to human habitation, from human footprints in beach sand and from occupied and unoccupied room air (Supplementary Fig. 1). Finally, we applied long-read shotgun sequencing and short-read sequencing human exome enrichment to obtain human-aligning sequences to reconstruct informative human haplotypes (genetic ancestry and mutations) from eDNA. Results Human-aligning reads were detected in all samples (Fig. 1b and Supplementary Table 1) of untargeted shotgun deep sequencing from water and sand eDNA generated for wildlife and pathogen monitoring8,17. Furthermore, in some wild (non-rehabi (...truncated)