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ABSTRACT RNA viruses are infamous for their ability to cross species barriers, posing threats to global health and security. Influenza A virus (IAV) is naturally found in avian hosts but periodically spills over into marine wildlife. IAV outbreaks occur in the Northwest Atlantic, but grey seals (Halichoerus grypus) appear to be less susceptible to IAV compared to other species. The subclinical nature of IAV infection in addition to life history factors suggest grey seals are a potential wild reservoir host for IAV. We investigated differential gene expression among grey seals naturally exposed to IAV to elucidate genetic mechanisms involved in grey seal disease resistance. RNA sequencing was conducted on blood samples (N = 31) collected from grey seal pups in Massachusetts, US between 2014 and 2019. Samples were grouped for analysis based on presence/absence of viral RNA and antibodies. In the presence of IAV RNA, we observed widespread down‐regulation of genes, including immune genes, potentially as a result of IAV‐induced host shutoff. Immune down‐regulation occurred in acute stage of IAV infection (+ viral RNA, − antibodies), followed by up‐regulation of protein production in peak stage (+ viral RNA, + antibodies), possibly as a result of increased viral replication. Evidence of an activated immune response was observed in late stage of infection (− viral RNA, + antibodies) with up‐regulated adaptive immunity genes. We hypothesize that the combination of down‐ and up‐regulated immune gene expression may prevent overstimulation of the immune response, acting as an adaptation in grey seals to resist IAV‐associated mortality. 

Marine mammals in the North Atlantic have experienced severe depletions due to overexploitation. While some species and populations have now recovered, there are numerous other anthropogenic activities impacting their North Atlantic ecosystem. Studying marine mammals is often associated with logistical challenges, and many species have an elusive nature, resulting in substantial knowledge gaps on the distribution, abundance and diversity of marine mammals in the North Atlantic. Environmental DNA (eDNA) is an emerging tool in biodiversity monitoring and has successfully been demonstrated to complement traditional monitoring methods for a wide range of marine taxonomic groups. The promising potential of seawater eDNA is owe to advances within an array of molecular methods used to extract, detect and/or sequence the genetic material of marine organisms from a single seawater sample.  We present a literature review of eDNA studies of marine mammals and discuss the potential applications and practical challenges of eDNA in marine mammal research, management and conservation.  Environmental DNA has already been introduced to a wide range of applications within marine mammal science, from detection of endangered species to population genetic assessments. Furthermore, eDNA has the power to capture other biologically important species in the marine ecosystem and food web, which could facilitate insight into the spatiotemporal variation of different marine communities in a changing environment. With methodological and technological standardization, eDNA based approaches have a promising potential to be integrated into regular monitoring practices and management strategies.