Metagenomic analysis of viruses associated with bivalves, seawater and marine mammals using a nanopore end-to-end sequencing workflow to address One Health surveillance

Metagenomic sequencing is a crucial tool for One Health surveillance, enabling the detection of vertebrate-associated viruses, including potential zoonotic threats. Bivalves and marine mammals serve as key sentinels in coastal ecosystems, bioaccumulating viruses from their environment and providing early indicators of emerging infectious diseases. This study applied a long-read nanopore sequencing workflow to identify vertebrate host viruses in oysters, mussels, seawater, and marine mammals California sea lions (Zalophus californianus) and bottlenose dolphins (Tursiops truncatus) from Barataria Bay (May to December 2023) and San Diego Bay (2018 to February 2024). Viral recovery rates from matrix spike experiments varied widely (1.08% to 167.26%), highlighting challenges in quantification but confirming virus retention during processing. Most sequencing reads (93.7%) aligned to unclassified viral types, with dsDNA and ssRNA(plus) viruses dominating across sample types. Vertebrate viral families varied temporally, with Orthoherpesviridae, Poxviridae, and Alloherpesviridae most prevalent. Shannon diversity was highest at San Diego piers, and PCoA revealed distinct viral clustering by sample type and location. Metagenomic assembly identified Avon-Heathcote Estuary associated circular virus 25 and Uncultured densovirus in San Diego marine environments. These findings reinforce the role of bivalves and marine mammals as environmental sentinels and enhance One Health surveillance by improving our understanding of viral ecology and aiding early detection of emerging vertebrate-associated viruses in coastal regions.