title: ENDEMIC INFECTION OF STRANDED SOUTHERN SEA OTTERS (ENHYDRA LUTRIS NEREIS) WITH NOVEL PARVOVIRUS, POLYOMAVIRUS, AND ADENOVIRUS.
abstract: Over the past century, the southern sea otter (SSO; Enhydra lutris nereis) population has been slowly recovering from near extinction due to overharvest. The SSO is a threatened subspecies under federal law and a fully protected species under California law, US. Through a multiagency collaborative program, stranded animals are rehabilitated and released, while deceased animals are necropsied and tissues are cryopreserved to facilitate scientific study. Here, we processed archival tissues to enrich particle-associated viral nucleic acids, which we randomly amplified and deeply sequenced to identify viral genomes through sequence similarities. Anelloviruses and endogenous retroviral sequences made up over 50% of observed viral sequences. Polyomavirus, parvovirus, and adenovirus sequences made up most of the remaining reads. We characterized and phylogenetically analyzed the full genome of sea otter polyomavirus 1 and the complete coding sequence of sea otter parvovirus 1 and found that the closest known viruses infect primates and domestic pigs ( Sus scrofa domesticus), respectively. We tested archived tissues from 69 stranded SSO necropsied over 14 yr (2000-13) by PCR. Polyomavirus, parvovirus, and adenovirus infections were detected in 51, 61, and 29% of examined animals, respectively, with no significant increase in frequency over time, suggesting endemic infection. We found that 80% of tested SSO were infected with at least one of the three DNA viruses, whose tissue distribution we determined in 261 tissue samples. Parvovirus DNA was most frequently detected in mesenteric lymph node, polyomavirus DNA in spleen, and adenovirus DNA in multiple tissues (spleen, retropharyngeal and mesenteric lymph node, lung, and liver). This study describes the virome in tissues of a threatened species and shows that stranded SSO are frequently infected with multiple viruses, warranting future research to investigate associations between these infections and observed lesions.
authors.affiliation: 1   Programa de Oncovirologia, Instituto Nacional de Câncer José Alencar Gomes da Silva, Coordenação de Pesquisa, Rua André Cavalcanti, 37-4° andar, Bairro de Fátima, Rio de Janeiro, CEP: 20231-050, Brazil.|2  Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, California 94118, USA.
authors.forename: Juliana D
authors.initials: JD
authors.lastname: Siqueira
authors.affiliation: 2  Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, California 94118, USA.|3  Division of Viral Diseases, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, Atlanta, Georgia 30333, USA.
authors.forename: Terry F
authors.initials: TF
authors.lastname: Ng
authors.affiliation: 4  Marine Wildlife Veterinary Care and Research Center, California Department of Fish and Wildlife, 1451 Shaffer Road, Santa Cruz, California 95060, USA.|5  Wildlife Health Center, University of California at Davis, One Shields Avenue, Davis, California 95616, USA.
authors.forename: Melissa
authors.initials: M
authors.lastname: Miller
authors.affiliation: 2  Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, California 94118, USA.|6  California Department of Public Health, Richmond, California 94804, USA.
authors.forename: Linlin
authors.initials: L
authors.lastname: Li
authors.affiliation: 2  Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, California 94118, USA.
authors.forename: Xutao
authors.initials: X
authors.lastname: Deng
authors.affiliation: 4  Marine Wildlife Veterinary Care and Research Center, California Department of Fish and Wildlife, 1451 Shaffer Road, Santa Cruz, California 95060, USA.
authors.forename: Erin
authors.initials: E
authors.lastname: Dodd
authors.affiliation: 4  Marine Wildlife Veterinary Care and Research Center, California Department of Fish and Wildlife, 1451 Shaffer Road, Santa Cruz, California 95060, USA.
authors.forename: Francesca
authors.initials: F
authors.lastname: Batac
authors.affiliation: 2  Blood Systems Research Institute, 270 Masonic Avenue, San Francisco, California 94118, USA.|7  Department of Laboratory Medicine, University of California at San Francisco, San Francisco, California 94118, USA.
authors.forename: Eric
authors.initials: E
authors.lastname: Delwart
mesh_terms: D000256:Adenoviridae / Q000302:isolation & purification*; D000818:Animals; D002140:California; D010041:Otters / Q000821:virology*; D017992:Parvovirus / Q000302:isolation & purification*; D011120:Polyomavirus / Q000302:isolation & purification*
keywords: Adenovirus; Enhydra lutris nereis; metagenomics; parvovirus; polyomavirus; southern sea otter; virome