1887

Abstract

To investigate viral pathogens potentially involved in a mortality event of 21 Pacific harbor seals () in California in 2000, viral metagenomics was performed directly on lung samples from five individuals. Metagenomics revealed a novel seal anellovirus (SealAV), which clusters phylogenetically with anelloviruses from California sea lions and domestic cats. Using specific PCR, SealAV was identified in lung tissue from two of five animals involved in the 2000 mortality event, as well as one of 20 harbor seal samples examined post-mortem in 2008. The identification of SealAV in multiple years demonstrates that this virus is persistent in the harbor seal population. SealAV is the second anellovirus reported in the lungs of pinnipeds, suggesting that anellovirus infections may be common amongst marine mammals and that more research is needed to understand the roles of these viruses in marine mammal health and disease.

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2011-06-01
2019-10-20
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References

  1. Abascal F. , Zardoya R. , Posada D. . ( 2005; ). ProtTest: selection of best-fit models of protein evolution. . Bioinformatics 21:, 2104–2105. [CrossRef] [PubMed]
    [Google Scholar]
  2. Altschul S. F. , Gish W. , Miller W. , Myers E. W. , Lipman D. J. . ( 1990; ). Basic local alignment search tool. . J Mol Biol 215:, 403–410.[PubMed] [CrossRef]
    [Google Scholar]
  3. Altschul S. F. , Madden T. L. , Schäffer A. A. , Zhang J. , Zhang Z. , Miller W. , Lipman D. J. . ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. . Nucleic Acids Res 25:, 3389–3402. [CrossRef] [PubMed]
    [Google Scholar]
  4. Biagini P. . ( 2009; ). Classification of TTV and related viruses (anelloviruses). . Curr Top Microbiol Immunol 331:, 21–33. [CrossRef] [PubMed]
    [Google Scholar]
  5. Biagini P. , Uch R. , Belhouchet M. , Attoui H. , Cantaloube J. F. , Brisbarre N. , de Micco P. . ( 2007; ). Circular genomes related to anelloviruses identified in human and animal samples by using a combined rolling-circle amplification/sequence-independent single primer amplification approach. . J Gen Virol 88:, 2696–2701. [CrossRef] [PubMed]
    [Google Scholar]
  6. Breitbart M. , Rohwer F. . ( 2005; ). Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. . Biotechniques 39:, 729–736. [CrossRef] [PubMed]
    [Google Scholar]
  7. Carstens E. B. . ( 2010; ). Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2009). . Arch Virol 155:, 133–146. [CrossRef] [PubMed]
    [Google Scholar]
  8. Cokol M. , Nair R. , Rost B. . ( 2000; ). Finding nuclear localization signals. . EMBO Rep 1:, 411–415. [CrossRef] [PubMed]
    [Google Scholar]
  9. Davidson I. , Shulman L. M. . ( 2008; ). Unraveling the puzzle of human anellovirus infections by comparison with avian infections with the chicken anemia virus. . Virus Res 137:, 1–15. [CrossRef] [PubMed]
    [Google Scholar]
  10. Delwart E. L. . ( 2007; ). Viral metagenomics. . Rev Med Virol 17:, 115–131. [CrossRef] [PubMed]
    [Google Scholar]
  11. de Villiers E.-M. , Kimmel R. , Leppik L. , Gunst K. . ( 2009; ). Intragenomic rearrangement in TT viruses: a possible role in the pathogenesis of disease. . Curr Top Microbiol Immunol 331:, 91–107. [CrossRef] [PubMed]
    [Google Scholar]
  12. Edwards R. A. , Rohwer F. . ( 2005; ). Viral metagenomics. . Nat Rev Microbiol 3:, 504–510. [CrossRef] [PubMed]
    [Google Scholar]
  13. Eizirik E. , Murphy W. J. , Koepfli K. P. , Johnson W. E. , Dragoo J. W. , Wayne R. K. , O’Brien S. J. . ( 2010; ). Pattern and timing of diversification of the mammalian order Carnivora inferred from multiple nuclear gene sequences. . Mol Phylogenet Evol 56:, 49–63. [CrossRef] [PubMed]
    [Google Scholar]
  14. Ellis J. A. , Allan G. , Krakowka S. . ( 2008; ). Effect of coinfection with genogroup 1 porcine torque teno virus on porcine circovirus type 2-associated postweaning multisystemic wasting syndrome in gnotobiotic pigs. . Am J Vet Res 69:, 1608–1614. [CrossRef] [PubMed]
    [Google Scholar]
  15. Fauquet C. M. , Mayo M. A. , Maniloff J. , Desselberger U. , Ball L. A. . (editors) ( 2005; ). Virus Taxonomy: Classification and Nomenclature of Viruses. Eighth Report of the International Committee on Taxonomy of Viruses. San Diego:: Elsevier Academic Press;.
    [Google Scholar]
  16. Gaffney P. , Colegrove K. , Gulland F. , Byrne B. , Jang S. , Edgar K. . ( 2008; ). Pathologic, microbiologic and epidemiologic characterization of Pseudomonas sp. in California sea lions (Zalophus californianus) and Pacific harbor seals (Phoca vitulina). In Proceedings of the 39th Annual Conference of the International Association for Aquatic Animal Medicine, 10–14 May 2008, Pomezia, Italy, p. 100. Edited by T. Reidarson. Rome: IAAAM.
  17. Hall T. A. . ( 1999; ). BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. . Nucleic Acids Symp Ser 41:, 95–98.
    [Google Scholar]
  18. Hijikata M. , Takahashi K. , Mishiro S. . ( 1999; ). Complete circular DNA genome of a TT virus variant (isolate name SANBAN) and 44 partial ORF2 sequences implicating a great degree of diversity beyond genotypes. . Virology 260:, 17–22. [CrossRef] [PubMed]
    [Google Scholar]
  19. Hino S. , Miyata H. . ( 2007; ). Torque teno virus (TTV): current status. . Rev Med Virol 17:, 45–57. [CrossRef] [PubMed]
    [Google Scholar]
  20. Huelsenbeck J. P. , Ronquist F. . ( 2001; ). mrbayes: Bayesian inference of phylogenetic trees. . Bioinformatics 17:, 754–755. [CrossRef] [PubMed]
    [Google Scholar]
  21. Jones M. S. , Kapoor A. , Lukashov V. V. , Simmonds P. , Hecht F. , Delwart E. . ( 2005; ). New DNA viruses identified in patients with acute viral infection syndrome. . J Virol 79:, 8230–8236. [CrossRef] [PubMed]
    [Google Scholar]
  22. Kamahora T. , Hino S. , Miyata H. . ( 2000; ). Three spliced mRNAs of TT virus transcribed from a plasmid containing the entire genome in COS1 cells. . J Virol 74:, 9980–9986. [CrossRef] [PubMed]
    [Google Scholar]
  23. Katoh K. , Kuma K. , Toh H. , Miyata T. . ( 2005; ). mafft version 5: improvement in accuracy of multiple sequence alignment. . Nucleic Acids Res 33:, 511–518. [CrossRef] [PubMed]
    [Google Scholar]
  24. Krakowka S. , Ellis J. A. . ( 2008; ). Evaluation of the effects of porcine genogroup 1 torque teno virus in gnotobiotic swine. . Am J Vet Res 69:, 1623–1629. [CrossRef] [PubMed]
    [Google Scholar]
  25. Kruse H. , Kirkemo A.-M. , Handeland K. . ( 2004; ). Wildlife as source of zoonotic infections. . Emerg Infect Dis 10:, 2067–2072.[PubMed] [CrossRef]
    [Google Scholar]
  26. Kuiken T. , Leighton F. A. , Fouchier R. A. M. , LeDuc J. W. , Peiris J. S. M. , Schudel A. , Stöhr K. , Osterhaus A. D. M. E. . ( 2005; ). Public health. Pathogen surveillance in animals. . Science 309:, 1680–1681. [CrossRef] [PubMed]
    [Google Scholar]
  27. Leary T. P. , Erker J. C. , Chalmers M. L. , Desai S. M. , Mushahwar I. K. . ( 1999; ). Improved detection systems for TT virus reveal high prevalence in humans, non-human primates and farm animals. . J Gen Virol 80:, 2115–2120.[PubMed]
    [Google Scholar]
  28. Maggi F. , Pifferi M. , Fornai C. , Andreoli E. , Tempestini E. , Vatteroni M. , Presciuttini S. , Marchi S. , Pietrobelli A. et al. ( 2003; ). TT virus in the nasal secretions of children with acute respiratory diseases: relations to viremia and disease severity. . J Virol 77:, 2418–2425. [CrossRef] [PubMed]
    [Google Scholar]
  29. Maggi F. , Pifferi M. , Tempestini E. , Lanini L. , De Marco E. , Fornai C. , Andreoli E. , Presciuttini S. , Vatteroni M. L. et al. ( 2004; ). Correlation between Torque tenovirus infection and serum levels of eosinophil cationic protein in children hospitalized for acute respiratory diseases. . J Infect Dis 190:, 971–974. [CrossRef] [PubMed]
    [Google Scholar]
  30. Ng T. F. F. , Suedmeyer W. K. , Wheeler E. , Gulland F. , Breitbart M. . ( 2009; a). Novel anellovirus discovered from a mortality event of captive California sea lions. . J Gen Virol 90:, 1256–1261. [CrossRef] [PubMed]
    [Google Scholar]
  31. Ng T. F. F. , Manire C. , Borrowman K. , Langer T. , Ehrhart L. , Breitbart M. . ( 2009; b). Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. . J Virol 83:, 2500–2509. [CrossRef] [PubMed]
    [Google Scholar]
  32. Ninomiya M. , Takahashi M. , Shimosegawa T. , Okamoto H. . ( 2007; ). Analysis of the entire genomes of fifteen torque teno midi virus variants classifiable into a third group of genus Anellovirus. . Arch Virol 152:, 1961–1975. [CrossRef] [PubMed]
    [Google Scholar]
  33. Ninomiya M. , Takahashi M. , Hoshino Y. , Ichiyama K. , Simmonds P. , Okamoto H. . ( 2009; ). Analysis of the entire genomes of torque teno midi virus variants in chimpanzees: infrequent cross-species infection between humans and chimpanzees. . J Gen Virol 90:, 347–358. [CrossRef] [PubMed]
    [Google Scholar]
  34. Nollens H. H. , Wellehan J. F. , Archer L. , Lowenstine L. J. , Gulland F. M. D. . ( 2010; ). Detection of a respiratory coronavirus from tissues archived during a pneumonia epizootic in free-ranging Pacific harbor seals Phoca vitulina richardsii . . Dis Aquat Organ 90:, 113–120. [CrossRef] [PubMed]
    [Google Scholar]
  35. Okamoto H. , Nishizawa T. , Tawara A. , Peng Y. , Takahashi M. , Kishimoto J. , Tanaka T. , Miyakawa Y. , Mayumi M. . ( 2000; ). Species-specific TT viruses in humans and nonhuman primates and their phylogenetic relatedness. . Virology 277:, 368–378. [CrossRef] [PubMed]
    [Google Scholar]
  36. Okamoto H. , Nishizawa T. , Takahashi M. , Tawara A. , Peng Y. H. , Kishimoto J. , Wang Y. . ( 2001; ). Genomic and evolutionary characterization of TT virus (TTV) in tupaias and comparison with species-specific TTVs in humans and non-human primates. . J Gen Virol 82:, 2041–2050.[PubMed]
    [Google Scholar]
  37. Okamoto H. , Takahashi M. , Nishizawa T. , Tawara A. , Fukai K. , Muramatsu U. , Naito Y. , Yoshikawa A. . ( 2002; ). Genomic characterization of TT viruses (TTVs) in pigs, cats and dogs and their relatedness with species-specific TTVs in primates and tupaias. . J Gen Virol 83:, 1291–1297.[PubMed]
    [Google Scholar]
  38. Rambaut, A. (2010). FigTree, version 1.3.1. Institute of Evolutionary Biology, University of Edinburgh.
  39. Symonds E. M. , Griffin D. W. , Breitbart M. . ( 2009; ). Eukaryotic viruses in wastewater samples from the United States. . Appl Environ Microbiol 75:, 1402–1409. [CrossRef] [PubMed]
    [Google Scholar]
  40. Taira O. , Ogawa H. , Nagao A. , Tuchiya K. , Nunoya T. , Ueda S. . ( 2009; ). Prevalence of swine Torque teno virus genogroups 1 and 2 in Japanese swine with suspected post-weaning multisystemic wasting syndrome and porcine respiratory disease complex. . Vet Microbiol 139:, 347–350. [CrossRef] [PubMed]
    [Google Scholar]
  41. Takahashi K. , Hijikata M. , Samokhvalov E. I. , Mishiro S. . ( 2000; ). Full or near full length nucleotide sequences of TT virus variants (Types SANBAN and YONBAN) and the TT virus-like mini virus. . Intervirology 43:, 119–123. [CrossRef] [PubMed]
    [Google Scholar]
  42. Wang D. , Coscoy L. , Zylberberg M. , Avila P. C. , Boushey H. A. , Ganem D. , DeRisi J. L. . ( 2002; ). Microarray-based detection and genotyping of viral pathogens. . Proc Natl Acad Sci U S A 99:, 15687–15692. [CrossRef] [PubMed]
    [Google Scholar]
  43. Willner D. , Furlan M. , Haynes M. , Schmieder R. , Angly F. E. , Silva J. , Tammadoni S. , Nosrat B. , Conrad D. , Rohwer F. . ( 2009; ). Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. . PLoS ONE 4:, e7370. [CrossRef] [PubMed]
    [Google Scholar]
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