1887

Abstract

Picornaviruses have been isolated from a variety of hosts, mainly mammals and birds. Here, we describe the sequence analysis of carp picornavirus 1 (CPV-1) F37/06 that was isolated from an organ pool (heart, brain, liver) of a common carp (). This carp perished after an accidental discharge of liquid manure into a fish pond and presented without obvious clinical symptoms. Experimental intraperitoneal infection of young carp with CPV-1 revealed no clinical signs, but the virus was re-isolated from various organs. Sequence analysis of almost the complete genome (7632 nt excluding the poly-A tract) revealed a novel picornavirus clade. In phylogenetic trees, the polymerase sequence clusters with parechoviruses, duck hepatitis A virus, eel picornavirus and aquamavirus A. The ORF includes 6807 nt and encodes a polyprotein of 2269 amino acids. CPV-1 has a genome layout like that of picornaviruses except for the presence of two aphthovirus 2A-like NPGP sequence motifs: VPg+5′UTR[1AB-1C-1D-2A1/2A2-2B-2C/3A-3B-3C-3D]3′UTR-poly-A. 2A1 and 2A2 are separated by 133 amino acids. The proteins 2A2, 2B, 3A and 3B have no significant similarity to the corresponding proteins of other picornaviruses. Amino acid identities of the orthologous proteins P1, 2C, 3C and 3D range from 16.4 to 40.8 % in the eel picornavirus/CPV-1 comparison. 3D shows the closest similarity to eel picornavirus, with an amino acid identity of 40.8 %, followed by human parechovirus (36.5 %), duck hepatitis A virus (32.7 %) and swine pasivirus (29.3 %). Both the unique genome organization and low sequence similarity support the assignment of CPV-1 to a novel picornavirus species within a novel genus.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/vir.0.058172-0
2014-01-01
2019-11-13
Loading full text...

Full text loading...

/deliver/fulltext/jgv/95/1/80.html?itemId=/content/journal/jgv/10.1099/vir.0.058172-0&mimeType=html&fmt=ahah

References

  1. Adams M. J., King A. M. Q., Carstens E. B.. ( 2013; ). Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2013). . Arch Virol 158:, 2023–2030. [CrossRef] [PubMed]
    [Google Scholar]
  2. Boros A., Pankovics P., Simmonds P., Reuter G.. ( 2011; ). Novel positive-sense, single-stranded RNA (+ssRNA) virus with di-cistronic genome from intestinal content of freshwater carp (Cyprinus carpio). . PLoS ONE 6:, e29145. [CrossRef] [PubMed]
    [Google Scholar]
  3. Dauber M., Schütze H., Fichtner D.. ( 2001; ). Development and characterisation of monoclonal antibodies raised against a viral haemorrhagic septicaemia virus (VHSV) isolate which failed to be identified by a commercial test kit. . Bull Eur Assoc Fish Pathol 21:, 170–177.
    [Google Scholar]
  4. Fichtner D., Philipps A., Groth M., Schmidt-Posthaus H., Granzow H., Dauber M., Platzer M., Bergmann S. M., Schrudde D.. & other authors ( 2013; ). Characterization of a novel picornavirus isolate from a diseased European eel (Anguilla anguilla). . J Virol 87:, 10895–10899. [CrossRef] [PubMed]
    [Google Scholar]
  5. Fijan N., Petrinec Z., Sulimanovic D., Zwillenberg L. O.. ( 1971; ). Isolation of the viral causative agent from the acute form of infectious dropsy of carp. . Vet Arh 41:, 125–138.
    [Google Scholar]
  6. Graff J., Richards O. C., Swiderek K. M., Davis M. T., Rusnak F., Harmon S. A., Jia X. Y., Summers D. F., Ehrenfeld E.. ( 1999; ). Hepatitis A virus capsid protein VP1 has a heterogeneous C terminus. . J Virol 73:, 6015–6023.[PubMed]
    [Google Scholar]
  7. Kapoor A., Simmonds P., Lipkin W. I., Zaidi S., Delwart E.. ( 2010; ). Use of nucleotide composition analysis to infer hosts for three novel picorna-like viruses. . J Virol 84:, 10322–10328. [CrossRef] [PubMed]
    [Google Scholar]
  8. Knowles N. J., Hovi T., Hyypiä T., King A. M. Q., Lindberg A. M., Pallansch M. A., Palmenberg A. C., Simmonds P., Skern T.. & other authors ( 2012; ). Picornaviridae . . In Virus Taxonomy, Ninth Report of the International Committee on Taxonomy of Viruses, pp. 855–880. Edited by King A. M. Q., Adams M. J., Carstens E. B., Lefkowitz E. J... Amsterdam:: Elsevier;.
    [Google Scholar]
  9. Koonin E. V., Dolja V. V.. ( 1993; ). Evolution and taxonomy of positive-strand RNA viruses: implications of comparative analysis of amino acid sequences. . Crit Rev Biochem Mol Biol 28:, 375–430. [CrossRef] [PubMed]
    [Google Scholar]
  10. Kozak M.. ( 1987; ). An analysis of 5′-noncoding sequences from 699 vertebrate messenger RNAs. . Nucleic Acids Res 15:, 8125–8148. [CrossRef] [PubMed]
    [Google Scholar]
  11. Langdon J. S., Humphrey J. D., Williams L. M.. ( 1988; ). Outbreaks of an EHNV-like iridovirus in cultured rainbow trout, Salmo gairdneri Richardson, in Australia. . J Fish Dis 11:, 93–96. [CrossRef]
    [Google Scholar]
  12. Luke G. A., de Felipe P., Lukashev A., Kallioinen S. E., Bruno E. A., Ryan M. D.. ( 2008; ). Occurrence, function and evolutionary origins of ‘2A-like’ sequences in virus genomes. . J Gen Virol 89:, 1036–1042. [CrossRef] [PubMed]
    [Google Scholar]
  13. Ng T. F. F., Marine R., Wang C., Simmonds P., Kapusinszky B., Bodhidatta L., Oderinde B. S., Wommack K. E., Delwart E.. ( 2012; ). High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage. . J Virol 86:, 12161–12175. [CrossRef] [PubMed]
    [Google Scholar]
  14. Philipps A., Dauber M., Groth M., Schirrmeier H., Platzer M., Krumbholz A., Wutzler P., Zell R.. ( 2012; ). Isolation and molecular characterization of a second serotype of the encephalomyocarditis virus. . Vet Microbiol 161:, 49–57. [CrossRef] [PubMed]
    [Google Scholar]
  15. Ronquist F., Huelsenbeck J. P.. ( 2003; ). MrBayes 3: Bayesian phylogenetic inference under mixed models. . Bioinformatics 19:, 1572–1574. [CrossRef] [PubMed]
    [Google Scholar]
  16. Shan T., Li L., Simmonds P., Wang C., Moeser A., Delwart E.. ( 2011; ). The fecal virome of pigs on a high-density farm. . J Virol 85:, 11697–11708. [CrossRef] [PubMed]
    [Google Scholar]
  17. Simmonds P.. ( 2012; ). SSE: a nucleotide and amino acid sequence analysis platform. . BMC Res Notes 5:, 50. [CrossRef] [PubMed]
    [Google Scholar]
  18. Stanway G., Brown F., Christian P., Hovi T., Hyypiä T., King A. M. Q., Knowles N. J., Lemon S. M., Minor P. D.. & other authors ( 2005; ). Picornaviridae. . In Virus Taxonomy. Eighth Report of the International Committee on Taxonomy of Viruses, pp. 757–778. Edited by Fauquet C. M., Mayo M. A., Maniloff J., Desselberger U., Ball L. A... Amsterdam:: Elsevier;.
    [Google Scholar]
  19. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011; ). MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef] [PubMed]
    [Google Scholar]
  20. Vestergård Jorgensen P., Grauballe P. C.. ( 1971; ). Problems in the serological typing of IPN virus. . Acta Vet Scand 12:, 145–147.[PubMed]
    [Google Scholar]
  21. Woo P. C. Y., Lau S. K. P., Choi G. K. Y., Huang Y., Teng J. L. L., Tsoi H. W., Tse H., Yeung M. L., Chan K. H.. & other authors ( 2012; ). Natural occurrence and characterization of two internal ribosome entry site elements in a novel virus, canine picodicistrovirus, in the picornavirus-like superfamily. . J Virol 86:, 2797–2808. [CrossRef] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/vir.0.058172-0
Loading
/content/journal/jgv/10.1099/vir.0.058172-0
Loading

Data & Media loading...

Most Cited This Month

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error