Consensus nested PCR amplification and sequencing of diverse reptilian, avian, and mammalian orthoreoviruses

Veterinary Microbiology

Volumn 133, Issue 1-2, 2009, Pages 34-42

  Wellehan Jr , James F X ^a   Childress, April L ^a   Marschang, Rachel E ^b   Johnson, April J ^a   Lamirande, Elaine W ^c   Roberts, John F ^a   Vickers, Mary L ^d   Gaskin, Jack M ^a   Jacobson, Elliott R ^a  

^a University of Florida College of Veterinary Medicine   (United States)

^b UNIVERSITY OF HOHENHEIM   (Germany)

^c SMITHSONIAN CONSERVATION BIOLOGY INSTITUTE   (United States)

^d UNIVERSITY OF KENTUCKY   (United States)

Author keywords

Birds; Consensus PCR; Nelson Bay virus; Orthoreovirus; Polymerase; Reovirus; Reptiles; Reptilian orthoreovirus

Indexed keywords

ARTICLE; AVIAN ORTHOREOVIRUS; BIRD; CONTROLLED STUDY; GENE AMPLIFICATION; MAMMALIAN ORTHOREOVIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARROT; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIMATE; REPTILE; RNA SEQUENCE; RNA VIRUS;

AMINO ACID SEQUENCE; ANIMALS; BAYES THEOREM; BIRDS; CLUSTER ANALYSIS; GENE AMPLIFICATION; GENOME, VIRAL; LIKELIHOOD FUNCTIONS; MAMMALS; MOLECULAR SEQUENCE DATA; ORTHOREOVIRUS; ORTHOREOVIRUS, AVIAN; ORTHOREOVIRUS, MAMMALIAN; PHYLOGENY; POLYMERASE CHAIN REACTION; REOVIRIDAE INFECTIONS; REPTILES; RNA, VIRAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY;

AQUAREOVIRUS; AVES; MAMMALIA; MAMMALIAN ORTHOREOVIRUSES; NELSON BAY VIRUS; ORTHOREOVIRUS; PRIMATES; PSITTACUS ERITHACUS; REPTILIA; REPTILIAN ORTHOREOVIRUS; RNA VIRUSES; VERTEBRATA;

EID: 55549091703     PISSN: 03781135     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.vetmic.2008.06.011     Document Type: Article

References (48)

1. Ahne W., Thomsen I., and Winton J. Isolation of a reovirus from the snake, Python regius. Arch. Virol. 94 (1987) 135-139
2. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
3. Attoui H., Fang Q., Jaafar F.M., Cantaloube J.F., Biagini P., de Micco P., and de Lamballerie X. Common evolutionary origin of aquareoviruses and orthoreoviruses revealed by genome characterization of Golden shiner reovirus, Grass carp reovirus, Striped bass reovirus and golden ide reovirus (genus Aquareovirus, family Reoviridae). J. Gen. Virol. 83 (2002) 1941-1951
4. Blahak S., and Göbel T. A case reported of a reovirus infection in an emerald tree boa (Corallus caninus). Proceedings of the 4th International Colloquium on the Pathology of Reptiles and Amphibians. Bad Nauheim (Germany) (1991) 13-16
5. Blahak S., Ott I., and Vieler E. Comparison of 6 different reoviruses of various reptiles. Vet. Res. 26 (1995) 470-476
6. Chappell J.D., Duncan R., Mertens P.P.C., and Dermody T.S. Orthoreovirus. In: Fauquet C.M., Mayo M.A., Maniloff J., Desselberger E., and Ball L.A. (Eds). Virus Taxonomy: Classification and Nomenclature of Viruses (2005), Academic Press, San Diego 455-465
7. Chua K.B., Crameri G., Hyatt A., Yu M., Tompang M.R., Rosli J., McEachern J., Crameri S., Kumarasamy V., Eaton B.T., and Wang L.F. A previously unknown reovirus of bat origin is associated with an acute respiratory disease in humans. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 11424-11429
8. Conzo G., Magnino S., Sironi G., Lavazza A., Vigo P.G., Fioretti A., and Kaleta E.F. Reovirus infection in two species of Psittaciformes recently imported into Italy. Avian Pathol. 30 (2001) 43-47
9. Day J.M., Pantin-Jackwood M.J., and Spackman E. Sequence and phylogenetic analysis of the S1 genome segment of turkey-origin reoviruses. Virus Genes 35 (2007) 235-242
10. Docherty D.E., Converse K.A., Hansen W.R., and Norman G.W. American woodcock (Scolopax minor) mortality associated with a Reovirus. Avian Dis. 38 (1994) 899-904
11. Drury S.E., Gough R.E., and Welchman Dde.B. Isolation and identification of a reovirus from a lizard, Uromastyx hardwickii, in the United Kingdom. Vet. Rec. 151 (2002) 637-638
12. Duncan R. Extensive sequence divergence and phylogenetic relationships between fusogenic and nonfusogenic orthoreoviruses: a species proposal. Virology 260 (1999) 316-328
13. Duncan R., Corcoran J., Shou J., and Stoltz D. Reptilian reovirus: a new fusogenic orthoreovirus species. Virology 319 (2004) 131-140
14. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004) 1792-1797
15. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
16. Felsenstein J. PHYLIP-phylogeny inference package. Cladistics 5 (1989) 164-166
17. Flynn J.J., Finarelli J.A., Zehr S., Hsu J., and Nedbal M.A. Molecular phylogeny of the Carnivora (Mammalia): assessing the impact of increased sampling on resolving enigmatic relationships. Syst. Biol. 54 (2005) 317-337
18. Gard G., and Compans R.W. Structure and cytopathic effects of Nelson Bay virus. J. Virol. 6 (1970) 100-106
19. Gonzalez J.M., Gomez-Puertas P., Cavanagh D., Gorbalenya A.E., and Enjuanes L. A comparative sequence analysis to revise the current taxonomy of the family Coronaviridae. Arch. Virol. 148 (2003) 2207-2235
20. Graham D.L. Characterization of a reo-like virus and its isolation from and pathogenicity for parrots. Avian Dis. 31 (1987) 411-419
21. Gravendyck M., Ammermann P., Marschang R.E., and Kaleta E.F. Paramyxoviral and reoviral infections of iguanas on Honduran Islands. J. Wildl. Dis. 34 (1998) 33-38
22. Jackson A.P., and Charleston M.A. A cophylogenetic perspective of RNA-virus evolution. Mol. Biol. Evol. 21 (2004) 45-57
23. Jacobson E.R. Viruses and viral associated diseases of reptiles. Acta Zool. Pathol. Antverp. 79 (1986) 73-90
24. Jones D.T., Taylor W.R., and Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8 (1992) 275-282
25. Kim J., Tao Y., Reinisch K.M., Harrison S.C., and Nibert M.L. Orthoreovirus and Aquareovirus core proteins: conserved enzymatic surfaces, but not protein-protein interfaces. Virus Res. 101 (2004) 15-28
26. Knopf C.W. Evolution of viral DNA-dependent DNA polymerases. Virus Genes 16 (1998) 47-58
27. Kosiol C., and Goldman N. Different versions of the Dayhoff rate matrix. Mol. Biol. Evol. 22 (2005) 193-199
28. Lamirande E.W., Nichols D.K., Owens J.W., Gaskin J.M., and Jacobson E.R. Isolation and experimental transmission of a reovirus pathogenic in ratsnakes (Elaphe species). Virus Res. 63 (1999) 135-141
29. Leary T.P., Erker J.C., Chalmers M.L., Cruz A.T., Wetzel J.D., Desai S.M., Mushahwar I.K., and Dermody T.S. Detection of mammalian reovirus RNA by using reverse transcription-PCR: sequence diversity within the lambda3-encoding L1 gene. J. Clin. Microbiol. 40 (2002) 1368-1375
30. Leland M.M., Hubbard G.B., Sentmore III H.T., Soike K.F., and Hilliard J.K. Outbreak of Orthoreovirus-induced meningoencephalomyelitis in baboons. Comp. Med. 50 (2000) 199-205
31. Macken C.A., Webby R.J., and Bruno W.J. Genotype turnover by reassortment of replication complex genes from avian influenza A virus. J. Gen. Virol. 87 (2006) 2803-2815
32. Marschang R.E., and Chitty J. Infectious diseases. In: Girling S.J., and Raiti P. (Eds). Manual of Reptiles (2004), British Small Animal Veterinary Association, Gloucester 330-345
33. Marschang R.E., Donahoe S., Manvell R., and Lemos-Espinal J. Paramyxovirus and reovirus infections in wild-caught Mexican lizards (Xenosaurus and Abronia spp.). J. Zoo. Wildl. Med. 33 (2002) 317-321
34. Nolte A.W., Freyhof J., Stemshorn K.C., and Tautz D. An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated from hybridization between old phylogeographic groups. Proc. Biol. Sci. 272 (2005) 2379-2387
35. Notredame C., Higgins D.G., and Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302 (2000) 205-217
36. Pulliam J.R.C. Viral host jumps: moving toward a predictive framework. Ecohealth 5 (2008) 80-91
37. Raynaud A., and Adrian M. Cutaneous lesions with papillomatous structure associated with viruses in the green lizard (Lacerta viridis Laur.). C. R. Acad. Sci. Hebd. Seances Acad. Sci. D 283 (1976) 845-847
38. Rieseberg L.H., Kim S.C., Randell R.A., Whitney K.D., Gross B.L., Lexer C., and Clay K. Hybridization and the colonization of novel habitats by annual sunflowers. Genetica 129 (2007) 149-165
39. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
40. Samal S.K., McPhillips T.H., Dinan D., and Rockemann D.D. Lack of restriction of growth for aquareovirus in mammalian cells. Arch. Virol. 143 (1998) 571-579
41. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignments through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
42. van den Brand J.M.A., Manvell R., Paul G., Kik M.J.L., and Dorrestein G.M. Reovirus infections associated with high mortality in psittaciformes in The Netherlands. Avian Pathol. 36 (2007) 293-299
43. VanDevanter D.R., Warrener P., Bennett L., Schultz E.R., Coulter S., Garber R.L., and Rose T.M. Detection and analysis of diverse herpesviral species by consensus primer PCR. J. Clin. Microbiol. 34 (1996) 1666-1671
44. Veerassamy S., Smith A., and Tillier E.R. A transition probability model for amino acid substitutions from blocks. J. Comput. Biol. 10 (2003) 997-1010
45. Vieler E., Baumgartner W., Herbst W., and Kohler G. Characterization of a reovirus isolate from a rattlesnake, Crotalus viridis, with neurological dysfunction. Arch. Virol. 138 (1994) 341-344
46. Wellehan J.F.X., Johnson A.J., Harrach B., Benkö M., Johnson C., Pessier A., Garner M.M., and Jacobson E.R. Detection and analysis of six lizard adenoviruses by consensus primer PCR provides further evidence of a reptilian origin for the atadenoviruses. J. Virol. 78 (2004) 13366-13369
47. Whelan S., and Goldman N. A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol. 18 (2001) 691-699
48. Woolhouse M.E., and Gowtage-Sequeria S. Host range and emerging and reemerging pathogens. Emerg. Infect. Dis. 11 (2005) 1842-1847