Detection, molecular characterization and phylogenetic analysis of full-length equine infectious anemia (EIAV) gag genes isolated from Shackleford Banks wild horses

Veterinary Microbiology

Volumn 157, Issue 3-4, 2012, Pages 320-332

  Capomaccio, S ^b   Willand, Z A ^a   Cook, S J ^a   Issel, C J ^a   Santos, E M ^c   Reis, J K P ^c   Cook, R F ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

^b UNIVERSITY OF PERUGIA   (Italy)

^c FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

Author keywords

Equine Infectious Anemia Virus (EIAV); Lentiviral gag gene; PCR; Sequence analysis; Shackleford Banks; Wild horse populations

Indexed keywords

GAG PROTEIN;

ANIMAL EUTHANASIA; ARTICLE; EQUINE INFECTIOUS ANEMIA; EQUINE INFECTIOUS ANEMIA VIRUS; GENE ISOLATION; HORSE; INFECTION CONTROL; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; VIRUS DETECTION;

AMINO ACID SEQUENCE; ANIMALS; EQUINE INFECTIOUS ANEMIA; GENES, GAG; GENES, VIRAL; HORSES; INFECTIOUS ANEMIA VIRUS, EQUINE; MOLECULAR SEQUENCE DATA; NORTH CAROLINA; PHYLOGENY; RNA, VIRAL; SEQUENCE ANALYSIS, RNA;

EQUIDAE; EQUINE INFECTIOUS ANEMIA VIRUS;

EID: 84860533279     PISSN: 03781135     EISSN: 18732542     Source Type: Journal    
DOI: 10.1016/j.vetmic.2012.01.015     Document Type: Article

References (43)

1. Anisimova M., Gascuel O. Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative. Syst. Biol. 2006, 55:539-552.
2. Arnold K., Bordoli L., Kopp J., Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006, 22:195-201.
3. Bordoli L., Kiefer F., Arnold K., Benkert P., Battey J., Schwede T. Protein structure homology modeling using SWISS-MODEL workspace. Nat. Protoc. 2009, 4:1-13.
4. Cheevers W.P., McGuire T.C. Equine infectious anemia virus: immunopathogenesis and persistence. Rev. Infect. Dis. 1985, 7:83-88.
5. Clabough D.L. Equine infectious anemia: the clinical signs, transmission, and diagnostic procedures. Vet. Med. 1990, 85:1007-1019.
6. Clabough D.L. The immunopathogenesis and control of equine infectious anemia. Vet. Med. 1990, 85:1020-1028.
7. Cook R.F., Leroux C., Cook S.J., Berger S.L., Lichtenstein D.L., Ghabrial N.N., Montelaro R.C., Issel C.J. Development and characterization of an in vivo pathogenic molecular clone of equine infectious anemia virus. J. Virol. 1998, 72:1383-1393.
8. Cook R.F., Cook S.J., Berger S.L., Leroux C., Ghabrial N.N., Gantz M., Bolin P.S., Mousel M.R., Montelaro R.C., Issel C.J. Enhancement of equine infectious anemia virus virulence by identification and removal of suboptimal nucleotides. Virology 2003, 313:588-603.
9. Cordes T.R., Issel C.J., Ostlund E.N., Schmitt B.J. Equine Infectious Anemia: 2001 Update 2001, APHIS United States Department of Agriculture, Washington, DC, pp. 1-36.
10. Cothran, E.G, 1997. Genetic Analysis of the Shackleford Banks Feral Horse Herd. Report for National Park Service.
11. Craigo J.K., Sturgeon T.J., Cook S.J., Issel C.J., Leroux C., Montelaro R.C. Apparent elimination of EIAV ancestral species in a long-term inapparent carrier. Virology 2006, 344:340-353.
12. Craigo J.K., Durkin S., Sturgeon T.J., Tagmyer T., Cook S.J., Issel C.J., Montelaro R.C. Immune suppression of challenged vaccinates as a rigorous assessment of sterile protection by lentiviral vaccines. Vaccine 2007, 25:834-845.
13. Craigo J.K., Zhang B., Barnes S., Tagmyer T.L., Cook S.J., Issel C.J., Montelaro R.C. Envelope variation as a primary determinant of lentiviral vaccine efficacy. Proc. Natl. Acad. Sci. U.S.A. 2007, 104:15105-15110.
14. Craigo J.K., Leroux C., Howe L., Steckbeck J.D., Cook S.J., Issel C.J., Montelaro R.C. Transient immune suppression of inapparent carriers infected with a principal neutralizing domain-deficient equine infectious anaemia virus induces neutralizing antibodies and lowers steady-state virus replication. J. Gen. Virol. 2002, 83:1353-1359.
15. FigTree 1.3.1. http://tree.bio.ed.ac.uk/software/figtree/.
16. Goodloe R.B., Warren R.J., Cothran E.G., Bratton S.P., Trembicki K.A. Genetic variation and its management applications in eastern U.S. feral horses. J. Wildlife Manage. 1991, 55:412-421.
17. Gouy M., Guindon S., Gascuel O. SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol. Biol. Evol. 2010, 27:221-224.
18. Guindon S., Dufayard J.F., Lefort V., Anisimova M., Hordijk W., Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 2010, 59:307-321.
19. Hatanaka H., Iourin O., Rao Z., Fry E., Kingsman A., Stuart D.I.a. Structure of equine infectious anemia virus matrix protein. J. Virol. 2002, 76(February (4)):1876-1883.
20. Jost S., Bernard M.C., Kaiser L., Yerly S., Hirschel B., Samri A., Autran B., Goh L.E., Perrin L. A patient with HIV-1 superinfection. N. Engl. J. Med. 2002, 347:731-736.
21. Koelsch K.K., Smith D.M., Little S.J., Ignacio C.C., Macaranas T.R., Brown A.J., Petropoulos C.J., Richman D.D., Wong J.K. Clade B HIV-1 superinfection with wild-type virus after primary infection with drug-resistant clade B virus. AIDS 2003, 17:F11-F16.
22. Kono Y., Kobayashi K., Fukunaga Y. Antigenic drift of equine infectious anemia virus in chronically infected horses. Arch. Virol. 1973, 41:1-10.
23. Kono Y., Hirasawa K., Fukunaga Y., Taniguchi T. Recrudescence of equine infectious anemia by treatment with immunosuppressive drugs. Natl. Inst. Anim. Health Q. 1976, 16:8-15.
24. Leroux C., Craigo J.K., Issel C.J., Montelaro R.C. Equine infectious anemia virus genomic evolution in progressor and nonprogressor ponies. J. Virol. 2001, 75:4570-4583.
25. Leroux C., Cadore J.L., Montelaro R.C. Equine Infectious Anemia Virus (EIAV): what has HIV's country cousin got to tell us?. Vet. Res. 2004, 35:485-512.
26. Leroux C., Issel C.J., Montelaro R.C. Novel and dynamic evolution of equine infectious anemia virus genomic quasispecies associated with sequential disease cycles in an experimentally infected pony. J. Virol. 1997, 71:9627-9639.
27. Malmquist W.A., Barnett D., Becvar C.S. Production of equine infectious anemia antigen in a persistently infected cell line. Arch. Virol. 1973, 42:361-370.
28. Montelaro R.C., Issel C.J., Payne S., Salinovich O. Antigenic variation during persistent infection by equine infectious anemia virus, a retrovirus. J. Biol. Chem. 1984, 259:10539-10544.
29. Payne S., Parekh B., Montelaro R.C., Issel C.J. Genomic alterations associated with persistent infections by equine infectious anaemia virus, a retrovirus. J. Gen. Virol. 1984, 65:1395-1399.
30. Payne S.L., Fang F.D., Liu C.P., Dhruva B.R., Rwambo P., Issel C.J., Montelaro R.C. Antigenic variation and lentivirus persistence: variations in envelope gene sequences during EIAV infection resemble changes reported for sequential isolates of HIV. Virology 1987, 161:321-331.
31. Posada D. jModelTest: phylogenetic model averaging. Mol. Biol. Evol. 2008, 25:1253-1256.
32. Quinlivan M., Cook R.F., Cullinane A. Real-time quantitative RT-PCR and PCR assays for a novel European field isolate of equine infectious anaemia virus based on sequence determination of the gag gene. Vet. Rec. 2007, 160:611-618.
33. Roy A., Kucukural A., Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protoc. 2010, 5:725-738.
34. Rwambo P.M., Issel C.J., Adams W.V.J., Hussain K.A., Miller M., Montelaro R.C. Equine infectious anemia virus (EIAV) humoral responses of recipient ponies and antigenic variation during persistent infection. Arch. Virol. 1990, 111:199-212.
35. Salinovich O., Payne S.L., Montelaro R.C., Hussain K.A., Issel C.J., Schnorr K.L. Rapid emergence of novel antigenic and genetic variants of equine infectious anemia virus during persistent infection. J. Virol. 1986, 57:71-80.
36. Smith D.M., Wong J.K., Hightower G.K., Ignacio C.C., Koelsch K.K., Petropoulos C.J., Richman D.D., Little S.J. HIV drug resistance acquired through superinfection. AIDS 2005, 19:1251-1256.
37. Tumas D.B., Hines M.T., Perryman L.E., Davis W.C., McGuire T.C. Corticosteroid immunosuppression and monoclonal antibody-mediated CD5+ T lymphocyte depletion in normal and equine infectious anaemia virus-carrier horses. J. Gen. Virol. 1994, 75:959-968.
38. van der Kuyl A.C., Kozaczynska K., Arien K.K., Gali Y., Balazs V.R., Dekker S.J., Zorgdrager F., Vanham G., Berkhout B., Cornelissen M. Analysis of infectious virus clones from two HIV-1 superinfection cases suggests that the primary strains have lower fitness. Retrovirology 2010, 7:60-75.
39. Yang O.O., Daar E.S., Jamieson B.D., Balamurugan A., Smith D.M., Pitt J.A., Petropoulos C.J., Richman D.D., Little S.J., Brown A.J. Human immunodeficiency virus type 1 clade B superinfection: evidence for differential immune containment of distinct clade B strains. J. Virol. 2005, 79:860-868.
40. Zhang Y. Template-based modeling and free modeling by I-TASSER in CASP7. Proteins 2007, 69(Suppl. 8):108-117.
41. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 2008, 9:40.
42. Zhang Y. I-TASSER: fully automated protein structure prediction in CASP8. Proteins 2009, 77(Suppl. 9):100-113.
43. Zheng Y.H., Sentsui H., Kono Y., Ikuta K. Mutations occurring during serial passage of Japanese equine infectious anemia virus in primary horse macrophages. Virus Res. 2000, 68:93-98.