Comparative genomics of serotype Asia 1 foot-and-mouth disease virus isolates from India sampled over the last two decades

Virus Research

Volumn 136, Issue 1-2, 2008, Pages 16-29

  Mohapatra, Jajati K ^a   Sanyal, Aniket ^a   Hemadri, Divakar ^a   Tosh, Chakradhar ^a   Biswas, Subhajit ^a   Knowles, Nick J ^b   Rasool, Thaha J ^a   Bandyopadhyay, Santanu K ^a   Pattnaik, Bramhadev ^a  

^a Indian Veterinary Research Institute Campus   (India)

^b INSTITUTE FOR ANIMAL HEALTH   (United Kingdom)

Author keywords

Comparative genomics; FMD virus; Serotype Asia 1

Indexed keywords

EPITOPE; PROTEINASE;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; ASIA; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; FOOT AND MOUTH DISEASE VIRUS; GENE DELETION; GENE LOCATION; GENE SEQUENCE; GENETIC VARIABILITY; INDIA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; SEROTYPE; T LYMPHOCYTE; VIRUS ISOLATION;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMALS; ANTIGENS, VIRAL; BASE SEQUENCE; CLUSTER ANALYSIS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; FOOT-AND-MOUTH DISEASE; FOOT-AND-MOUTH DISEASE VIRUS; GENOME, VIRAL; GENOTYPE; INDIA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION, MISSENSE; NUCLEIC ACID CONFORMATION; PHYLOGENY; RECOMBINATION, GENETIC; RNA, VIRAL; SELECTION (GENETICS); SEQUENCE ANALYSIS, DNA; SEQUENCE DELETION; SEQUENCE HOMOLOGY; SEROTYPING; VIRAL PROTEINS;

FOOT-AND-MOUTH DISEASE VIRUS;

EID: 46249087034     PISSN: 01681702     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virusres.2008.04.010     Document Type: Article

References (81)

1. Barnett P.V., Samuel A.R., Pullen L., Ansell D., Butcher R.N., and Parkhouse R.M.E. Monoclonal antibodies against type O1 serotype of foot-and-mouth disease virus, from a natural bovine host, recognize similar antigenic feature to those defined by the mouse. J. Gen. Virol. 79 (1998) 1687-1697
2. Basavappa R., Syed R., Flore O., Icenogle J.P., and Filman D.J. Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: structure of the empty capsid assembly intermediate at 2.9 Å resolution. Protein Sci. 3 (1994) 1651-1669
3. Beard C.W., and Mason P.W. Genetic determinants of altered virulence of Taiwanese foot-and-mouth disease virus. J. Virol. 74 (2000) 987-991
4. Biswas S., Sanyal A., Hemadri D., Tosh C., Mohapatra J.K., Manoj Kumar R., and Bandyopadhyay S.K. Genetic comparison of large fragment of the 5′ untranslated region among foot-and-mouth disease viruses with special reference to serotype Asia 1. Arch. Virol. 150 (2005) 2217-2239
5. Biswas S., Sanyal A., Hemadri D., Tosh C., Mohapatra J.K., Manoj Kumar R., and Bandyopadhyay S.K. Sequence analysis of the non-structural 3A and 3C protein-coding regions of foot-and-mouth disease virus serotype Asia 1 field isolates from an endemic country. Vet. Microbiol. 116 (2006) 187-193
6. Blanco E., Garcia-Briones M., Sanz-Parra A., Gomes P., De Oliveira E., Valero M.L., Andreu D., Ley V., and Sobrino F. Identification of T-cell epitopes in non-structural proteins of foot-and-mouth disease virus. J. Virol. 75 (2001) 3164-3174
7. Carrillo C., Tulman E.R., Delhon G., Lu Z., Carreno A., Vagnozzi A., Kutish G.F., and Rock D.L. Comparative genomics of foot-and-mouth disease virus. J. Virol. 79 (2005) 6487-6504
8. Cooper P.D., Agol V.I., Bachrach H.L., Brown F., Ghendan Y., Giggs A.L., Gillespie J.H., Lonberg-Holm K., Mandel B., Melnick J.L., Mohanty S.B., Povey R.C., Rueckert R.R., Schaffer F.L., and Tyrrell D.A.J. Picornaviridae: second report. Intervirology 10 (1978) 165-180
9. Dever T.E., Glynias M.J., and Merrick W.C. GTP-binding domain: three consensus sequence elements with distinct spacing. Proc. Natl. Acad. Sci. 84 (1987) 1814-1818
10. Domingo E., Baranowski E., Escarmis C., and Sobrino F. Foot-and-mouth disease virus. Comp. Immunol. Microbiol. Infect. Dis. 25 (2002) 297-308
11. Donnelly M.L., Gani D., Flint M., Monaghan S., and Ryan M.D. The cleavage activities of aphthovirus and cardiovirus 2A proteins. J. Gen. Virol. 78 (1997) 13-21
12. Escarmis C., Dopazo J., Davila M., Palma E.L., and Domingo E. Large deletions in the 5′-untranslated region of foot-and mouth disease virus of serotype C. Virus. Res. 35 (1995) 155-167
13. Feng Q., Yu H., Liu Y., He C., Hu J., Sang H., Ding N., Ding M., Fung Y.W., Lau L., Yu A.C., and Chen J. Genome comparison of a novel foot-and-mouth disease virus with other FMDV strains. Biochem. Biophys. Res. Commun. 323 (2004) 254-263
14. Fry E., Lea S.M., Jackson T., Newman J.W.I., Ellard F.M., Blakemore W.E., Abu-Ghazaleh R., Samuel A., King A.M.Q., and Stuart D.I. The structure and function of a foot and mouth disease virus-oligosaccharide receptor complex. EMBO J. 18 (1999) 543-554
15. George, M., 2000. Molecular cloning and expression of the nonstructural proteins of foot-and-mouth disease virus serotype Asia 1. Ph.D. Thesis submitted to the Deemed University, Indian Veterinary Research Institute, Izatnagar/Mukteswar, Uttar Pradesh, India.
16. Giraudo A.T., Beck E., Strebel K., de Mello P.A., La Torre J.L., Scodeller E.A., and Bergmann I.E. Identification of a nucleotide deletion in parts of polypeptide 3A in two independent attenuated aphthovirus strains. Virology 177 (1990) 780-783
17. Giraudo A.T., Sagedahl A., Bergmann I.E., La Torre J.L., and Scodeller E.A. Isolation and characterization of recombinants between attenuated and virulent aphthovirus strains. J. Virol. 61 (1987) 419-425
18. Grazioli, S., Francesca Fallacara, F., Brocchi, E., 2004. Mapping of neutralising sites on FMD virus type Asia 1 and relationships with sites. Rpt. Sess. Res. Gp. Stand. Tech. Comm. Eur. Comm. Control of FMD (FAO), Crete (Greece), Appendix 44, pp. 277-287.
19. Grubman M.J., Zellner M., Bablanian G., Mason P.W., and Piccone M.E. Identification of the active-site residues of the 3C proteinase of foot-and-mouth disease virus. Virology 213 (1995) 581-589
20. Guarné A., Tormo J., Kirchweger R., Pfistermueller D., Fita I., and Skern T. Structure of the foot-and-mouth disease virus leader protease: a papain-like fold adapted for self-processing and eIF4G recognition. EMBO J. 17 (1998) 7469-7479
21. Gurumurthy, C.B., 2000. Antigenic sites of foot-and mouth disease virus type Asia 1. Ph.D. Thesis submitted to the Deemed University, IVRI, Izatnagar/Mukteswar, India.
22. Hagenbuchle O., Santer M., and Steitz J.A. Conservation of the primary structure at the 3′end of 18S rRNA from eucaryotic cells. Cell 13 (1978) 551-563
23. Haydon D.T., Bastos A.D.S., and Awadalla P. Low linkage disequilibrium indicative of recombination in foot-and-mouth disease virus gene sequence alignments. J. Gen. Virol. 85 (2004) 1095-1100
24. Hofmann K., and Stoffel W. TMBase, a database of membrane spanning protein segments. Biol. Chem. Hoppe-Seyler 347 (1993) 166
25. International Committee on Taxonomy of Viruses (ICTV), Van Regenmortel, M.H.V., International Union of Microbiological Societies, Virology Division, 2000. Family: Picornaviridae. Virus Taxonomy: Classification and Nomenclature of Viruses. Seventh report of the International Committee on Taxonomy of Viruses. Academic Press, Inc., San Diego, CA, pp. 657-678.
26. Jackson T., Ellard F.M., Ghazaleh R.A., Brookes S.M., Blakemore W.E., Corteyn A.H., Stuart D.I., Newman J.W., and King A.M. Efficient infection of cells in culture by type O foot-and-mouth disease virus requires binding to cell surface heparan sulfate. J. Virol. 70 (1996) 5282-5287
27. Juretic D., Jeroncic A., and Zucic D. Sequence analysis of membrane proteins with the web server SPLIT. Croat. Chem. Acta 72 (1999) 975-997
28. Kanno T., Yamakawa M., Yosida K., and Sakamoto K. The complete nucleotide sequence of the PanAsia strain of foot-and-mouth disease virus isolated in Japan. Virus Genes 25 (2002) 119-125
29. King A.M.Q. Recombination in positive strand RNA viruses. In: Domingo E., Holland J.J., and Ahlquist P. (Eds). RNA Genetics vol. 2 (1988), CRC Press, Boca Raton, FL 149-165
30. Kitson J.D.A., McCahon D., and Belsham G.J. Sequence analysis of monoclonal antibody resistant mutants of type O foot and mouth disease virus: evidence for the involvement of the three surface exposed capsid proteins in four antigenic sites. Virology 179 (1990) 26-34
31. Knowles N.J., Davies P.R., Henry T., O'Donnell V., Pacheco J.M., and Mason P.W. Emergence in Asia of foot-and-mouth disease viruses with altered host range: characterization of alterations in the 3A protein. J. Virol. 75 (2001) 1551-1556
32. Knowles, N.J., Samuel, A.R., 1995. Polymerase chain reaction amplification and cycle sequencing of the 1D (VP1) gene of foot-and-mouth disease viruses. Rpt. Sess. Res. Gp. Stand. Tech. Comm. Eur. Comm. Control of FMD (FAO), Vienna, Austria, September 1994, pp. 45-53.
33. Komarov A., and Goldsmit L. Avianized modified foot and mouth disease viruses. Paper presented at the International Farmers Convention. Israel, 1959 (1959) 333-353
34. Koonin E.V. The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J. Gen. Virol. 72 (1991) 2197-2206
35. Krebs O., and Marquardt O. Identification and characterization of foot-and-mouth disease virus O1 Burgwedel 1987 as an intertypic recombinant. J. Gen. Virol. 73 (1993) 613-619
36. Kuhn R., Norbert L., and Beck E. Functional analysis of the internal translation initiation site of foot-and-mouth disease virus. J. Virol. 64 (1990) 4625-4631
37. Kumar S., Tamura K., Jakobsen I.B., and Nei M. MEGA2: Molecular Evolutionary Genetics Analysis software (2001), Arizona State University, Tempe, AZ, USA
38. Kweon C.H., Ko Y.J., Kim W.I., Kwon B.J., Hyun B.H., Sohn H.J., Choi K.S., and Shin J.H. Molecular characterization of foot-and-mouth disease virus O/SKR/2000. Virus Res. 90 (2002) 15-22
39. Li D., Shang Y.J., Liu Z.X., Liu X.T., and Cai X.P. Molecular relationships between type Asia 1 new strain from China and type O Panasia strains of foot-and-mouth-disease virus. Virus Genes 35 (2007) 273-279
40. Lopez de Quinto S., and Martinez-Salas E. Conserved structural motifs located in distal loops of aphthovirus internal ribosome entry site domain 3 are required for internal initiation of translation. J. Virol. 71 (1997) 4171-4175
41. Lu J., Zhang J., Wang X., Jiang H., Liu C., and Hu Y. In vitro and in vivo identification of structural and sequence elements in the 5′ untranslated region of Ectropis oblique picorna-like virus required for internal initiation. J. Gen. Virol. 87 (2006) 3667-3677
42. Luz N., and Beck E. Interaction of a cellular 57-kDa protein with the internal translation initiation site of foot-and-mouth disease virus. J. Virol. 65 (1991) 6486-6494
43. Manoj Kumar R., Sanyal A., Hemadri D., Tosh C., Mohapatra J.K., and Bandyopadhyay S.K. Characterization of foot-and-mouth disease serotype Asia 1 viruses grown in the presence of polyclonal antisera in serology and nucleotide sequence analysis. Arch. Virol. 149 (2004) 1801-1814
44. Marquardt O., Rahman M.M., and Freiberg B. Genetic and antigenic variance of foot-and-mouth disease virus type Asia 1. Arch. Virol. 145 (2000) 149-157
45. Martinez-Salas E., Ortin J., and Domingo E. Sequence of the viral replicase gene from foot-and-mouth disease virus C1-Santa Pau (C-S8). Gene 35 (1985) 55-61
46. Mason P.W., Bezborodova S.V., and Henry T.M. Identification and characterization of a cis-acting replication element (cre) adjacent to the internal ribosome entry site of foot-and-mouth disease virus. J. Virol. 76 (2002) 9686-9694
47. Mason P.W., Grubman M.J., and Baxt B. Molecular basis of pathogenesis of FMDV. Virus Res. 91 (2003) 9-32
48. Mason P.W., Pacheco J.M., Zhao Q.Z., and Knowles N.J. Comparisons of the complete genomes of Asian, African and European isolates of a recent foot-and-mouth disease virus type O pandemic strain (PanAsia). J. Gen. Virol. 84 (2003) 1583-1593
49. Mohapatra J.K., Sanyal A., Hemadri D., Tosh C., Sabarinath G.P., Manoj Kumar R., Venkataramanan R., and Bandyopadhyay S.K. Sequence variability in the structural protein-encoding region of foot-and-mouth disease virus serotype Asia 1field isolates. Res. Vet. Sci. 77 (2004) 153-161
50. Mohapatra J.K., Sanyal A., Hemadri D., Tosh C., Sabarinath G.P., and Venkataramanan R. Sequence and phylogenetic analysis of the L and VP1 genes of foot-and-mouth disease virus serotype Asia 1. Virus Res. 87 (2002) 107-118
51. Oem J.K., Lee K.N., Cho I.S., Kye S.J., Park J.H., and Joo Y.S. Comparison and analysis of the complete nucleotide sequence of foot-and-mouth disease viruses from animals in Korea and other PanAsia strains. Virus Genes 29 (2004) 63-71
52. Pacheco J.M., Henry T.M., O'Donnell V.K., Gregory J.B., and Mason P.W. Role of nonstructural proteins 3A and 3B in host range and pathogenicity of foot-and-mouth disease virus. J. Virol. 77 (2003) 13017-13027
53. Pattnaik B., Sanyal A., George M., Tosh C., Hemadri D., and Venkataramanan R. Evaluation of primers for PCR amplification of RNA polymerase gene sequences of foot-and-mouth disease virus. Acta Virol. 41 (1997) 333-336
54. Paul A.V., van Boom J.H., Filippov D., and Wimmer E. Protein-primed RNA synthesis by purified poliovirus RNA polymerase. Nature 393 (1998) 280-284
55. Pereda A.J., Konig G.A., Chimeno Zoth S.A., Borca M., Palma E.L., and Piccone M.E. Full length nucleotide sequence of foot-and-mouth disease virus strain O1 Campos/Bra/58. Arch. Virol. 147 (2002) 2225-2230
56. Perez Filgueira M., Wigdorovitz A., Romera A., Zamorano P., Borca M.V., and Sadir A.M. Detection and characterization of functional T-cell epitopes on the structural proteins VP2, VP3, and VP4 of foot and mouth disease virus O1 Campos. Virology 271 (2000) 234-239
57. Piccone M.E., Rieder E., Mason P.W., and Grubman M.J. The foot-and-mouth disease virus leader proteinase gene is not required for viral replication. J. Virol. 69 (1995) 5376-5382
58. Ray, S.C., 1999. SimPlot for Windows 95, version 2.5. Distributed by the author (www.med.jhu.edu/deptmed/sray/download).
59. Roberts P.J., and Belsham G. Identification of critical amino acids within the foot-and-mouth disease virus leader protein, a cysteine protease. Virology 213 (1995) 140-160
60. Rust C.R., Ochs K., Meyer K., Beck E., and Niepmann M. Interaction of eukaryotic initiation factor eIF4B with the internal ribosome entry site of foot and mouth disease virus is independent of polypyrimidine tract-binding protein. J. Virol. 73 (1999) 6111-6113
61. Sabarinath, G.P., 2001. Comparison of nucleotide sequence of structural protein encoding (P1) region of foot-and-mouth disease virus serotype O isolates. M.V.Sc. Thesis Submitted to Deemed University, Indian Veterinary Research Institute, Izatnagar/Mukteswar, UP, India.
62. Sa-Carvalho D., Rieder E., Baxt B., Rodarte R., Tanuri A., and Mason P.W. Tissue culture adaptation of foot-and-mouth disease virus selects viruses that bind to heparin and are attenuated in cattle. J. Virol. 71 (1997) 5115-5123
63. Saleh L., Rust C.R., Fullkrug R., Beck E., Bassili G., Ochs K., and Niepman M. Functional interaction of translation initiation factor eIF-4G with the foot-and-mouth disease virus internal ribosome entry site. J. Gen. Virol. 82 (2001) 757-763
64. Sanyal A., Gurumurthy C.B., Venkataramanan R., Hemadri D., and Tosh C. Antigenic characterization of Foot and mouth disease virus serotype Asia 1 field isolates using polyclonal and monoclonal antibodies. Vet. Microbiol. 93 (2003) 1-11
65. Sanyal A., Hemadri D., Tosh C., and Bandyopadhyay S.K. Emergence of a novel subgroup within the widely circulating lineage of Foot-and-Mouth Disease virus serotype Asia 1 in India. Res. Vet. Sci. 76 (2004) 151-156
66. Sanyal A., Mohapatra J.K., Manoj Kumar R., Biswas S., Hemadri D., Tosh C., Sabarinath G.P., Gupta S.K., Mittal M., Giridharan P., and Bandyopadhyay S.K. Complete nucleotide sequence analysis of a vaccine strain (IND491/97) and a field isolate of foot-and-mouth disease virus serotype Asia 1 with an insertion in VP1 genomic region. Acta Virol. 48 (2004) 65-72
67. Sanyal A., Venkataramanan R., and Pattnaik B. Antigenic features of foot-and-mouth disease virus serotype Asia 1 as revealed by monoclonal antibodies and neutralization-escape mutants. Virus Res. 50 (1997) 107-117
68. Strimmer K., and von Haeseler A. Quartet Puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13 (1996) 964-969
69. Tamura K., and Nei M. Estimation of the number of nucleotide substitution in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10 (1993) 512-526
70. Tesar M., and Marquardt O. Serological probes for some foot-and-mouth disease virus nonstructural proteins. Virus Genes 3 (1989) 29-44
71. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The Clustal X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24 (1997) 4876-4882
72. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
73. Toja M., Escarmis C., and Domingo E. Genomic nucleotide sequence of a foot-and-mouth disease virus clone and its persistent derivatives. Implications for the evolution of viral quasispecies during a persistent infection. Virus Res. 64 (1999) 161-172
74. Tosh C., Hemadri D., and Sanyal A. Evidence of recombination in the capsid-coding region of type A foot-and-mouth disease virus. J. Gen. Virol. 83 (2002) 2455-2460
75. Tosh C., Hemadri D., Sanyal A., and Bandyopadyay S.K. Genetic and antigenic analysis of two recently circulating genotypes of type A foot-and-mouth disease virus in India: evidence for positive selection in the capsid-coding genes. Arch. Virol. 148 (2003) 853-869
76. Van Rensberg H., Haydon D., Joubert F., Bastos A., Heath L., and Nel L. Genetic heterogeneity in the foot-and-mouth disease virus Leader and 3C proteinases. Gene 289 (2002) 19-29
77. Von Heijne G. Membrane protein structure prediction: hydrophobicity analysis and the "positive inside" rule. J. Mol. Biol. 225 (1992) 487-494
78. Xiang W., Cuconati A., Hope D., Kirkegaard K., and Wimmer E. Complete protein linkage map of poliovirus P3 proteins: interaction of polymerase 3Dpol with VPg and with genetic variants of 3AB. J. Virol. 72 (1998) 6732-6741
79. Yang, Z., 1999. Plylogenetic analysis by maximum likelihood (PAML) (http://abacus.gene.ucl.ac.uk/software/paml.html). University College London, London.
80. Yang Z., Nielsen R., Goldman N., and Pedersen A.M.K. Codon substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155 (2000) 431-449
81. Zuker M., Mathews D.H., and Turner D.H. Algorithms and thermodynamics for RNA secondary structure prediction. In: Barciszewski J., and Clark B.F.C. (Eds). A Practical Guide in RNA Biochemistry and Biotechnology (1999), Kluwer Academic Publishers NATO ASI Series