Rapid subgroup identification of the flaviviruses using degenerate primer E-gene RT-PCR and site specific restriction enzyme analysis

Journal of Virological Methods

Volumn 128, Issue 1-2, 2005, Pages 113-127

  Gaunt, M W ^a,b   Gould, E A ^b  

^a LONDON SCHOOL OF HYGIENE AND TROPICAL MEDICINE   (United Kingdom)

^b CENTRE FOR ECOLOGY AND HYDROLOGY   (United Kingdom)

Author keywords

Conserved restriction sites; Degenerate primers; Flavivirus identification; Flaviviruses; Restriction enzyme analysis; RT PCR; Universal primers

Indexed keywords

COMPLEMENTARY DNA; OLIGONUCLEOTIDE; VIRUS DNA; VIRUS VECTOR;

ARTICLE; CLINICAL PROTOCOL; CONTROLLED STUDY; DENGUE VIRUS; ENTEBBE BAT VIRUS; FLAVIVIRUS; GENE IDENTIFICATION; GENE SEQUENCE; JAPANESE ENCEPHALITIS VIRUS; KOKOBERA FLAVIVIRUS; MODOC FLAVIVIRUS; NONHUMAN; NTAYA FLAVIVIRUS; ORGANIZATION; PRIORITY JOURNAL; REACTION TIME; RESTRICTION MAPPING; RESTRICTION SITE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RIO BRAVO FLAVIVIRUS; SENSITIVITY AND SPECIFICITY; SPONDWENI FLAVIVIRUS; TAXONOMY; TICK BORNE ENCEPHALITIS FLAVIVIRUS; VIRUS DETECTION; VIRUS GENE; VIRUS IDENTIFICATION; YELLOW FEVER FLAVIVIRUS;

ANIMALS; DNA PRIMERS; DNA, COMPLEMENTARY; FLAVIVIRUS; FLAVIVIRUS INFECTIONS; HUMANS; RESTRICTION MAPPING; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA, VIRAL; SPECIES SPECIFICITY; TIME FACTORS; VIRAL ENVELOPE PROTEINS;

FLAVIVIRUS;

EID: 22144442717     PISSN: 01660934     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jviromet.2005.04.006     Document Type: Article

References (44)

1. R. Anderson, A.D. King, and B.L. Innis Correlation of E protein binding cell susceptibility to dengue 4 virus infection J. Gen. Virol. 69 1992 695 700
2. F. Billoir, R. de Chesse, H. Tolou, P. de Micco, E.A. Gould, and X. de Lamballerie Phylogeny of the genus Flavivirus using complete coding sequences of arthropod-borne viruses and viruses with no known vector J. Gen. Virol. 81 2000 781 790
3. J. Blok, M. McWilliam, A.J. Butler, A.J. Gibbs, G. Weiller, B.L. Herring, A.C. Hemsley, J.G. Aaskov, S. Yoksan, and N. Bhamarapravati Comparison of a dengue-2 virus and its candidate vaccine derivative, sequence relationships with the flaviviruses and other viruses Virology 187 1992 573 590
4. T.M. Brown, G.J. Chang, C.B. Cropp, K.E. Robbins, and T.F. Tsai Detection of yellow fever by polymerase chain reaction Clin. Diagn. Virol. 2 1994 41 51
5. C.H. Calisher, N. Karabatsos, J.M. Dalrymple, R.E. Shope, J.S. Porterfield, E.G. Westerway, and W.E. Brandt Antigenic relationships between flaviviruses as determined by cross-neutralisation tests with polyclonal antisera J. Gen. Virol. 70 1989 37 43
6. G.-J. Chang, D.W. Trent, A.V. Vorndam, E. Vergne, R.M. Kinney, and C.J. Mitchell An integrated target sequence and signal amplification assay, reverse transcriptase-PCR enzyme-linked immunosorbent assay to detect and characterise flaviviruses J. Clin. Microbiol. 32 1994 477 483
7. N. Charlier, P. Leyssen, C.W. Pleij, P. Lemey, F. Billoir, K. van Laethem, A.M. Vandamme, E. De Clercq, X. de Lamballerie, and J. Neyts Complete genome sequence of Montana Myotis leukoencephalitis virus, phylogenetic analysis and comparative study of the 3′ untranslated region of flaviviruses with no known vector J. Gen. Virol. 83 2002 1875 1885
8. Chastel, C. Guiguen, G. Le Lay, M.C. Quillien, J.Y. Monnat, and J.C. Beaucournu The identification of Meaban virus, a new Flavivirus from the seabird Ornithodoros Alectorobius maritimus in France Arch. Virol. 83 1985 45 56
9. V.T. Chow, C.L. Seah, and Y.C. Chan Use of NS3 consensus primers for the polymerase chain reaction amplification and sequencing of dengue viruses and other flaviviruses Arch. Virol. 133 1993 157 170
10. G. Coimbra, E.S. Nassar, A.H. Nagamori, I.B. Ferreira, L.E. Pereira, I.M. Rocco, M. Ueda-ito, and N.S. Romano Iguape, a newly recognised flavivirus from Sao Paulo state Brazil. Intervirol. 36 1993 144 152
11. X. de Lamballerie, S. Crochu, F. Billoir, J. Neyts, P. de Micco, E.C. Holmes, and E.A. Gould Genome sequence analysis of Tamana bat virus and its relationship with the genus Flavivirus J. Gen. Virol. 83 2002 2443 2454
12. V. Deubel, M. Laille, J.P. Hugnot, E. Chungue, J.L. Guesdon, M.T. Drouet, B. Bassot, and D. Chevier Identification of dengue sequences by genomic amplification, rapid diagnosis of dengue virus serotypes in peripheral blood J. Med. Virol. 30 1990 41 54
13. Z.A. Eldadah, D.A. Asher, M.S. Godec, K.L. Pomeroy, L.G. Goldfard, S.M. Feinstone, H. Levitan, C.J. Gibbs Jr., and D.C. Gajdusek Detection of flavivirus by reverse transcription chain reaction J. Med. Virol. 33 1991 260 267
14. G.F. Gao, M.H. Hussain, H.W. Reid, and E.A. Gould Classification of a new member of the TBE flavivirus subgroup by its immunological, pathogenetic and molecular characteristics, identification of subgroup-specific pentapeptides Virus Res. 30 1993 129 144
15. G.F. Gao, W.R. Jiang, M.H. Hussan, K. Venugopal, T. Gritsun, H.W. Reid, and E.A. Gould Sequencing and antigenic studies of a Norwegian virus isolated from encephalomyelitic sheep confirm the existence of louping ill virus outside Great Britain and Ireland J. Gen. Virol. 74 1993 109 114
16. M.W. Gaunt, L.D. Jones, K. Laurenson, P.J. Hudson, H.W. Reid, and E.A. Gould Definitive identification of louping ill virus by RT-PCR and sequencing in field populations of Ixodes ricinus on the Lochindorb Estate Arch. Virol. 142 1997 1181 1191
17. M.W. Gaunt, A.A. Sall, X. de Lamballerie, A.K. Falconar, T.I. Dzhivanian, and E.A. Gould Phylogenetic relationships of flaviviruses correlate with their epidemiology, disease association and biogeography J. Gen. Virol. 82 2001 1867 1876
18. E.A. Gould, A. Buckley, S. Higgs, and S. Gaidamovich Antigenicity of flaviviruses Arch. Virol. Suppl. 1 1990 137 152
19. T.S. Gritsun, and E.A. Gould Infectious Transcripts of tick-borne encephalitis virus, generated in days by RT-PCR Virology 214 1995 611 618
20. T.S. Gritsun, V.A. Lashkevich, and E.A. Gould Nucleotide and deduced amino acid sequence of the envelope protein of Omsk haemorrhagic fever virus, comparison with other flaviviruses J. Gen. Virol. 74 1993 287 291
21. F.X. Heinz Epitope mapping of flavivirus glycoproteins Adv. Virus Res. 31 1986 103 135
22. F.X. Heinz, M.S. Collett, R.H. Purcell, E.A. Gould, C.R. Howard, M. Houghton, R.J.M. Moormann, C.M. Rice, and H.J. Thiel Family Flaviviridae M.V.E. Regenmortel C.M. Fauquet D.H.L. Bishop E. Carstens S. Lemon J. Maniloff M.A. Mayo D. McGeogch C.R. Pringle R.B. Wickner Virus Taxonomy. Seventh International Committee for the Taxonomy of Viruses 2000 Academic Press San Diego 859 878
23. E.A. Henchal, S.L. Polo, V. Vorndam, C. Yaemsiri, B.L. Innis, and C.L. Hoke Sensitivity and specificity of a universal primer set for rapid diagnosis of dengue virus infections by polymerase chain reaction and nucleic acid hybridisation Am. J. Trop. Med. Hyg. 45 1991 418 428
24. N. Karabatsos International Catalogue of Arboviruses fourth ed. 1995 American Society of Tropical Medicine and Hygiene San Antonia
25. G. Kuno Universal diagnostic RT-PCR protocol for arboviruses J. Virol. Meth. 72 1998 27 41
26. G. Kuno, G.J.J. Chang, K.R. Tsuchiya, N. Karabatsos, and C.B. Cropp Phylogeny of the genus Flavivirus J. Virol. 72 1998 73 83
27. P. Leyssen, N. Charlier, P. Lemey, F. Billoir, A.M. Vandamme, E. de Clercq, X. de Lamballerie, and J. Neyts Complete genome sequence, taxonomic assignment, and comparative analysis of the untranslated regions of the Modoc virus, a flavivirus with no known vector Virology 293 2002 125 140
28. O. Lopes, T.L.M. Coimbra, L. Sacchetta, and A. de Emergence of a new arbovirus in Brazil. I. Isolation and characterisation of the etiologic agent, Rocio virus Am. J. Epidemiol. 107 1978 444 449
29. O. Lopes, L. Sacchetta, A. de, and T.L.M. Coimbra Epidemiological studies on, 1975 epidemic Am. J. Epidemiol. 108 1978 394 401
30. D.E. Macfarlene, and C.E. Dahle Isolating RNA from whole blood - the dawn of RNA diagosis Nature 362 1993 186 188
31. M.S. Marin, P.M. Zanotto, A. de, T.S. Gritsun, and E.A. Gould Phylogeny of TYU, SRE and CFA virus, different evolutionary rates in the genus Flavivirus Virology 206 1995 1133 1139
32. M.S. Marin, J. MacKenzie, G.F. Gao, H.W. Reid, A. Antoniadis, and E.A. Gould The virus causing encephalomyelitis in sheep in Spain, a new member of the tick-borne encephalitis group Res. Vet. Sci. 58 1995 11 13
33. T.P. Monath, and F.X. Heinz Flaviviruses B.N. Fields D.M. Knipe P.M. Howley Fields Virology third ed. 1995 New York Raven Press 961 1031
34. V. Pierre, M-T. Drouet, and V. Deubel Identification of mosquito-borne flaviviruses using universal primers and reverse transcription/polymerase chain reaction Res. Virol. 145 1994 93 104
35. M. Poidinger, R.A. Hall, and J.S. Mackenzie Molecular characterization of the Japanese encephalitis serocomplex of the Flavivirus genus Virology 218 1996 417 421
36. B. Puri, E.A. Henchal, J. Burans, K.R. Porter, W. Nelson, D.M. Watts, and C.G. Hayes A rapid method for detection and identification of flaviviruses by polymerase chain reaction and nucleic hybridisation Arch. Virol. 134 1994 29 37
37. R.K. Saiki, D.H. Gelfand, S. Stoffel, St. Scharf, R. Higuchi, G.T. Horn, K. Mullis, and H. Erlich Primer-directed enzymatic amplification of DNA with a thermosTable DNA polymerase Science 239 1988 487 491
38. S.Y.W. Shiu, M.D. Ayres, and E.A. Gould Genomic sequence of the structural proteins of louping ill virus, comparative analysis with tick-borne encephalitis virus Virology 180 1991 411 415
39. M. Tanaka Rapid identification of Flavivirus using the polymerase chain reaction J. Virol. Meth. 41 1993 311 322
40. K. Venugopal, A. Buckley, H.W. Reid, and E.A. Gould Nucleotide sequence of the envelope glycoprotein of Negishi virus shows very close homology to louping ill virus Virology 190 1992 515 521
41. K. Venugopal, T. Gritsun, V.A. Lashkevich, and E.A. Gould Analysis of the structural protein gene sequence of sequence shows Kyasanur Forest disease virus as a distinct member in the tick-borne encephalitis virus serocomplex J. Gen. Virol. 75 1994 227 232
42. J.E. Whitby, H. Ni, H.E. Whitby, A.D. Jennings, L.M. Bradley, J.M. Lee, G. Lloyd, J.R. Stephenson, and A.D.T. Barrett Rapid detection of viruses of the tick-borne encephalitis virus complex by RT-PCR of viral RNA J. Gen. Virol. 45 1993 103 114
43. T.H. Work, and H. Trapido Kyasanur Forest disease, a new virus disease in India J. Med. Sci. 11 1957 341 345
44. P.M. Zanotto, A. de, E.A. Gould, G.F. Gao, P.H. Harvey, and E.C. Holmes Population dynamics of flaviviruses revealed by molecular phylogenies Proc. Natl. Acad. Sci. 93 1996 548 553