Genomic characterisation of Almpiwar virus, Harrison Dam virus and Walkabout Creek virus; three novel rhabdoviruses from northern Australia

Virology Reports

Volumn 3, Issue , 2014, Pages 1-17

  McAllister, Jane ^a   Gauci, Penelope J ^a   Mitchell, Ian R ^a   Boyle, David B ^b   Bulach, Dieter M ^b,c   Weir, Richard P ^d   Melville, Lorna F ^d   Davis, Steven S ^d   Gubala, Aneta J ^a  

^a DEFENCE SCIENCE AND TECHNOLOGY ORGANISATION   (Australia)

^b CSIRO   (Australia)

^c MONASH UNIVERSITY   (Australia)

^d Berrimah Veterinary Laboratories   (Australia)

Author keywords

Almpiwar virus; Arbovirus; Genome characterisation; Harrison Dam virus; Rhabdovirus; Walkabout Creek virus

Indexed keywords

COMPLEMENTARY DNA; CORE PROTEIN; EPITOPE; RNA DIRECTED RNA POLYMERASE; UNCLASSIFIED DRUG; VIRUS ANTIBODY; VIRUS PROTEIN G; VIRUS PROTEIN L; VIRUS PROTEIN M; VIRUS PROTEIN N; VIRUS PROTEIN P; VIRUS RNA;

ALMPIWAR VIRUS; AMINO ACID SEQUENCE; ARTICLE; AUSTRALIA; CERATOPOGONIDAE; CROSS REACTION; CULEX QUINQUEFASCIATUS; DNA SEQUENCE; GENETIC SIMILARITY; GENETIC VARIABILITY; HARRISON DAM VIRUS; HIGH THROUGHPUT SEQUENCING; MAXIMUM LIKELIHOOD METHOD; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; OVERLAPPING GENE; PARAINFLUENZA VIRUS 1; POLYMERASE CHAIN REACTION; PROTEIN ANALYSIS; PROTEIN RNA BINDING; RHABDOVIRUS; RNA EXTRACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SQUAMATE; TRANSCRIPTION INITIATION; VIRUS GENOME; VIRUS NEUTRALIZATION; WALKABOUT CREEK VIRUS;

EID: 84919382581     PISSN: 22146695     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.virep.2014.09.001     Document Type: Article

References (50)

1. Allison A.B., Palacios G., Travassos da Rosa A., Popov V.L., Lu L., Xiao S.Y., DeToy K., Briese T., Lipkin W.I., Keel M.K., Stallknecht D.E., Bishop G.R., Tesh R.B. Characterization of Durham virus, a novel rhabdovirus that encodes both a C and SH protein. Virus Res. 2011, 155(1):112-122.
2. Bexfield N., Kellam P. Metagenomics and the molecular identification of novel viruses. Vet. J. 2011, 190(2):191-198.
3. Bourhy H., Cowley J.A., Larrous F., Holmes E.C., Walker P.J. Phylogenetic relationships among rhabdoviruses inferred using the L polymerase gene. J. Gen. Virol. 2005, 86(10):2849-2858.
4. Boyle D.B., Bulach D.M., Amos-Ritchie R., Adams M.M., Walker P.J., Weir R. Genomic sequences of australian bluetongue virus prototype serotypes reveal global relationships and possible routes of entry into Australia. J. Virol. 2012, 86(12):6724-6731.
5. Brandt W.E., Buescher E.L., Hetrick F.M. Production and characterization of arbovirus antibody in mouse ascitic fluid. Am. J. Trop. Med. Hyg. 1967, 16(3):339-347.
6. Calisher C.H., Karabatsos N., Zeller H., Digoutte J.P., Tesh R.B., Shope R.E., Travassos da Rosa A.P., St George T.D. Antigenic relationships among rhabdoviruses from vertebrates and hematophagous arthropods. Intervirology 1989, 30(5):241-257.
7. Carley J.G., Standfast H.A., Kay B.H. Multiplication of viruses isolated from arthopods and vertebrates in Australia in experimentally infected mosquitoes. J. Med. Entomol. 1973, 10(3):244-249.
8. Dietzgen R.G. Morphology, genome organisation, transcription and replication of rhabdoviruses. Rhabdoviruses: Molecular Taxonomy, Evolution, Genomics, Ecology, Host-Vector Interactions, Cytopathology and Control 2012, Caister Academic Press, Norfolk. R.G. Dietzgen, I.V. Kuzmin (Eds.).
9. Dietzgen R.G., Calisher C.H., Kurath G., Kuzmin I.V., Rodriguez L.L., Stone D.M., Tesh R.B., Tordo N., Walker P.J., Wetzel T., Whitfield A.E. Rhabdoviridae. Virus Taxonomy: Ninth Report of the International Committee on the Taxonomy of Viruses 2012, 654-681. Elsevier Academic Press, San Diego, TX, USA. A.M.Q. King (Ed.).
10. Doherty R.L., Whitehead R.H., Wetters E.J., Gorman B.M., Carley J.G. A survey of antibody to 10 arboviruses (Koongol group, Mapputta group and ungrouped) isolated in Queensland. Trans. R. Soc. Trop. Med. Hyg. 1970, 64(5):748-753.
11. Drummond A.J., Suchard M.A., Xie D., Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 2012, 29(8):1969-1973.
12. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32(5):1792-1797.
13. Gan S.W., Tan E., Lin X., Yu D., Wang J., Tan G.M.Y., Vararattanavech A., Yeo C.Y., Soon C.H., Soong T.W., Pervushin K., Torres J. The small hydrophobic protein of the human respiratory syncytial virus forms pentameric ion channels. J. Biol. Chem. 2012, 287(29):24671-24689.
14. Grard G., Fair J.N., Lee D., Slikas E., Steffen I., Muyembe J.J., Sittler T., Veeraraghavan N., Ruby J.G., Wang C., Makuwa M., Mulembakani P., Tesh R.B., Mazet J., Rimoin A.W., Taylor T., Schneider B.S., Simmons G., Delwart E., Wolfe N.D., Chiu C.Y., Leroy E.M. A novel rhabdovirus associated with acute hemorrhagic fever in Central Africa. PLoS Pathog. 2012, 8(9).
15. Gubala A. Characterisation of novel viruses isolated from vertebrates and insects in Australia 2009, (PhD thesis), School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Australia.
16. Gubala A. Recent advances in the characterization of animal rhabdoviruses. Rhabdoviruses: Molecular Taxonomy, Evolution, Genomics, Ecology, Host-Vector Interactions, Cytopathology and Control 2012, 165-203. Caister Academic Press, Norfolk, UK. R.G. Dietzgen, I.V. Kuzmin (Eds.).
17. Gubala A.J., Proll D.F., Barnard R.T., Cowled C.J., Crameri S.G., Hyatt A.D., Boyle D.B. Genomic characterisation of Wongabel virus reveals novel genes within the Rhabdoviridae. Virology 2008, 376(1):13-23.
18. Gubala A., Davis S., Weir R., Melville L., Cowled C., Walker P., Boyle D. Ngaingan virus, a macropod-associated rhabdovirus, contains a second glycoprotein gene and seven novel open reading frames. Virology 2010, 399(1):98-108.
19. Humphery-Smith I., Cybinski D.H., Byrnes K.A., St George T.D. Seroepidemiology of arboviruses among seabirds and island residents of the Great Barrier Reef and Coral Sea. Epidemiol. Infect. 1991, 107(2):435-440.
20. Käll L., Krogh A., Sonnhammer E.L.L. A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 2004, 338(5):1027-1036.
21. The American Committee on Arthropod-borne Viruses: International Catalog of Arboviruses Including Certain Other Viruses of Vertebrates 1985, American Society for Tropical Medicine and Hygiene, San Antonio, Texas, USA. 3rd ed. N. Karabatsos (Ed.).
22. Kouznetzoff A., Buckle M., Tordo N. Identification of a region of the rabies virus N protein involved in direct binding to the viral RNA. J. Gen. Virol. 1998, 79(5):1005-1013.
23. Kurz W., Gelderblom H., Flugel R.M., Darai G. Isolation and characterization of a tupaia rhabdovirus. Intervirology 1986, 25(2):88-96.
24. Kuzmin I.V., Hughes G.J., Rupprecht C.E. Phylogenetic relationships of seven previously unclassified viruses within the family Rhabdoviridae using partial nucleoprotein gene sequences. J. Gen. Virol. 2006, 87(8):2323-2331.
25. Li J., Rahmeh A., Morelli M., Whelan S.P.J. A conserved motif in region V of the large polymerase proteins of nonsegmented negative-sense RNA viruses that is essential for mRNA capping. J. Virol. 2008, 82(2):775-784.
26. Monath T.P., Cropp C.B., Frazier C.L., Murphy F.A., Whitfield S.G. Viruses isolated from reptiles: identification of three new members of the family Rhabdoviridae. Arch. Virol. 1979, 60(1):1-12.
27. Nadin-Davis S.A., Abdel-Malik M., Armstrong J., Wandeler A.I. Lyssavirus P gene characterisation provides insights into the phylogeny of the genus and identifies structural similarities and diversity within the encoded phosphoprotein. Virology 2002, 298(2):286-305.
28. Petersen T.N., Brunak S., Von Heijne G., Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 2011, 8(10):785-786.
29. Poch O., Sauvaget I., Delarue M., Tordo N. Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. Embo J. 1989, 8(12):3867-3874.
30. Quan P.L., Williams D.T., Johansen C.A., Jain K., Petrosov A., Diviney S.M., Tashmukhamedova A., Hutchison S.K., Tesh R.B., Mackenzie J.S., Briese T., Lipkin W.I. Genetic characterization of K13965, a strain of Oak Vale virus from Western Australia. Virus Res. 2011, 160(1-2):206-213.
31. Reed L.J., Muench H. A simple method of estimating fifty percent endpoints. Am. J. Hyg. 1938, 27:493-497.
32. Rice P., Longden L., Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 2000, 16(6):276-277.
33. Rost B., Liu J. The PredictProtein server. Nucleic Acids Res. 2003, 31(13):3300-3304.
34. Sievers F., Wilm A., Dineen D., Gibson T.J., Karplus K., Li W., Lopez R., McWilliam H., Remmert M., Söding J., Thompson J.D., Higgins D.G. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 2011, 7.
35. Spiropoulou C.F., Nichol S.T. A small highly basic protein is encoded in overlapping frame within the P gene of vesicular stomatitis virus. J. Virol. 1993, 67(6):3103-3110.
36. Springfeld C., Darai G., Cattaneo R. Characterization of the Tupaia rhabdovirus genome reveals a long open reading frame overlapping with P and a novel gene encoding a small hydrophobic protein. J. Virol. 2005, 79(11):6781-6790.
37. Standfast H.A., Dyce A.L., St George T.D., Muller M.J., Doherty R.L., Carley J.G., Filippich C. Isolation of arboviruses from insects collected at Beatrice Hill, Northern Territory of Australia, 1974-1976. Aust. J. Biol. Sci. 1984, 37(5-6):351-366.
38. Talavera G., Castresana J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 2007, 56(4):564-577.
39. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 2011, 28(10):2731-2739.
40. Tao J.J., Zhou G.Z., Gui J.F., Zhang Q.Y. Genomic sequence of mandarin fish rhabdovirus with an unusual small non-transcriptional ORF. Virus Res. 2008, 132(1-2):86-96.
41. Tesh R.B., Travassos Da Rosa A.P., Travassos Da Rosa J.S. Antigenic relationship among rhabdoviruses infecting terrestrial vertebrates. J. Gen. Virol. 1983, 64(1):169-176.
42. Triantafilou K., Kar S., Vakakis E., Kotecha S., Triantafilou M. Human respiratory syncytial virus viroporin SH: a viral recognition pathway used by the host to signal inflammasome activation. Thorax 2013, 68(1):66-75.
43. Vasilakis N., Widen S., Mayer S.V., Seymour R., Wood T.G., Popov V., Guzman H., Travassos da Rosa A.P.A., Ghedin E., Holmes E.C., Walker P.J., Tesh R.B. Niakha virus: a novel member of the family Rhabdoviridae isolated from phlebotomine sandflies in Senegal. Virology 2013, 444(1-2):80-89.
44. Walker P.J., Kongsuwan K. Deduced structural model for animal rhabdovirus glycoproteins. J. Gen. Virol. 1999, 80(5):1211-1220.
45. Walker P.J., Dietzgen R.G., Joubert D.A., Blasdell K.R. Rhabdovirus accessory genes. Virus Res. 2011, 162(1-2):110-125.
46. Walker P.J., Blasdell K.R., Joubert D.A. Ephemeroviruses: arthropod-borne rhabdoviruses of ruminants, with large, complex genomes. Rhabdoviruses: Molecular Taxonomy, Evolution, Genomics, Ecology, Host-Vector Interactions, Cytopathology and Control 2012, 59-89. Caister Academic Press, Norfolk, UK. R.G. Dietzgen, I.V. Kuzmin (Eds.).
47. Weir R. Classification and identification of viruses isolated from mosquitoes in the Northern Territory, 1982-1992, using a range of techniques 2002, (PhD thesis), Faculty of Medicine, University of Sydney, Australia.
48. Wellehan J.F.X., Pessier A.P., Archer L.L., Childress A.L., Jacobson E.R., Tesh R.B. Initial sequence characterization of the rhabdoviruses of squamate reptiles, including a novel rhabdovirus from a caiman lizard (Dracaena guianensis). Vet. Microbiol. 2012, 158(3-4):274-279.
49. Wilkins M.R., Gasteiger E., Bairoch A., Sanchez J.C., Williams K.L., Appel R.D., Hochstrasser D.F. Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol. 1999, 112:531-552.
50. Zhu R.L., Lei X.Y., Ke F., Yuan X.P., Zhang Q.Y. Genome of turbot rhabdovirus exhibits unusual non-coding regions and an additional ORF that could be expressed in fish cell. Virus Res. 2011, 155(2):495-505.