Sequence analysis of the VP6-encoding genome segment of avian group F and G rotaviruses

Virology

Volumn 412, Issue 2, 2011, Pages 384-391

  Johne, Reimar ^a   Otto, Peter ^b   Roth, Bernhard ^c   Löhren, Ulrich ^d   Belnap, David ^e   Reetz, Jochen ^a   Trojnar, Eva ^a,f  

^a FEDERAL INSTITUTE FOR RISK ASSESSMENT   (Germany)

^b FEDERAL RESEARCH INSTITUTE FOR ANIMAL HEALTH   (Germany)

^c Novartis Vaccines and Diagnostics GmbH   (Germany)

^d BWE Brüterei Weser Ems GmbH and Co KG   (Germany)

^e Brigham Young University   (United States)

^f FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

Avian viruses; Phylogenetic analysis; Rotavirus; Taxonomic grouping; VP6

Indexed keywords

ARGININE; GLUTAMIC ACID; NUCLEOTIDE; PROTEIN VP6;

AMINO ACID SEQUENCE; ARTICLE; CHICKEN; CONTROLLED STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; ROTAVIRUS; ROTAVIRUS A; ROTAVIRUS B; ROTAVIRUS D; ROTAVIRUS F; ROTAVIRUS G; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; VIRUS GENOME;

AMINO ACID SEQUENCE; ANIMALS; ANTIGENS, VIRAL; CAPSID PROTEINS; CHICKENS; CLUSTER ANALYSIS; GENOTYPE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; POULTRY DISEASES; RNA, VIRAL; ROTAVIRUS; ROTAVIRUS INFECTIONS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID;

AVES; GALLUS GALLUS; MAMMALIA; MIRIDAE; ROTAVIRUS; ROTAVIRUS B;

EID: 79952625737     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2011.01.031     Document Type: Article

References (40)

1. Attoui H., Billoir F., Cantaloube J.F., Biagini P., De Micco P., De Lamballerie X. Strategies for the sequence determination of viral dsRNA genomes. J. Virol. Meth. 2000, 89:147-158.
2. Bridger J.C. Non-group A rotaviruses. Viral Infections of the Gastrointestinal Tract 1994, 369-407. Marcel Dekker Inc. New York, Basel, Hong Kong. 2nd ed. A.Z. Kapikian (Ed.).
3. Buragohain M., Cherian S.S., Prabhakar G., Chitambar S.D. VP6 capsid protein of chicken rotavirus strain CH2: sequence, phylogeny and in silico antigenic analyses. Virus Res. 2008, 137:173-178.
4. Desselberger U. Genome rearrangements of rotaviruses. Adv. Virus Res. 1996, 46:69-95.
5. Deo R.C., Groft C.M., Rajashankar K.R., Burley S.K. Recognition of the rotavirus mRNA 3_ consensus by an asymmetric NSP3 homodimer. Cell 2002, 108:71-81.
6. Estes M.K., Kapikian A.Z. Rotaviruses. Fields Virology 2007, 1917-1974. Philadelphia, Lippincott Williams and Wilkins. 5th edn. D.M. Knipe, P.M. Howley, D.E. Griffin, R.A. Lamb, M.A. Martin, B. Roizman, S.E. Straus (Eds.).
7. Elschner M., Hotzel H., Reetz J., Diller R., Otto P. Isolation, identification and characterization of group A rotavirus from chicken: the inner capsid protein sequence shows only a distant phylogenetic relationship to most other avian group A rotaviruses. J. Vet. Med. Ser. B 2005, 52:211-213.
8. Fischer T.K., Viboud C., Parashar U., Malek M., Steiner C., Glass R., Simonsen L. Hospitalizations and deaths from diarrhea and rotavirus among children <5years of age in the United States, 1993-2003. J. Infect. Dis. 2007, 195:1117-1125.
9. Ito H., Sugiyama M., Masubuchi Y., Mori Y., Minamoto N. Complete nucleotide sequence of a group A avian rotavirus genome and comparison with its counterparts of mammalian rotaviruses. Virus Res. 2001, 75:123-138.
10. Jiang S., Ji S., Tang Q., Cui X., Yang H., Kan B., Gao S. Molecular characterization of a novel adult diarrhoea rotavirus strain J19 isolated in China and its significance for the evolution and origin of group B rotaviruses. J. Gen. Virol. 2008, 89:2622-2629.
11. Kang S.Y., Nagaraja K.V., Newman J.A. Electropherotypic analysis of rotaviruses isolated from turkeys. Avian Dis. 1986, 30:794-801.
12. Kapikian A.Z., Hoshino Y., Chanock R.M. Rotaviruses. Fields Virology 2001, 1787-1833. Philadelphia, Lippincott Williams and Wilkins. 4th ed. D.M. Knipe, P.M. Howley (Eds.).
13. Lambden P.R., Cooke S.J., Caul E.O., Clarke I.N. Cloning of noncultivatable human rotavirus by single primer amplification. J. Virol. 1992, 66:1817-1822.
14. Maan S., Rao S., Maan N.S., Anthony S.J., Attoui H., Samuel A.R., Mertens P.P. Rapid cDNA synthesis and sequencing techniques for the genetic study of bluetongue and other dsRNA viruses. J. Virol. Meth. 2007, 143:132-139.
15. Martella V., Bányai K., Matthijnssens J., Buonavoglia C., Ciarlet M. Zoonotic aspects of rotaviruses. Vet. Microbiol. 2010, 140:246-255.
16. Mathieu M., Petitpas I., Navaza J., Lepault J., Kohli E., Pothier P., Prasad B.V.V., Cohen J., Rey F.A. Atomic structure of the major capsid protein of rotavirus: implications for the architecture of the virion. EMBO J. 2001, 20:1485-1497.
17. Matthijnssens J., Ciarlet M., Rahman M., Attoui H., Bányai K., Estes M.K., Gentsch J.R., Iturriza-Gómara M., Kirkwood C.D., Martella V., Mertens P.P., Nakagomi O., Patton J.T., Ruggeri F.M., Saif L.J., Santos N., Steyer A., Taniguchi K., Desselberger U., Van Ranst M. Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments. Arch. Virol. 2008, 153:1621-1629.
18. Matthijnssens J., Ciarlet M., Heiman E., Arijs I., Delbeke T., Mc-Donald S.M., Palombo E.A., Iturriza-Gomara M., Maes P., Patton J.T., Rahman M., Van Ranst M. Full genome-based classification of rotaviruses reveals a common origin between human Wa-like and porcine rotavirus strains and human DS-1-like and bovine rotavirus strains. J. Virol. 2008, 82:3204-3219.
19. McDonald S.M., Aguayo D., Gonzalez-Nilo F.D., Patton J.T. Shared and group-specific features of the rotavirus RNA polymerase reveal potential determinants of gene reassortment restriction. J. Virol. 2009, 83:6135-6148.
20. McNulty M.S., Allan G.M., Todd D., McFerran J.B., McKillop E.R., Collins D.S., McCracken R.M. Isolation of rotaviruses from turkeys and chickens: demonstration of distinct serotypes and RNA electropherotypes. Avian Pathol. 1980, 9:363-375.
21. McNulty M.S., Todd D., Allan G.M., Mc Ferran J.B., Greene J.A. Epidemiology of rotavirus infection in broiler chickens: recognition of four serogroups. Arch. Virol. 1984, 81:113-121.
22. McNulty M.S., Reynolds D.L. Rotavirus infections. Diseases of Poultry 2008, 338-350. Iowa State Press, Ames. 12th ed. Y.M. Saif (Ed.).
23. Mertens P.P.C., Arella M., Attoui H., Belloncik A., Bergoin S., Boccardo M.G., Booth T.F., Chiu W., Diprose J.M., Duncan R., Estes M.K., Gorziglia M., Gouet P., Gould A.R., Grimes J.M., Hewat E., Holmes I.H., Hoshino Y., Hill C., Joklik W.K., Knowles N., Ferber M.L., Malby R., Marzachi C., McCrae M.A., Milne R.G., Nibert M., Nunn M., Omura T., Prasad B.V.V., Pritchard I., Roy P., Samal S.K., Schoehn G., Shikata E., Stoltz D.B., Stuart D.I., Suzuki N., Upahyaya N., Uyeda I., Waterhouse P., Williams C.F., Winton J.R., Zhou H.Z. Family reoviridae. Virus taxonomy, 7th report 2000, 395-480. Academic Press, San Diego. M.H.V. van Regenmortel, C.M. Fauquet, D.H.L. Bishop (Eds.).
24. Nagashima S., Kobayashi N., Ishino M., Alam M.M., Ahmed M.U., Paul S.K., Ganesh B., Chawla-Sarkar M., Krishnan T., Naik T.N., Wang Y.H. Whole genomic characterization of a human rotavirus strain B219 belonging to a novel group of the genus Rotavirus. J. Med. Virol. 2008, 80:2023-2033.
25. Otto P., Liebler-Tenorio E.M., Elschner M., Reetz J., Löhren U., Diller R. Detection of rotaviruses and intestinal lesions in broiler chicks from flocks with runting and stunting syndrome (RSS). Avian Dis. 2006, 50:411-418.
26. Otto P., Schulze P., Herbst W. Demonstration of group C rotaviruses in fecal samples of diarrheic dogs from Germany. Arch. Virol. 1999, 144:2467-2473.
27. Pantin-Jackwood M.J., Spackman E., Day J.M., Rives D. Periodic monitoring of commercial turkeys for enteric viruses indicates continuous presence of astrovirus and rotavirus on the farms. Avian Dis. 2007, 51:674-680.
28. Parashar U.D., Hummelman E.G., Bresee J.S., Miller M.A., Glass R.I. Global illness and deaths caused by rotavirus disease in children. Emerg. Infect. Dis. 2003, 9:565-572.
29. Parashar U.D., Gibson C.J., Bresee J.S., Glass R.I. Rotavirus and severe childhood diarrhea. Emerg. Infect. Dis. 2006, 12:304-306.
30. Pedley S., Bridger J.C., Chasey D., McCrae M.A. Definition of two new groups of atypical rotaviruses. J. Gen. Virol. 1986, 67:131-137.
31. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25:1605-1612.
32. Ramig R.F., Ciarlet M., Mertens P.P.C., Dermody T.S. Genus Rotavirus. Virus Taxonomy. Eighth Report of the ICTV 2005, 484-496. Elsevier Academic Press, Amsterdam etc. C.M. Fauquet, M.A. Mayo, J. Maniloff, U. Desselberger, L.A. Ball (Eds.).
33. Saif L.J., Rosen B.I., Parwani A.V. Animal rotaviruses. Viral infections of the gastrointestinal tract»» 1994, 279-367. Marcel Dekker Inc. New York, Basel, Hong Kong. 2nd ed. A.Z. Kapikian (Ed.).
34. Saif L.J., Jiang B. Nongroup A rotaviruses of humans and animals. Curr. Top. Microbiol. Immunol. 1994, 185:339-371.
35. Schumann T., Hotzel H., Otto P., Johne R. Evidence of interspecies transmission and reassortment among avian group A rotaviruses. Virology 2009, 386:334-343.
36. Settembre E.C., Chen J.Z., Dormitzer P.R., Grigorieff N., Harrison S.C. Atomic model of an infectious rotavirus particle. EMBO J. 2011, 30:408-416.
37. Theil K.W., Reynolds D.L., Saif Y.M. Genomic cariation among rotavirus-like viruses detected by polyacrylamide gel electrophoresis. Avian Dis. 1986, 30:829-834.
38. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 1994, 22:4673-4680.
39. Trojnar E., Otto P., Johne R. The first complete genome sequence of a chicken group A rotavirus indicates independent evolution of mammalian and avian strains. Virology 2009, 386:325-333.
40. Trojnar E., Otto P., Roth B., Reetz J., Johne R. The genome segments of group D rotavirus possess group A-like conserved termini but encode group-specific proteins. J. Virol. 2010, 84:10254-10265.