Comparison of novel MLB-clade, VA-clade and classic human astroviruses highlights constrained evolution of the classic human astrovirus nonstructural genes

Virology

Volumn 436, Issue 1, 2013, Pages 8-14

  Jiang, Hongbing ^a   Holtz, Lori R ^a   Bauer, Irma ^a   Franz, Carl J ^a   Zhao, Guoyan ^a   Bodhidatta, Ladaporn ^b   Shrestha, Sanjaya K ^c   Kang, Gagandeep ^d   Wang, David ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b ARMED FORCES RESEARCH INSTITUTE OF MEDICAL SCIENCES   (Thailand)

^c Walter Reed/AFRIMS Research Unit Nepal   (Nepal)

^d CHRISTIAN MEDICAL COLLEGE   (India)

Author keywords

Astrovirus discovery; Constrained evolution; Diarrhea; Nonstructural genes

Indexed keywords

COMPLEMENTARY DNA; VIRUS PROTEIN;

5' UNTRANSLATED REGION; ARTICLE; ASTROVIRUS; ASTROVIRUS MLB; ASTROVIRUS MLB1; ASTROVIRUS MLB2; ASTROVIRUS VA; ASTROVIRUS VA1; ASTROVIRUS VA2; ASTROVIRUS VA3; CLADISTICS; COMPARATIVE STUDY; CONSENSUS SEQUENCE; CONTROLLED STUDY; DIARRHEA; FECES ANALYSIS; GENE MUTATION; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC DISTANCE; HUMAN; INDIA; NEPAL; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; UNINDEXED SEQUENCE; VIRUS CAPSID; VIRUS GENOME; VIRUS IDENTIFICATION;

3' UNTRANSLATED REGIONS; 5' UNTRANSLATED REGIONS; ASTROVIRIDAE INFECTIONS; CAPSID; CAPSID PROTEINS; CHILD; DIARRHEA; EVOLUTION, MOLECULAR; FECES; GENES, VIRAL; GENOME, VIRAL; HUMANS; MAMASTROVIRUS; MOLECULAR SEQUENCE DATA; PEPTIDE HYDROLASES; PHYLOGENY; RNA REPLICASE; RNA, VIRAL; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; VIRAL NONSTRUCTURAL PROTEINS;

ASTROVIRIDAE; HUMAN ASTROVIRUS; MIRIDAE;

EID: 84872193015     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2012.09.040     Document Type: Article

References (27)

1. Ajjampur S.S., Rajendran P., Ramani S., Banerjee I., Monica B., Sankaran P., Rosario V., Arumugam R., Sarkar R., Ward H., Kang G. Closing the diarrhoea diagnostic gap in Indian children by the application of molecular techniques. J. Med. Microbiol. 2008, 57:1364-1368.
2. Abascal F., Zardoya R., Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 2005, 21:2104-2105.
3. Boom R., Sol C.J., Salimans M.M., Jansen C.L., Wertheim-van Dillen P.M., van der Noordaa J. Rapid and simple method for purification of nucleic acids. J. Clin. Microbiol. 1990, 28:495-503.
4. Burbelo P.D., Ching K.H., Esper F., Iadarola M.J., Delwart E., Lipkin W.I., Kapoor A. Serological studies confirm the novel astrovirus HMOAstV-C as a highly prevalent human infectious agent. PloS One 2011, 6:e22576.
5. Finkbeiner S.R. Detection of newly described astrovirus MLB1 in stool samples from children. Emerging Infect. Dis. 2009, 15:441-444.
6. Finkbeiner S.R., Allred A.F., Tarr P.I., Klein E.J., Kirkwood C.D., Wang D. Metagenomic analysis of human diarrhea: viral detection and discovery. PloS Pathog. 2008, 4:e1000011.
7. Finkbeiner S.R., Holtz L.R., Jiang Y., Rajendran P., Franz C.J., Zhao G., Kang G., Wang D. Human stool contains a previously unrecognized diversity of novel astroviruses. Virol. J. 2009, 6:161.
8. Finkbeiner S.R., Li Y., Ruone S., Conrardy C., Gregoricus N., Toney D., Virgin H.W., Anderson L.J., Vinje J., Wang D., Tong S. Identification of a novel astrovirus (astrovirus VA1) associated with an outbreak of acute gastroenteritis. J. Virol. 2009, 83:10836-10839.
9. 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.
10. Holtz L.R., Bauer I.K., Rajendran P., Kang G., Wang D. Astrovirus MLB1 is not associated with diarrhea in a cohort of Indian children. PloS One 2011, 6:e28647.
11. Holtz L.R., Wylie K.M., Sodergren E., Jiang Y., Franz C.J., Weinstock G.M., Storch G.A., Wang D. Astrovirus MLB2 viremia in febrile child. Emerging Infect. Dis. 2011, 17:2050-2052.
12. Jiang B., Monroe S.S., Koonin E.V., Stine S.E., Glass R.I. RNA sequence of astrovirus: distinctive genomic organization and a putative retrovirus-like ribosomal frameshifting signal that directs the viral replicase synthesis. Proc. Nat. Acad. Sci. USA 1993, 90:10539-10543.
13. Jonassen C.M., Jonassen T.O., Grinde B. A common RNA motif in the 3' end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus. J. Gen. Virol. 1998, 79:715-718. Pt 4.
14. Kapoor A., Li L., Victoria J., Oderinde B., Mason C., Pandey P., Zaidi S.Z., Delwart E. Multiple novel astrovirus species in human stool. J. Gen. Virol. 2009, 90:2965-2972.
15. Kirkwood C.D., Clark R., Bogdanovic-Sakran N., Bishop R.F. A 5-year study of the prevalence and genetic diversity of human caliciviruses associated with sporadic cases of acute gastroenteritis in young children admitted to hospital in Melbourne, Australia (1998-2002). J. Med. Virol. 2005, 77:96-101.
16. Kjeldsberg E. Serotyping of human astrovirus strains by immunogold staining electron microscopy. J. Virol. Methods 1994, 50:137-144.
17. Madeley C.R., Cosgrove B.P. Letter: 28nm particles in faeces in infantile gastroenteritis. Lancet 1975, 2:451-452.
18. Mendez, E., Arias, C.F., 2007. Astrovirus. In: Knipe, D.M., Howley, P.M. (Eds.), Fields Virolog, 5th ed., vol. 1. Lippincott Williams & Wilkins, Phiadelphia, pp. 981-1000.
19. Monceyron C., Grinde B., Jonassen T.O. Molecular characterisation of the 3'-end of the astrovirus genome. Arch. Virol. 1997, 142:699-706.
20. Nei M., Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 1986, 3:418-426.
21. Quan P.L., Wagner T.A., Briese T., Torgerson T.R., Hornig M., Tashmukhamedova A., Firth C., Palacios G., Baisre-De-Leon A., Paddock C.D., Hutchison S.K., Egholm M., Zaki S.R., Goldman J.E., Ochs H.D., Lipkin W.I. Astrovirus encephalitis in boy with X-linked agammaglobulinemia. Emerging Infect. Dis. 2010, 16:918-925.
22. Sakamoto T., Negishi H., Wang Q.H., Akihara S., Kim B., Nishimura S., Kaneshi K., Nakaya S., Ueda Y., Sugita K., Motohiro T., Nishimura T., Ushijima H. Molecular epidemiology of astroviruses in Japan from 1995 to 1998 by reverse transcription-polymerase chain reaction with serotype-specific primers (1-8). J. Med. Virol. 2000, 61:326-331.
23. Soares C.C., Maciel de Albuquerque M.C., Maranhao A.G., Rocha L.N., Ramirez M.L., Benati F.J., Timenetsky Mdo C., Santos N. Astrovirus detection in sporadic cases of diarrhea among hospitalized and non-hospitalized children in Rio De Janeiro, Brazil, from 1998 to 2004. J. Med. Virol. 2008, 80:113-117.
24. Steitz T.A. DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 1999, 274:17395-17398.
25. 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, 28:2731-2739.
26. Walter J.E., Briggs J., Guerrero M.L., Matson D.O., Pickering L.K., Ruiz-Palacios G., Berke T., Mitchell D.K. Molecular characterization of a novel recombinant strain of human astrovirus associated with gastroenteritis in children. Arch. Virol. 2001, 146:2357-2367.
27. Wang D., Urisman A., Liu Y.T., Springer M., Ksiazek T.G., Erdman D.D., Mardis E.R., Hickenbotham M., Magrini V., Eldred J., Latreille J.P., Wilson R.K., Ganem D., DeRisi J.L. Viral discovery and sequence recovery using DNA microarrays. PLoS Biol. 2003, 1:E2.