Discovery of rosavirus 2, a novel variant of a rodent-associated picornavirus, in children from The Gambia

Virology

Volumn 454-455, Issue 1, 2014, Pages 25-33

  Lim, Efrem S ^a   Cao, Song ^a   Holtz, Lori R ^a   Antonio, Martin ^b   Stine, O Colin ^c   Wang, David ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b MEDICAL RESEARCH COUNCIL LABORATORIES   (Gambia)

^c UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

Author keywords

Developing country; Emerging viruses; Picornavirus; Virus discovery

Indexed keywords

NUCLEOTIDE; VIRUS RNA;

3' UNTRANSLATED REGION; ARTICLE; CHILD; COHORT ANALYSIS; CONTROLLED STUDY; DISEASE ASSOCIATION; ETHNIC GROUP; FECES ANALYSIS; FEMALE; GAMBIA; GAMBIAN; GENETIC CONSERVATION; HUMAN; INFECTIOUS DIARRHEA; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PICORNAVIRUS; POPULATION BASED CASE CONTROL STUDY; PREDICTION; PRESCHOOL CHILD; PREVALENCE; PRIORITY JOURNAL; RNA STRUCTURE; RODENT; ROSAVIRUS 2; STRUCTURE ANALYSIS; UNITED STATES; VIRUS CLASSIFICATION; VIRUS DETECTION; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS STRAIN;

DEVELOPING COUNTRY; EMERGING VIRUSES; PICORNAVIRUS; VIRUS DISCOVERY;

ADOLESCENT; CASE-CONTROL STUDIES; CHILD; CHILD, PRESCHOOL; COHORT STUDIES; FECES; FEMALE; GAMBIA; GENOME, VIRAL; HUMANS; INFANT; MALE; MOLECULAR SEQUENCE DATA; PICORNAVIRIDAE; PICORNAVIRIDAE INFECTIONS; RNA, VIRAL; SEQUENCE ANALYSIS, DNA;

EID: 84896541044     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2014.01.018     Document Type: Article

References (40)

1. Adams M.J., King A.M., Carstens E.B. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2013). Arch. Virol. 2013, 158:2023-2030.
2. Ambert-Balay K., Lorrot M., Bon F., Giraudon H., Kaplon J., Wolfer M., Lebon P., Gendrel D., Pothier P. Prevalence and genetic diversity of Aichi virus strains in stool samples from community and hospitalized patients. J. Clin. Microbiol. 2008, 46:1252-1258.
3. Boros A., Nemes C., Pankovics P., Kapusinszky B., Delwart E., Reuter G. Identification and complete genome characterization of a novel picornavirus in turkey (Meleagris gallopavo). J. Gen. Virol. 2012, 93:2171-2182.
4. Bradley R.K., Roberts A., Smoot M., Juvekar S., Do J., Dewey C., Holmes I., Pachter L. Fast statistical alignment. PLoS Comput. Biol. 2009, 5:e1000392.
5. Chikhi-Brachet R., Bon F., Toubiana L., Pothier P., Nicolas J.C., Flahault A., Kohli E. Virus diversity in a winter epidemic of acute diarrhea in France. J. Clin. Microbiol. 2002, 40:4266-4272.
6. Correll C.C., Swinger K. Common and distinctive features of GNRA tetraloops based on a GUAA tetraloop structure at 1.4A resolution. RNA 2003, 9:355-363.
7. Denno, D.M., Klein, E.J., Young, V.B., Fox, J.G., Wang, D., Tarr, P.I., 2007. Explaining unexplained diarrhea and associating risks and infections. In: Proceedings of the Conference of Research Workers in Animal Diseases. Anim. Health Res. Rev. 8, 69-80.
8. Drummond, A.J., Andrew, R., 2009. Tracer v1.5.
9. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32:1792-1797.
10. Fauquet C.M., Mayo M.A., Maniloff J., Desselberger U., Ball L.A. Virus Taxonomy: Eighth report of the International Committee on Taxonomy of Viruses 2005, Elsevier Academic Press, San Diego, CA.
11. Fernandez-Miragall O., Ramos R., Ramajo J., Martinez-Salas E. Evidence of reciprocal tertiary interactions between conserved motifs involved in organizing RNA structure essential for internal initiation of translation. RNA 2006, 12:223-234.
12. Guindon S., Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 2003, 52:696-704.
13. Herold J., Andino R. Poliovirus RNA replication requires genome circularization through a protein-protein bridge. Mol. Cell 2001, 7:581-591.
14. Hird T.R., Grassly N.C. Systematic review of mucosal immunity induced by oral and inactivated poliovirus vaccines against virus shedding following oral poliovirus challenge. PLoS Pathog. 2012, 8:e1002599.
15. Holtz L.R., Finkbeiner S.R., Zhao G., Kirkwood C.D., Girones R., Pipas J.M., Wang D. Klassevirus 1, a previously undescribed member of the family Picornaviridae, is globally widespread. Virol. J. 2009, 6:86.
16. Huelsenbeck J.P., Ronquist F. MRBAYES: bayesian inference of phylogenetic trees. Bioinformatics 2001, 17:754-755.
17. Kapikian A.Z. Viral gastroenteritis. JAMA: J. Am. Med. Assoc. 1993, 269:627-630.
18. Kapoor A., Victoria J., Simmonds P., Slikas E., Chieochansin T., Naeem A., Shaukat S., Sharif S., Alam M.M., Angez M., Wang C., Shafer R.W., Zaidi S., Delwart E. A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Proc. Natl. Acad. Sci. U S A 2008, 105:20482-20487.
19. Knowles, N.J., Hovi, T., Hyypiä, T., King, A.M.Q., Lindberg, A.M., Pallansch, M.A., Palmenberg, A.C., Simmonds, P., Skern, T., Stanway, G., Yamashita, T.Zell, R., 2012. Virus taxonomy: classification and nomenclature of viruses. In: Proceedings of the Ninth Report of the International Committee on Taxonomy of Viruses. Picornaviridae. pp. 855-880.
20. Koonin E.V., Wolf Y.I., Nagasaki K., Dolja V.V. The big bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat. Rev. Microbiol. 2008, 6:925-939.
21. Kotloff K.L., Blackwelder W.C., Nasrin D., Nataro J.P., Farag T.H., van Eijk A., Adegbola R.A., Alonso P.L., Breiman R.F., Faruque A.S., Saha D., Sow S.O., Sur D., Zaidi A.K., Biswas K., Panchalingam S., Clemens J.D., Cohen D., Glass R.I., Mintz E.D., Sommerfelt H., Levine M.M. The Global Enteric Multicenter Study (GEMS) of diarrheal disease in infants and young children in developing countries: epidemiologic and clinical methods of the case/control study. Clin. Infect. Dis. 2012, 55(Suppl 4):S232-S245.
22. Le Gall O., Christian P., Fauquet C.M., King A.M., Knowles N.J., Nakashima N., Stanway G., Gorbalenya A.E. Picornavirales, a proposed order of positive-sense single-stranded RNA viruses with a pseudo-T=3 virion architecture. Arch. Virol. 2008, 153:715-727.
23. Li L.L., Victoria J., Kapoor A., Blinkova O., Wang C.L., Babrzadeh F., Mason C.J., Pandey P., Triki H., Bahri O., Oderinde B.S., Baba M.M., Bukbuk D.N., Besser J.M., Bartkus J.M., Delwart E.L. A novel picornavirus associated with gastroenteritis. J. Virol. 2009, 83:12002-12006.
24. Lim E.S., Reyes A., Antonio M., Saha D., Ikumapayi U.N., Adeyemi M., Stine O.C., Skelton R., Brennan D.C., Mkakosya R.S., Manary M.J., Gordon J.I., Wang D. Discovery of STL polyomavirus, a polyomavirus of ancestral recombinant origin that encodes a unique T antigen by alternative splicing. Virology 2013, 436:295-303.
25. Lole K.S., Bollinger R.C., Paranjape R.S., Gadkari D., Kulkarni S.S., Novak N.G., Ingersoll R., Sheppard H.W., Ray S.C. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J. Virol. 1999, 73:152-160.
26. Martinez-Salas E. The impact of RNA structure on picornavirus IRES activity. Trends Microbiol. 2008, 16:230-237.
27. Nylander J.A., Wilgenbusch J.C., Warren D.L., Swofford D.L. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 2008, 24:581-583.
28. Pham N.T., Khamrin P., Nguyen T.A., Kanti D.S., Phan T.G., Okitsu S., Ushijima H. Isolation and molecular characterization of Aichi viruses from fecal specimens collected in Japan, Bangladesh, Thailand, and Vietnam. J. Clin. Microbiol. 2007, 45:2287-2288.
29. Phan T.G., Kapusinszky B., Wang C., Rose R.K., Lipton H.L., Delwart E.L. The fecal viral flora of wild rodents. PLoS Pathog. 2011, 7:e1002218.
30. Phan T.G., Vo N.P., Simmonds P., Samayoa E., Naccache S., Chiu C.Y., Delwart E. Rosavirus: the prototype of a proposed new genus of the Picornaviridae family. Virus genes. 2013.
31. Pickett B.E., Sadat E.L., Zhang Y., Noronha J.M., Squires R.B., Hunt V., Liu M., Kumar S., Zaremba S., Gu Z., Zhou L., Larson C.N., Dietrich J., Klem E.B., Scheuermann R.H. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Res. 2012, 40:D593-598.
32. Ren L., Gonzalez R., Xiao Y., Xu X., Chen L., Vernet G., Paranhos-Baccala G., Jin Q., Wang J. Saffold cardiovirus in children with acute gastroenteritis, Beijing, China. Emerg. Infect. Dis. 2009, 15:1509-1511.
33. Sanfacon H., Wellink J., Le Gall O., Karasev A., van der Vlugt R., Wetzel T. Secoviridae: a proposed family of plant viruses within the order Picornavirales that combines the families Sequiviridae and Comoviridae, the unassigned genera Cheravirus and Sadwavirus, and the proposed genus Torradovirus. Arch. Virol. 2009, 154:899-907.
34. Serrano P., Gomez J., Martinez-Salas E. Characterization of a cyanobacterial RNase P ribozyme recognition motif in the IRES of foot-and-mouth disease virus reveals a unique structural element. RNA 2007, 13:849-859.
35. Shan T., Wang C., Cui L., Yu Y., Delwart E., Zhao W., Zhu C., Lan D., Dai X., Hua X. Picornavirus salivirus/klassevirus in children with diarrhea, China. Emerg. Infect. Dis. 2010, 16:1303-1305.
36. Toyoda H., Franco D., Fujita K., Paul A.V., Wimmer E. Replication of poliovirus requires binding of the poly(rC) binding protein to the cloverleaf as well as to the adjacent C-rich spacer sequence between the cloverleaf and the internal ribosomal entry site. J. Virol. 2007, 81:10017-10028.
37. Walker C.L., Aryee M.J., Boschi-Pinto C., Black R.E. Estimating diarrhea mortality among young children in low and middle income countries. PLoS One 2012, 7:e29151.
38. Woo P.C., Lau S.K., Choi G.K., Huang Y., Teng J.L., Tsoi H.W., Tse H., Yeung M.L., Chan K.H., Jin D.Y., Yuen K.Y. Natural occurrence and characterization of two internal ribosome entry site elements in a novel virus, canine picodicistrovirus, in the picornavirus-like superfamily. J. Virol. 2012, 86:2797-2808.
39. Zhao G., Krishnamurthy S., Cai Z., Popov V.L., Travassos da Rosa A.P., Guzman H., Cao S., Virgin H.W., Tesh R.B., Wang D. Identification of novel viruses using virushunter - an automated data analysis pipeline. PLoS One 2013, 8:e78470.
40. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.