Sequence analysis of the whole genomes of five African human G9 rotavirus strains

Infection, Genetics and Evolution

Volumn 16, Issue , 2013, Pages 62-77

  Nyaga, Martin M ^a   Jere, Khuzwayo C ^a,b   Peenze, Ina ^a   Mlera, Luwanika ^b   van Dijk, Alberdina A ^b   Seheri, Mapaseka L ^a   Mphahlele, M Jeffrey ^a  

^a SEFAKO MAKGATHO HEALTH SCIENCES UNIVERSITY   (South Africa)

^b NORTH WEST UNIVERSITY   (South Africa)

Author keywords

454 Pyrosequencing; Africa; Reassortment; Rotavirus G9P 6 and G9P 8 strains; Sequence analysis; Whole genome

Indexed keywords

AFRICA; ARTICLE; CAMEROON; CENTRAL AFRICA; CONTROLLED STUDY; GENE CLUSTER; GENE SEQUENCE; GENOTYPE; GENOTYPING TECHNIQUE; HUMAN G9 ROTAVIRUS; HUMAN ROTAVIRUS; KENYA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SOUTH AFRICA; VIRUS GENOME; VIRUS STRAIN; ZIMBABWE;

AFRICA; FECES; GENOME, VIRAL; HUMANS; PHYLOGENY; RNA, VIRAL; ROTAVIRUS; ROTAVIRUS INFECTIONS; SEQUENCE ANALYSIS, RNA;

EID: 84875274732     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2013.01.005     Document Type: Article

References (36)

1. Armah G.E., Steele A.D., Esona M.D., Akran V.A., Nimzing L., Pennap G. Diversity of rotavirus strains circulating in West Africa from 1996 to 2000. J. Infect. Dis. 2010, 10:64-71.
2. Bányai K., László B., Duque J., Steele A.D., Nelson E.A., Gentsch J.R., Parashar U.D. Systematic review of regional and temporal trends in global rotavirus strain diversity in the pre rotavirus vaccine era: insights for understanding the impact of rotavirus vaccination programs. Vaccine 2012, 30(suppl. 1):A122-A130.
3. Cao D., Santos N., Jones R.W., Tatsumi M., Gentsch J.R., Hoshino Y. The VP7 genes of two G9 rotaviruses isolated in 1980 from diarrheal stool samples collected in Washington, DC, are unique molecularly and serotypically. J. Virol. 2008, 82:4175-4179.
4. Cunliffe N.A., Gondwe J.S., Broadhead R.L., Molyneux M.E., Woods P.A., Bresee J.S., Glass R.I., Gentsch J.R., Hart C.A. Rotavirus G and P types in children with acute diarrhea in Blantyre, Malawi, from 1997 to 1998: predominance of novel P[6]G8 strains. J. Med. Virol. 1999, 57:308-312.
5. Das B.K., Gentsch J.R., Cicirello H.G., Woods P.A., Gupta A., Ramachandran M., Kumar R., Bhan M.K., Glass R.I. Characterization of rotavirus strains from newborns in New Delhi, India. J. Clin. Microbiol. 1994, 32:1820-1822.
6. Estes M., Kapikian A. Rotaviruses. Fields Virology 2007, 1917-1974. Lippincott Williams and Wilkins, Philadelphia. fifth ed. D.M. Knipe, P.M. Howley, D.E. Griffin, R.A. Lamb, M.A. Martin, B. Roizman, S.E. Straus (Eds.).
7. Ghosh S., Kobayashi N. Whole-genomic analysis of rotavirus strains: current status and future prospects. Future Microbiol. 2011, 6:1049-1065.
8. Ghosh S., Urushibara N., Taniguchi K., Kobayashi N. Whole genomic analysis reveals the porcine origin of human G9P[19] rotavirus strains Mc323 and Mc345. Infect. Genet. Evol. 2012, 12:471-477.
9. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 1999, 41:95-98.
10. Heiman E.M., McDonald S.M., Barro M., Taraporewala Z.F., Bar-Magen T., Patton J.T. Group A human rotavirus genomics: evidence that gene constellations are influenced by viral protein interactions. J. Virol. 2008, 82:11106-11116.
11. Jere K.C., Mlera L., O'Neill H.G., Potgieter A.C., Page N.A., Seheri M.L., Van Dijk A.A. Whole genome analyses of African G2, G8, G9, and G12 rotavirus strains using sequence-independent amplification and 454® pyrosequencing. J. Med. Virol. 2011, 83:2018-2042.
12. Jere K.C., Mlera L., Page N.A., Van Dijk A.A., O'Neill H.G. Whole genome analysis of multiple rotavirus strains from a single stool specimen using sequence-independent amplification and 454® pyrosequencing reveals evidence of intergenotype genome segment recombination. Infect. Genet. Evol. 2011, 11:2072-2082.
13. Maes P., Matthijnssens J., Rahman M., Van Ranst M. RotaC: a web-based tool for the complete genome classification of group A rotaviruses. BMC Microbiol. 2009, 9:238.
14. Martinez-Laso J., Román A., Head J., Cervera I., Rodríguez M., Rodríguez-Avial I., Picazo J.J. Phylogeny of G9 rotavirus genotype: a possible explanation of its origin and evolution. J. Clin. Virol. 2009, 44:52-57.
15. Matthijnssens J., Heylen E., Zeller M., Rahman M., Lemey P., Van Ranst M. Phylodynamic analyses of rotavirus genotypes G9 and G12 underscore their potential for swift global spread. Mol. Biol. Evol. 2010, 27:2431-2436.
16. Matthijnssens J., Ciarlet M., McDonald S.M., Attoui H., Banyai K., Brister J.R., Buesa J., Esona M.D., Estes M.K., Gentsch J.R., Iturriza-Gomara M., Johne R., Kirkwood C.D., Martella V., Mertens P.P., Nakagomi O., Parreno V., Rahman M., Ruggeri F.M., Saif L.J., Santos N., Steyer A., Taniguchi K., Patton J.T., Desselberger U., Van Ranst M. Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch. Virol. 2011, 156:1397-1413.
17. Matthijnssens J., Otto P.H., Ciarlet M., Desselberger U., Van Ranst M., Johne R. VP6-sequence-based cutoff values as a criterion for rotavirus species demarcation. Arch. Virol. 2012, 157:1177-1182.
18. Matthijnssens J., Van Ranst M. Genotype constellation and evolution of group A rotaviruses infecting humans. Curr. Opin. Virol. 2012, 2:426-433.
19. Mukherjee A., Dutta D., Ghosh S., Bagchi P., Chattopadhyay S., Nagashima S., Kobayashi N., Dutta P., Krishnan T., Naik T.N., Chawla-Sarkar M. Full genomic analysis of a human group A rotavirus G9P[6] strain from Eastern India provides evidence for porcine-to-human interspecies transmission. Arch. Virol. 2009, 154:733-746.
20. Mwenda J.M., Ntoto K.M., Adebe A., Enweronu-Laryea C., Amina I., Mchomvu J., Kisakye Mpabalwani E.M., Pazvakavambwa I., Armah G.E., Seheri L.M., Kiulia N.M., Page N., Widdowson M.A., Steele A.D. Burden and epidemiology of rotavirus diarrhoea in selected African countries: preliminary results from the African Rotavirus Surveillance Network. J. Infect. Dis. 2010, 202:5-11.
21. Nakagomi T., Ohshima A., Akatani K., Ikegami N., Katsushima N., Nakagomi O. Isolation and molecular characterization of a serotype 9 human rotavirus strain. Microbiol. Immunol. 1990, 34:77-82.
22. Page N., Esona M., Armah G., Nyangao J., Mwenda J., Sebunya T., Basu G., Pyndiah N., Potgieter N., Geyer A., Steele D. Emergence and characterization of serotype G9 rotavirus strains from Africa. J. Infect. Dis. 2010, 202:55-63.
23. Parashar U.D., Burton A., Lanata C., Boschi-Pinto C., Shibuya K., Steele D., Birmingham M., Glass R.I. Global mortality associated with rotavirus disease among children in 2004. J. Infect. Dis. 2009, 200:9-15.
24. Phan T.G., Okitsu S., Maneekarn N., Ushijima H. Genetic heterogeneity, evolution and recombination in emerging G9 rotaviruses. Infect. Genet. Evol. 2007, 7:656-663.
25. Potgieter A.C., Page N.A., Liebenberg J., Wright L.M., Landt O., Van Dijk A.A. Improved strategies for sequence-independent amplification and sequencing of viral double-stranded RNA genomes. J. Gen. Virol. 2009, 90:1423-1432.
26. Rahman M., Matthijnssens J., Yang X., Delbeke T., Arijs I., Taniguchi K., Iturriza-Gómara M., Iftekharuddin N., Azim T., Van Ranst M. Evolutionary history and global spread of the emerging g12 human rotaviruses. J. Virol. 2007, 81:2382-2390.
27. Ramachandran M., Kirkwood C.D., Unicomb L., Cunliffe N.A., Ward R.L., Bhan M.K., Clark H.F., Glass R.I., Gentsch J.R. Molecular characterization of serotype G9 rotavirus strains from a global collection. Virology 2000, 278:436-444.
28. Santos N., Lima R.C.C., Nozawa C.M., Linhares R.E., Gouvea V. Detection of porcine rotavirus type G9 and of a mixture of types G1 and G5 associated with Wa-like VP4 specificity: evidence for natural human-porcine reassortment. J. Clin. Microbiol. 1999, 37:2734-2736.
29. Santos N., Hoshino Y. Global distribution of rotavirus serotypes/genotypes and its implication for the development and implementation of an effective rotavirus vaccine. Rev. Med. Virol. 2005, 15:29-56.
30. Tamura K., Dudley J., Nei M., Kumar S. MEGA 4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
31. Tate J.E., Burton A.H., Boschi-Pinto C., Steele A.D., Duque J., Parashar U.D. The WHO-coordinated Global Rotavirus Surveillance Network., 2012. 2008 Estimate of worldwide rotavirus-associated mortality in children younger than 5 years before the introduction of universal rotavirus vaccination programmes: a systematic review and meta-analysis. Lancet Infect. Dis. 2012, 12:136-141.
32. Teodoroff T.A., Tsunemitsu H., Okamoto K., Katsuda K., Kohmoto M., Kawashima K., Nakagomi T., Nakagomi O. Predominance of porcine rotavirus G9 in Japanese piglets with diarrhea: close relationship of their VP7 genes with those of recent human G9 strains. J. Clin. Microbiol. 2005, 43:1377-1384.
33. Urasawa S., Hasegawa A., Urasawa T., Taniguchi K., Wakasugi F., Suzuki H., Inouye S., Pongprot B., Supawadee J., Suprasert S., Rangsiyanond P., Tonusin S., Yamazi Y. Antigenic and genetic analysis of human rotaviruses in Chiang Mai. Thailand: evidence for a close relationship between human and animal rotaviruses. J. Infect. Dis. 1992, 166:227-234.
34. Vesikari T. Rotavirus vaccines. Scand. J. Infect. Dis. 2008, 40:691-695.
35. Ward R.L., Nakagomi O., Knowlton D.R., McNeal M.M., Nakagomi T., Clemens J.D., Sack D.A., Schiff G.M. Evidence for natural reassortants of human rotaviruses belonging to different genogroups. J. Virol. 1990, 64:3219-3225.
36. Zeller M., Heylen E., De Coster S., Van Ranst M., Matthijnssen J. Full genome characterization of a porcine-like human G9P[6] rotavirus strain isolated from an infant in Belgium. Infect. Genet. Evol. 2012, 12:1492-1500.