Phylogenetic analysis of G1P[6] group A rotavirus strains detected in Northeast Brazilian children fully vaccinated with Rotarix™

Infection, Genetics and Evolution

Volumn 19, Issue , 2013, Pages 395-402

  Gómez, Mariela Martínez ^a   da Silva, Marcelle Figueira Marques ^a   Zeller, Mark ^c   Heylen, Elisabeth ^c   Matthijnssens, Jelle ^c   Ichihara, Maria Yuri Travassos ^b   Rose, Tatiana Lundgren ^a   de Mello Volotão, Eduardo ^a   Leite, Jose Paulo Gagliardi ^a  

^a INSTITUTO OSWALDO CRUZ   (Brazil)

^b FEDERAL UNIVERSITY OF BAHIA   (Brazil)

^c REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

Author keywords

Complete genome analysis; G1P 6 ; Group A rotavirus; Phylogenetic analysis; Rotarix

Indexed keywords

ROTAVIRUS VACCINE;

ACUTE GASTROENTERITIS; AFRICA; ARTICLE; ASIA; BRAZIL; CHILD; CHILDHOOD MORTALITY; CONTROLLED STUDY; DRUG EFFICACY; HOST; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; ROTAVIRUS; ROTAVIRUS INFECTION; SEQUENCE HOMOLOGY; VACCINATION; VIRAL GENETICS; VIRUS GENE; VIRUS GENOME; VIRUS IDENTIFICATION; VIRUS STRAIN;

ROTAVIRUS A;

COMPLETE GENOME ANALYSIS; G1P[6]; GROUP A ROTAVIRUS; PHYLOGENETIC ANALYSIS; ROTARIX(™);

BRAZIL; CHILD, PRESCHOOL; FECES; GENOME, VIRAL; GENOTYPE; HUMANS; INFANT; PHYLOGENY; ROTAVIRUS; ROTAVIRUS INFECTIONS; ROTAVIRUS VACCINES; VACCINES, ATTENUATED;

EID: 84885180230     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2013.03.028     Document Type: Article

References (59)

1. Araujo I.T., Ferreira M.S., Fialho A.M., Assis R.M., Cruz C.M., Rocha M., Leite J.P. Rotavirus genotypes P[4]G9, P[6]G9, and P[8]G9 in hospitalized children with acute gastroenteritis in Rio de Janeiro, Brazil. J. Clin. Microbiol. 2001, 39:1999-2001.
2. Armah, G.E., Steele, A.D., Esona, M.D., Akran, V.A., Nimzing, L., Pennap, G., 2010. Diversity of rotavirus strains circulating in west Africa from 1996 to 2000. J. Infect. Dis. Sep 1; 202 Suppl: S64-71.
3. Black R.E., Cousens S., Johnson H.L., Lawn J.E., Rudan I., Bassani D.G., Jha P., Campbell H., Walker C.F., Cibulskis R., Eisele T., Liu L., Mathers C. Global, regional, and national causes of child mortality in 2008: a systematic analysis. Lancet 2010, 375:1969-1987.
4. 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.
5. Carvalho-Costa F.A., Volotao Ede M., de Assis R.M., Fialho A.M., de Andrade Jda S., Rocha L.N., Tort L.F., da Silva M.F., Gomez M.M., de Souza P.M., Leite J.P. Laboratory-based rotavirus surveillance during the introduction of a vaccination program, Brazil, 2005-2009. Pediatr. Infect. Dis. J. 2011, 30:S35-S41.
6. Centers for Disease Control and Prevention (CDC). Progress in the introduction of rotavirus vaccine - Latin America and the Caribbean, 2006-2010. MMWR Morb. Mortal Wkly Rep. 2011 2, 60 (47), 1611-1614.
7. Desselberger U., Huppertz H.I. Immune responses to rotavirus infection and vaccination and associated correlates of protection. J. Infect. Dis. 2011, 203:188-195.
8. doCarmo G.M., Yen C., Cortes J., Siqueira A.A., de Oliveira W.K., Cortez-Escalante J.J., Lopman B., Flannery B., de Oliveira L.H., Carmo E.H., Patel M. Decline in diarrhea mortality and admissions after routine childhood rotavirus immunization in Brazil a time-series analysis. PLoS Med. 2011, 8:e1001024.
9. Esona M.D., Mijatovic-Rustempasic S., Conrardy C., Tong S., Kuzmin I.V., Agwanda B., Breiman R.F., Banyai K., Niezgoda M., Rupprecht C.E., Gentsch J.R., Bowen M.D. Reassortant group A rotavirus from straw-colored fruit bat (Eidolon helvum). Emerg. Infect. Dis. 2010, 16:1844-1852.
10. Estes M.K., Kapikian A.Z. Rotaviruses. Fields Virology 2007, 1917-1974. Lippincott, Williams and Wilkins, Philadelphia. fifth ed. K. DM, H. PM, G. DE, M. MA, L. RA (Eds.).
11. Fumian T.M., Leite J.P., Rose T.L., Prado T., Miagostovich M.P. One year environmental surveillance of rotavirus specie A (RVA) genotypes in circulation after the introduction of the Rotarix(R) vaccine in Rio de Janeiro, Brazil. Water Res. 2011, 45:5755-5763.
12. Gentsch J.R., Glass R.I., Woods P., Gouvea V., Gorziglia M., Flores J., Das B.K., Bhan M.K. Identification of group A rotavirus gene four types by polymerase chain reaction. J. Clin. Microbiol. 1992, 30:1365-1373.
13. Gómez M.M., Volotao E.M., de Mendonca M.C., Tort L.F., da Silva M.F., Leite J.P. Detection of uncommon rotavirus A strains P[8]G8 and P[4]G8 in the city of Rio de Janeiro, 2002. J. Med. Virol. 2010, 82:1272-1276.
14. Gómez M.M., de Mendonca M.C., Volotao Ede M., Tort L.F., da Silva M.F., Cristina J., Leite J.P. Rotavirus A genotype P[4]G2: genetic diversity and reassortment events among strains circulating in Brazil between 2005 and 2009. J. Med. Virol. 2011, 83:1093-1106.
15. Guo D., Liu J., Lu Y., Sun Y., Yuan D., Jiang Q., Lin H., Li C., Si C., Qu L. Full genomic analysis of rabbit rotavirus G3P[14] strain N5 in China: identification of a novel VP6 genotype. Infect. Genet. Evol. 2012, 12:1567-1576.
16. Gurgel R.Q., Correia J.B., Cuevas L.E. Effect of rotavirus vaccination on circulating virus strains. Lancet 2008, 371:301-302.
17. 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.
18. Heylen E., Zeller M., Ciarlet M., De Coster S., Van Ranst M., Matthijnssens J. Complete genetic characterization of human G2P[6] and G3P[6] rotavirus strains. Infect. Genet. Evol. 2012, 12:27-35.
19. 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.
20. Kirkwood C.D., Gentsch J.R., Hoshino Y., Clark H.F., Glass R.I. Genetic and antigenic characterization of a serotype P[6]G9 human rotavirus strain isolated in the United States. Virology 1999, 256:45-53.
21. Le V.P., Kim J.B., Shon D.H., Chung I.S., Yoon Y., Kim K., Chung S.I., Lim I., Kim W. Molecular characterization of rare G12P[6] rotavirus isolates closely related to G12 strains from the United States, CAU 195 and CAU 214. Arch. Virol. 2011, 156:511-516.
22. Leite J.P., Alfieri A.A., Woods P.A., Glass R.I., Gentsch J.R. Rotavirus G and P types circulating in Brazil: characterization by RT-PCR, probe hybridization, and sequence analysis. Arch. Virol. 1996, 141:2365-2374.
23. Leite J.P., Carvalho-Costa F.A., Linhares A.C. Group A rotavirus genotypes and the ongoing Brazilian experience. a review. Mem. Instrum. Oswaldo Cruz 2008, 103:745-753.
24. Linhares A.C., Mascarenhas J.D., Gusmao R.H., Gabbay Y.B., Fialho A.M., Leite J.P. Neonatal rotavirus infection in Belem, northern Brazil: nosocomial transmission of a P[6] G2 strain. J. Med. Virol. 2002, 67:418-426.
25. Maranhao A.G., Vianez-Junior J.L., Benati F.J., Bisch P.M., Santos N. Polymorphism of rotavirus genotype G1 in Brazil: In silico analysis of variant strains circulating in Rio de Janeiro from 1996 to 2004. Infect. Genet. Evol. 2012, 12:1397-1404.
26. Mascarenhas J.D., Linhares A.C., Gabbay Y.B., Leite J.P. Detection and characterization of rotavirus G and P types from children participating in a rotavirus vaccine trial in Belem, Brazil. Mem. Instrum. Oswaldo Cruz 2002, 97:113-117.
27. Mascarenhas J.D., Linhares A.C., Bayma A.P., Lima J.C., Sousa M.S., Araujo I.T., Heinemann M.B., Gusmao R.H., Gabbay Y.B., Leite J.P. Molecular analysis of VP4, VP7, and NSP4 genes of P[6]G2 rotavirus genotype strains recovered from neonates admitted to hospital in Belem, Brazil. J. Med. Virol. 2006, 78:281-289.
28. Mascarenhas J.D., Linhares A.C., Gabbay Y.B., Lima C.S., Guerra Sde F., Soares L.S., Oliveira D.S., Lima J.C., Macedo O., Leite J.P. Molecular characterization of VP4 and NSP4 genes from rotavirus strains infecting neonates and young children in Belem, Brazil. Virus Res. 2007, 126:149-158.
29. Matthijnssens J., Van Ranst M. Genotype constellation and evolution of group A rotaviruses infecting humans. Curr. Opin. Virol. 2012, 2:426-433.
30. Matthijnssens J., Rahman M., Yang X., Delbeke T., Arijs I., Kabue J.P., Muyembe J.J., Van Ranst M. G8 rotavirus strains isolated in the Democratic Republic of Congo belong to the DS-1-like genogroup. J. Clin. Microbiol. 2006, 44:1801-1809.
31. Matthijnssens J., Rahman M., Van Ranst M. Two out of the 11 genes of an unusual human G6P[6] rotavirus isolate are of bovine origin. J. Gen. Virol. 2008, 89:2630-2635.
32. 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.
33. McDonald S.M., Matthijnssens J., McAllen J.K., Hine E., Overton L., Wang S., Lemey P., Zeller M., Van Ranst M., Spiro D.J., Patton J.T. Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations. PLoS Pathog. 2009, 5:e1000634.
34. Mwenda J.M., Ntoto K.M., Abebe A., Enweronu-Laryea C., Amina I., McHomvu J., Kisakye A., 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 diarrhea in selected African countries: preliminary results from the African Rotavirus Surveillance Network. J. Infect. Dis. 2010, 202(Suppl):S5-S11.
35. Nakagomi O., Kaga E. Distinctness of NSP1 gene of human rotavirus AU-1 from NSP1 gene of other human genogroups. Res. Virol. 1995, 146:423-428.
36. Nordgren J., Nitiema L.W., Sharma S., Ouermi D., Traore A.S., Simpore J., Svensson L. Emergence of unusual G6P[6] rotaviruses in children, Burkina Faso, 2009-2010. Emerg. Infect. Dis. 2012, 18:589-597.
37. Papp H., Al-Mutairi L.Z., Chehadeh W., Farkas S.L., Lengyel G., Jakab F., Martella V., Szucs G., Bányai K. Novel NSP4 genotype in a camel G10P[15] rotavirus strain. Acta Microbiol. Immunol. Hung 2012, 59:411-421.
38. Pietsch C., Liebert U.G. Human infection with G12 rotaviruses, Germany. Emerg. Infect. Dis. 2009, 15:1512-1515.
39. Rahman M., Sultana R., Ahmed G., Nahar S., Hassan Z.M., Saiada F., Podder G., Faruque A.S., Siddique A.K., Sack D.A., Matthijnssens J., Van Ranst M., Azim T. Prevalence of G2P[4] and G12P[6] rotavirus, Bangladesh. Emerg. Infect. Dis. 2007, 13:18-24.
40. 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.
41. Ramani S., Kang G. Burden of disease & molecular epidemiology of group A rotavirus infections in India. Indian J. Med. Res. 2007, 125(5):619-632.
42. Rippinger C.M., Patton J.T., McDonald S.M. Complete genome sequence analysis of candidate human rotavirus vaccine strains RV3 and 116E. Virology 2010, 405:201-213.
43. Santos N., Gouvea V., Timenetsky M.C., Clark H.F., Riepenhoff-Talty M., Garbarg-Chenon A. Comparative analysis of VP8* sequences from rotaviruses possessing M37-like VP4 recovered from children with and without diarrhoea. J. Gen. Virol. 1994, 75:1775-1780.
44. Soares Lda S., Lobo Pdos S., Mascarenhas J.D., Neri D.L., Guerra Sde F., de Oliveira Ado S., Maestri R.P., Oliveira Dde S., de Menezes E.M., Linhares Ada C. Identification of lineage III of G12 rotavirus strains in diarrheic children in the Northern Region of Brazil between 2008 and 2010. Arch. Virol. 2012, 157:135-139.
45. 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.
46. Than V.T., Le V.P., Lim I., Kim W. Complete genomic characterization of cell culture adapted human G12P[6] rotaviruses isolated from South Korea. Virus Genes 2011, 42:317-322.
47. 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, 11:4673-4680.
48. Timenetsky M.C., Santos N., Gouvea V. Survey of rotavirus G and P types associated with human gastroenteritis in Sao Paulo, Brazil, from 1986 to 1992. J. Clin. Microbiol. 1994, 32:2622-2624.
49. Todd, S., Page, N.A., Duncan Steele, A., Peenze, I., Cunliffe, N.A., 2010. Rotavirus strain types circulating in Africa: Review of studies published during 1997-2006. J. Infect. Dis. Sep 1; 202 Suppl:S34-42.
50. Tort L.F., Volotao Ede M., de Mendonca M.C., da Silva M.F., Siqueira A.A., Assis R.M., Moratorio G., Cristina J., Leite J.P. Phylogenetic analysis of human P[8]G9 rotavirus strains circulating in Brazil reveals the presence of a novel genetic variant. J. Clin. Virol. 2010, 47:345-355.
51. Trojnar E., Sachsenroder J., Twardziok S., Reetz J., Otto P.H., Johne R. Identification of an avian group A rotavirus containing a novel VP4 gene of close relationship to those of mammalian rotaviruses. J. Gen. Virol. 2012, 10.
52. United Nations Children's Fund (UNICEF)/World Health Organization (WHO), 2009. Diarrhoea: Why children are still dying and what can be done.
53. Varghese V., Ghosh S., Das S., Bhattacharya S.K., Krishnan T., Karmakar P., Kobayashi N., Naik T.N. Characterization of VP1, VP2 and VP3 gene segments of a human rotavirus closely related to porcine strains. Virus Genes 2006, 32:241-247.
54. Volotao E.M., Soares C.C., Maranhao A.G., Rocha L.N., Hoshino Y., Santos N. Rotavirus surveillance in the city of Rio de Janeiro-Brazil during 2000-2004: detection of unusual strains with G8P[4] or G10P[9] specificities. J. Med. Virol. 2006, 78:263-272.
55. Wang Y.H., Kobayashi N., Nagashima S., Zhou X., Ghosh S., Peng J.S., Hu Q., Zhou D.J., Yang Z.Q. Full genomic analysis of a porcine-bovine reassortant G4P[6] rotavirus strain R479 isolated from an infant in China. J. Med. Virol. 2010, 82:1094-1102.
56. World Health Organization Meeting of the Immunization Strategic Advisory Group of Experts, April 2009 - conclusions and recommendations. Wkly Epidemiol. Rec. 2009, 84:220-236.
57. Yen C., Tate J.E., Patel M.M., Cortese M.M., Lopman B., Fleming J., Lewis K., Jiang B., Gentsch J., Steele D., Parashar U.D. Rotavirus vaccines: update on global impact and future priorities. Hum. Vaccin. 2011, 7:1282-1290.
58. Zeller M., Heylen E., De Coster S., Van Ranst M., Matthijnssens 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.
59. Zeller M., Patton J.T., Heylen E., De Coster S., Ciarlet M., Van Ranst M., Matthijnssens J. Genetic analyses reveal differences in the VP7 and VP4 antigenic epitopes between human rotaviruses circulating in Belgium and rotaviruses in Rotarix and RotaTeq. J. Clin. Microbiol. 2012, 50:966-976.