Phylogenetic analysis of novel G12 rotaviruses in the united states: A molecular search for the origin of a new strain

Journal of Medical Virology

Volumn 81, Issue 4, 2009, Pages 736-746

  Freeman, M M ^a,c   Kerin, T ^a   Hull, J ^a   Teel, E ^a   Esona, M ^a   Parashar, U ^a   Glass, R I ^b   Gentsch, J R ^a  

^a CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c Mail Stop C 03 ^*  (United States)

Author keywords

Classification; Evolution; Genetic shift; Rotavirus; Vaccine

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENOTYPE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; ROTAVIRUS; SEROTYPE; VIRUS DETECTION; VIRUS STRAIN; ANIMAL; CLASSIFICATION; DNA SEQUENCE; FECES; GENETIC REASSORTMENT; GENETICS; HUMAN; ISOLATION AND PURIFICATION; MOLECULAR EVOLUTION; MOLECULAR GENETICS; SWINE; UNITED STATES; VIROLOGY; VIRUS INFECTION;

MIRIDAE; ROTAVIRUS; SUS;

CAPSID PROTEIN; VIRUS ANTIGEN; VP4 PROTEIN, ROTAVIRUS; VP7 PROTEIN, ROTAVIRUS;

ANIMALS; ANTIGENS, VIRAL; CAPSID PROTEINS; EVOLUTION, MOLECULAR; FECES; GENOTYPE; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; REASSORTANT VIRUSES; ROTAVIRUS; ROTAVIRUS INFECTIONS; SEQUENCE ANALYSIS, DNA; SWINE; UNITED STATES;

EID: 62849100236     PISSN: 01466615     EISSN: 10969071     Source Type: Journal    
DOI: 10.1002/jmv.21446     Document Type: Article

References (51)

1. Banyai K, Bogdan A, Kisfali P, Molnar P, Mihaly I, Melegh B, Martella V, Gentsch JR, Szucs G. 2007. Emergence of serotype G12 rotaviruses, Hungary. Emerg Infect Dis 13:916-919.
2. Castello AA, Arguelles MH, Rota RP, Olthoff A, Jiang B, Glass RI, Gentsch JR, Glikmann G. 2006. Molecular epidemiology ofgroup A rotavirus diarrhea among children in Buenos Aires, Argentina, from 1999 to 2003 and emergence of the infrequent genotype G12. J Clin Microbiol 44:2046-2050.
3. Clark HF, Hoshino Y, Bell LM, Groff J, Hess G, Bachman P, Offit PA. 1987. Rotavirus isolate WI61 representing a presumptive new human serotype. J Clin Microbiol 25:1757-1762.
4. Cunliffe NA, Gondwe JS, Broadhead RL, Molyneux ME, Woods PA, Bresee JS, Glass RI, Gentsch JR, Hart CA. 1999. 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 57:308-312.
5. Das BK, Gentsch JR, Cicirello HG, Woods PA, Gupta A, Ramachandran M, Kumar R, Bhan MK, Glass RI. 1994. Characterization of rotavirus strains from newborns in New Delhi, India. J Clin Microbiol 32:1820-1822.
6. Das S, Varghese V, Chaudhury S, Barman P, Mahapatra S, Kojima K, Bhattacharya SK, Krishnan T, Ratho RK, Chhotray GP, Phukan AC, Kobayashi N, Naik TN. 2003. Emergence ofnovel human group A rotavirus G12 strains in India. J Clin Microbiol 41:2760-2762.
7. Desselberger U, Iturriza-Gomara M, Gray JJ. 2001. Rotavirus epidemiology and surveillance. Novartis Found Symp 238:125-147; discussion 147-152.
8. Esona GA, Banyai K, Page N, Aminu M, Armah GE. Novel human rotavirus genotype G5P[7] from child with diarrhea, Cameroon. Emerg Infect Dis [serial on the Internet] (in press).
9. Esona MD, Geyer A, Banyai K, Page N, Aminu M, Armah GE, Hull J, Steele DA, Glass RI, Gentsch JR. 2009. Novel human rotavirus genotype G5P[7] from child with diarrhea, Cameroon. Emerg Infect Dis 15:83-86.
10. Estes MK, Kapikian AZ. 2007. Rotaviruses. In: Knipe DM, Howley PM, Griffin DE, Lamb RA, Martin MA, Roizman B, Straus SE, editors. Fields virology. 5th edition. Lippincott Williams & Wilkins. Philadelphia: pp 1917-1974.
11. Felsenstein J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791. Fischer TK, Viboud C, Parashar U, Malek M, Steiner C, Glass R, Simonsen L. 2007. Hospitalizations and deaths from diarrhea and rotavirus among children <5 years of age in the United States, 1993-2003. J Infect Dis 195:1117-1125.
12. Freeman MM, Kerin TK, Hull J, McCaustland K, Gentsch JR. 2008. Enhancement of detection and quantification of rotavirus in stool using a modified real-time RT-PCR assay. J Med Virol 80:1489-1496.
13. Gentsch JR, Glass RI, Woods P, Gouvea V, Gorziglia M, Flores J, Das BK, Bhan MK. 1992. Identification of group A rotavirus gene 4 types by polymerase chain reaction. J Clin Microbiol 30:1365-1373.
14. Gentsch JR, Laird AR, Bielfelt B, Griffin DD, Banyai K, Ramachandran M, Jain V, Cunliffe NA, Nakagomi O, Kirkwood CD, Fischer TK, Parashar UD, Bresee JS, Jiang B, Glass RI. 2005. Serotype diversity and reassortment between human and animal rotavirus strains: Implications for rotavirus vaccine programs. J Infect Dis 192:S146-S159.
15. Ghosh S, Varghese V, Samajdar S, Bhattacharya SK, Kobayashi N, Naik TN. 2006. Molecular characterization of a porcine Group A rotavirus strain with G12 genotype specificity. Arch Virol 151:1329-1344.
16. Gouvea V, Glass RI, Woods P, Tanguchi K, Clark HF, Forrester B, Fang ZY. 1990. Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens. J Clin Microbiol 28:276-282.
17. Gouvea V, Decastro L, Timenetsky MD, Greenberg H, Santos N. 1994. Rotavirus serotype-G5 associated with diarrhea in Brazilian children. J Clin Microbiol 32:1408-1409.
18. Griffin DD, Nakagomi T, Hoshino Y, Nakagomi O, Kirkwood CD, Parashar UD, Glass RI, Gentsch JR. 2002. Characterization of nontypeable rotavirus strains from the United States: Identification of a new rotavirus reassortant (P2A[6], G12) and rare P3[9] strains related to bovine rotaviruses. Virology 294:256-269.
19. Iturriza Gomara M, Wong C, Blome S, Desselberger U, Gray J. 2002. Molecular characterization of VP6 genes of human rotavirus isolates: Correlation of genogroups with subgroups and evidence of independent segregation. J Virol 76:6596-6601.
20. Iturriza-Gomara M, Isherwood B, Desselberger U, Gray J. 2001. Reassortment in vivo: Driving force for diversity of human rotavirus strains isolated in the United Kingdom between 1995 and 1999. J Virol 75:3696-3705.
21. Kerin TK, Kane EM, Glass R, Gentsch JR. 2007. Characterization of VP6 genes from rotavirus strains collected in the United States from 1996-2002. Virus Genes 35:489-495.
22. Kheyami AM, Nakagomi T, Nakagomi O, Dove W, Hart CA, Cunliffe NA. 2008. Molecular epidemiology of rotavirus diarrhea among children in Saudi Arabia: First detection of G9 and G12 strains. J Clin Microbiol 46:1185-1191.
23. Le VP, Kim JY, Cho SL, Nam SW, Lim I, Lee HJ, Kim K, Chung SI, Song W, Lee KM, Rhee MS, Lee JS, Kim W. 2008. Detection of unusual rotavirus genotypes G8P[8] and G12P[6] in South Korea. J Med Virol 80:175-182.
24. Matthijnssens J, Ciarlet M, Heiman E, Arijs I, Delbeke T, McDonald SM, Palombo EA, Iturriza-Gomara M, Maes P, Patton JT, Rahman M, Van Ranst M. 2008a. 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 82:3204-3219.
25. Matthijnssens J, Ciarlet M, Rahman M, Attoui H, Banyai K, Estes MK, Gentsch JR, Iturriza-Gomara M, Kirkwood CD, Martella V, Mertens PPC, Nakagomi O, Patton JT, Ruggeri FM, Saif LJ, Santos N, Steyer A, Taniguchi K, Desselberger U, Van Ranst M. 2008b. Recommendations for the classification of group A rotaviruses using all 11 genomic RNA segments. Arch Virol 153:1621-1629.
26. Maunula L, Von Bonsdorff CH. 2002. Frequent reassortments may explain the genetic heterogeneity of rotaviruses: Analysis of Finnish rotavirus strains. J Virol 76:11793-11800. McDonald SM, Patton JT. 2008. Molecular characterization of a subgroup specificity associated with the rotavirus inner capsid protein VP2. J Virol 82:2752-2764.
27. Nakagomi O, Nakagomi T, Akatani K, Ikegami N. 1989. Identification of rotavirus genogroups by RNA-RNA hybridization. Mol Cell Probes 3:251-261.
28. Palombo EA, Masendycz PJ, Bugg HC, Bogdanovic-Sakran N, Barnes GL, Bishop RF. 2000. Emergence ofserotype G9 human rotaviruses in Australia. J Clin Microbiol 38:1305-1306.
29. Parashar UD, Hummelman EG, Bresee JS, Miller MA, Glass RI. 2003. Global illness and deaths caused by rotavirus disease in children. Emerg Infect Dis 9:565-572.
30. Parashar UD, Gibson CJ, Bresee JS, Glass RI. 2006. Rotavirus and severe childhood diarrhea. Emerg Infect Dis 12:304-306.
31. Payne DC, Staat MA, Edwards KM, Szilagyi PG, Gentsch JR, Stockman LJ, Curns AT, Griffin M, Weinberg GA, Hall CB, Fairbrother G, Alexander J, Parashar UD. 2008. Active, population-based surveillance for severe rotavirus gastroenteritis in children in the United States. Pediatrics 122:1235-1243.
32. Phan TG, Okitsu S, Maneekarn N, Ushijima H. 2007. Genetic heterogeneity, evolution and recombination in emerging G9 rotaviruses. Infect Genet Evol 7:656-663.
33. Pietruchinski E, Benati F, Lauretti F, Kisielius J, Ueda M, Volotao EM, Soares CC, Hoshino Y, Linhares REC, Nozawa C, Santos N. 2006. Rotavirus diarrhea in children and adults in a southern city of Brazil in 2003: Distribution of G/P types and finding of a rare G12 strain. J Med Virol 78:1241-1249. Pongsuwanna Y, Guntapong R, Chiwakul M, Tacharoenmuang R, Onvimala N, Wakuda M, Kobayashi N, Taniguchi K. 2002. Detection of a human rotavirus with G12 and P[9] specificity in Thailand. J Clin Microbiol 40:1390-1394.
34. Pun SB, Nakagomi T, Sherchand JB, Pandey BD, Cuevas LE, Cunliffe NA, Hart CA, Nakagomi O. 2007. Detection of G12 human rotaviruses in Nepal. Emerg Infect Dis 13:482 -484.
35. Rahman M, Matthijnssens J, Yang XL, Delbeke T, Arijs I, Taniguchi K, Iturriza-Gomara M, Iftekharuddin N, Azim T, Van Ranst M. 2007a. Evolutionary history and global spread of the emerging G12 human rotaviruses. J Virol 81:2382-2390.
36. Rahman M, Sultana R, Ahmed G, Nahar S, Hassan ZM, Saiada F, Podder G, Faruque ASG, Siddique AK, Sack DA, Matthijnssens J, Van Ranst M, Azim T. 2007b. Prevalence of G2P[4] and G12P[6] rotavirus, Bangladesh. Emerg Infect Dis 13:18-24.
37. Ramani S, Banerjee I, Gladstone BP, Sarkar R, Selvapandian D, Le Fevre AM, Jaffar S, Iturriza-Gomara M, Gray JJ, Estes MK, Brown DW, Kang G. 2007. Geographic information systems and genotyp- ing in identification of rotavirus G12 infections in residents of an urban slum with subsequent detection in hospitalized children: Emergence of G12 genotype in south India. J Clin Microbiol 45:432-437.
38. Ruiz-Palacios GM, Perez-Schael I, Velazquez FR, Abate H, Breuer T, Clemens SC, Cheuvart B, Espinoza F, Gillard P, Innis BL, Cervantes Y, Linhares AC, Lopez P, Macias-Parra M, Ortega- Barria E, Richardson V, Rivera-Medina DM, Rivera L, Salinas B, Pavia-Ruz N, Salmeron J, Ruttimann R, Tinoco JC, Rubio P, Nunez E, Guerrero ML, Yarzabal JP, Damaso S, Tornieporth N, Saez- Llorens X, Vergara RF, Vesikari T, Bouckenooghe A, Clemens R, De Vos B, O'Ryan M. 2006. Safety and efficacy of an attenuated vaccine against severe rotavirus gastroenteritis. N Engl J Med 354:11-22.
39. Saitou N, Nei M. 1987. The neighbor-joining method- A new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425.
40. Samajdar S, Varghese V, Barman P, Ghosh S, Mitra U, Dutta P, Bhattacharya SK, Narasimham MV, Panda P, Krishnan T, Kobayashi N, Naik TN. 2006. Changing pattern of human group A rotaviruses: Emergence of G12 as an important pathogen among children in eastern India. J Clin Virol 36:183-188.
41. Santos N, Hoshino Y. 2005. Global distribution of rotavirus serotypes/ genotypes and its implication for the development and implementation of an effective rotavirus vaccine. Rev Med Virol 15:29-56.
42. Sharma S, Ray P, Gentsch JR, Glass RI, Kalra V, Bhan MK. 2008. Emergence of G12 rotavirus strains in Delhi, India, in 2000 to 2007. J Clin Microbiol 46:1343-1348.
43. Shinozaki K, Okada M, Nagashima S, Kaiho I, Taniguchi K. 2004. Characterization of human rotavirus strains with G12 and P[9] detected in Japan. J Med Virol 73:612-616.
44. Steele AD, Ivanoff B. 2003. Rotavirus strains circulating in Africa during 1996-1999: Emergence of G9 strains and P[6] strains. Vaccine 21:361-367.
45. Steyer A, Pojsak-Prijatelj M, Bufon TL, Marcun- Varda N, Marin J. 2007. Rotavirus genotypes in Slovenia: Unexpected detection of G8P[8] and G12P[8] genotypes. JMed Virol 79:626-632.
46. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEG A4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596-1599.
47. Taniguchi K, Urasawa T, Kobayashi N, Gorziglia M, Urasawa S. 1990. Nucleotide sequence of VP4 and VP7 genes of human rotaviruses with subgroup I specificity and long RNA pattern: Implication for new G serotype specificity. J Virol 64:5640-5644.
48. Uchida R, Pandey BD, Sherchand JB, Ahmed K, Yokoo M, Nakagomi T, Cuevas LE, Cunliffe NA, Hart CA, Nakagomi O. 2006. Molecular epidemiology of rotavirus diarrhea among children and adults in
49. Nepal: Detection of G12 strains with P[6] or P[8] and a G11P[25] strain. J Clin Microbiol 44:3499-3505.
50. Vesikari T, Matson DO, Dennehy P, Van Damme P, Santosham M, Rodriguez Z, Dallas MJ, Heyse JF, Goveia MG, Black SB, Shinefield HR, Christie CDC, Ylitalo S, Itzler RF, Coia ML, Onorato MT, Adeyi BA, Marshall GS, Gothefors L, Campens D, Karvonen A, Watt JP, O'Brien KL, DiNubile MJ, Clark HF, Boslego JW, Offit PA, Heaton PM. 2006. Safety and efficacy of a pentavalent human-bovine (WC3) reassortant rotavirus vaccine. N Engl J Med 354:23-33.
51. Widdowson MA, Meltzer MI, Zhang X, Bresee JS, Parashar UD, Glass RI. 2007. Cost-effectiveness and potential impact of rotavirus vaccination in the United States [see comment]. Pediatrics 119:684-697.