Epidemiology and phylogenetic analysis of VP7 and VP4 genes of rotaviruses circulating in Rawalpindi, Pakistan during 2010

Infection, Genetics and Evolution

Volumn 14, Issue 1, 2013, Pages 161-168

  Tamim, S ^a   Hasan, F ^a   Matthijnssens, J ^b   Sharif, S ^c   Shaukat, S ^c   Alam, M M ^c   Angez, M ^c   Suleman Rana, M ^c   Khurshid, A ^c   Zaidi, S S Z ^c  

^a QUAID I AZAM UNIVERSITY   (Pakistan)

^b REGA INSTITUTE FOR MEDICAL RESEARCH   (Belgium)

^c NATIONAL INSTITUTE OF HEALTH   (Pakistan)

Author keywords

Diarrhea; Genotype; Group A rotavirus; Pakistan; Phylogeny; VP4; VP7

Indexed keywords

PROTEIN VP4; PROTEIN VP7;

AGE DISTRIBUTION; ARTICLE; ASIA; CHILD; CROSS-SECTIONAL STUDY; EASTERN EUROPE; FECES ANALYSIS; GENE AMPLIFICATION; GENETIC EPIDEMIOLOGY; GENETIC LINKAGE; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HUMAN; MIXED INFECTION; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; PRESCHOOL CHILD; PREVALENCE; PRIORITY JOURNAL; ROTAVIRUS; SEQUENCE ANALYSIS; TREND STUDY; VIRUS DETECTION; VIRUS GENE; VIRUS LOAD; VIRUS STRAIN; VIRUS TRANSMISSION; VP4 GENE; VP7 GENE;

ANTIGENS, VIRAL; CAPSID PROTEINS; CHILD, PRESCHOOL; GENOTYPE; HUMANS; INFANT; INFANT, NEWBORN; MOLECULAR SEQUENCE DATA; PAKISTAN; PHYLOGENY; PREVALENCE; ROTAVIRUS; ROTAVIRUS INFECTIONS;

BOVINAE; ROTAVIRUS; ROTAVIRUS A;

EID: 84872668374     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2012.10.009     Document Type: Article

References (49)

1. Alam M.M., Malik S.A., Shaukat S., Naeem A., Sharif S., Angez M., Rana M.S., Khurshid A., Zaidi S.Z. Genetic characterization of rotavirus subtypes in Pakistan-first report of G12 genotype from Pakistan under WHO-Eastern Mediterranean region. Virus Res. 2009, 144:280-284.
2. Araujo I.T., Assis R.M., Fialho A.M., Mascarenhas J.D., Heinemann M.B., Leite J.P. Brazilian P[8], G1, P[8], G5, P[8], G9, and P[4], G2 rotavirus strains: nucleotide sequence and phylogenetic analysis. J. Med. Virol. 2007, 79:995-1001.
3. Arista S., Giammanco G.M., De Grazia S., Ramirez S., Lo Biundo C., Colomba C., Cascio A., Martella V. Heterogeneity and temporal dynamics of evolution of G1 human rotaviruses in a settled population. J. Virol. 2006, 80:10724-10733.
4. Banerjee I., Ramani S., Primrose B., Moses P., Iturriza-Gomara M., Gray J.J., Jaffar S., Monica B., Muliyil J.P., Brown D.W., Estes M.K., Kang G. Comparative study of the epidemiology of rotavirus in children from a community-based birth cohort and a hospital in South India. J. Clin. Microbiol. 2006, 44:2468-2474.
5. Banyai K., Gentsch J.R., Schipp R., Jakab F., Bene J., Melegh B., Glass R.I., Szucs G. Molecular epidemiology of human P[8], G9 rotaviruses in Hungary between 1998 and 2001. J. Med. Microbiol. 2004, 53:791-801.
6. Bresee J.S., Hummelman E., Nelson E.A., Glass R.I. Rotavirus in Asia: The value of surveillance for informing decisions about the introduction of new vaccines. J. Infect. Dis. 2005, 192(Suppl. 1):S1-S5.
7. Chen K.T., Fan S.F., Tang R.B., Huang Y.F., Lee P.I., Chen P.Y., Tang C.W., Chen H.C. Hospital-based study of the economic burden associated with rotavirus diarrhea in Taiwan. Vaccine 2007, 25:4266-4272.
8. Dey S.K., Hayakawa Y., Rahman M., Islam R., Mizuguchi M., Okitsu S., Ushijima H. G2 strain of rotavirus among infants and children, Bangladesh. Emerg. Infect. Dis. 2009, 15:91-94.
9. Estes M.E. Rotaviruses and their replication. Fields Virology 2001, Lippincott Williams &Wilkins, Philadelphia, Pa. fourth ed. D. Howley (Ed.).
10. Estes M.K., Kang G., Zeng C.Q., Crawford S.E., Ciarlet M. Pathogenesis of rotavirus gastroenteritis. Novartis Found Symp. 2001, 238:82-96. discussion 96-100.
11. Fischer T.K., Anh D.D., Antil L., Cat N.D., Kilgore P.E., Thiem V.D., Rheingans R., Tho le H., Glass R.I., Bresee J.S. Health care costs of diarrheal disease and estimates of the cost-effectiveness of rotavirus vaccination in Vietnam. J. Infect. Dis. 2005, 192:1720-1726.
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 4 types by polymerase chain reaction. J. Clin. Microbiol. 1992, 30:1365-1373.
13. Ghosh S., Kobayashi N., Nagashima S., Chawla-Sarkar M., Krishnan T., Ganesh B., Naik T.N. Full genomic analysis and possible origin of a porcine G12 rotavirus strain RU172. Virus Genes 2010, 40:382-388.
14. Gomara M.I., Cubitt D., Desselberger U., Gray J. Amino acid substitution within the VP7 protein of G2 rotavirus strains associated with failure to serotype. J. Clin. Microbiol. 2001, 39:3796-3798.
15. Gouvea V., Glass R.I., Woods P., Taniguchi K., Clark H.F., Forrester B., Fang Z.Y. Polymerase chain reaction amplification and typing of rotavirus nucleic acid from stool specimens. J. Clin. Microbiol. 1990, 28:276-282.
16. Gouvea V., Santos N., Timenetsky Mdo C. Identification of bovine and porcine rotavirus G types by PCR. J. Clin. Microbiol. 1994, 32:1338-1340.
17. Gouvea V., Santos N., Timenetsky Mdo C. VP4 typing of bovine and porcine group A rotaviruses by PCR. J. Clin. Microbiol. 1994, 32:1333-1337.
18. Han T.H., Kim C.H., Chung J.Y., Park S.H., Hwang E.S. Genetic characterization of rotavirus in children in South Korea from 2007 to 2009. Arch. Virol. 2010, 155:1663-1673.
19. Jin H., Wang B., Fang Z., Duan Z., Gao Q., Liu N., Zhang L., Qian Y., Gong S., Zhu Q., Shen X., Wu Q. Hospital-based study of the economic burden associated with rotavirus diarrhea in eastern China. Vaccine 2011, 29:7801-7806.
20. Kawai K., O'Brien M.A., Goveia M.G., Mast T.C., El Khoury A.C. Burden of rotavirus gastroenteritis and distribution of rotavirus strains in Asia: a systematic review. Vaccine 2012, 30:1244-1254.
21. Keating G.M. Rotavirus vaccine RIX4414 (Rotarix). Paediatr. Drugs 2006, 8:389-395. discussion 396-387.
22. 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.
23. Lu C.Y., Lauderdale T.L., Fang Y.H., Wang C.Y., Ho Y.H., Hung C.L., Chang L.Y., Lee C.Y., Huang L.M. Disease burden and related medical costs of rotavirus infections in Taiwan. BMC Infect. Dis. 2006, 6:176.
24. Matthijnssens J., Ciarlet M., Heiman E., Arijs I., Delbeke T., McDonald S.M., Palombo E.A., Iturriza-Gomara M., Maes P., Patton J.T., Rahman M., Van Ranst M. 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. 2008, 82:3204-3219.
25. Matthijnssens, J., Mustafizur R., Ciarlet M, Van Ranst M., 2008. Emerging Human Rotavirus Genotypes, Inc. in: C., A.E.P.a.K. (Ed.). Research Signpost, Trivandrum, India, pp. 171-219.
26. Matthijnssens J., Bilcke J., Ciarlet M., Martella V., Banyai K., Rahman M., Zeller M., Beutels P., Van Damme P., Van Ranst M. Rotavirus disease and vaccination: impact on genotype diversity. Future Microbiol. 2009, 4:1303-1316.
27. Matthijnssens J., Joelsson D.B., Warakomski D.J., Zhou T., Mathis P.K., van Maanen M.H., Ranheim T.S., Ciarlet M. Molecular and biological characterization of the 5 human-bovine rotavirus (WC3)-based reassortant strains of the pentavalent rotavirus vaccine, RotaTeq. Virology 2010, 403:111-127.
28. 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.
29. 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.
30. Mendelsohn A.S., Asirvatham J.R., Mkaya Mwamburi D., Sowmynarayanan T.V., Malik V., Muliyil J., Kang G. Estimates of the economic burden of rotavirus-associated and all-cause diarrhoea in Vellore, India. Trop. Med. Int. Health 2008, 13:934-942.
31. Nelson E.A., Tam J.S., Yu L.M., Ng Y.C., Bresee J.S., Poon K.H., Ng C.H., Ip K.S., Mast T.C., Chan P.K., Parashar U.D., Fok T.F., Glass R.I. Hospital-based study of the economic burden associated with rotavirus diarrhea in Hong Kong. J. Infect. Dis. 2005, 192(Suppl. 1):S64-S70.
32. Parashar U.D., Hummelman E.G., Bresee J.S., Miller M.A., Glass R.I. Global illness and deaths caused by rotavirus disease in children. Emerg. Infect. Dis. 2003, 9:565-572.
33. Parashar U.D., Alexander J.P., Glass R.I. Prevention of rotavirus gastroenteritis among infants and children. Recommendations of the Advisory Committee on Immunization Practices (ACIP). MMWR Recomm. Rep. 2006, 55:1-13.
34. Parashar U.D., Gibson C.J., Bresee J.S., Glass R.I. Rotavirus and severe childhood diarrhea. Emerg. Infect. Dis. 2006, 12:304-306.
35. Phan T.G., Khamrin P., Quang T.D., Dey S.K., Takanashi S., Okitsu S., Maneekarn N., Ushijima H. Detection and genetic characterization of group A rotavirus strains circulating among children with acute gastroenteritis in Japan. J. Virol. 2007, 81:4645-4653.
36. Qazi R., Sultana S., Sundar S., Warraich H., un-Nisa T., Rais A., Zaidi A.K. Population-based surveillance for severe rotavirus gastroenteritis in children in Karachi, Pakistan. Vaccine 2009, 27(Suppl. 5):F25-F30.
37. Rahman M., Goegebuer T., De Leener K., Maes P., Matthijnssens J., Podder G., Azim T., Van Ranst M. Chromatography paper strip method for collection, transportation, and storage of rotavirus RNA in stool samples. J. Clin. Microbiol. 2004, 42:1605-1608.
38. 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.
39. Ruiz L.P. Rotavirus vaccines. N. Engl. J. Med. 2006, 354:1747-1751. author reply: 1747-1751.
40. Samajdar S., Ghosh S., Dutta D., Chawla-Sarkar M., Kobayashi N., Naik T.N. Human group A rotavirus P[8] Hun9-like and rare OP354-like strains are circulating among diarrhoeic children in Eastern India. Arch. Virol. 2008, 153:1933-1936.
41. 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.
42. Sato T., Nakagomi T., Nakagomi O. Cost-effectiveness analysis of a universal rotavirus immunization program in Japan. Jpn. J. Infect. Dis. 2011, 64:277-283.
43. Sharma S., Ray P., Gentsch J.R., Glass R.I., Kalra V., Bhan M.K. Emergence of G12 rotavirus strains in Delhi, India, in 2000 to 2007. J. Clin. Microbiol. 2008, 46:1343-1348.
44. 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.
45. Tate J.E., Chitambar S., Esposito D.H., Sarkar R., Gladstone B., Ramani S., Raghava M.V., Sowmyanarayanan T.V., Gandhe S., Arora R., Parashar U.D., Kang G. Disease and economic burden of rotavirus diarrhoea in India. Vaccine 2009, 27(Suppl. 5):F18-F24.
46. Vesikari T., Matson D.O., Dennehy P., Van Damme P., Santosham M., Rodriguez Z., Dallas M.J., Heyse J.F., Goveia M.G., Black S.B., Shinefield H.R., Christie C.D., Ylitalo S., Itzler R.F., Coia M.L., Onorato M.T., Adeyi B.A., Marshall G.S., Gothefors L., Campens D., Karvonen A., Watt J.P., O'Brien K.L., DiNubile M.J., Clark H.F., Boslego J.W., Offit P.A., Heaton P.M. Safety and efficacy of a pentavalent human-bovine (WC3) reassortant rotavirus vaccine. N. Engl. J. Med. 2006, 354:23-33.
47. Wilopo S.A., Kilgore P., Kosen S., Soenarto Y., Aminah S., Cahyono A., Ulfa M., Tholib A. Economic evaluation of a routine rotavirus vaccination programme in Indonesia. Vaccine 2009, 27(Suppl. 5):F67-F74.
48. Zaman K., Yunus M., Faruque A.S., El Arifeen S., Hossain I., Azim T., Rahman M., Podder G., Roy E., Luby S., Sack D.A. Surveillance of rotavirus in a rural diarrhoea treatment centre in Bangladesh, 2000-2006. Vaccine 2009, 27(Suppl. 5):F31-F34.
49. 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.