Genotyping of mumps viruses based on SH gene: Development of a server using alignment-free and alignment-based methods

Immunome Research

Volumn 7, Issue 3, 2011, Pages

  Kolekar, Pandurang S ^a   Kale, Mohan M ^a   Kulkarni Kale, Urmila ^a  

^a UNIVERSITY OF PUNE   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; CONFERENCE PAPER; CONTROLLED STUDY; DATA BASE; GENE SEQUENCE; GENOTYPE; GEOGRAPHIC DISTRIBUTION; METHODOLOGY; MOLECULAR PHYLOGENY; MOLECULAR PHYLOGENY ANALYSIS; MUMPS VIRUS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PREDICTION; QUALITY CONTROL; RELIABILITY; RETURN TIME DISTRIBUTION METHOD; SEQUENCE ALIGNMENT; SH GENE; VALIDATION PROCESS; VIRUS GENE;

MUMPS VIRUS; PARAMYXOVIRIDAE; RUBULAVIRUS;

EID: 84866150638     PISSN: None     EISSN: 17457580     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (33)

1. Paterson RG, Lamb RA: RNA editing by G-nucleotide insertion in mumps virus P-gene mRNA transcripts. J Virol 1990, 64(9):4137-4145. (Pubitemid 20279820)
2. Jin L, Beard S, Brown DW: Genetic heterogeneity of mumps virus in the United Kingdom: identification of two new genotypes. J Infect Dis 1999, 180 (3):829-833. (Pubitemid 29411371)
3. Jin L, Rima B, Brown D, Orvell C, Tecle T, Afzal M, Uchida K, Nakayama T, Song JW, Kang C et al: Proposal for genetic characterisation of wild-type mumps strains: preliminary standardisation of the nomenclature. Arch Virol 2005, 150(9):1903-1909. (Pubitemid 41176643)
4. Kim SH, Song KJ, Shin YK, Kim JH, Choi SM, Park KS, Baek LJ, Lee YJ, Song JW: Phylogenetic analysis of the small hydrophobic (SH) gene of mumps virus in Korea: identification of a new genotype. Microbiol Immunol 2000, 44(3):173-177. (Pubitemid 30190914)
5. Tecle T, Bottiger B, Orvell C, Johansson B: Characterization of two decades of temporal co-circulation of four mumps virus genotypes in Denmark: identification of a new genotype. J Gen Virol 2001, 82 (Pt 11):2675-2680. (Pubitemid 32998645)
6. Echevarría JE, Castellanos A, Sanz JC, de Aragón MVM, Rey IP, Mosquera M, de Ory F, Royuela E: Mumps Virus Genotyping: Basis and Known Circulating Genotypes. Open Vaccine Journal 2010, 3:37-41.
7. Santos CL, Ishida MA, Foster PG, Sallum MA, Benega MA, Borges DB, Correa KO, Constantino CR, Afzal MA, Paiva TM: Detection of a new mumps virus genotype during parotitis epidemic of 2006-2007 in the state of Sao Paulo, Brazil. J Med Virol 2008, 80 (2):323-329.
8. Folb PI, Bernatowska E, Chen R, Clemens J, Dodoo AN, Ellenberg SS, Farrington CP, John TJ, Lambert PH, Macdonald NE et al: A global perspective on vaccine safety and public health: the Global Advisory Committee on Vaccine Safety. Am J Public Health 2004, 94(11):1926-1931. (Pubitemid 39434822)
9. Furesz J: Safety of live mumps virus vaccines. J Med Virol 2002, 67 (3):299-300.
10. Galazka AM, Robertson SE, Kraigher A: Mumps and mumps vaccine: a global review. Bull World Health Organ 1999, 77 (1):3-14. (Pubitemid 29282133)
11. Afzal MA, Buchanan J, Dias JA, Cordeiro M, Bentley ML, Shorrock CA, Minor PD: RT-PCR based diagnosis and molecular characterisation of mumps viruses derived from clinical specimens collected during the 1996 mumps outbreak in Portugal. Journal of Medical Virology 1997, 52 (4):349-353. (Pubitemid 27356178)
12. Briss PA, Fehrs LJ, Parker RA, Wright PF, Sannella EC, Hutcheson RH, Schaffner W: Sustained transmission of mumps in a highly vaccinated population: assessment of primary vaccine failure and waning vaccine-induced immunity. J Infect Dis 1994, 169(1):77-82.
13. Hersh BS, Fine PE, Kent WK, Cochi SL, Kahn LH, Zell ER, Hays PL, Wood CL: Mumps outbreak in a highly vaccinated population. J Pediatr 1991, 119(2):187-193.
14. Orvell C, Alsheikhly AR, Kalantari M, Johansson B: Characterization of genotype-specific epitopes of the HN protein of mumps virus. J Gen Virol 1997, 78 (Pt 12):3187-3193. (Pubitemid 27511309)
15. Pons C, Pelayo T, Pachon I, Galmes A, Gonzalez L, Sanchez C, Martinez F: Two outbreaks of mumps in children vaccinated with the Rubini strain in Spain indicate low vaccine efficacy. Euro Surveill 2000, 5 (7):80-84.
16. Richard JL, Zwahlen M, Feuz M, Matter HC: Comparison of the effectiveness of two mumps vaccines during an outbreak in Switzerland in 1999 and 2000: a case-cohort study. Eur J Epidemiol 2003, 18(6):569-577. (Pubitemid 36899563)
17. Tecle T, Johansson B, Jejcic A, Forsgren M, Orvell C: Characterization of three co-circulating genotypes of the small hydrophobic protein gene of mumps virus. J Gen Virol 1998, 79 (Pt 12):2929-2937. (Pubitemid 29002327)
18. Vandermeulen C, Roelants M, Vermoere M, Roseeuw K, Goubau P, Hoppenbrouwers K: Outbreak of mumps in a vaccinated child population: a question of vaccine failure? Vaccine 2004, 22 (21-22):2713-2716. (Pubitemid 38900645)
19. Kulkarni-Kale U, Ojha J, Manjari GS, Deobagkar DD, Mallya AD, Dhere RM, Kapre SV: Mapping antigenic diversity and strain specificity of mumps virus: a bioinformatics approach. Virology 2007, 359 (2):436-446. (Pubitemid 46274873)
20. Nojd J, Tecle T, Samuelsson A, Orvell C: Mumps virus neutralizing antibodies do not protect against reinfection with a heterologous mumps virus genotype. Vaccine 2001, 19(13-14):1727-1731. (Pubitemid 32175734)
21. CDC: Update: multistate outbreak of mumps - United States, January 1-May 2, 2006. MMWR Morb Mortal Wkly Rep 2006, 55 (20):559-563.
22. WHO: Global status of mumps immunization and surveillance. Wkly Epidemiol Rec 2005, 80(48):418-424.
23. Takahashi M, Nakayama T, Kashiwagi Y, Takami T, Sonoda S, Yamanaka T, Ochiai H, Ihara T, Tajima T: Single genotype of measles virus is dominant whereas several genotypes of mumps virus are co-circulating. J Med Virol 2000, 62 (2):278-285.
24. Gnaneshan S, Ijaz S, Moran J, Ramsay M, Green J: HepSEQ: International Public Health Repository for Hepatitis B. Nucl Acids Res 2007, 35 (suppl-1):D367-370.
25. Myers RE, Gale CV, Harrison A, Takeuchi Y, Kellam P: A statistical model for HIV-1 sequence classification using the subtype analyser (STAR). Bioinformatics 2005, 21(17):3535-3540. (Pubitemid 41235998)
26. de Oliveira T, Deforche K, Cassol S, Salminen M, Paraskevis D, Seebregts C, Snoeck J, van Rensburg EJ, Wensing AM, van de Vijver DA et al: An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics 2005, 21(19):3797-3800. (Pubitemid 41535530)
27. Kolekar PS, Kale MM, Kulkarni-Kale U: 'Inter-Arrival Time' Inspired Algorithm and its Application in Clustering and Molecular Phylogeny. AIP Conference Proceedings 2010, 1298 (1):307-312.
28. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW: GenBank. Nucleic Acids Research 2011, 39(suppl 1):D32-D37.
29. Sneath PHAS, R. R.: Numerical Taxonomy: the Principles and Practice of Numerical Classification. San Francisco: W. H. Freeman.; 1973.
30. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4(4):406-425.
31. Rubin S, Mauldin J, Chumakov K, Vanderzanden J, Iskow R, Carbone K: Serological and phylogenetic evidence of monotypic immune responses to different mumps virus strains. Vaccine 2006, 24(14):2662-2668. (Pubitemid 43290398)
32. Saito H, Takahashi Y, Harata S, Tanaka K, Sato H, Suto T, Yamada A, Yamazaki S, Morita M: Cloning and sequence analysis of genomic RNA from the mumps virus strain with high incidence of aseptic meningitis. Microbiology and Immunology 1998, 42:133-137. (Pubitemid 28101048)
33. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215 (3):403-410.