Genotyping of GII.4 and GIIb norovirus RT-PCR amplicons by RFLP analysis

Journal of Virological Methods - Tập 147 Số 2 - Trang 250-256 - 2008
Stefania Ramirez1, Anna Giammanco, Simona De Grazia, Claudia Colomba, Vito Martella, Serenella Arista
1Department of Hygiene and Microbiology, University of Palermo, via del Vespro 133, Palermo, Italy.

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Adah, 1997, Nigerian rotavirus serotype G8 could not be typed by PCR due to nucleotide mutation at the 3′ end of the primer-binding site, Arch. Virol., 142, 1881, 10.1007/s007050050206

Ambert-Balay, 2005, Characterization of new recombinant noroviruses, J. Clin. Microbiol., 43, 5179, 10.1128/JCM.43.10.5179-5186.2005

Blanton, 2006, Molecular and epidemiologic trends of caliciviruses associated with outbreaks of acute gastroenteritis in the United States, 2000–2004, J. Infect. Dis., 193, 413, 10.1086/499315

Boom, 1990, Rapid and simple method for purification of nucleic acids, J. Clin. Microbiol., 28, 495, 10.1128/jcm.28.3.495-503.1990

Buesa, 2002, Molecular epidemiology of caliciviruses causing outbreaks and sporadic cases of acute gastroenteritis in Spain, J. Clin. Microbiol., 40, 2854, 10.1128/JCM.40.8.2854-2859.2002

Bull, 2005, Norovirus recombination in ORF1/ORF2 overlap, Emerg. Infect. Dis., 11, 1079, 10.3201/eid1107.041273

Bull, 2006, Emergence of a new norovirus genotype II.4 variant associated with global outbreaks of gastroenteritis, J. Clin. Microbiol., 44, 327, 10.1128/JCM.44.2.327-333.2006

Centers for Disease Control and Prevention, 2006

De Jong, 1999, Adenoviruses from human immunodeficiency virus-infected individuals, including two strains that represent new candidate serotypes Ad50 and Ad51 of species B1 and D, respectively, J. Clin. Microbiol., 37, 3940, 10.1128/JCM.37.12.3940-3945.1999

Dingle, 2004, Mutation in a Lordsdale norovirus epidemic strain as a potential indicator of transmission routes, J. Clin. Microbiol., 42, 3950, 10.1128/JCM.42.9.3950-3957.2004

Fankhauser, 1998, Molecular epidemiology of “Norwalk-like viruses” in outbreaks of gastroenteritis in the United States, J. Infect. Dis., 178, 1571, 10.1086/314525

Fankhauser, 2002, Epidemiologic and molecular trends of “Norwalk-like viruses” associated with outbreaks of gastroenteritis in the United States, J. Infect. Dis., 186, 1, 10.1086/341085

Fauquet, 2005, Caliciviridae

Gallimore, 2006, Environmental monitoring for gastroenteric viruses in a pediatric primary immunodeficiency unit, J. Clin. Microbiol., 44, 395, 10.1128/JCM.44.2.395-399.2006

Hutson, 2004, Norovirus disease: changing epidemiology and host susceptibility factors, Trends Microbiol., 12, 279, 10.1016/j.tim.2004.04.005

Ike, 2006, Molecular epidemiology of norovirus in outbreaks of gastroenteritis in southwest Germany from 2001 to 2004, J. Clin. Microbiol., 44, 1262, 10.1128/JCM.44.4.1262-1267.2006

Iritani, 2003, Prevalence of Norwalk-like virus infections in cases of viral gastroenteritis among children in Osaka City, Japan, J. Clin. Microbiol., 41, 1756, 10.1128/JCM.41.4.1756-1759.2003

Iturriza Gomara, 2002, Rotavirus subgroup characterisation by restriction endonuclease digestion of a cDNA fragment of the VP6 gene, J. Virol. Methods, 105, 99, 10.1016/S0166-0934(02)00087-3

Iturriza-Gomara, 2000, Diversity within the VP4 gene of rotavirus P[8] strains: implications for reverse transcription-PCR genotyping, J. Clin. Microbiol., 38, 898, 10.1128/JCM.38.2.898-901.2000

Koopmans, 2004, Foodborne viruses: an emerging problem, Int. J. Food Microbiol., 90, 23, 10.1016/S0168-1605(03)00169-7

Leao, 2005, Profiling Mycobacterium ulcerans with hsp65, Emerg. Infect. Dis., 11, 1795, 10.3201/eid1111.050234

Lindell, 2005, Molecular epidemiology of norovirus infections in Stockholm, Sweden, during the years 2000–2003: association of the GGIIb genetic cluster with infection in children, J. Clin. Microbiol., 43, 1086, 10.1128/JCM.43.3.1086-1092.2005

Lopman, 2003, Viral gastroenteritis outbreaks in Europe, 1995–2000, Emerg. Infect. Dis., 9, 90, 10.3201/eid0901.020184

Lopman, 2004, Increase in viral gastroenteritis outbreaks in Europe and epidemic spread of new norovirus variant, Lancet, 363, 682, 10.1016/S0140-6736(04)15641-9

Monica, 2007, Human caliciviruses in symptomatic and asymptomatic infections in children in Vellore, South India, J. Med. Virol., 79, 544, 10.1002/jmv.20862

National Institute of Allergy and Infectious Diseases, 2006

O’Halloran, 2002, Application of restriction fragment length polymorphism analysis of VP7-encoding genes: fine comparison of Irish and global rotavirus isolates, J. Clin. Microbiol., 40, 524, 10.1128/JCM.40.2.524-531.2002

Prammananan, 2006, Distribution of hsp65 PCR-restriction enzyme analysis patterns among Mycobacterium avium complex isolates in Thailand, J. Clin. Microbiol., 44, 3819, 10.1128/JCM.02495-05

Ramirez, 2006, Detection of the norovirus variants GGII.4 Hunter and GGIIb/Hilversum in Italian children with gastroenteritis, J. Med. Virol., 78, 1656, 10.1002/jmv.20751

Reuter, 2005, Evidence of the etiological predominance of norovirus in gastroenteritis outbreaks-emerging new-variant and recombinant noroviruses in Hungary, J. Med. Virol., 76, 598, 10.1002/jmv.20403

Reuter, 2006, Epidemic spread of recombinant noroviruses with four capsid types in Hungary, J. Clin. Virol., 35, 84, 10.1016/j.jcv.2005.07.012

Rodriguez-Castillo, 2006, Analysis of human rotavirus G1P[8] strains by RFLP reveals higher genetic drift in the VP7 than the VP4 gene during a 4-year period in Mexico, J. Virol. Methods, 138, 177, 10.1016/j.jviromet.2006.08.013

Rodriguez-Nava, 2006, Use of PCR-restriction enzyme pattern analysis and sequencing database for hsp65 gene-based identification of Nocardia species, J. Clin. Microbiol., 44, 536, 10.1128/JCM.44.2.536-546.2006

Rohayem, 2005, Evidence of recombination in the norovirus capsid gene, J. Virol., 79, 4977, 10.1128/JVI.79.8.4977-4990.2005

Sanchez-Fauquier, 2005, Surveillance of human calicivirus in Spain, Emerg. Infect. Dis., 11, 1327, 10.3201/eid1108.041166

Thompson, 1994, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 22, 4673, 10.1093/nar/22.22.4673

Vainio, 2006, Molecular epidemiology of norovirus outbreaks in Norway during 2000–2005 and comparison of four norovirus real-time reverse transcriptase PCR assays, J. Clin. Microbiol., 44, 3695, 10.1128/JCM.00023-06

Vinje, 1996, Molecular detection and epidemiology of small round-structured viruses in outbreaks of gastroenteritis in the Netherlands, J. Infect. Dis., 174, 610, 10.1093/infdis/174.3.610

Vinje, 2000, Simultaneous detection and genotyping of “Norwalk-like viruses” by oligonucleotide array in a reverse line blot hybridization format, J. Clin. Microbiol., 38, 2595, 10.1128/JCM.38.7.2595-2601.2000

Vinje, 2003, International collaborative study to compare reverse transcriptase PCR assays for detection and genotyping of noroviruses, J. Clin. Microbiol., 41, 1423, 10.1128/JCM.41.4.1423-1433.2003

Vinje, 2004, Development and application of a capsid VP1 (region D) based reverse transcription PCR assay for genotyping of genogroup I and II noroviruses, J. Virol. Methods, 116, 109, 10.1016/j.jviromet.2003.11.001

Zheng, 2006, Norovirus classification and proposed strain nomenclature, Virology, 346, 312, 10.1016/j.virol.2005.11.015

Zintz, 2005, Prevalence and genetic characterization of caliciviruses among children hospitalized for acute gastroenteritis in the United States, Infect. Genet. Evol., 5, 281, 10.1016/j.meegid.2004.06.010