Detection of circulating norovirus genotypes: Hitting a moving target

Virology Journal

Volumn 11, Issue 1, 2014, Pages

  Rooney, Brenda Lee ^a   Pettipas, Janice ^a   Grudeski, Elsie ^b   Mykytczuk, Oksana ^c   Pang, Xiao Li ^d,e   Booth, Tim F ^b   Hatchette, Todd F ^a   Leblanc, Jason J ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

^b PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^c HEALTH CANADA   (Canada)

^d PROVINCIAL LABORATORY FOR PUBLIC HEALTH   (Canada)

^e UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Epidemiology; Genotyping; Norovirus; Proficiency testing; Quantitative RT PCR

Indexed keywords

CALICIVIRIDAE INFECTIONS; GASTROENTERITIS; GENETICS; GENOTYPE; HUMAN; NOROVIRUS; REAL TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; VIROLOGY;

CALICIVIRIDAE INFECTIONS; GASTROENTERITIS; GENOTYPE; HUMANS; NOROVIRUS; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY;

EID: 84904272468     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-11-129     Document Type: Article

References (47)

1. Systematic literature review of role of noroviruses in sporadic gastroenteritis. Patel MM, Widdowson MA, Glass RI, Akazawa K, Vinje J, Parashar UD, Emerg Infect Dis 2008 14 1224 1231
2. Updated norovirus outbreak management and disease prevention guidelines. Hall AJ, Vinjé J, Lopman B, Park GW, Yen C, Gregoricus N, Parashar U, MMWR 2011 60 1 15
3. European multicenter evaluation of commercial enzyme immunoassays for detecting norovirus antigen in fecal samples. Gray JJ, Kohli E, Ruggeri FM, Vennema H, Sánchez-Fauquier A, Schreier E, Gallimore CI, Iturriza-Gomara M, Giraudon H, Pothier P, Di Bartolo I, Inglese N, De Bruin E, van der Veer B, Moreno S, Montero V, De Llano MC, Höhne M, Diedrich SM, Clin Vaccine Immunol 2007 14 1349 1355 (Pubitemid 350012979)
4. Evaluation of the RIDAQUICK immunochromatographic norovirus detection assay using specimens from Australian gastroenteritis incidents. Bruggink LD, Witlox KJ, Sameer R, Catton MG, Marshall JA, J Virol Methods 2011 173 121 126
5. Of gastro and the gold standard: evaluation and policy implications of norovirus test performance for outbreak detection. Fisman DN, Greer AL, Brouhanski G, Drews SJ, J Transl Med 2009 7 23
6. Analytical performance of norovirus real-time RT-PCR detection protocols in Canadian laboratories. Mattison K, Grudeski E, Auk B, Brassard J, Charest H, Dust K, Gubbay J, Hatchette TF, Houde A, Jean J, Jones T, Lee BE, Mamiya H, McDonald R, Mykytczuk O, Pang X, Petrich A, Plante D, Ritchie G, Wong J, Booth TF, J Clin Virol 2011 50 109 113
7. Multicenter comparison of two norovirus ORF2-based genotyping protocols. Mattison K, Grudeski E, Auk B, Charest H, Drews SJ, Fritzinger A, Gregoricus N, Hayward S, Houde A, Lee BE, Pang XL, Wong J, Booth TF, Vinjé J, J Clin Microbiol 2009 47 3927 3932
8. Detection and differentiation of antigenically distinct small round-structured viruses (Norwalk-like viruses) by reverse transcription-PCR and southern hybridization. Ando T, Monroe SS, Gentsch JR, Jin Q, Lewis DC, Glass RI, J Clin Microbiol 1995 33 64 71 (Pubitemid 24382400)
9. Broadly reactive and highly sensitive assay for Norwalk-like viruses based on real-time quantitative reverse transcription-PCR. Kageyama T, Kojima S, Shinohara M, Uchida K, Fukushi S, Hoshino FB, Takeda N, Katayama K, J Clin Microbiol 2003 41 1548 1557 (Pubitemid 36428103)
10. Use of TaqMan real-time reverse transcriptase-PCR for rapid detection, quantification, and typing of noroviruses. Trujillo A, McCaustland K, Zheng D, Hadley L, Vaughn G, Adams S, Ando T, Glass R, Monroe S, J Clin Microbiol 2006 44 1405 1412
11. Molecular detection and epidemiology of small round-structured viruses in outbreaks of gastroenteritis in the Netherlands. Vinjé J, Koopmans MP, J Infect Dis 1996 174 610 615 (Pubitemid 26299697)
12. Proposal for a unified norovirus nomenclature and genotyping. Kroneman A, Vega E, Vennema H, Vinjé J, White PA, Hansman G, Green K, Martella V, Katayama K, Koopmans M, Arch Virol 2013 158 2059 2068
13. Norovirus classification and proposed strain nomenclature. Zheng DP, Ando T, Fankhauser RL, Beard RS, Glass RI, Monroe SS, Virology 2006 346 312 323 (Pubitemid 43357875)
14. Novel surveillance network for norovirus gastroenteritis outbreaks, United States. Vega E, Barclay L, Gregoricus N, Williams K, Lee D, Vinjé J, Emerg Infect Dis 2011 17 1389 1395
15. Sensitive and rapid detection of norovirus using duplex TaqMan reverse transcription-polymerase chain reaction. Ishida S, Yoshizumi S, Ikeda T, Miyoshi M, Okano M, Okui T, J Med Virol 2008 80 913 920 (Pubitemid 351500042)
16. Environmental detection of genogroup I, II, and IV noroviruses by using a generic real-time reverse transcription-PCR assay. Miura T, Parnaudeau S, Grodzki M, Okabe S, Atmar RL, Le Guyader FS, Appl Environ Microbiol 2013 79 6585 6592
17. Broadly reactive nested reverse transcription-PCR using an internal RNA standard control for detection of noroviruses in stool samples. Medici MC, Martinelli M, Ruggeri FM, Abelli LA, Bosco S, Arcangeletti MC, Pinardi F, De Conto F, Calderaro A, Chezzi C, Dettori G, J Clin Microbiol 2005 43 3772 3778 (Pubitemid 41129659)
18. Multiplex real time RT-PCR for the detection and quantitation of norovirus genogroups I and II in patients with acute gastroenteritis. Pang XL, Preiksaitis JK, Lee B, J Clin Virol 2005 33 168 171 (Pubitemid 40725311)
19. Genogroup I and II noroviruses detected in stool samples by real-time reverse transcription-PCR using highly degenerate universal primers. Richards GP, Watson MA, Fankhauser RL, Monroe SS, Appl Environ Microbiol 2004 70 7179 7184 (Pubitemid 39643781)
20. Emergence of new pandemic GII.4 Sydney norovirus strain correlates with escape from herd immunity. Debbink K, Lindesmith LC, Donaldson EF, Costantini V, Beltramello M, Corti D, Swanstrom J, Lanzavecchia A, Vinjé J, Baric RS, J Infect Dis 2013 208 1877 1887
21. Rapid evolution of pandemic noroviruses of the GII.4 lineage. Bull RA, Eden JS, Rawlinson WD, White PA, PLoS Pathog 2010 6 1000831
22. Notes from the field: Emergence of new norovirus strain GII.4 Sydney-United States, 2012. Centers for Disease Control and Prevention (CDC), MMWR 2013 62 55 55
23. Emergence of a new norovirus GII.4 variant and changes in the historical biennial pattern of norovirus outbreak activity in Alberta, Canada, from 2008 to 2013. Hasing ME, Lee BE, Preiksaitis JK, Tellier R, Honish L, Senthilselvan A, Pang XL, J Clin Microbiol 2013 51 2204 2211
24. New strains of norovirus and the mystery of viral gastroenteritis epidemics. Lee BE, Pang XL, CMAJ 2013 185 1381 1382
25. Influence of novel norovirus GII.4 variants on gastroenteritis outbreak dynamics in Alberta and the Northern Territories, Canada between 2000 and 2008. Pang XL, Preiksaitis JK, Wong S, Li V, Lee BE, PLoS One 2010 5 11599
26. Indications for worldwide increased norovirus activity associated with emergence of a new variant of genotype II.4, late 2012. Van Beek J, Ambert-Balay K, Botteldoorn N, Eden JS, Fonager J, Hewitt J, Iritani N, Kroneman A, Vennema H, Vinjé J, White PA, Koopmans M, NoroNet, Euro Surveill 2013 18 8 9
27. Emergence of norovirus strain GII.4 Sydney (2012) in BC. Prystajecky N, Isaac-Renton J, Auk B, Fung J, Wong B, Kong C, BCMJ 2013 55 142 143
28. Genotypic and epidemiologic trends of norovirus outbreaks in the United States, 2009-2013. Vega E, Barclay L, Gregoricus N, Shirley SH, Lee D, Vinjé J, J Clin Microbiol 2014 52 147 155
29. Molecular characterization of noroviruses and rotaviruses involved in a large outbreak of gastroenteritis in Northern Italy. Di Bartolo I, Monini M, Losio MN, Pavoni E, Lavazza A, Ruggeri FM, Appl Environ Microbiol 2011 77 5545 5548
30. Foodborne norovirus outbreak: the role of an asymptomatic food handler. Barrabeig I, Rovira A, Buesa J, Bartolomé R, Pintó R, Prellezo H, Domínguez A, BMC Infect Dis 2010 10 269
31. Food-borne outbreak of gastroenteritis associated with genogroup I calicivirus. Johansson PJ, Torvén M, Hammarlund AC, Björne U, Hedlund KO, Svensson L, J Clin Microbiol 2002 40 794 798 (Pubitemid 34208625)
32. Phylogenetic analysis of norovirus isolates involved in some Canadian gastroenteritis outbreaks in 2004 and 2005. Lamhoujeb S, Charest H, Fliss I, Ngazoa S, Jean J, Can J Microbiol 2007 53 1133 1140 (Pubitemid 350178701)
33. Genetic diversity among food-borne and waterborne norovirus strains causing outbreaks in Sweden. Lysén M, Thorhagen M, Brytting M, Hjertqvist M, Andersson Y, Hedlund KO, J Clin Microbiol 2009 47 2411 2418
34. New target tissue for food-borne virus detection in oysters. Wang D, Wu Q, Yao L, Wei M, Kou X, Zhang J, Lett Appl Microbiol 2008 47 405 409
35. Genetic diversity and molecular epidemiology of Norwalk-like viruses. Gonin P, Couillard M, D'Halewyn MA, J Infect Dis 2000 182 691 697
36. Selection of more appropriate PCR primer pairs for improved efficiency in detecting Norwalk-like virus (NLV) RNA. Naitou H, Morita T, J Gen Appl Microbiol 2001 47 241 246 (Pubitemid 34196308)
37. Evolutionary dynamics of GII.4 noroviruses over a 34-year period. Bok K, Abente EJ, Realpe-Quintero M, Mitra T, Sosnovtsev SV, Kapikian AZ, Green KY, J Virol 2009 83 11890 11901
38. Comparative evolution of GII.3 and GII.4 norovirus over a 31-year period. Boon D, Mahar JE, Abente EJ, Kirkwood CD, Purcell RH, Kapikian AZ, Green KY, Bok K, J Virol 2011 85 8656 8666
39. Detection of false positives with a commonly used Norovirus RT-PCR primer set. Wollants E, Van Ranst M, J Clin Virol 2013 56 84 85
40. Probabilities in norovirus outbreak diagnosis. Duizer E, Pielaat A, Vennema H, Kroneman A, Koopmans M, J Clin Virol 2007 40 38 42 (Pubitemid 47302861)
41. Specimen collection and confirmation of norovirus outbreaks. Plantenga MS, Shiferaw B, Keene WE, Biggs C, Terry JM, Grenz L, Cieslak PR, Emerg Infect Dis 2011 17 1553 1555
42. Next-generation whole genome sequencing identifies the direction of norovirus transmission in linked patients. Kundu S, Lockwood J, Depledge DP, Chaudhry Y, Aston A, Rao K, Hartley JC, Goodfellow I, Breuer J, Clin Infect Dis 2013 57 407 414
43. A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. Batty EM, Wong TH, Trebes A, Argoud K, Attar M, Buck D, Ip CL, Golubchik T, Cule M, Bowden R, Manganis C, Klenerman P, Barnes E, Walker AS, Wyllie DH, Wilson DJ, Dingle KE, Peto TE, Crook DW, Piazza P, PLoS One 2013 8 66129
44. Finney DJ, Probit Analysis UK: Cambridge university press, Cambridge 3 1971
45. Statistical Methods for Rates and Proportions. Fleiss JL, Levin B, Paik MC, New York: John Wiley & Sons, Shewart WA, Wilks SS, 2003 ISBN: 9780471526292
46. Genogroup-specific PCR primers for detection of Norwalk-like viruses. Kojima S, Kageyama T, Fukushi S, Hoshino FB, Shinohara M, Uchida K, Natori K, Takeda N, Katayama K, J Virol Methods 2002 100 107 114 (Pubitemid 34003629)
47. Development and application of a capsid VP1 (region D) based reverse transcription PCR assay for genotyping of genogroup I and II noroviruses. Vinjé J, Hamidjaja RA, Sobsey MD, J Virol Methods 2004 116 109 117 (Pubitemid 38117075)