Typing of Human Rhinoviruses Based on Sequence Variations in the 5' Non-coding Region

Torgersen, Helge; Skern, Tim; Blaas, Dieter

doi:10.1099/0022-1317-70-11-3111

Cited by 29 publications

(18 citation statements)

References 18 publications

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“…To detect the large number of rhinovirus serotypes, regions within the conserved noncoding 5Ј untranslated region of the genome are amplified (54), leading to cross-reactions with many enteroviruses. Several methods have been used to detect rhinoviruses specifically: a nested procedure, the use of primers spanning a region between the 5Ј untranslated region and the VP2/VP4 region, hybridization with specific probes (69), and differentiation on the basis of the size of the amplicons (89,141,196) or sequencing (131). Nevertheless, Johnston et al (91) could identify only 8 of 30 positive samples as rhinoviruses on the basis of either acid lability or the length of the amplicon, with 73% remaining "unclassified picornaviruses."…”

Section: Molecular Diagnostic Techniques For Acute Respiratory Tract mentioning

confidence: 99%

Relevance of nucleic acid amplification techniques for the diagnosis of respiratory tract infections in the clinical laboratory

Ieven¹

1996

Journal of Microbiological Methods

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Section: Molecular Diagnostic Techniques For Acute Respiratory Tract mentioning

confidence: 99%

Relevance of nucleic acid amplification techniques for the diagnosis of respiratory tract infections in the clinical laboratory

Ieven¹

1996

Journal of Microbiological Methods

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“…These presumably have sequence-specific, critical roles in virus replication although these have not yet been elucidated. Conserved sequences of this kind are at present finding use for broad-range virus detection systems based on the polymerase chain reaction (PCR) (Gama et al, 1988(Gama et al, , 1989Hyypi~i et al, 1989;Torgersen et al, 1989) or oligonucleotide hybridization . An interesting aspect of the 5' UTR is that in the closely related entero-and rhinoviruses the regions align for the first 600 nucleotides, showing 60% homology; then the enteroviruses have a relative insertion of 100 to 140 nucleotides.…”

Section: The 5' Untranslated Regionmentioning

confidence: 99%

Structure, function and evolution of picornaviruses

Stanway

1990

Journal of General Virology

161

105

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“…Primers and probes used are listed in Table 1. The primers initially used (pd 904, pd 905, pd 906, and pd 907) were based on the published sequences of the RV 5Ј NCRs (4,6,27,38). The 5Ј end of the P1 primers is a T7 RNA polymerase promoter sequence followed by a stretch of nucleotides complementary to the sequence of the target RNA.…”

Section: Virusmentioning

confidence: 99%

Improved Detection of Rhinoviruses by Nucleic Acid Sequence-Based Amplification after Nucleotide Sequence Determination of the 5′ Noncoding Regions of Additional Rhinovirus Strains

et al. 2003

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The isothermal nucleic acid sequence-based amplification (NASBA) system was applied for the detection of rhinoviruses using primers targeted at the 5 noncoding region (5 NCR) of the viral genome. The nucleotide sequence of the 5 NCRs of 34 rhinovirus isolates was determined to map the most conserved regions and design more appropriate primers and probes. The assay amplified RNA extracted from 30 rhinovirus reference strains and 88 rhinovirus isolates, it did not amplify RNA from 49 enterovirus isolates and other respiratory viruses. The assay allows one to discriminate between group A and B rhinoviruses. Sensitivities for the detection of group B and group A rhinoviruses was 20 and 200 50% tissue culture infective doses, respectively.Rhinoviruses (RVs) are the most frequent cause of acute upper respiratory tract infections in humans and are usually associated with the common cold (22,24). However, they can also cause lower respiratory tract infections resulting in severe disease in children, in the elderly (17,19,23,26), and in immunosuppressed patients (11,43 P1006, 1999). RVs have been isolated in association with an underlying disease, such as cystic fibrosis (37), and in cases of otitis media (3) and sinusitis (31). In addition, RV infections may exacerbate chronic bronchitis and asthma (9,15,16,28).Andries et al., through evaluation of capsid-binding compounds, classified the RVs into two groups: A and B (2). This classification correlates with sequence similarities.Detection of RVs by tissue culture is slow and cumbersome due to the specific culture conditions required. This limits diagnostic capabilities to a few reference laboratories (29). Serologic diagnosis is virtually impossible because of the existence of more than 100 serotypes.Several studies have shown RT-PCR to be more sensitive than culture for the detection of RVs (1,10,14,15,16,31,33). These assays are based on known sequences of the RV serovars.Nucleic acid sequence-based amplification (NASBA) (Organon Teknika, Boxtel, The Netherlands) might offer an interesting alternative to reverse transcriptase PCR (RT-PCR), because it directly amplifies RNA. It uses the simultaneous enzymatic activities of avian myeloblastosis virus (AMV) RT, RNase H, and T7 RNA polymerase under isothermal conditions. The NASBA technique has already been successfully applied for the detection of human immunodeficiency virus type 1 (HIV-1) RNA (18) We applied NASBA for the detection of RVs. Because the sensitivity of the assay based on the known sequences of RVs was unsatisfactory, we determined the sequence of the 5Ј nocoding regions (NCRs) of 34 additional RV strains, selected new primers and probes, and assessed their specificities and sensitivities for RV strains. MATERIALS AND METHODSVirus strains. The 30 RV reference strains (group A: 4, 6, 13, 14, 17, 26, 27, 43, 45, 52, 69, 70, 72, 84, 86, and 91; group B: 2, 15, 29, 30, 31, 39, 41, 44, 51, 56, 59, 63, 85, 89) were kindly provided by K. Andries, Janssen Research Foundation, Beerse, Belgium (2). RVs were cult...

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Typing of Human Rhinoviruses Based on Sequence Variations in the 5' Non-coding Region

Cited by 29 publications

References 18 publications

Relevance of nucleic acid amplification techniques for the diagnosis of respiratory tract infections in the clinical laboratory

Relevance of nucleic acid amplification techniques for the diagnosis of respiratory tract infections in the clinical laboratory

Structure, function and evolution of picornaviruses

Improved Detection of Rhinoviruses by Nucleic Acid Sequence-Based Amplification after Nucleotide Sequence Determination of the 5′ Noncoding Regions of Additional Rhinovirus Strains

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