Amplification of rhinovirus specific nucleic acids from clinical samples using the polymerase chain reaction

Gama, R; Horsnell, Philip R.; Hughes, Pamela J.; North, Christine; Bruce, Christine; Al‐Nakib, W.; Stanway, Glyn

doi:10.1002/jmv.1890280204

Cited by 110 publications

(87 citation statements)

References 18 publications

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“…The DNA fragments so generated may be typed by subsequent hybridization analysis or sequencing, as performed here and by Puchta & S/inger (1989), or by restriction enzyme cleavage, as has been done for distinguishing products of rhinovirus PCR amplification (Gama et al, 1989). The latter two techniques in particular give rise to data which can be used directly for classification purposes.…”

Section: Discussionmentioning

confidence: 99%

Detection and typing of maize streak virus and other distantly related geminiviruses of grasses by polymerase chain reaction amplification of a conserved viral sequence

Rybicki

Hughes

1990

Journal of General Virology

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The application of the polymerase chain reaction DNA amplification technique to the detection and typing of isolates of maize streak virus (MSV) and other related geminiviruses of grasses is described. The oligonucleotide primers used for amplification were 17-mers which contained a number of degeneracies. An approximately 250 base pair fragment was amplified from all geminivirus-infected grass and cereal samples tested. The amplification reaction was specific, working down to a concentration of 50 fg/ml of MSV-specific plasmid-cloned DNA and with a 10 -9 dilution of MSVinfected maize DNA extract. DNA could also be amplified from distantly related geminiviruses, including two different sugarcane viruses, digitaria streak virus and another as yet uncharacterized virus of a Panicum sp. Amplified DNA from a Mauritian sugarcane isolate (SSV-M) was cloned and sequenced. Sequence comparison and phylogenetic analysis showed that this sequence differed sufficiently from the analogous region of other geminiviruses for SSV-M to be considered a distinct virus. The use of the polymerase chain reaction for the amplification of gemini-and other virus genomes or genomic fragments for typing, mapping, phylogenetic analysis and taxonomy is discussed.

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Section: Discussionmentioning

confidence: 99%

Detection and typing of maize streak virus and other distantly related geminiviruses of grasses by polymerase chain reaction amplification of a conserved viral sequence

Rybicki

Hughes

1990

Journal of General Virology

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“…Specimens from symptomatic children who tested positive for KIV or WUV were also screened for human bocavirus (HBoV); human metapneumovirus (hMPV); human coronaviruses (HCoV) 229E, NL63, and HKU1; and human picornaviruses (including rhinoviruses [HRV]) by using previously described methods (6)(7)(8)(9)(10)(11)(12). To screen for human parainfl uenzavirus type 4 and HCoV OC43, RNA extraction and reverse transcription were performed as previously described (7).…”

Section: The Studymentioning

confidence: 99%

Role of Human Polyomaviruses in Respiratory Tract Disease in Young Children

Wattier¹,

Vázquez²,

Weibel³

et al. 2008

Emerg. Infect. Dis.

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KI virus was detected in respiratory secretions of 8/367 (2.2%) symptomatic and 0/96 asymptomatic children (p = 0.215). WU virus was detected in 26/367 (7.1%) of symptomatic children and 6/96 (6.3%) asymptomatic children (p = 1.00). These human polyomaviruses may not independently cause respiratory tract disease in young children. I n 2007, 2 new human polyomaviruses, KI virus (KIV)and WU virus (WUV), were identifi ed by molecular screening of respiratory secretions from children <2 years of age with symptomatic respiratory tract disease (1,2). Both viruses have since been detected in asymptomatic children and in those concurrently infected with other respiratory viruses, suggesting that KIV and WUV may not cause respiratory tract disease (3-5). To further understand the epidemiology of these viruses in young children and to clarify their association with symptomatic respiratory tract infections in this age group, we screened respiratory specimens from both asymptomatic and symptomatic children for the presence of KIV and WUV. The StudyRespiratory specimens from 2 groups of children (all <2 years of age) were collected in 2004 and screened for KIV and WUV. The fi rst group comprised symptomatic children whose respiratory specimens were submitted to the Clinical Virology Laboratory, Yale-New Haven Hospital, New Haven, Connecticut. These respiratory specimens tested negative for respiratory syncytial virus (RSV), parainfl uenza viruses (types 1-3), infl uenza viruses A and B, and adenovirus by direct fl uorescence antibody assay. The second group comprised asymptomatic children at the hospital-affi liated pediatric clinic for well-child care. Nucleic acids were extracted from each specimen by using QIAamp nucleic acid purifi cation kits (QIAGEN, Valencia, CA, USA). Samples were screened by nested PCR for both KIV and WUV (for WUV, the fi rst primers were those used by Gaynor et. al., and the nested primers were 5′-GCGCATCAAGAGGCACAGCTACTATTTC-3′ and 5′-GCGCCTAGCCTGTGAACTCCATC-3′). The G/C clamp for each primer is underlined. (1,2). Positive and negative controls were included in each set of PCRs. All PCR products were sequenced. Any child who had multiple specimens with positive results was included once in the total number of children whose specimens tested positive for a given virus.Specimens from symptomatic children who tested positive for KIV or WUV were also screened for human bocavirus (HBoV); human metapneumovirus (hMPV); human coronaviruses (HCoV) 229E, NL63, and HKU1; and human picornaviruses (including rhinoviruses [HRV]) by using previously described methods (6-12). To screen for human parainfl uenzavirus type 4 and HCoV OC43, RNA extraction and reverse transcription were performed as previously described (7). The primers used to amplify hPIV4 were 5′-GCGAGAGGATCCAGCTGGTGGC-3′ and 5′-GCGCCCTAATCTTTCCTGTTGATGG-3′. The primers for HCoV-OC43 were 5′-GCATAAGCCCC GCCAGAAGAGGAG-3′ and 5′-GCGCTGACGCTGTG GTTTTGGACT-3′.We tested 423 direct fl uorescent antibody-negative respiratory specimens, from 367 children,...

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“…Nasopharyngeal and induced sputum samples were analysed using a reverse transcriptase (RT)-PCR method with rhinovirus-specific primers [14,15]. In a class I microbiological safety cabinet, 250 mL nasal aspirate or induced sputum were added to 200 mL Trizol1 Reagent (Life Technologies, Paisley, UK), the mixture agitated on a vortex mixer for 30 s and then placed on ice.…”

Section: Laboratory Analysismentioning

confidence: 99%

Detection of rhinovirus in induced sputum at exacerbation of chronic obstructive pulmonary disease

Seemungal

Harper-Owen²,

Bhowmik³

et al. 2000

Eur Respir J

309

208

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Common colds are associated with exacerbations of chronic obstructive pulmonary disease (COPD). However, the role of the common cold virus (human rhinovirus) in the production of symptoms and lower airway inflammation at COPD exacerbation is unknown.Thirty three patients with moderate-to-severe COPD were seen at baseline, when the number of chest infections in the previous year was noted, and acutely at COPD exacerbation. Within 48 h after the onset of the exacerbation and at baseline, nasal aspirates and induced sputum were taken for rhinovirus reverse transcriptase polymerase chain reaction (RT-PCR) analysis and determination of cytokine levels. Symptoms, recorded on diary cards, were noted and forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) measured.At exacerbation, mean FEV1 and FVC fell significantly from baseline (p<0.001). Ten of 43 exacerbations were associated with rhinovirus infection, detected in induced sputum. In four of these, nasophageal samples contained no detectable rhinovirus. All baseline samples were negative for rhinovirus. The simultaneous presence of increased nasal discharge/nasal congestion (in 26 of the 43 exacerbations) and increased sputum (29 exacerbations) was strongly associated with the presence of rhinovirus (odds ratio 6.15; p=0.036). Total symptom scores were greater for rhinovirus as compared to nonrhinovirus exacerbations (p=0.039). Median baseline sputum interleukin-6 levels rose from 90.2 to 140.3 pg . mL -1 at exacerbation (p=0.005); the change was greater in the presence of rhinovirus infection (p=0.008).Rhinovirus infection can be detected at chronic obstructive pulmonary disease exacerbation. This is associated with elevation of lower airway interleukin-6 levels, which may mediate lower airway symptom expression during chronic obstructive pulmonary disease exacerbations. Eur Respir J 2000; 16: 677±683.

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Amplification of rhinovirus specific nucleic acids from clinical samples using the polymerase chain reaction

Cited by 110 publications

References 18 publications

Detection and typing of maize streak virus and other distantly related geminiviruses of grasses by polymerase chain reaction amplification of a conserved viral sequence

Detection and typing of maize streak virus and other distantly related geminiviruses of grasses by polymerase chain reaction amplification of a conserved viral sequence

Role of Human Polyomaviruses in Respiratory Tract Disease in Young Children

Detection of rhinovirus in induced sputum at exacerbation of chronic obstructive pulmonary disease

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