5′ Noncoding Region Alone Does Not Unequivocally Determine Genetic Type of Human Rhinovirus Strains

Savolainen-Kopra, Carita; Blomqvist, Soile; Smura, Teemu; Roivainen, Merja; Hovi, Tapani

doi:10.1128/jcm.02130-08

Cited by 30 publications

(38 citation statements)

References 19 publications

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“…This is itself a likely outcome of a recombination event that occurred in the evolutionary history of some species C variants. For these reasons and despite the recent promotion of 5Ј UTR-based HRV (sero)type identification methods (12,18), we concur with Savolainen-Kopra and colleagues that P1-coding sequences are required for reliable species and serotype assignments (32). We therefore supplemented our screening method with a second PCR for typing of VP4-VP2 using nested primers to ensure reliability and sensitivity for direct use with clinical specimens.…”

Section: Discussionmentioning

confidence: 94%

“…However, in addition to detection, identification of the infecting species or serotype is of key importance diagnostically for the detection of mixed infections or a reinfection with different HRV serotypes, as well as in broader clinical investigations of the relationship between a serotype or species with disease severity and in epidemiological investigations of the circulation and turnover of HRVs (20). Unfortunately, the amplicons generated by most screening assays (including the 5Ј UTR-based methods described in this paper) are usually too short and lack sufficient variability to allow serotypes or, often, species to be reliably identified (32). Furthermore, while the recombination events that occur in HRV have not been documented to be as extensive as those that occur in HEV (14,25,30,33), the 5Ј UTR-P1 boundary is a recombination hot spot in other picornavirus groups and genera.…”

Section: Discussionmentioning

confidence: 99%

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Screening Respiratory Samples for Detection of Human Rhinoviruses (HRVs) and Enteroviruses: Comprehensive VP4-VP2 Typing Reveals High Incidence and Genetic Diversity of HRV Species C

et al. 2009

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Rhinovirus infections are the most common cause of viral illness in humans, and there is increasing evidence of their etiological role in severe acute respiratory tract infections (ARTIs). Human rhinoviruses (HRVs) are classified into two species, species A and B, which contain over 100 serotypes, and a recently discovered genetically heterogeneous third species (HRV species C). To investigate their diversity and population turnover, screening for the detection and the genetic characterization of HRV variants in diagnostic respiratory samples was performed by using nested primers for the efficient amplification of the VP4-VP2 region of HRV (and enterovirus) species and serotype identification. HRV species A, B, and C variants were detected in 14%, 1.8%, and 6.8%, respectively, of 456 diagnostic respiratory samples from 345 subjects (6 samples also contained enteroviruses), predominantly among children under age 10 years. HRV species A and B variants were remarkably heterogeneous, with 22 and 6 different serotypes, respectively, detected among 73 positive samples. Similarly, by using a pairwise distance threshold of 0.1, species C variants occurring worldwide were provisionally assigned to 47 different types, of which 15 were present among samples from Edinburgh, United Kingdom. There was a rapid turnover of variants, with only 5 of 43 serotypes detected during both sampling periods. By using divergence thresholds and phylogenetic analysis, several species A and C variants could provisionally be assigned to new types. An initial investigation of the clinical differences between rhinovirus species found HRV species C to be nearly twice as frequently associated with ARTIs than other rhinovirus species, which matches the frequencies of detection of respiratory syncytial virus. The study demonstrates the extraordinary genetic diversity of HRVs, their rapid population turnover, and their extensive involvement in childhood respiratory disease.

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Section: Discussionmentioning

confidence: 94%

Section: Discussionmentioning

confidence: 99%

Screening Respiratory Samples for Detection of Human Rhinoviruses (HRVs) and Enteroviruses: Comprehensive VP4-VP2 Typing Reveals High Incidence and Genetic Diversity of HRV Species C

et al. 2009

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“…Genetic characterization of HRV-C amplified from clinical specimens has provided evidence for extensive heterogeneity in the VP4/VP2 region, the existence of two phylogenetically separate groups of sequences in the 59-UTR (one resembling sequences found in species A rhinoviruses; Han et al, 2009;Huang et al, 2009;Savolainen-Kopra et al, 2009b;Wisdom et al, 2009a) and substantial sequence divergence throughout the genome of the 11 full-length HRV-C sequences obtained to date (Lamson et al, 2006;Lau et al, 2007;Kistler et al, 2007;McErlean et al, 2007;Huang et al, 2009;Tapparel et al, 2009b;Arden et al, 2010b). Although we currently lack the means to classify HRV-C serologically (as has been achieved for other rhinovirus and enterovirus species), we recognize and are responding to the need to develop a classification system for this species.…”

Section: Proposal Aimsmentioning

confidence: 99%

“…For enteroviruses and rhinoviruses whose type assignments are dependent on the capsid genes (and the encoded differences in antigenic properties), regions that undergo extremely frequent recombination (such as the 59-UTR, P2 and P3 non-structural gene regions in HEV) cannot therefore contribute to their (sero)type classification (Savolainen-Kopra et al, 2009b).…”

Section: Rhinovirus Recombinationmentioning

confidence: 99%

Proposals for the classification of human rhinovirus species C into genotypically assigned types

Simmonds

McIntyre

Savolainen-Kopra

et al. 2010

Journal of General Virology

212

163

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Human rhinoviruses (HRVs) are common respiratory pathogens associated with mild upper respiratory tract infections, but also increasingly recognized in the aetiology of severe lower respiratory tract disease. Wider use of molecular diagnostics has led to a recent reappraisal of HRV genetic diversity, including the discovery of HRV species C (HRV-C), which is refractory to traditional virus isolation procedures. Although it is heterogeneous genetically, there has to date been no attempt to classify HRV-C into types analogous to the multiple serotypes identified for HRV-A and -B and among human enteroviruses. Direct investigation of cross-neutralization properties of HRV-C is precluded by the lack of methods for in vitro culture, but sequences from the capsid genes (VP1 and partial VP4/VP2) show evidence for marked phylogenetic clustering, suggesting the possibility of a genetically based system comparable to that used for the assignment of new enterovirus types. We propose a threshold of 13 % divergence for VP1 nucleotide sequences for type assignment, a level that classifies the current dataset of 86 HRV-C VP1 sequences into a total of 33 types. We recognize, however, that most HRV-C sequence data have been collected in the VP4/VP2 region (currently 701 sequences between positions 615 and 1043). We propose a subsidiary classification of variants showing .10 % divergence in VP4/ VP2, but lacking VP1 sequences, to 28 provisionally assigned types (subject to confirmation once VP1 sequences are determined). These proposals will assist in future epidemiological and clinical studies of HRV-C conducted by different groups worldwide, and provide the foundation for future exploration of type-associated differences in clinical presentations and biological properties. IntroductionHuman rhinoviruses (HRVs) are highly prevalent respiratory pathogens, most commonly associated with mild upper respiratory tract disease and exacerbations of preexisting respiratory disease such as asthma. They are also increasingly recognized as underlying more severe disease manifestations, such as bronchiolitis in young children and in the immunosuppressed. The increasing use of molecular methods for respiratory virus screening has contributed to this reappraisal of rhinoviruses, as has the recent discovery of an entirely novel rhinovirus group, refractory to previously used virus isolation methods but now known to be highly prevalent and widely circulating worldwide (Arden et al., 2006;Kaiser et al., 2006;Lamson et al., 2006;Kistler et al., 2007;Lau et al., 2007;Lee et al., 2007;McErlean et al., 2007;Renwick et al., 2007;Olenec et al., 2010).These newly characterized rhinoviruses have been proposed to belong to a novel species of rhinovirus (designated species C; HRV-C), recognizing their substantial sequence divergence from other classified species within the genus Enterovirus of picornaviruses (Carstens, 2010;Knowles, 2010) (Fig. 1a). Clinically and biologically, they share many attributes with the other designated HRV species, HRV-A and -B....

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“…15 Sequencing of the rhinovirus 59 nontranslated region is a suitable approach for evaluation of short-term transmission. 18,19 Briefly 12.5 mL of iQ supermix (Bio-Rad) was mixed within a 25-mL PCR reaction containing 200 nM of both a biotinylated forward primer (biotin-TGGACAAGGTGCGAAGAGC) and a reverse primer (GGTTAGCCGCATTCAGGG) and 1 mL of the rhinovirus qPCR amplimer 15 and nuclease-free water to volume. Thermocycling was completed by using a Bio-Rad C1000 thermocycler and the following protocol: (1) 1.5 minutes, 95°C, (2) 95°C, 15 seconds, (3) 60°C, 1 minute, repeat 50 times, (4) 72°C, 5 minutes, and (5) indefinite hold at 4°C.…”

Section: Molecular Virological Studiesmentioning

confidence: 99%

Duration of Rhinovirus Shedding in the Upper Respiratory Tract in the First Year of Life

Loeffelholz¹,

Trujillo

Pyles

et al. 2014

Pediatrics

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WHAT'S KNOWN ON THIS SUBJECT: Rhinoviruses are commonly detected in both acutely ill and asymptomatic infants and children. The finding may represent new infection or prolonged presence of rhinovirus RNA in the respiratory tract. WHAT THIS STUDY ADDS:In young, otherwise healthy infants, shedding of RNA from the same rhinovirus strain rarely persisted longer than 30 days. abstract BACKGROUND: Current molecular diagnostic methods have detected rhinovirus RNA in a high proportion of asymptomatic infants and children, raising the question of the clinical significance of these findings. This study investigates the prevalence of prolonged rhinovirus RNA presence in the upper respiratory tract of infants during the first year of life. METHODS:In a longitudinal study, infants were followed from birth up to 12 months. Nasopharyngeal specimens were collected monthly (months 1-6 and month 9) and during an upper respiratory infection. Rhinoviruses were detected by quantitative reverse-transcription polymerase chain reaction. Presence of repeated rhinovirus RNA was evaluated by nucleotide sequence analysis. RESULTS:A total of 2153 specimens from 362 infants were studied; 341 distinct rhinovirus infections in 216 infants were identified. Follow-up specimens were available within 30 days for 179 infections, creating the sample set to assess prolonged rhinovirus presence. Of the 179 infections, 46 involved the detection of the same rhinovirus strain in repeated specimens, including 8 events of prolonged presence of the same strain (detected in specimens collected .30 days apart), representing 4.5% of the evaluable rhinovirus infections. There were 26 events in which a rhinovirus strain was replaced by a different strain within a 30-day interval, representing 14.5% of the 179 infections. CONCLUSIONS:Although rhinovirus infections are common in healthy infants, prolonged presence of rhinovirus RNA in the respiratory tract after an upper respiratory infection was uncommon (,5%). Detection of rhinovirus RNA in an infant most likely represents an infection within a 30-day period. Dr Loeffelholz co-conceptualized and co-designed the study and wrote the initial manuscript; Dr Trujillo coordinated data collection; Dr Pyles conceptualized and supervised molecular virology studies and reviewed and revised the manuscript; Mr Miller performed molecular virology studies and provided interpretation of the data for inclusion in the manuscript; Dr Alvarez-Fernandez supervised data collection; Dr Pong performed molecular virology studies and performed data collection and analysis; Dr Chonmaitree conceptualized and designed the study, provided overall study supervision, and revised the manuscript; and all authors approved the final manuscript as submitted and agree to be accountable for all aspects of the work. 4,5 A study in adult volunteers showed that cultivatable rhinoviruses were routinely recovered for ∼2 weeks after infection. 6 Recurrent rhinovirus infection has been described in patients with asthma 7 and in those at risk of developing...

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5′ Noncoding Region Alone Does Not Unequivocally Determine Genetic Type of Human Rhinovirus Strains

Cited by 30 publications

References 19 publications

Screening Respiratory Samples for Detection of Human Rhinoviruses (HRVs) and Enteroviruses: Comprehensive VP4-VP2 Typing Reveals High Incidence and Genetic Diversity of HRV Species C

Screening Respiratory Samples for Detection of Human Rhinoviruses (HRVs) and Enteroviruses: Comprehensive VP4-VP2 Typing Reveals High Incidence and Genetic Diversity of HRV Species C

Proposals for the classification of human rhinovirus species C into genotypically assigned types

Duration of Rhinovirus Shedding in the Upper Respiratory Tract in the First Year of Life

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