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Journal of Clinical Microbiology, February 2008, p. 533-539, Vol. 46, No. 2
0095-1137/08/$08.00+0 doi:10.1128/JCM.01739-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
Real-Time Reverse Transcription-PCR Assay for Comprehensive Detection of Human Rhinoviruses
Xiaoyan Lu,1
Brian Holloway,2
Ryan K. Dare,1
Jane Kuypers,3
Shigeo Yagi,4
John V. Williams,5
Caroline B. Hall,6 and
Dean D. Erdman1*
Gastroenteritis and Respiratory Virus Laboratory Branch, Division of Viral Diseases,1
Biotechnology Core Facility Branch, Centers for Disease Control and Prevention, Atlanta, Georgia,2
Department of Laboratory Medicine, University of Washington, Seattle, Washington,3
Viral and Rickettsial Disease Laboratory, California Department of Health Services, Richmond, California,4
Departments of Pediatrics and Microbiology and Immunology, Vanderbilt School of Medicine, Nashville, Tennessee,5
Department of Infectious Diseases, University of Rochester School of Medicine and Dentistry, Rochester, New York6
Received 31 August 2007/
Returned for modification 11 October 2007/
Accepted 7 November 2007

ABSTRACT
Human rhinoviruses (HRVs) are important contributors to respiratory
disease, but their healthcare burden remains unclear, primarily
because of the lack of sensitive, accurate, and convenient means
of determining their causal role. To address this, we developed
and clinically validated the sensitivity and specificity of
a real-time reverse transcription-PCR (RT-PCR) assay targeting
the viral 5' noncoding region defined by sequences obtained
from all 100 currently recognized HRV prototype strains and
85 recently circulating field isolates. The assay successfully
amplified all HRVs tested and could reproducibly detect 50 HRV
RNA transcript copies, with a dynamic range of over 7 logs.
In contrast, a quantified RNA transcript of human enterovirus
68 (HEV68) that showed the greatest sequence homology to the
HRV primers and probe set was not detected below a concentration
of 5
x 10
5 copies per reaction. Nucleic acid extracts of 111
coded respiratory specimens that were culture positive for HRV
or HEV were tested with the HRV real-time RT-PCR assay and by
two independent laboratories that used different in-house HRV/HEV
RT-PCR assays. Eighty-seven HRV-culture-positive specimens were
correctly identified by the real-time RT-PCR assay, and 4 of
the 24 HEV-positive samples were positive for HRV. HRV-specific
sequences subsequently were identified in these four specimens,
suggesting HRV/HEV coinfection in these patients. The assay
was successfully applied in an investigation of a coincidental
outbreak of HRV respiratory illness among laboratory staff.

INTRODUCTION
Human rhinovirus (HRV) infections are among the most frequent
causes of the common cold (
42), and more recent studies have
linked HRVs to more severe lower respiratory illnesses in otherwise
healthy young children (
34,
35), the elderly (
16,
36,
48), and
the immunocompromised (
13,
19). Persons with underlying respiratory
diseases, like asthma, chronic bronchitis, and cystic fibrosis
(
12,
26,
46), also may have an increased risk of severe HRV-associated
complications.
Together with the human enteroviruses (HEVs), HRVs are classified within the family Picornaviridae (27). There are currently 100 distinct HRV serotypes assigned to two species, A and B (2), and new genetic variants of HRV have been reported recently (29, 33); one former HRV serotype, HRV87, recently was shown by sequence analysis to be a strain of HEV68 (6, 43). The clinical presentation of HRV infection is of little diagnostic value, and laboratory diagnosis has been complicated by the failure of some strains to grow in cell culture and by their extreme antigenic variability, precluding the routine use of antigen detection methods or serology. Moreover, distinguishing HRVs from HEVs, which also may be present in respiratory specimens, by acid liability testing has been shown to be ineffective for many strains (5, 17, 18). Reverse transcription-PCR (RT-PCR) assays therefore have become the method of choice for the sensitive detection and differentiation of HRVs and have greatly enhanced our appreciation of the role of these viruses in human disease.
Numerous molecular assays have been described for the HRVs/HEVs. These assays typically target the 5' noncoding region (5'NCR) of the viral genome that contains highly conserved sequences suitable for molecular assay development. However, most of these assays require postamplification processing of the amplicon by gel electrophoresis, probe hybridization, sequencing, or restriction analysis to confirm and differentiate HRVs from HEVs (1, 3, 4, 5, 14, 24, 31, 34, 41). More recently, real-time RT-PCR assays have been described for HRVs/HEVs (8, 9, 25, 38, 44) that offer potentially rapid, sensitive, and quantitative results and that are less prone to amplicon contamination. However, because of the more extensive genetic variability of the HRVs and the lack of available sequence data in the public domain, few real-time RT-PCR assays have been described specifically for the HRVs (8, 9, 44, 51), and none to our knowledge has been shown to successfully detect all recognized HRV prototype strains. In this study, we sequenced a portion of the 5'NCR of all HRV prototype strains as well as multiple recently circulating field isolates and used these data to develop and evaluate an HRV real-time RT-PCR assay.
(Data from this report were presented in part at the 23rd Clinical Virology Symposium, Clearwater, FL, 29 April to 2 May 2007.)

MATERIALS AND METHODS
Virus strains and clinical specimens.
One hundred HRV prototype strains (HRV1A, HRV1B, HRV2 to HRV86,
and HRV88 to HRV100) kindly provided by ViroPharma Inc. (
30)
and 85 HRV field isolates obtained from several sources between
1999 and 2007 were available for study. HRV isolates were sequenced
directly or after one additional passage in HeLa Ohio cells.
Infected cells were incubated at 35°C in 5% CO
2 with gentle
rocking until reaching full cytopathic effect. Isolates then
were freeze-thawed twice and clarified by low-speed centrifugation,
and supernatants were collected and stored at –70°C.
Forty-eight HEV laboratory strains grown in primary monkey kidney
or human RD cells and prepared as described above included echoviruses
1 to 6, 8, 9, 11 to 25, and 29 to 31; coxsackievirus types A2,
A4 to A6, A8 to A10, A16, A21, A24, and B1 to B6; enterovirus
types 68, 70, and 71; and poliovirus types 1, 2, and 3. Other
respiratory viruses available for specificity testing included
respiratory syncytial virus, human metapneumovirus, human parainfluenza
viruses 1 to 4, adenovirus, coronaviruses 229E and OC43, influenza
viruses A and B, and human bocavirus (
32). Coded respiratory
specimens culture positive for HRV or HEV were provided by the
California Department of Health Services, the University of
Washington, the Vanderbilt Medical Center, and the University
of Rochester Medical Center for clinical validation studies.
Nasal and throat swab specimens were self obtained by symptomatic
laboratory staff and were expressed in 2 ml of chilled viral
transport medium (Hank's buffered salt solution with 0.5% gelatin)
and frozen at –70°C prior to testing.
Sample extraction.
Total nucleic acid extracts were prepared from 100 µl of infected cell culture lysate or 200 µl of clinical specimen using the NucliSens easyMAG extraction system by following the manufacturer's instructions (bioMérieux, Durham, NC).
Partial 5'NCR sequencing.
Extracted viral RNA was reverse transcribed using random hexamer primers (Promega, Madison, WI) at 52°C for 60 min with Superscript III reverse transcriptase (Invitrogen, Carlsbad, CA) by following the manufacturer's instructions. Five microliters of the cDNA then was amplified in two separate PCRs using HRV species A- and B-specific primer sets (Table 1) with the HotStarTaq master mix kit (Qiagen, Chatsworth, CA). PCR cycling conditions were the following: an initial activation step at 95°C for 15 min, followed by 35 cycles of 95°C for 1 min, 55°C for 1 min, and 72°C for 1 min, with a final extension of 72°C for 5 min on a GeneAmp PCR system 9700 (Applied Biosystems). Amplified products were purified with the QIAquick PCR purification kit (Qiagen), and sequencing was performed in both directions using the amplification primers and the ABI Prism BigDye Terminator cycle sequencing ready reaction kit, version 3.1, on an ABI 3100 DNA sequencer (Applied Biosystems). Sequencher software (version 3.1.1; Gene Codes, Ann Arbor, MI) was used for sequence assembly and editing.
Primers and probes.
Conserved regions of the 5'NCR were identified from alignments
of nucleotide sequences available in the GenBank database (HEV
sequence accession numbers: AF108187, AF169670, AF303040, AF405316,
AF405321, AF412341 to AF412376, AF412383, AJ007342, AY028214
to AY028218, AY062275, L76395, L76409, L76411, L76413, L76411,
L76412, X89534, X89535, X89539, and z78133; HRV sequence accession
numbers: AF108149 to AF108186, AF542419 to AF542421, AF542424
to AF542448, D00239, DQ473485 to DQ473512, DQ473509, E01069,
EF186077, L24917, M16248, NC_001490, and X02316) or were obtained
during this study (HRV sequence accession numbers EU095987 to
EU096086). Primers and probes were selected with the aid of
Primer Express software, version 2.0.0 (Applied Biosystems,
Foster City, CA), and Netprimer (Premier Biosoft International).
Primers and probes that showed no major nonspecific homologies
on BLAST analysis were synthesized by the Centers for Disease
Control and Prevention (CDC) Biotechnology Core Facility. TaqMan
probes were labeled at the 5' end with the reporter molecule
6-carboxyfluorescein and at the 3' end with the quencher Black
Hole Quencher 1 (Biosearch Technologies, Inc., Novato, CA).
Locked nucleic acid (Exiqon A/S, Vedbaek, Denmark) analogues
(LNA) that increase thermodynamic stability (
37) were introduced
during oligonucleotide synthesis to achieve a balanced melting
temperature between the forward and reverse primers. Optimal
primer and probe concentrations were determined by checkerboard
titrations against synthetic RNA transcripts (see below). Primer
and probe sets that gave the highest amplification efficiencies
at optimized conditions and with no identifiable cross-reactions
were chosen for further study (Table
1).
Real-time RT-PCR assay.
The real-time RT-PCR assay was performed using the iScript one-step RT-PCR kit for probes (Bio-Rad, Hercules, CA). Each 25-µl reaction mixture contained 1 µM forward and reverse primers, 0.1 µM probe, and 5 µl of nucleic acid extract. The amplification was performed on an iCycler iQ real-time detection system (Bio-Rad) using the following thermocycling conditions: 10 min at 48°C for RT, 3 min at 95°C for polymerase activation, and then 45 cycles of 15 s at 95°C and 1 min at 60°C. Each run included template and nontemplate controls. Specimen extracts also were tested for the human RNase P gene to monitor specimen quality as previously described (10).
RNA transcript synthesis.
RNA transcripts were prepared from the 5'NCR of representative HRV and HEV strains for analytical sensitivity and specificity studies. PCR amplicons were prepared from HRV14 and HEV68 using primers that bracketed the real-time RT-PCR signature and that contained 5'-end T7 and Sp6 promoter sequences to serve as templates for RNA polymerase (Table 1). The expected sequences were confirmed by amplicon sequencing. The transcripts were synthesized and purified using MegaScript and MegaClear kits (Ambion, Inc., Austin, TX), respectively, and were quantified using the NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Positive-sense transcripts for HRV14 and HEV68 were 951 and 545 nucleotides (nt) in length, respectively, with RNA yields of 2.03 x 1011 copies/µl for HRV14 and 3.10 x 1012 copies/µl for HEV68. To generate standard curves for quantitative determinations, replicate serial 10-fold dilutions of the transcripts were prepared in 10 mM Tris-EDTA buffer containing yeast tRNA (50 ng/ml) (Ambion) and were stored at –70°C until use.
Nucleotide sequence accession numbers.
The HRV sequences determined in the course of this work were deposited in GenBank under accession numbers EU095987 to EU096086.

RESULTS
Assay development and optimization.
The 5'NCR of all 100 HRV prototype strains and 85 recently circulating
field isolates were sequenced and aligned with those of representative
HRV/HEV strains available from GenBank (NIH). A conserved region
identified between nt 356 and 563 (HRV1B accession no. D00239)
(Fig.
1) was selected to develop primer and probe sets for evaluation.
The sets that gave the best initial performance with several
representative HRV strains were chosen for subsequent studies.
The reverse primer and probe were highly conserved among all
available HRV/HEV sequences. In contrast, the forward primer
was located in a variable region that contained a signature
T indel at nt 367 that distinguished all HRVs from HEVs and
that could be exploited for differential amplification. To compensate
for the necessarily shorter length of the forward primer, LNA
were introduced to achieve a balanced midpoint temperature with
the reverse primer. The performance of the assay was optimized
using the iScript one-step RT-PCR kit for probes (Bio-Rad).
Limited examinations of other commercial real-time RT-PCR reagent
kits found that the QuantiTect probe PCR kit (Qiagen) and Ag-Path-ID
one-step RT-PCR kit (Applied Biosystems) performed comparably
to the iScript kit, whereas amplification was less efficient
with the TaqMan one-step RT-PCR master mix (Applied Biosystems)
or failed entirely with the SuperScript III platinum one-step
quantitative RT-PCR kit (Invitrogen) on repeat evaluations (data
not shown).

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FIG. 1. Alignment of partial 5'NCR sequences of 100 HRV and 52 HEV serotypes in regions corresponding to primers and probes used for the HRV real-time RT-PCR assay. Consensus sequences and nucleotide variations from the consensus are shown for each alignment. A blank square indicates that that base is identical to the consensus sequence base. The dash indicates the presence of an indel at position 367. , Not determined. The nucleotide position numbering is based on the sequence of HRV1B (accession no. D00239). Letters in the Sequences column indicate the following HRV strains: A, 3, 4, 6, 13, 14, 17 to 19, 27, 37, 41, 48, 49, 53, 61, 73, 79, 82 to 84, 90, 92, 93, 96, and 97; B, 2, 8 to 11, 15, 16, 20, 21, 23 to 25, 29, 30, 32, 34, 38, 40, 44, 46, 50, 54 to 57, 60, 62, 66 to 68, 74, 76, 80, 81, 85, 95, 98, and 100; C, 1A, 1B, 22, 43, 51, 64, 71, 75, 86, and 94; D, 7, 12, 31, 36, 39, 45, 47, 58, and 89; E, 5, 35, 42, 52, 65, 69, and 91; F, 26 and 99; G, 59 and 63; H, 28; I, 33; J, 70; K, 72; L, 77; M, 78; and N, 88. Letters in the Sequences column indicate the following HEV types: O, coxsackievirus types A1, A2, A11, A13, A15, A17 to A22, and A24, HEV68 and HEV70, and poliovirus types 1 and 3; P, coxsackievirus types A3 to A7, A10, A12, and A14, coxsackievirus types B1, B3, and B5, echoviruses 1, 6 to 8, 13, 16 to 21, 27, 29, 31, and 32, and enterovirus types 69 and 71; Q, echovirus types 4, 14, and 15; R, poliovirus type 2; S, coxsackievirus type A8; T, echovirus type 11; U, echovirus type 26; and V, echovirus type 33. Ref. Acc. No., reference accession number.
|
Assay evaluation with HRV/HEV isolates.
Viral culture lysates of all 100 HRV prototype strains, 85 HRV
field isolates, and 48 HEV laboratory strains were tested by
the real-time RT-PCR assay. Undiluted RNA extracts of all HRV
prototype strains and field isolates gave strongly positive
reactions (median cycle threshold [
CT] value, 13.7; range, 9.3
to 25.3). In contrast, 34 HEVs were nonreactive, and 14 (echoviruses
1, 3, 5, 6, 13, and 21; poliovirus types 1 and 2; enterovirus
types 68 and 71; coxsackievirus types A4, A6, and A24; and coxsackievirus
type B1) gave weakly positive reactions (median
CT value, 34;
range, 33 to 34.8); positive reactions with HEVs appeared to
be related to the virus titer and not to any particular virus
type. Tenfold serial dilutions of total nucleic acid extracts
of HRV2, HRV5, HRV33, HRV88, echovirus 1 and coxsackievirus
type B1 were tested in parallel by the real-time RT-PCR assay
and a conventional RT-PCR assay that amplifies an

115-bp region
of the 5'NCR of both HRVs and HEVs (
45). Whereas the relative
sensitivities of the two assays for the HRVs were equivalent,
the real-time RT-PCR assay was

10
5-fold less sensitive than
the conventional assay with HEVs echovirus 1 and coxsackievirus
type B1.
Assay analytical sensitivity and specificity.
Serial 10-fold dilutions of HRV14 RNA transcripts that showed 100% sequence identity with the real-time RT-PCR primers and probe set were tested to assess the amplification efficiency. A linear amplification was achieved over a 7-log dynamic range from 5 x 101 to 5 x 107 copies per reaction (Fig. 2). The assay's detection limit was determined with 24 replicates of 50, 5, and 1 transcript copy per reaction. At 50 copies, 100% of the replicates were positive; at 5 copies, 9 (37.5%) of the replicates were positive; and at 1 copy, 2 (8.3%) of the replicates were positive. In contrast, the HEV68 transcript was not detected below a concentration of approximately 5 x 105 copies per reaction. Nucleic acid extracts of other respiratory viruses, including human respiratory syncytial virus, human metapneumovirus, parainfluenza viruses 1 to 4, adenovirus, coronaviruses 229E and OC43, influenza viruses A and B, and human bocavirus were negative by the real-time RT-PCR assay.
Assay reproducibility.
To assess intra- and interassay reproducibility, 10-fold serial
dilutions of the HRV14 RNA transcripts, from 5
x 10
1 to 5
x 10
7 copies per reaction, were tested in triplicate on three
succeeding days. Over the linear range of the assay, the coefficient
of variation of the mean
CT values ranged from 0.24 to 0.94%
within runs and from 0.91 to 2.68% between runs.
Assay evaluation with clinical specimens.
To assess the performance of the real-time RT-PCR assay with clinical samples, extracts of 111 coded respiratory specimens previously determined to be culture positive for HRV or HEV were prepared and tested simultaneously with the HRV real-time RT-PCR assay and by two independent laboratories (laboratories A and B) that used different in-house HRV/HEV RT-PCR assays. Of 87 HRV culture-positive specimens tested, all were identified as HRV by the real-time RT-PCR assay (median CT value, 26.3; range, 14.9 to 38.5) (Table 2); HRV also was identified in all 87 specimens by one or both of the reference in-house RT-PCR assays. Of 24 HEV culture-positive specimens, 4 were positive for HRV by the real-time RT-PCR assay (median CT value, 28.8; range, 26.2 to 32.1); one of these four also was identified as HRV by laboratory B. HEV isolates available from three of the four specimens were not amplified by the real-time RT-PCR, whereas amplicon sequences obtained from all four clinical specimens were found to be HRV, suggesting that these specimens contained both HRV and HEV.
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TABLE 2. Comparison of HRV real-time RT-PCR assay to reference assays for detection of HRV and HEV in clinical specimensc
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Outbreak investigation.
Between 10 and 22 September 2006, six CDC laboratory staff members
developed respiratory illnesses characterized by one or more
of the following symptoms: cough, congestion, myalgia, chills,
or fever, and five were absent from work for 1 or more days.
Testing samples from these individuals with a comprehensive
panel of respiratory virus PCR assays identified five cases
of HRV infection. Serial throat and nasal swab specimens were
self collected from four of the HRV-positive individuals beginning
2 and 6 days after the onset of symptoms and continued until
at least two consecutive specimens tested negative (Fig.
3).
The duration of detectable HRV ranged from 11 to 21 days (median,
12.5 days). With the exception of case A, in which HRV was detected
at comparable levels from both throat and nasal swabs, throat
swabs either were consistently negative for HRV (cases B and
C) or became negative earlier than did nasal swabs (case D).
The duration of symptoms for the five HRV-positive cases ranged
from 12 to 24 days (median, 16 days); one individual (case D)
had a prolonged paroxysmal cough that persisted for 24 days.
The duration of reported symptoms exceeded the duration of detectable
HRV by real-time RT-PCR for all cases. The sequencing of a partial
region of the HRV VP1 gene from the specimens obtained from
the five cases identified two genetically distinct HRV strains
that showed the closest sequence identities to HRV86 (amino
acid identity score, 83.5%) and HRV69 (amino acid identity score,
84.6%), respectively.

DISCUSSION
The 5'NCR has long been the preferred site for designing molecular
diagnostic assays for HRVs/HEVs due to the availability of highly
conserved sequences that support the complex secondary structures
of the HRV/HEV internal ribosome entry site (
50). Whereas the
locations of these conserved sequences offer considerable flexibility
for designing targeted primers/probes for HEV real-time RT-PCR
assays (
25,
38,
47), the development of comparable assays for
HRVs has been hampered by their greater genetic variability
and the paucity of published HRV sequence data from the 5'NCR.
The few real-time assays that have been described for HRVs were
not evaluated against or failed to detect all known HRV serotypes
(
8,
9,
44,
51), or they used Sybr green instead of probe-based
fluorescence detection (
8); the results of Sybr green testing
can be difficult to interpret (
49). A comprehensive analysis
of HRV 5'NCR sequences obtained in this study identified a region
suitable for the development of an HRV-specific probe-based
real-time RT-PCR assay that was demonstrated to detect all HRV
prototype stains, multiple recently circulating field isolates,
including newly identified genetic variants (
33), and HRV culture-positive
clinical specimens. The assay was further shown to discriminate
between HRVs and HEVs in clinical specimens and successfully
identified HRV coinfections in specimens that were culture positive
only for HEV.
During the course of this study, an outbreak of HRV respiratory illness occurred among laboratory workers that was investigated to assess the viral shedding patterns in four of those affected. HRV was detected by real-time RT-PCR for up to 3 weeks after the onset of symptoms in one case; however, most cases showed progressively decreasing virus loads, becoming RT-PCR negative within 2 weeks of the onset of symptoms, and all cases continued to be symptomatic after the cessation of HRV shedding. Studies of children have found HRV for up to 5 to 6 weeks by RT-PCR (20); however, results of epidemiological and human volunteer studies of shedding patterns in healthy adults are more consistent with our findings (15). In most cases, nasal swabs were better than throat swabs for virus recovery, reflecting the preferred site of HRV replication in the anterior nasal mucosa (21). The ability of the real-time RT-PCR assay to detect two genetically novel HRV strains responsible for this outbreak and its primer/probe sequence compatibility with the newly recognized group of HRVs represented by strain HRV-QPM (33) confirm its robust diagnostic capabilities.
Despite these advantages, our real-time RT-PCR assay has several potential limitations. Although all HRV strains evaluated were successfully detected, the full genetic diversity of HRVs may not be fully represented in our study. Unrecognized genetic heterogeneity in the primer/probe region could compromise assay performance. Moreover, despite our efforts to design an HRV-specific assay, some HEVs present at high titers in the respiratory specimen could be misidentified as HRV. In addition to these technical issues, the potential for long-term shedding of HRVs in some populations (20, 23, 28, 51) and the high rates of asymptomatic HRV infection found in some studies (11, 39, 51) make it more difficult to establish an etiologic link to disease. By restricting the testing to HRVs alone, other members of the Picornaviridae that have been implicated in acute respiratory disease would not be identified. Respiratory illnesses indistinguishable from those caused by HRVs occur in up to 21% of non-poliovirus HEV infections (40), and picornaviruses of the more recently identified Parechovirus genus also have been linked to respiratory disease (22). Therefore, a more comprehensive diagnostic strategy would combine the HRV real-time RT-PCR assay with real-time assays for the other respiratory picornavirus pathogens (7).
Our real-time RT-PCR assay permits rapid, sensitive, and specific detection of HRVs in a format more convenient for diagnostic laboratories. Expanding routine testing for these viruses will help better define the epidemiology of HRV infection and the spectrum and burden of HRV disease.

ACKNOWLEDGMENTS
We thank David Schnurr of the Viral and Rickettsial Disease
Laboratory, California Department of Health Services, and Kenneth
Schnabel of the University of Rochester School of Medicine and
Dentistry for providing clinical specimens for this study.
The findings and conclusions in this report are those of the author(s) and do not necessarily represent the views of the funding agency.

FOOTNOTES
* Corresponding author. Mailing address: 1600 Clifton Road, N.E., Mailstop G04, Atlanta, GA 30333. Phone: (404) 639-3727. Fax: (404) 639-4416. E-mail:
dde1{at}cdc.gov 
Published ahead of print on 5 December 2007. 

REFERENCES
1 - Andeweg, A. C., T. M. Bestebroer, M. Huybreghs, T. G. Kimman, and J. C. de Jong. 1999. Improved detection of rhinoviruses in clinical samples by using a newly developed nested reverse transcription-PCR assay. J. Clin. Microbiol. 37:524-530.[Abstract/Free Full Text]
2 - Andries, K., B. Dewindt, J. Snoeks, L. Wouters, H. Moereels, P. J. Lewi, and P. A. Janssen. 1990. Two groups of rhinoviruses revealed by a panel of antiviral compounds present sequence divergence and differential pathogenicity. J. Virol. 64:1117-1123.[Abstract/Free Full Text]
3 - Atmar, R. L., and P. R. Georghiou. 1993. Classification of respiratory tract picornavirus isolates as enteroviruses or rhinoviruses by using reverse transcription-polymerase chain reaction. J. Clin. Microbiol. 31:2544-2546.[Abstract/Free Full Text]
4 - Billaud, G., S. Peny, V. Legay, B. Lina, and M. Valette. 2003. Detection of rhinovirus and enterovirus in upper respiratory tract samples using a multiplex nested PCR. J. Virol. Methods 108:223-228.[CrossRef][Medline]
5 - Blomqvist, S., A. Skytta, M. Roivainen, and T. Hovi. 1999. Rapid detection of human rhinoviruses in nasopharyngeal aspirates by a microwell reverse transcription-PCR-hybridization assay. J. Clin. Microbiol. 37:2813-2816.[Abstract/Free Full Text]
6 - Blomqvist, S., C. Savolainen, L. Raman, M. Roivainen, and T. Hovi. 2002. Human rhinovirus 87 and enterovirus 68 represent a unique serotype with rhinovirus and enterovirus features. J. Clin. Microbiol. 40:4218-4223.[Abstract/Free Full Text]
7 - Corless, C. E., M. Guiver, R. Borrow, V. Edwards-Jones, A. J. Fox, E. B. Kaczmarski, and K. J. Mutton. 2002. Development and evaluation of a real-time RT-PCR for the detection of enterovirus and parechovirus RNA in CSF and throat swab samples. J. Med. Virol. 67:555-562.[CrossRef][Medline]
8 - Dagher, H., H. Donninger, P. Hutchinson, R. Ghildyal, and P. Bardin. 2004. Rhinovirus detection: comparison of real-time and conventional PCR. J. Virol. Methods 117:113-121.[CrossRef][Medline]
9 - Deffernez, C., W. Wunderli, Y. Thomas, S. Yerly, L. Perrin, and L. Kaiser. 2004. Amplicon sequencing and improved detection of human rhinovirus in respiratory samples. J. Clin. Microbiol. 42:3212-3218.[Abstract/Free Full Text]
10 - Emery, S. L., D. D. Erdman, M. D. Bowen, B. R. Newton, J. M. Winchell, R. F. Meyer, S. Tong, B. T. Cook, B. P. Holloway, K. A. McCaustland, P. A. Rota, B. Bankamp, L. E. Lowe, T. G. Ksiazek, W. J. Bellini, and L. J. Anderson. 2004. Real-time reverse transcription-polymerase chain reaction assay for SARS-associated coronavirus. Emerg. Infect. Dis. 10:311-316.[Medline]
11 - Fox, J. P., M. K. Cooney, C. E. Hall, and H. M. Foy. 1985. Rhinoviruses in Seattle families, 1975-1979. Am. J. Epidemiol. 122:830-846.[Abstract/Free Full Text]
12 - Friedlander, S. L., and W. W. Busse. 2005. The role of rhinovirus in asthma exacerbations. J. Allergy Clin. Immunol. 116:267-273.[CrossRef][Medline]
13 - Ghosh, S., R. Champlin, R. Couch, J. England, I. Raad, S. Malik, M. Luna, and E. Whimbey. 1999. Rhinovirus infections in myelosuppressed adult blood and marrow transplant recipients. Clin. Infect. Dis. 29:528-532.[Medline]
14 - Halonen, P., E. Rocha, J. Hierholzer, B. Holloway, T. Hyypia, P. Hurskainen, and M. Pallansch. 1995. Detection of enteroviruses and rhinoviruses in clinical specimens by PCR and liquid-phase hybridization. J. Clin. Microbiol. 33:648-653.[Abstract/Free Full Text]
15 - Hendley, J. O., and J. M. Gwaltney. 1988. Mechanisms of transmission of rhinovirus infections. Epidemiol. Rev. 10:243-258.[Medline]
16 - Hicks, L. A., C. W. Shepard, P. H. Britz, D. D. Erdman, M. Fischer, B. L. Flannery, A. J. Peck, X. Lu, W. L. Thacker, R. F. Benson, M. L. Tondella, M. E. Moll, C. G. Whitney, L. J. Anderson, and D. R. Feikin. 2006. Two outbreaks of severe respiratory disease in nursing homes associated with rhinovirus. J. Am. Geriatr. Soc. 54:284-289.[CrossRef][Medline]
17 - Hyypiä, T., T. Puhakka, O. Ruuskanen, M. Mäkelä, A. Arola, and P. Arstila. 1998. Molecular diagnosis of human rhinovirus infections: comparison with virus isolation. J. Clin. Microbiol. 36:2081-2083.[Abstract/Free Full Text]
18 - Ireland, D. C., J. Kent, and K. G. Nicholson. 1993. Improved detection of rhinoviruses in nasal and throat swabs by seminested RT-PCR. J. Med. Virol. 40:96-101.[Medline]
19 - Ison, M. G., F. G. Hayden, L. Kaiser, L. Corey, and M. Boeckh. 2003. Rhinovirus infections in hematopoietic stem cell transplant recipients with pneumonia. Clin. Infect. Dis. 36:1139-1143.[CrossRef][Medline]
20 - Jartti, T., P. Lehtinen, T. Vuorinen, M. Koskenvuo, and O. Ruuskanen. 2004. Persistence of rhinovirus and enterovirus RNA after acute respiratory illness in children. J. Med. Virol. 72:695-699.[CrossRef][Medline]
21 - Johnston, S. L., and D. A. J. Tyrreil. 1995. Rhinoviruses, p. 553-563. In E. H. Lennette, D. A. Lennette, and E. T. Lennette (ed.), Diagnostic procedures for viral, rickettsial, and chlamydial infections, 7th ed. American Public Health Association, Washington, DC.
22 - Joki-Korpela, P., and T. Hyypia. 2001. Parechoviruses, a novel group of human picornaviruses. Ann. Med. 33:466-471.[Medline]
23 - Kaiser, L., J. D. Aubert, J. C. Pache, C. Deffernez, T. Rochat, J. Garbino, W. Wunderli, P. Meylan, S. Yerly, L. Perrin, I. Letovanec, L. Nicod, C. Tapparel, and P. M. Soccal. 2006. Chronic rhinoviral infection in lung transplant recipients. Am. J. Respir. Crit. Care Med. 174:1392-1399.[Abstract/Free Full Text]
24 - Kämmerer, U., B. Kunkel, and K. Korn. 1994. Nested PCR for specific detection and rapid identification of human picornaviruses. J. Clin. Microbiol. 32:285-291.[Abstract/Free Full Text]
25 - Kares, S., M. Lonnrot, P. Vuorinen, S. Oikarinen, S. Taurianen, and H. Hyoty. 2004. Real-time PCR for rapid diagnosis of entero- and rhinovirus infections using LightCycler. J. Clin. Virol. 29:99-104.[CrossRef][Medline]
26 - Khetsuriani, N., N. N. Kazerouni, D. D. Erdman, X. Lu, S. C. Redd, L. J. Anderson, and W. G. Teague. 2007. Prevalence of viral respiratory tract infections in children with asthma. J. Allergy Clin. Immunol. 119:314-321.[CrossRef][Medline]
27 - King, A. M. Q., F. Brown, P. Christian, T. Hovi, T. Hyypiä, N. J. Knowles, S. M. Lemon, P. D. Minor, A. C. Palmenberg, T. Skern, and G. Stanway. 2000. Picornaviridae, p. 657-678. In M. H. V. van Regenmortel, C. M. Fauquet, D. H. L. Bishop, E. B. Carstens, M. K. Estes, S. M. Lemon, J. Maniloff, M. A. Mayo, D. J. McGeoch, C. R. Pringle, and R. B. Wickner (ed.), Virus taxonomy. Seventh report of the International Committee for the Taxonomy of Viruses. Academic Press, San Diego, CA.
28 - Kling, S., H. Donninger, Z. Williams, J. Vermeulen, E. Weinberg, K. Latiff, R. Ghildyal, and P. Bardin. 2005. Persistence of rhinovirus RNA after asthma exacerbation in children. Clin. Exp. Allergy 35:672-678.[CrossRef][Medline]
29 - Lamson, D., N. Renwick, V. Kapoor, Z. Liu, G. Palacios, J. Ju, A. Dean, K. St. George, T. Briese, and W. I. Lipkin. 2006. MassTag polymerase-chain-reaction detection of respiratory pathogens, including a new rhinovirus genotype that caused influenza-like illness in New York State during 2004-2005. J. Infect. Dis. 194:1398-1402.[CrossRef][Medline]
30 - Ledford, R. M., N. R. Patel, T. M. Demenczuk, A. Watanyar, T. Herbertz, M. S. Collett, and D. C. Pevear. 2004. VP1 sequencing of all human rhinovirus serotypes: insights into genus phylogeny and susceptibility to antiviral capsid-binding compounds. J. Virol. 78:3663-3674.[Abstract/Free Full Text]
31 - Loens, K., H. Goossens, C. de Laat, H. Foolen, P. Oudshoorn, S. Pattyn, P. Sillekens, and M. Ieven. 2006. Detection of rhinoviruses by tissue culture and two independent amplification techniques, nucleic acid sequence-based amplification and reverse transcription-PCR, in children with acute respiratory infections during a winter season. J. Clin. Microbiol. 44:166-171.[Abstract/Free Full Text]
32 - Lu, X., M. Chittaganpitch, S. J. Olsen, I. M. Mackay, T. P. Sloots, A. M. Fry, and D. D. Erdman. 2006. Real-time PCR assays for detection of bocavirus in human specimens. J. Clin. Microbiol. 44:3231-3235.[Abstract/Free Full Text]
33 - McErlean, P., L. A. Shackelton, S. B. Lambert, M. D. Nissen, T. P. Sloots, and I. M. Mackay. 2007. Characterisation of a newly identified human rhinovirus, HRV-QPM, discovered in infants with bronchiolitis. J. Clin. Virol. 39:67-75.[CrossRef][Medline]
34 - Miller, E. K., X. Lu, D. D. Erdman, K. A. Poehling, Y. Zhu, M. R. Griffin, T. V. Hartert, L. J. Anderson, G. A. Weinberg, C. B. Hall, M. K. Iwane, K. M. Edwards, and the New Vaccine Surveillance Network. 2007. Rhinovirus-associated hospitalizations in young children. J. Infect. Dis. 195:773-781.[CrossRef][Medline]
35 - Monto, A. S., A. M. Fendrick, and M. W. Sarnes. 2001. Respiratory illness caused by picornavirus infection: a review of clinical outcomes. Clin. Ther. 23:1615-1627.[CrossRef][Medline]
36 - Nicholson, K. G., J. Kent, V. Hammersley, and E. Cancio. 1996. Risk factors for lower respiratory complications of rhinovirus infections in elderly people living in the community: prospective cohort study. Br. Med. J. 313:1119-1123.[Abstract/Free Full Text]
37 - Nielsen, C. B., S. K. Singh, J. Wengel, and J. P. Jacobsen. 1999. The solution structure of a locked nucleic acid (LNA) hybridized to DNA. J. Biomol. Struct. Dyn. 17:175-191.[Medline]
38 - Nijhuis, M., N. van Maarseveen, R. Schuurman, S. Verkuijlen, M. de Vos, K. Hendriksen, and A. M. van Loon. 2002. Rapid and sensitive routine detection of all members of the genus enterovirus in different clinical specimens by real-time PCR. J. Clin. Microbiol. 40:3666-3670.[Abstract/Free Full Text]
39 - Nokso-Koivisto, J., T. J. Kinnari, P. Lindahl, T. Hovi, and A. Pitkäranta. 2002. Human picornavirus and coronavirus RNA in nasopharynx of children without concurrent respiratory symptoms. J. Med. Virol. 66:417-420.[CrossRef][Medline]
40 - Pallansch, M. A., and R. P. Roos. 2001. Enteroviruses: polioviruses, coxsackieviruses, echoviruses, and newer enterovirus, p. 723-775. In D. M. Knipe, P. M. Howley, D. E. Griffin, R. A. Lamb, M. A. Martin, B. Roizman, and S. E. Straus (ed.), Fields virology, 4th ed. Lippincott Williams & Wilkins, Philadelphia, PA.
41 - Papadopoulos, N. G., J. Hunter, G. Sanderson, J. Meyer, and S. L. Johnston. 1999. Rhinovirus identification by BglI digestion of picornavirus RT-PCR amplicons. J. Virol. Methods 80:179-185.[CrossRef][Medline]
42 - Pitkäranta, A., and F. G. Hayden. 1998. Rhinoviruses: important respiratory pathogens. Ann. Med. 30:529-537.[Medline]
43 - Savolainen, C., S. Blomqvist, M. N. Mulders, and T. Hovi. 2002. Genetic clustering of all 102 human rhinovirus prototype strains: serotype 87 is close to human enterovirus 70. J. Gen. Virol. 83:333-340.[Abstract/Free Full Text]
44 - Scheltinga, S. A., K. E. Templeton, M. F. Beersma, and E. C. Claas. 2005. Diagnosis of human metapneumovirus and rhinovirus in patients with respiratory tract infections by an internally controlled multiplex real-time RNA PCR. J. Clin. Virol. 33:306-311.[CrossRef][Medline]
45 - Schrag, S. J., J. T. Brooks, C. Van Beneden, U. D. Parashar, P. M. Griffin, L. J. Anderson, W. J. Bellini, R. F. Benson, D. D. Erdman, A. Klimov, T. G. Ksiazek, T. C. Peret, D. F. Talkington, W. L. Thacker, M. L. Tondella, J. S. Sampson, A. W. Hightower, D. F. Nordenberg, B. D. Plikaytis, A. S. Khan, N. E. Rosenstein, T. A. Treadwell, C. G. Whitney, A. E. Fiore, T. M. Durant, J. F. Perz, A. Wasley, D. Feikin, J. L. Herndon, W. A. Bower, B. W. Klibourn, D. A. Levy, V. G. Coronado, J. Buffington, C. A. Dykewicz, R. F. Khabbaz, and M. E. Chamberland. 2004. SARS surveillance during emergency public health response, United States, March-July 2003. Emerg. Infect. Dis. 10:185-194.[Medline]
46 - Smyth, A. R., R. L. Smyth, C. Y. Tong, C. A. Hart, and D. P. Heaf. 1995. Effect of respiratory virus infections including rhinovirus on clinical status in cystic fibrosis. Arch. Dis. Child. 73:117-120.[Abstract/Free Full Text]
47 - Verstrepen, W. A., S. Kuhn, M. M. Kockx, M. E. Van De Vyvere, and A. H. Mertens. 2001. Rapid detection of enterovirus RNA in cerebrospinal fluid specimens with a novel single-tube real-time reverse transcription-PCR assay. J. Clin. Microbiol. 39:4093-4096.[Abstract/Free Full Text]
48 - Wald, T., P. Shult, P. Krause, B. Miller, P. Drinka, and S. Gravenstein. 1995. A rhinovirus outbreak among residents of a long-term care facility. Ann. Intern. Med. 123:588-593.[Abstract/Free Full Text]
49 - Wittwer, C. T., M. G. Herrmann, A. A. Moss, and R. P. Rasmussen. 1997. Continuous fluorescence monitoring of rapid cycle DNA amplification. BioTechniques 22:130-138.[Medline]
50 - Witwer, C., S. Rauscher, I. L. Hofacker, and P. F. Stadler. 2001. Conserved RNA secondary structures in Picornaviridae genomes. Nucleic. Acids Res. 29:5079-5089.[Abstract/Free Full Text]
51 - Wright, P. F., A. M. Deatly, R. A. Karron, R. B. Belshe, J. R. Shi, W. C. Gruber, Y. Zhu, and V. B. Randolph. 2007. Comparison of results of detection of rhinovirus by PCR and viral culture in human nasal wash specimens from subjects with and without clinical symptoms of respiratory illness. J. Clin. Microbiol. 45:2126-2129.[Abstract/Free Full Text]
Journal of Clinical Microbiology, February 2008, p. 533-539, Vol. 46, No. 2
0095-1137/08/$08.00+0 doi:10.1128/JCM.01739-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
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