A recently identified rhinovirus genotype is associated with severe respiratory-tract infection in children in Germany

Molecular detection of rhinoviruses

Rhinoviruses are a frequent cause of the common cold and more serious illnesses, such as otitis media, sinusitis and asthma exacerbations and, more infrequently, have been implicated in lower airway infections, including pneumonia and exacerbations of chronic obstructive pulmonary disease and cystic fibrosis. Diagnosis of rhinovirus infections is best achieved using sensitive and specific reverse-transcription (RT)-PCR assays. The article by Do et al. describes the development and validation of a new one-step, TaqMan RT-PCR assay targeting the rhinovirus noncoding region for the detection of rhinovirus RNA in respiratory specimens from children with upper respiratory symptoms. The assay was rapid and specific and sensitive compared with cell culture. The recent use of RT-PCR assays for the detection of rhinoviruses in clinical specimens has provided more accurate information about the disease burden and epidemiology of these ubiquitous viruses.

Association between human rhinovirus C and severity of acute asthma in children

A new and potentially more pathogenic group of human rhinovirus (HRV), group C (HRVC), has recently been discovered. We hypothesised that HRVC would be present in children with acute asthma and cause more severe attacks than other viruses or HRV groups. Children with acute asthma (n = 128; age 2-16 yrs) were recruited on presentation to an emergency department. Asthma exacerbation severity was assessed, and respiratory viruses and HRV strains were identified in a nasal aspirate. The majority of the children studied had moderate-to-severe asthma (85.2%) and 98.9% were admitted to hospital. HRV was detected in 87.5% and other respiratory viruses in 14.8% of children, most of whom also had HRV. HRVC was present in the majority of children with acute asthma (59.4%) and associated with more severe asthma. Children with HRVC (n = 76) had higher asthma severity scores than children whose HRV infection was HRVA or HRVB only (n = 34; p = 0.018), and all other children (n = 50; p = 0.016). Of the 19 children with a non-HRV virus, 13 had HRV co-infections, seven of these being HRVC. HRVC accounts for the majority of asthma attacks in children presenting to hospital and causes more severe attacks than previously known HRV groups and other viruses.

[Bronchiolitis viruses]

In Normandy (France), human respiratory syncytial virus (hRSV) was detected in 64.1% of acute bronchiolitis in hospitalized children, rhinovirus in 26.8%, human metapneumovirus (hMPV) in 7.6%, and parainfluenza virus (PIV) in 3.4%. The viruses causing acute bronchiolitis in the community were hRSV (42%), rhinovirus (19.5%), coronavirus (8%), PIV (3.5%), and hMPV (2.5%). In 53.7% of the cases, hRSV infected infants (86.9%), 53.7% being less than 6 months of age. Of the hRSV cases, 48.2% were detected in November and December and 44.5% in January and February. The hRSV epidemic started the 1st or 2nd week of October but it varied from one year to another and from one region to another. hRSV acute bronchiolitis increased from 261 cases in epidemics from 1999-2003 to 341 cases from 2004-2009. Rhinoviruses gave acute bronchiolitis in 38.4% of cases. A rate of 54.6% of viruses was detected in September and October and 38.5% in March and April. A total of 34.2% of infected infants were under 6 months of age, 37.8% between 6 months and 2 years, and 19.5% were between 2 and 5 years old. hMPV epidemics coincided with hRSV epidemics, but they accounted for one-sixth the number of cases. HMPV infected infants (74%) who were older than those infected with hRSV, and the diagnosis was bronchiolitis (59%) and pneumonia (17%). PIV infections (about 100 cases per year) included PIV3 (62.7%), PIV1 (25.3%), and PIV2 (7.3%). PIV1 infections occurred every 2 years in the fall. PIV3 infections were observed every year during the fall and winter, with peaks of infections in the spring in the years without PIV1. There were acute cases of bronchiolitis in 29.8% of PIV3 infections and 18.3% in PIV1 infections.

The ABCs of rhinoviruses, wheezing, and asthma

Human rhinoviruses (HRVs) were discovered as common cold pathogens over 50 years ago. Recent advances in molecular viral diagnostics have led to an appreciation of their role in more-significant respiratory illnesses, including bronchiolitis in infancy, childhood pneumonia, and acute exacerbations of chronic respiratory diseases such as asthma, chronic obstructive lung disease, and cystic fibrosis. Until a few years ago, only two groups of HRVs (A and B) had been recognized. However, full and partial sequencing of HRVs led to the discovery of a third species of HRV (HRV-C) that has distinct structural and biologic features. Risk factors and pathogenic mechanisms for more-severe HRV infections are being defined, and yet fundamental questions persist about mechanisms relating this common pathogen to allergic diseases and asthma. The close relationship between HRV infections and asthma suggests that antiviral treatments could have a major impact on the morbidity associated with this chronic respiratory disease.

Analysis of genetic diversity and sites of recombination in human rhinovirus species C

Human rhinoviruses (HRVs) are a highly prevalent and diverse group of respiratory viruses. Although HRV-A and HRV-B are traditionally detected by virus isolation, a series of unculturable HRV variants have recently been described and assigned as a new species (HRV-C) within the picornavirus Enterovirus genus. To investigate their genetic diversity and occurrence of recombination, we have performed comprehensive phylogenetic analysis of sequences from the 5' untranslated region (5' UTR), VP4/VP2, VP1, and 3Dpol regions amplified from 89 HRV-C-positive respiratory samples and available published sequences. Branching orders of VP4/VP2, VP1, and 3Dpol trees were identical, consistent with the absence of intraspecies recombination in the coding regions. However, numerous tree topology changes were apparent in the 5' UTR, where >60% of analyzed HRV-C variants showed recombination with species A sequences. Two recombination hot spots in stem-loop 5 and the polypyrimidine tract in the 5' UTR were mapped using the program GroupingScan. Available HRV-C sequences showed evidence for additional interspecies recombination with HRV-A in the 2A gene, with breakpoints mapping precisely to the boundaries of the C-terminal domain of the encoded proteinase. Pairwise distances between HRV-C variants in VP1 and VP4/VP2 regions fell into two separate distributions, resembling inter- and intraserotype distances of species A and B. These observations suggest that, without serological cross-neutralization data, HRV-C genetic groups may be equivalently classified into types using divergence thresholds derived from distance distributions. The extensive sequence data from multiple genome regions of HRV-C and analyses of recombination in the current study will assist future formulation of consensus criteria for HRV-C type assignment and identification.

Newly identified human rhinoviruses: molecular methods heat up the cold viruses

Human rhinovirus (HRV) infections cause at least 70% of virus‐related wheezing exacerbations and cold and flu‐like illnesses. They are associated with otitis media, sinusitis and pneumonia. Annually, the economic impact of HRV infections costs billions in healthcare and lost productivity. Since 1987, 100 officially recognised HRV serotypes reside in two genetically distinct species; HRV A and HRV B, within the genus Enterovirus, family Picornaviridae. Sequencing of their ∼7kb genomes was finalised in 2009. Since 1999, many globally circulating, molecularly‐defined ‘strains’, perhaps equivalent to novel serotypes, have been discovered but remain uncharacterised. Many of these currently unculturable strains have been assigned to a proposed new species, HRV C although confusion exists over the membership of the species. There has not been sufficient sampling to ensure the identification of all strains and no consensus criteria exist to define whether clinical HRV detections are best described as a distinct strain or a closely related variant of a previously identified strain (or serotype). We cannot yet robustly identify patterns in the circulation of newly identified HRVs (niHRVs) or the full range of associated illnesses and more data are required. Many questions arise from this new found diversity: what drives the development of so many distinct viruses compared to other species of RNA viruses? What role does recombination play in generating this diversity? Are there species‐ or strain‐specific circulation patterns and clinical outcomes? Are divergent strains sensitive to existing capsid‐binding antivirals? This update reviews the findings that trigger these and other questions arising during the current cycle of intense rhinovirus discovery. Copyright © 2010 John Wiley & Sons, Ltd.

Human rhinoviruses in Chinese adults with acute respiratory tract infection

Objective

To evaluate the roles of human rhinoviruses (HRVs) in acute respiratory tract infections (ARTIs) in Chinese adults and determine the association between species of HRV and clinical presentations.

Methods

RT-PCR methods were used to detect HRVs in throat and nasal swabs collected from 6104 adult patients with ARTIs from December 2005 to April 2008 in Beijing, China.

Results

HRV strains were detected in 271 ARTIs cases, 65% of which tested positive for HRV-A, 25% for HRV-B, and 10% for HRV-C. Aside from fever, pharyngeal congestion and headache were the most common clinical symptoms observed in the HRVs infected patients. HRV-A infected patients had a higher percentage of upper respiratory symptoms than patients infected by the two other HRV species. Systemic symptoms such as chilliness and myalgia were more frequent in people infected by HRV-B. The three HRV species exhibited unique infection timing when analyzed monthly.

Conclusion

HRV-C can be detected in adult patients with acute upper respiratory tract infections, but is not the predominant species in this population.

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

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.

Prospective evaluation of a novel multiplex real-time PCR assay for detection of fifteen respiratory pathogens-duration of symptoms significantly affects detection rate

BACKGROUND

Nucleic acid amplification techniques have improved the diagnostic possibilities in respiratory tract infections, although their clinical applicability is not yet fully defined. We have evaluated a multiplex real-time PCR method for the detection of 13 respiratory viruses and 2 bacteria (Mycoplasma and Chlamydophila) in a clinical setting.

OBJECTIVES

The aim of the present study was to evaluate the diagnostic performance and clinical use of a novel multiplex PCR method in adults with community-acquired respiratory viral infection, and the impact of duration of symptoms on detection rates.

STUDY DESIGN

Nasopharyngeal swab samples were prospectively collected from 209 adult outpatients with respiratory infections and 100 asymptomatic controls.

RESULTS

An infectious agent was identified in 43% of samples from patients and 2% of asymptomatic controls. The detection rate was significantly higher in samples from patients with a duration of symptoms of 6 days or less (51%) than in samples from patients with a duration of symptoms of 7 days or more (30%, p<0.01). For human corona viruses, and influenza virus A and B there was a correlation between the amount of virus in each patient sample as measured Ct values and duration of symptoms.

CONCLUSIONS

Duration of symptoms significantly affects the detection rate of respiratory pathogens by multiplex real-time PCR in nasopharyngeal swab samples from adult patients with respiratory infections. Our finding should be taken into account when using these tests in clinical practise.

Genetics, recombination and clinical features of human rhinovirus species C (HRV-C) infections; interactions of HRV-C with other respiratory viruses

To estimate the frequency, molecular epidemiological and clinical associations of infection with the newly described species C variants of human rhinoviruses (HRV), 3243 diagnostic respiratory samples referred for diagnostic testing in Edinburgh were screened using a VP4-encoding region-based selective polymerase chain reaction (PCR) for HRV-C along with parallel PCR testing for 13 other respiratory viruses. HRV-C was the third most frequently detected behind respiratory syncytial virus (RSV) and adenovirus, with 141 infection episodes detected among 1885 subjects over 13 months (7.5%). Infections predominantly targeted the very young (median age 6–12 months; 80% of infections in those <2 years), occurred throughout the year but with peak incidence in early winter months. HRV-C was detected significantly more frequently among subjects with lower (LRT) and upper respiratory tract (URT) disease than controls without respiratory symptoms; HRV-C mono-infections were the second most frequently detected virus (behind RSV) in both disease presentations (6.9% and 7.8% of all cases respectively). HRV variants were classified by VP4/VP2 sequencing into 39 genotypically defined types, increasing the current total worldwide to 60. Through sequence comparisons of the 5′untranslated region (5′UTR), the majority grouped with species A (n = 96; 68%, described as HRV-Ca), the remainder forming a phylogenetically distinct 5′UTR group (HRV-Cc). Multiple and bidirectional recombination events between HRV-Ca and HRV-Cc variants and with HRV species A represents the most parsimonious explanation for their interspersed phylogeny relationships in the VP4/VP2-encoding region. No difference in age distribution, seasonality or disease associations was identified between HRV-Ca and HRV-Cc variants. HRV-C-infected subjects showed markedly reduced detection frequencies of RSV and other respiratory viruses, providing evidence for a major interfering effect of HRV-C on susceptibility to other respiratory virus infections. HRV-C's disease associations, its prevalence and evidence for interfering effects on other respiratory viruses mandates incorporation of rhinoviruses into future diagnostic virology screening.

All known human rhinovirus species are present in sputum specimens of military recruits during respiratory infection

Human rhinoviruses (HRV) are known to cause common cold as well as more complicated respiratory infections. HRV species -A, -B and -C have all been associated with lower respiratory infections and exacerbations of asthma. However, the type distribution of strains connected to different kinds of lower respiratory conditions is not clearly known. We have analysed the presence of HRV in sputum specimens derived from military recruits with and without pre-diagnosed asthma at times of acute respiratory infection (CIAS Study, 2004-2005). The analysis was performed with HRV and HEV real-time RT-PCR assays. Subsequently we studied type distribution of HRV strains by genetic typing in the VP4/VP2 genomic region. In total 146 (38.8%) specimens were HRV-positive and 36 (9.3%) HEV-positive. No difference was found in HRV detection between the asthmatic vs. non-asthmatic patients. Most of the genetically typed strains, 18 (62.1%), belonged to HRV-A, while HRV-B strains constituted five (17.2%) of the HRV-positive strains. HRV-C strain was typed four times from the HRV-positive cases and a HEV-D strain twice. We further typed six HEV positive strains in the partial VP1 region. Three of these belonged to HRV-A and three to HEV-D. HRV-A strains were discovered throughout the study period, while HRV-C strains originated from winter and spring specimens. Interestingly, four out of five typed HRV-B strains originated from the summer season specimens.

Full-genome sequence and analysis of a novel human rhinovirus strain within a divergent HRV-A clade

Genome sequences of human rhinoviruses (HRV) have primarily been from stocks collected in the 1960s, with genomes and phylogeny of modern HRVs remaining undefined. Here, two modern isolates (hrv-A101 and hrv-A101-v1) collected approximately 8 years apart were sequenced in their entirety. Incorporation into our full-genome HRV alignment with subsequent phylogenetic network inference indicated that these represent a unique HRV-A, localized within a distinct divergent clade. They appear to have resulted from recombination of the hrv-65 and hrv-78 lineages. These results support our contention that there are unrecognized distinct HRV-A strains, and that recombination is evident in currently circulating strains.

Clinical and molecular epidemiology of human rhinovirus C in children and adults in Hong Kong reveals a possible distinct human rhinovirus C subgroup

BackgroundA novel human rhinovirus (HRV) species, HRV-C, was recently discovered, but its clinical features and epidemiology, compared with HRV-A and HRV-B, remains poorly understood, especially in adults

MethodsOne thousand two hundred nasopharyngeal aspirate samples obtained from hospitalized children and adults during a 1-year period were subject to reverse-transcriptase polymerase chain reaction to detect HRV. The clinical and molecular epidemiology of the 3 HRV species was analyzed

ResultsHRVs were detected in 178 (29.7%) of 600 nasopharyngeal aspirate samples from children and 42 (7%) of 600 nasopharyngeal aspirate samples from adults. HRV-A was most prevalent (n=111), followed by HRV-C (n=91) and HRV-B (n=18). Although upper respiratory tract infection was the most common presentation in children, 8 (62%) of the 13 adults with HRV-C infection had pneumonia, compared with 6 (27%) of the 22 adults with HRV-A infection (P<.05). Wheezing episodes were also more common among individuals with HRV-C (37%) and HRV-A (20%) infection than among those with HRV-B (0%) infection (P<.05). Clinical and molecular data analysis revealed HRV-C as a frequent cause of community and institutionalized outbreaks. A diverse set of HRV-C genotypes was circulating throughout the year, among which a potential distinct subgroup of strains was observed

ConclusionHRV-C is associated with pneumonia in adults and outbreaks of respiratory infections requiring hospitalization. A potential novel HRV-C subgroup was identified

Diagnostics and discovery in viral hemorrhagic fevers

The rate of discovery of new microbes and of new associations of microbes with health and disease is accelerating. Many factors contribute to this phenomenon including those that favor the true emergence of new pathogens as well as new technologies and paradigms that enable their detection and characterization. This chapter reviews recent progress in the field of pathogen surveillance and discovery with a focus on viral hemorrhagic fevers.

Rhinovirus infections in children: a retrospective and prospective hospital-based study

To analyze clinical characteristics and prevalence of rhinovirus infections in children in the hospital, we reviewed a retrospective dataset from a 20-year period, and conducted a short-term prospective study. Records of children and adolescents treated at our hospital during 1987-2006 with a documented rhinovirus infection were reviewed and compared with patients with other respiratory virus infections. Prospective study included all children >or=1 month of age admitted to pediatric infectious disease ward during an autumn period. Rhinoviruses were detected by reverse transcription-PCR and/or culture, and sequence analysis was used for virus typing. In the retrospective study, the median age of 580 children with rhinovirus infection was 1.9 years (interquartile range, 1.0-4.3 years), and 27% had an underlying medical condition. Eighty-four children (16% of in-patients) were treated at pediatric intensive care unit. Twenty-one children (4%) had a hospital-acquired rhinovirus infection. In the prospective study, rhinoviruses were detected in 28% of 163 hospital episodes. Acute wheezing illness was diagnosed in 61% of children with rhinovirus and in 31% of children with respiratory syncytial virus, enterovirus, or no study virus (P < 0.001). One-half of sequence-analyzed rhinovirus strains belonged to the newly identified C group. In conclusion, rhinovirus infections are a frequent cause of pediatric hospitalizations, and they are common also at the intensive care unit. Acute wheezing is the most frequent manifestation in hospital setting, but the range of clinical presentations is wide. Group C rhinoviruses may account for a large part of rhinovirus hospitalizations.

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

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.

Evidence of recombination and genetic diversity in human rhinoviruses in children with acute respiratory infection

Background

Human rhinoviruses (HRVs) are a highly prevalent cause of acute respiratory infection in children. They are classified into at least three species, HRV-A, HRV-B and HRV-C, which are characterized by sequencing the 5′ untranslated region (UTR) or the VP4/VP2 region of the genome. Given the increased interest for novel HRV strain identification and their worldwide distribution, we have carried out clinical and molecular diagnosis of HRV strains in a 2-year study of children with acute respiratory infection visiting one district hospital in Shanghai.

Methodology/Findings

We cloned and sequenced a 924-nt fragment that covered part of the 5′UTR and the VP4/VP2 capsid genes. Sixty-four HRV-infected outpatients were diagnosed amongst 827 children with acute low respiratory tract infection. Two samples were co-infected with HRV-A and HRV-B or HRV-C. By comparative analysis of the VP4/VP2 sequences of the 66 HRVs, we showed a high diversity of strains in HRV-A and HRV-B species, and a prevalence of 51.5% of strains that belonged to the recently identified HRV-C species. When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. We confirmed the close relationship of their structural proteins but showed apparent additional recombination events in the 2A gene and 3′UTR of the HRV-Ca strain. Double or triple infections with HRV-C and respiratory syncytial virus and/or bocavirus were diagnosed in 33.3% of the HRV-infected patients, but no correlation with severity of clinical outcome was observed.

Conclusion

Our study showed a high diversity of HRV strains that cause bronchitis and pneumonia in children. A predominance of HRV-C over HRV-A and HRV-B was observed, and two subspecies of HRV-C were identified, the diversity of which seemed to be related to recombination with former HRV-A strains. None of the HRV-C strains appeared to have a higher clinical impact than HRV-A or HRV-B on respiratory compromise.

Detection of tick-borne pathogens by MassTag polymerase chain reaction

MassTag polymerase chain reaction (PCR) is a platform that enables microbe detection using primers labeled through a photocleavable link with tags that vary in molecular weight. After multiplex PCR, tags are released by ultraviolet irradiation and analyzed by mass spectroscopy. The identification of a microbe in a sample is determined by its cognate tags. Here we describe establishment and implementation of a MassTag PCR panel for surveillance of microbes implicated in tick-vectored infectious diseases.

Bugs and asthma: a different disease?

The prevalence of asthma has dramatically increased in recent decades. Exacerbations of asthma are a large contributor to asthma-related costs, and are primarily caused by viral and atypical bacterial infections. Rhinoviruses (RVs) are the most common viruses detected after an asthma exacerbation. RVs, respiratory syncytial virus (RSV), and human metapneumovirus (hMPV) viral infections early in life can induce wheezing and are associated with the development of asthma later in life. Atypical bacterial infections from Mycoplasma pneumoniae and Chlamydia pneumoniae have also been linked to chronic asthma and potential asthma exacerbations. In this article, we will discuss recent developments in viral infections, specifically RV, RSV, and hMPV, and atypical bacterial infections as causes of asthma exacerbations, including new data focusing on the host immune response in airway epithelial cells and animal models of infection.

New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses

Increased genomic diversity of these viruses is demonstrated.

Rhinoviruses and enteroviruses are leading causes of respiratory infections. To evaluate genotypic diversity and identify forces shaping picornavirus evolution, we screened persons with respiratory illnesses by using rhinovirus-specific or generic real-time PCR assays. We then sequenced the 5′ untranslated region, capsid protein VP1, and protease precursor 3CD regions of virus-positive samples. Subsequent phylogenetic analysis identified the large genotypic diversity of rhinoviruses circulating in humans. We identified and completed the genome sequence of a new enterovirus genotype associated with respiratory symptoms and acute otitis media, confirming the close relationship between rhinoviruses and enteroviruses and the need to detect both viruses in respiratory specimens. Finally, we identified recombinants among circulating rhinoviruses and mapped their recombination sites, thereby demonstrating that rhinoviruses can recombine in their natural host. This study clarifies the diversity and explains the reasons for evolution of these viruses.

Prevalence of human respiratory viruses in adults with acute respiratory tract infections in Beijing, 2005-2007

To determine the aetiological role and epidemiological profile of common respiratory viruses in adults with acute respiratory tract infections (ARTIs), a 2-year study was conducted in Beijing, China, from May 2005 to July 2007. Nose and throat swab samples from 5808 ARTI patients were analysed by PCR methods for common respiratory viruses, including influenza viruses (IFVs) A, B, and C, parainfluenza viruses (PIVs) 1-4, enteroviruses (EVs), human rhinoviruses (HRVs), respiratory syncytial virus (RSV), human metapneumovirus (HMPV), human coronaviruses (HCoVs) OC43, 229E, NL63, and HKU1, and adenoviruses (ADVs). Viral pathogens were detected in 34.6% of patient samples, and 1.6% of the patients tested positive for more than one virus. IFVs (19.3%) were the dominant agents detected, followed by HRVs (6.5%), PIVs (4.3%), EVs (3.2%), and HCoVs (1.1%). ADVs, RSV and HMPV were also detected (<1%). The viral detection rates differed significantly between infections of the lower and upper respiratory tracts in the sample population: PIVs, the second most commonly detected viral agents in lower acute respiratory tract infections (LRTIs), were more prevalent than in upper acute respiratory tract infections, indicating that the pathogenic role of PIVs in LRTIs should be investigated. Currently, this study is the largest-scale investigation of respiratory virus infections in China with multiple agent detection, providing baseline data for further studies of respiratory virus infections in adults with ARTIs.

Pneumonia and pericarditis in a child with HRV-C infection: a case report

Human rhinovirus type C is a recently discovered species that has been associated with respiratory tract infections of unusual severity in some cases. However, the precise type of diseases associated with this new human rhinovirus needs to be investigated. In the present report, we used adapted real-time PCR assays to screen different clinical specimens collected from a 14-month-old boy presenting an acute lower respiratory tract disease complicated by a severe pericarditis. RT-PCR identified picornavirus RNA in the bronchoalveolar lavage (BAL) specimen, pericardial fluid, plasma and stools. This supported the existence of a disseminated viral infection that extended to the pericardial space. 5′UTR and VP1 sequence analysis performed directly from the BAL sample allowed genotyping of the virus as a human rhinovirus C. This observation highlights the need for adapted diagnostic tools and the potential for the new rhinovirus species C to cause complications, including pericarditis.

Detection of human rhinovirus C in children with acute lower respiratory tract infections in South Korea

Recently, HRV-C was identified as a new species of HRV, but its spectrum of clinical disease is still not clear. The purpose of this study was to investigate the molecular epidemiology of HRVs in children with acute lower respiratory tract infections (LRTIs). A total of 54 HRV-positive samples that were negative for other respiratory viruses were sequenced. HRV-A was detected in 33, HRV-B in 4, and HRV-C in 17 of these samples. All HRV-C-positive patients showed favorable clinical outcomes. We confirmed the presence of HRV-C in children with LRTIs, but its association with clinical severity is not clear.

New molecular detection tools adapted to emerging rhinoviruses and enteroviruses

Human rhinoviruses (HRV), and to a lesser extent human enteroviruses (HEV), are important respiratory pathogens. Like other RNA viruses, these picornaviruses have an intrinsic propensity to variability. This results in a large number of different serotypes as well as the incessant discovery of new genotypes. This large and growing diversity not only complicates the design of real-time PCR assays but also renders immunofluorescence unfeasible for broad HRV and HEV detection or quantification in cells. In this study, we used the 5' untranslated region, the most conserved part of the genome, as a target for the development of both a real-time PCR assay (Panenterhino/Ge/08) and a peptide nucleic acid-based hybridization oligoprobe (Panenterhino/Ge/08 PNA probe) designed to detect all HRV and HEV species members according to publicly available sequences. The reverse transcription-PCR assay has been validated, using not only plasmid and viral stocks but also quantified RNA transcripts and around 1,000 clinical specimens. These new generic detection PCR assays overcame the variability of circulating strains and lowered the risk of missing emerging and divergent HRV and HEV. An additional real-time PCR assay (Entero/Ge/08) was also designed specifically to provide sensitive and targeted detection of HEV in cerebrospinal fluid. In addition to the generic probe, we developed specific probes for the detection of HRV-A and HRV-B in cells. This investigation provides a comprehensive toolbox for accurate molecular identification of the different HEV and HRV circulating in humans.

Epidemiological and clinical study of viral respiratory tract infections in children from Italy

Impact of recently discovered viruses on epidemiology of acute respiratory tract infections (ARTI) is still unclear. We studied the impact of recently discovered human metapneumovirus (hMPV), human bocavirus (HBoV), and new coronaviruses (HCoV‐NL63 and HKU1) on the global epidemiology of ARTI. From October 2006 to April 2007, 237 pediatric patients affected by ARTI were enrolled in our study. Specimens were tested for respiratory viruses by polymerase chain reaction. One hundred twenty‐four out of 237 samples (52.3%) were positive for one or more viruses. Picornaviruses were the most prevalent viruses (n = 61, 43.6%), followed by respiratory syncytial virus (n = 34, 24.3%) and Adenovirus (n = 25, 17.9%); hMPV (n = 9, 6.4%) was the fourth most common virus detected. HBoV and HCoV showed a low prevalence (respectively 2.9% and 2.1%). RSV was the prevalent agent of LRTI (38%). Viruses were identified in more than 50% of the studied ARTI, providing useful information on clinical features and epidemiology of specific agents affecting children in cold months. Although routine surveillance of respiratory viruses does not seem cost‐effective, continuous monitoring of ARTI etiology could be a useful tool for planning resources for the development of new vaccines and antiviral agents. J. Med. Virol. 81:750–756, 2009 © 2009 Wiley‐Liss, Inc.

Novel human rhinoviruses and exacerbation of asthma in children

To determine links between human rhinoviruses (HRV) and asthma, we used data from a case–control study, March 2003–February 2004, among children with asthma. Molecular characterization identified several likely new HRVs and showed that association with asthma exacerbations was largely driven by HRV-A and a phylogenetically distinct clade of 8 strains, genogroup C.

Etiology of community-acquired pneumonia in hospitalized children based on WHO clinical guidelines

Community-acquired pneumonia (CAP) is a major cause of death in developing countries and of morbidity in developed countries. The objective of the study was to define the causative agents among children hospitalized for CAP defined by WHO guidelines and to correlate etiology with clinical severity and surrogate markers. Investigations included an extensive etiological workup. A potential causative agent was detected in 86% of the 99 enrolled patients, with evidence of bacterial (53%), viral (67%), and mixed (33%) infections. Streptococcus pneumoniae was accounted for in 46% of CAP. Dehydration was the only clinical sign associated with bacterial pneumonia. CRP and PCT were significantly higher in bacterial infections. Increasing the number of diagnostic tests identifies potential causes of CAP in up to 86% of children, indicating a high prevalence of viruses and frequent co-infections. The high proportion of pneumococcal infections re-emphasizes the importance of pneumococcal immunization.

A novel group of rhinoviruses is associated with asthma hospitalizations

BACKGROUND

Although recent studies have identified new group C human rhinoviruses (HRVCs), their spectrum of pediatric disease is unknown.

OBJECTIVE

We sought to determine the presentation and burden of disease caused by HRVCs among young hospitalized children.

METHODS

We conducted prospective population-based surveillance in 2 US counties among children less than 5 years of age hospitalized with acute respiratory illness or fever from October 2001 through September 2003. Nasal/throat swabs were obtained and tested for HRVs, as determined by means of RT-PCR and then characterized by means of partial sequencing.

RESULTS

Of 1052 children enrolled and tested during the 2-year period, 167 (16%) had HRVs detected. Of 147 samples successfully sequenced, 64 were group A HRVs, 6 were group B HRVs, and 77 were HRVCs. Children with HRVCs were significantly more likely than those with group A HRVs to have underlying high-risk conditions, such as asthma (42% vs 23%, P = .023) and to have had a discharge diagnosis of asthma (55% vs 36%, P = .022).

CONCLUSIONS

Overall, HRVCs were detected in 7% of children hospitalized for fever or respiratory conditions and constituted almost half of all rhinovirus-associated hospitalizations, suggesting that this novel group causes a substantial burden of pediatric disease.

Novel species of human rhinoviruses in acute otitis media

We have studied human rhinovirus (HRV) recovered from nasopharyngeal aspirates and middle ear fluids collected during acute otitis media with RT-PCR sequencing followed by phylogenetic analysis. In addition to a great diversity of traditional HRV types we found genetic relatives of the novel HRV species, suggested HRV-C, in both sample types. Our results indicate the presence of HRV-C in the middle ear for the first time.

Epidemiology

The common cold is the result of an upper respiratory tract infection causing an acute syndrome characterised by a combination of non-specific symptoms, including sore throat, cough, fever, rhinorrhoea, malaise, headache, and myalgia. Respiratory viruses, alone or in combination, are the most common cause. The course f illness can be complicated by bacterial agents, causing pharyngitis or sinusitis, but the are a rare cause of cold and flu-like illnesses (CFLIs). Our understanding of CFLI epidemiology has been enhanced by molecular detection methods, particularly polymerase chain reaction (PCR) testing. PCR has not only improved detection of previously known viruses, but within the last decade has resulted in the detection of many divergent novel respiratory virus species. Human rhinovirus (HRV) infections cause nearly all CFLIs and they can be responsible for asthma and chronic obstructive pulmonary disease exacerbations. HRVs are co-detected with other respiratory viruses in statistically significant patterns, with HRVs occurring in the lowest proportion of co-detections, compared to most other respiratory viruses. Some recently identified rhinoviruses may populate an entirely new putative HRV species; HRV C. Further work is required to confirm a causal role for these newly identified viruses in CFLIs. The burden of illness associated with CFLIs is poorly documented, but where data are available, the impact of CFLIs is considerable. Individual infections, although they do not commonly result in more severe respiratory tract illness, are associated with substantial direct and indirect resource use. The product of frequency and burden for CFLIs is likely to be greater in magnitude than for any other respiratory syndrome, but further work is required to document this. Our understanding of the viral causes of CLFIs, although incomplete, has improved in recent years. Documenting burden is also an important step in progress towards improved control and management of these illnesses.

Rhinoviruses are a major cause of wheezing and hospitalization in children less than 2 years of age

BACKGROUND

Human rhinoviruses (HRV) are now considered major respiratory pathogens. We sought to determine whether HRV are a cause of wheezing and/or hospitalization in children <2 years old.

METHODS

A polymerase chain reaction assay was used to screen for HRV infection in 4 categories of children <2 years old: (1) with symptoms of respiratory tract disease without wheezing; (2) with wheezing with or without other symptoms; (3) who were asymptomatic and; (4) who had a respiratory specimen submitted to a diagnostic laboratory. All specimens were collected between January and December 2004. Phylogenetic analyses were performed on most HRV isolates.

RESULTS

Twenty-eight (17%) of 165 children with symptoms of respiratory infection without wheezing; 21 (26.3%) of 80 children with wheezing; 3 (3%) of 93 asymptomatic children; and 47 (23.3%) of 202 children with specimens submitted to the diagnostic laboratory tested positive for HRV. The difference between the rates of infection in the asymptomatic group and in each of the 3 other categories was statistically significant (P </= 0.01). Among HRV-positive children with samples submitted to the diagnostic laboratory, 55% were hospitalized, which was similar to that observed for respiratory syncytial virus (52.7%) among children of a similar age group and time period (P = 0.85). Diverse groups of HRV were circulating during the 1-year study period.

CONCLUSIONS

HRV are important pathogens among children <2 years old and are responsible for a significant proportion of wheezing this age group. The hospitalization rates of HRV-positive children seem to be similar to that of respiratory syncytial virus.

Multiplex MassTag-PCR for respiratory pathogens in pediatric nasopharyngeal washes negative by conventional diagnostic testing shows a high prevalence of viruses belonging to a newly recognized rhinovirus clade

BACKGROUND

Respiratory infections are the most common infectious diseases in humans worldwide and are a leading cause of death in children less than 5 years of age.

OBJECTIVES

Identify candidate pathogens in pediatric patients with unexplained respiratory disease.

STUDY DESIGN

Forty-four nasopharyngeal washes collected during the 2004-2005 winter season from pediatric patients with respiratory illnesses that tested negative for 7 common respiratory pathogens by culture and direct immunofluorescence assays were analyzed by MassTag-PCR. To distinguish human enteroviruses (HEV) and rhinoviruses (HRV), samples positive for picornaviruses were further characterized by sequence analysis.

RESULTS

Candidate pathogens were detected by MassTag PCR in 27 of the 44 (61%) specimens that previously were rated negative. Sixteen of these 27 specimens (59%) contained picornaviruses; of these 9 (57%) contained RNA of a recently discovered clade of rhinoviruses. Bocaviruses were detected in three patients by RT-PCR.

CONCLUSIONS

Our study confirms that multiplex MassTag-PCR enhances the detection of pathogens in clinical specimens, and shows that previously unrecognized rhinoviruses, that potentially form a species HRV-C, may cause a significant amount of pediatric respiratory disease.

Assay for 5' noncoding region analysis of all human rhinovirus prototype strains

Increasing recognition of the association of rhinovirus with severe lower respiratory tract illnesses has clarified the need to understand the relationship between specific serotypes of rhinovirus and their clinical consequences. To accomplish this, a specific and sensitive assay to detect and serotype rhinovirus directly from clinical specimens is needed. Traditional methods of serotyping using culture and serum neutralization are time-consuming, limited to certain reference laboratories, and complicated by the existence of over 100 serotypes of human rhinoviruses (HRVs). Accordingly, we have developed a sequence-based assay that targets a 390-bp fragment accounting for approximately two-thirds of the 5' noncoding region (NCR). Our goal was to develop an assay permitting amplification of target sequences directly from clinical specimens and distinction among all 101 prototype strains of rhinoviruses. We determined the sequences of all 101 prototype strains of HRV in this region to enable differentiation of virus genotypes in both viral isolates and clinical specimens. We evaluated this assay in a total of 101 clinical viral isolates and 24 clinical specimens and compared our findings to genotyping results using a different region of the HRV genome (the VP4-VP2 region). Five specimens associated with severe respiratory disease in children did not correlate with any known serotype of rhinovirus and were found to belong to a novel genogroup of rhinovirus, genogroup C. Isolates were also found that corresponded to the genogroup A2 variant identified in New York and Australia and two other novel group A clusters (GAC1 and GAC2).

Human rhinoviruses: the cold wars resume

BACKGROUND

Human rhinoviruses (HRVs) are the most common cause of viral illness worldwide but today, less than half the strains have been sequenced and only a handful examined structurally. This viral super-group, known for decades, has still to face the full force of a molecular biology onslaught. However, newly identified viruses (NIVs) including human metapneumovirus and bocavirus and emergent viruses including SARS-CoV have already been exhaustively scrutinized. The clinical impact of most respiratory NIVs is attributable to one or two major strains but there are 100+ distinct HRVs and, because we have never sought them independently, we must arbitrarily divide the literature's clinical impact findings among them. Early findings from infection studies and use of inefficient detection methods have shaped the way we think of 'common cold' viruses today.

OBJECTIVES

To review past HRV-related studies in order to put recent HRV discoveries into context.

RESULTS

HRV infections result in undue antibiotic prescriptions, sizable healthcare-related expenditure and exacerbation of expiratory wheezing associated with hospital admission.

CONCLUSION

The finding of many divergent and previously unrecognized HRV strains has drawn attention and resources back to the most widespread and frequent infectious agent of humans; providing us the chance to seize the advantage in a decades-long cold war.

The cis-acting replication elements define human enterovirus and rhinovirus species

Replication of picornaviruses is dependent on VPg uridylylation, which is linked to the presence of the internal cis-acting replication element (cre). Cre are located within the sequence encoding polyprotein, yet at distinct positions as demonstrated for poliovirus and coxsackievirus-B3, cardiovirus, and human rhinovirus (HRV-A and HRV-B), overlapping proteins 2C, VP2, 2A, and VP1, respectively. Here we report a novel distinct cre element located in the VP2 region of the recently reported HRV-A2 species and provide evolutionary evidence of its functionality. We also experimentally interrogated functionality of recently identified HRV-B cre in the 2C region that is orthologous to the human enterovirus (HEV) cre and show that it is dispensable for replication and appears to be a nonfunctional evolutionary relic. In addition, our mutational analysis highlights two amino acids in the 2C protein that are crucial for replication. Remarkably, we conclude that each genetic clade of HRV and HEV is characterized by a unique functional cre element, where evolutionary success of a new genetic lineage seems to be associated with an invention of a novel cre motif and decay of the ancestral one. Therefore, we propose that cre element could be considered as an additional criterion for human rhinovirus and enterovirus classification.

Global distribution of novel rhinovirus genotype

Global surveillance for a novel rhinovirus genotype indicated its association with community outbreaks and pediatric respiratory disease in Africa, Asia, Australia, Europe, and North America. Molecular dating indicates that these viruses have been circulating for at least 250 years.

Rapid sequence-based diagnosis of viral infection

With globalization of microbial threats and an increasing appreciation for the role of infection in chronic as well as acute diseases, there is burgeoning interest in the development of specific antiviral drugs. Less attention has been focused on the establishment and implementation of rapid viral diagnostic methods, without which it will not be possible to obtain the full benefit of new therapies. Here we review the current status of viral diagnostics and the utility of various sequence-based diagnostic platforms for applications in clinical microbiology, surveillance and pathogen discovery.