Molecular epidemiological study of human rhinovirus species A, B and C from patients with acute respiratory illnesses in Japan

Update on virus-induced asthma exacerbations

INTRODUCTION

Viral infections are common triggers for asthma exacerbation. Subjects with asthma are more susceptible to viral infections and develop more severe or long-lasting lower respiratory tract symptoms than healthy individuals owing to impaired immune responses. Of the many viruses associated with asthma exacerbation, rhinovirus (RV) is the most frequently identified virus in both adults and children.

AREAS COVERED

We reviewed epidemiological and clinical links and mechanistic studies on virus-associated asthma exacerbations. We included sections on severe acute respiratory syndrome coronavirus 2 (SARS-CoV2), the latest evidence of coronavirus disease 2019 (COVID-19) in asthma patients, and past and future searches for therapeutic and prevention targets.

EXPERT OPINION

Early treatment or prevention of viral infections might significantly reduce the rate of asthma exacerbation, which is one of the key points of disease management. Although it is hypothetically possible nowadays to interfere with every step of the infectious cycle of respiratory tract viruses, vaccination development has provided some of the most encouraging results. Future research should proceed toward the development of a wider spectrum of vaccines to achieve a better quality of life for patients with asthma and to reduce the economic burden on the healthcare system.

Etiologies of Acute Bronchiolitis in Children at Risk for Asthma, with Emphasis on the Human Rhinovirus Genotyping Protocol

This research aims to determine acute bronchiolitis' causative virus(es) and establish a viable protocol to classify the Human Rhinovirus (HRV) species. During 2021-2022, we included children 1-24 months of age with acute bronchiolitis at risk for asthma. The nasopharyngeal samples were taken and subjected to a quantitative polymerase chain reaction (qPCR) in a viral panel. For HRV-positive samples, a high-throughput assay was applied, directing the VP4/VP2 and VP3/VP1 regions to confirm species. BLAST searching, phylogenetic analysis, and sequence divergence took place to identify the degree to which these regions were appropriate for identifying and differentiating HRV. HRV ranked second, following RSV, as the etiology of acute bronchiolitis in children. The conclusion of the investigation of all available data in this study distributed sequences into 7 HRV-A, 1 HRV-B, and 7 HRV-C types based on the VP4/VP2 and VP3/VP1 sequences. The nucleotide divergence between the clinical samples and the corresponding reference strains was lower in the VP4/VP2 region than in the VP3/VP1 region. The results demonstrated the potential utility of the VP4/VP2 region and the VP3/VP1 region for differentiating HRV genotypes. Confirmatory outcomes were yielded, indicating how nested and semi-nested PCR can establish practical ways to facilitate HRV sequencing and genotyping.

Trends and Intensity of Rhinovirus Invasions in Kilifi, Coastal Kenya, Over a 12-Year Period, 2007-2018

Background

Rhinoviruses (RVs) are ubiquitous pathogens and the principal etiological agents of common cold. Despite the high frequency of RV infections, data describing their long-term epidemiological patterns in a defined population remain limited.

Methods

Here, we analyzed 1070 VP4/VP2 genomic region sequences sampled at Kilifi County Hospital on the Kenya coast. The samples were collected between 2007 and 2018 from hospitalized pediatric patients (<60 months of age) with acute respiratory illness.

Results

Of 7231 children enrolled, RV was detected in 1497 (20.7%) and VP4/VP2 sequences were recovered from 1070 samples (71.5%). A total of 144 different RV types were identified (67 Rhinovirus A, 18 Rhinovirus B, and 59 Rhinovirus C) and at any month, several types co-circulated with alternating predominance. Within types, multiple genetically divergent variants were observed. Ongoing RV infections through time appeared to be a combination of (1) persistent types (observed up to 7 consecutive months), (2) reintroduced genetically distinct variants, and (3) new invasions (average of 8 new types annually).

Conclusions

Sustained RV presence in the Kilifi community is mainly due to frequent invasion by new types and variants rather than continuous transmission of locally established types/variants.

Human Rhinoviruses in Adult Patients in a Tertiary Care Hospital in Germany: Molecular Epidemiology and Clinical Significance

Rhinoviruses (RVs) constitute a substantial public health burden. To evaluate their abundance and genetic diversity in adult patients, RV RNA in respiratory samples was assessed using real-time RT-PCR and the partial nucleic acid sequencing of viral genomes. Additionally, clinical data were retrieved from patient charts to determine the clinical significance of adult RV infections. In total, the respiratory specimens of 284 adult patients (18-90 years), collected from 2013 to 2017, were analyzed. Infections occurred throughout the entire year, with peaks occurring in fall and winter, and showed a remarkably high intra- and interseasonal diversity of RV genotypes. RV species were detected in the following ratios: 60.9% RV-A 173, 12.7% RV-B, and 26.4% RV-C. No correlations between RV species and underlying comorbidities such as asthma (p = 0.167), COPD (p = 0.312) or immunosuppression (p = 0.824) were found. However, 21.1% of the patients had co-infections with other pathogens, which were associated with a longer hospital stay (p = 0.024), LRTI (p < 0.001), and pneumonia (p = 0.01). Taken together, this study shows a pronounced genetic diversity of RV in adults and underlines the important role of co-infections. No correlation of specific RV species with a particular clinical presentation could be deduced.

Genetic diversity and epidemiology of human rhinovirus among children with severe acute respiratory tract infection in Guangzhou, China

BACKGROUND

Human rhinovirus (HRV) is one of the major viruses of acute respiratory tract disease among infants and young children. This work aimed to understand the epidemiological and phylogenetic features of HRV in Guangzhou, China. In addition, the clinical characteristics of hospitalized children infected with different subtype of HRV was investigated.

METHODS

Hospitalized children aged < 14 years old with acute respiratory tract infections were enrolled from August 2018 to December 2019. HRV was screened for by a real-time reverse-transcription PCR targeting the viral 5'UTR.

RESULTS

HRV was detected in 6.41% of the 655 specimens. HRV infection was frequently observed in children under 2 years old (57.13%). HRV-A and HRV-C were detected in 18 (45%) and 22 (55%) specimens. All 40 HRV strains detected were classified into 29 genotypes. The molecular evolutionary rate of HRV-C was estimated to be 3.34 × 10^-3 substitutions/site/year and was faster than HRV-A (7.79 × 10^-4 substitutions/site/year). Children who experienced rhinorrhoea were more common in the HRV-C infection patients than HRV-A. The viral load was higher in HRV-C detection group than HRV-A detection group (p = 0.0148). The median peak symptom score was higher in patients with HRV-C infection as compared to HRV-A (p = 0.0543), even though the difference did not significance.

CONCLUSION

This study revealed the molecular epidemiological characteristics of HRV in patients with respiratory infections in southern China. Children infected with HRV-C caused more severe disease characteristics than HRV-A, which might be connected with higher viral load in patients infected with HRV-C. These findings will provide valuable information for the pathogenic mechanism and treatment of HRV infection.

Genotypes of rhinovirus detected among children in two communities of South-West Nigeria

Rhinoviruses (RVs) are the most common etiological agent implicated in respiratory infections among infants and children. There are currently no approved antivirals and vaccine for use against the virus; hence, the need for information on the genotypes of rhinovirus from developing countries of the world with high burden of the infection. This study determined the genotypes of rhinovirus circulating among children in selected cities in Nigeria. Nasopharyngeal and oropharyngeal samples were carefully collected from children showing signs of respiratory infection in two communities in South-west Nigeria. Polymerase Chain Reaction was used to amplify the hypervariable part of the 5'- non-coding region, the entire viral protein gene 4 and the 5' terminus of the VP2 gene of RV. Nucleotide BLAST and phylogenetic analyses were used to genotype the isolates. Of the samples analysed, 12.7% showed rhinovirus positivity. All the three genotypes of rhinovirus were detected with genotype C (71.4%), being the predominant. Multiple strains of rhinovirus were found circulating. We showed for the first time the genotypes and strains of rhinovirus circulating in Nigeria. Further studies are required to highlight transmission patterns and disease severity among rhinovirus species in Nigeria.

Unveiling Viruses Associated with Gastroenteritis Using a Metagenomics Approach

Acute infectious gastroenteritis is an important illness worldwide, especially on children, with viruses accounting for approximately 70% of the acute cases. A high number of these cases have an unknown etiological agent and the rise of next generation sequencing technologies has opened new opportunities for viral pathogen detection and discovery. Viral metagenomics in routine clinical settings has the potential to identify unexpected or novel variants of viral pathogens that cause gastroenteritis. In this study, 124 samples from acute gastroenteritis patients from 2012–2014 previously tested negative for common gastroenteritis pathogens were pooled by age and analyzed by next generation sequencing (NGS) to elucidate unidentified viral infections. The most abundant sequences detected potentially associated to acute gastroenteritis were from Astroviridae and Caliciviridae families, with the detection of norovirus GIV and sapoviruses. Lower number of contigs associated to rotaviruses were detected. As expected, other viruses that may be associated to gastroenteritis but also produce persistent infections in the gut were identified including several Picornaviridae members (EV, parechoviruses, cardioviruses) and adenoviruses. According to the sequencing data, astroviruses, sapoviruses and NoV GIV should be added to the list of viral pathogens screened in routine clinical analysis.

Ingredients Acting as a Physical Barrier for the Prevention and Treatment of the Rhinovirus Infection

Although the common cold, usually caused by human rhinoviruses, is responsible for enormous damage to the economy and health every year, there are hardly any treatment options or prophylaxis for rhinovirus infections. In this work, the potential of a hydrogel complex, based on polymers and an aqueous extract of Icelandic moss in isla® medic lozenges (Engelhard Arzneimittel, Niederdorfelden, Germany), and two other hydrogels (based on solely xanthan gum or sodium hyaluronate) are investigated for the first time in order to prevent and treat rhinovirus infections. By means of rheological investigations, we demonstrate that isla® medic and containing polymers cause artificial saliva to thicken. Additionally, we demonstrate that the thickening results in the formation of a physical diffusion barrier, which leads to a significant reduction in plaques in a preventive plaque assay with rhinovirus 14 (RV-14). Furthermore, it is shown in a curative plaque assay that the hydrogel complex also has a curative effect on rhinovirus infections in that it reduces the spread of the RV-14-infection on H1-HeLa cell monolayers. Overall, polymer-based hydrogels and related products, such as isla® medic, could contribute to the prevention and treatment of rhinovirus infections.

An Intensive, Active Surveillance Reveals Continuous Invasion and High Diversity of Rhinovirus in Households

We report on infection patterns in 5 households (78 participants) delineating the natural history of human rhinovirus (HRV). Nasopharyngeal collections were obtained every 3-4 days irrespective of symptoms, over a 6-month period, with molecular screening for HRV and typing by sequencing VP4/VP2 junction. Overall, 311/3468 (8.9%) collections were HRV positive: 256 were classified into 3 species: 104 (40.6%) HRV-A; 14 (5.5%) HRV-B, and 138 (53.9%) HRV-C. Twenty-six known HRV types (13 HRV-A, 3 HRV-B, and 10 HRV-C) were identified (A75, C1, and C35 being most frequent). We observed continuous invasion and temporal clustering of HRV types in households (range 5-13 over 6 months). Intrahousehold transmission was independent of clinical status but influenced by age. Most (89.0%) of HRV infection episodes were limited to <14 days. Individual repeat infections were frequent (range 1-7 over 6 months), decreasing with age, and almost invariably heterotypic, indicative of lasting type-specific immunity and low cross-type protection.

Non-neutralizing Antibody Responses against VP1 in Enterovirus A, B, C and Rhinovirus A species among Infants and Children in Shanghai

The overall non-neutralizing antibody responses against EV infections among infants and children remain unknown. The non-neutralizing antibody responses against VP1 of EV-A species (Enterovirus 71 (EV71), Coxsackievirus A16 (CA16)), EV-B species (Coxsackievirus B3 (CB3)), EV-C species (Poliovirus 1 (PV1)) and RV-A species (Rhinovirus A N13 (RV13)) were detected and analyzed using a novel evolved immunoglobulin-binding molecule (NEIBM)-based ELISA among infants and children aged 1 day to 6 years in Shanghai. The anti-VP1 reactivity against these EVs changed similarly in an age-related dynamic: being high level in the 1-28-day age group, declining to the lowest level in the 1-12-month age group, gradually increasing to the peak level in the 13-60-month age group, and remarkably declining in the 61-72-month age group, which reflects the conversion from maternally-derived to primary antibody responses. The anti-RV13 VP1 antibodies were demonstrated at the highest level, with anti-CB3 and PV1 VP1 antibodies at the second highest level and anti-CA16 and EV71 VP1 antibodies at the lowest level. These findings are the first to describe the overall non-neutralizing antibody responses against VP1 of the EV-A, B, C and RV-A viruses among the infants and children and could be helpful for further understanding the ubiquitous EV infections among children.

Epidemiological analysis and follow-up of human rhinovirus infection in children with asthma exacerbation

To determine the prevalence of human rhinovirus (HRV) infection in children with acute asthma exacerbations, investigation of HRV viral load and severity of asthma exacerbations is also required. Nasopharyngeal aspirates and swabs were collected and assessed for respiratory viruses. HRV-positive samples were sequenced to identify types and determine viral load. Outpatients with asthma exacerbations underwent follow-up evaluations, their swabs were collected and clinical outcomes were recorded at their next clinic visit 4 weeks later. One hundred forty-three inpatients and 131 outpatients, including 88 patients with asthma exacerbations and 43 controls with stable asthma were recruited. HRV-A was mainly detected in September and February (45.5% and 33.3%, respectively), while HRV-C was mainly detected in November and April (70.0% and 55.6%, respectively). HRV-C was the primary type and was primarily found in inpatients with severe asthma exacerbations. HRV-A viral load in the group of inpatients with severe exacerbations was higher than in the mild and moderate groups (P < 0.001 and P = 0.022). The HRV-A viral load of both inpatients and outpatients was higher than that of HRV-C (P < 0.001 and P = 0.036). The main genotypes were HRV-C53 and HRV-A20 among inpatients, and this genotype caused more severe clinical manifestations. HRV persisted for no more than 4 weeks, and their symptoms or signs of disease were well-controlled well. HRV-C was most frequently detected in asthma exacerbations. HRV-A with high viral load led to severe asthma exacerbations.

Association of Different Human Rhinovirus Species with Asthma in Children: A Preliminary Study

Background:

Human rhinoviruses (HRVs) are divided into three genetic species: HRV-A, HRV-B, and HRV-C. The association of different HRV species with asthma in children in China has not yet been evaluated. This preliminary study aimed to assess the associations between different HRV species, particularly HRV-C, and asthma in young children in China.

Methods:

A total of 702 nasopharyngeal aspirates were obtained from 155 children with asthma (asthma group), 461 children with acute respiratory infection (ARI) without asthma (nonasthma ARI group), and 86 children from the control group. Semi-nested polymerase chain reaction (PCR) was used to detect HRVs, and PCR products were sequenced for species identification. Epidemiological characteristics of HRV-positive cases were analyzed.

Results:

HRVs were the most common pathogen (15.4%; 108/702) in the patients in this study. The prevalence of HRV was significantly different (F = 20.633, P = 0.000) between the asthma (25.8%) and nonasthma ARI groups (11.1%). Phylogenetic analysis indicated that in the 108 cases positive for HRVs, 41 were identified as HRV-A, 8 as HRV-B, and 56 as HRV-C. Comparing the asthma with the nonasthma ARI group, Spearman's rank correlation analysis revealed an association between HRV-A (P < 0.05) and C (P < 0.01) and asthma, confirmed by regression analysis, with odds ratios of 2.2 (HRV-A) and 4.2 (HRV-C).

Conclusions:

Our data revealed a high prevalence of HRVs in children in China, regardless of clinical status. HRV-C was the dominant species and may be one of the key factors in the association of HRVs with asthma.

Pathogen profiles and molecular epidemiology of respiratory viruses in Japanese inpatients with community-acquired pneumonia

Background

The etiological profile of viruses among adult patients with community-acquired pneumonia (CAP) has not been characterized yet. The aim of this study was twofold: first, investigate the pathogen profiles and the molecular epidemiology of respiratory viruses among Japanese CAP patients; and second, explore the clinical significance of viral infections.

Methods

A cross-sectional observational study was conducted at Kyorin University Hospital. To identify respiratory pathogens, hospitalized CAP patients were enrolled, and reverse transcriptase–polymerase chain reaction technology was applied alongside conventional microbiological methods. Phylogenetic and pairwise distance analyses of 10 viruses were performed. CAP patients were divided into four etiological groups (virus alone, bacteria alone, co-detection of virus and bacteria, and not detected) and the clinical findings were compared.

Results

Seventy-six patients were enrolled. Bacteria alone were detected in 39.5% (n=30) of CAP patients. Virus alone or co-detection were found in 10.5% (n=8) and 11.8% (n=9) of cases, respectively. Streptococcus pneumoniae and human metapneumovirus were the most frequently detected bacterium and virus, respectively. Phylogenetic analyses of human metapneumovirus, human rhinovirus, and human respiratory syncytial virus showed that different subgroups and genotypes might be associated with CAP. Respiratory failure was more common when a virus was detected (both virus alone and co-detection groups; n=17, 100%, p<0.05) than when a bacteria alone was detected (n=17, 56.7%).

Conclusion

Prevalence of respiratory virus infection in CAP inpatients was 22.3%. The detected viruses display high genetic divergence and correlate with increased respiratory failure.

Serotype and genetic diversity of human rhinovirus strains that circulated in Kenya in 2008

Background

Human rhinoviruses (HRVs) are a well‐established cause of the common cold and recent studies indicated that they may be associated with severe acute respiratory illnesses (SARIs) like pneumonia, asthma, and bronchiolitis. Despite global studies on the genetic diversity of the virus, the serotype diversity of these viruses across diverse geographic regions in Kenya has not been characterized.

Objectives

This study sought to characterize the serotype diversity of HRV strains that circulated in Kenya in 2008.

Methods

A total of 517 archived nasopharyngeal samples collected in a previous respiratory virus surveillance program across Kenya in 2008 were selected. Participants enrolled were outpatients who presented with influenza‐like (ILI) symptoms. Real‐time RT‐PCR was employed for preliminary HRV detection. HRV‐positive samples were amplified using RT‐PCR and thereafter the nucleotide sequences of the amplicons were determined followed by phylogenetic analysis.

Results

Twenty‐five percent of the samples tested positive for HRV. Phylogenetic analysis revealed that the Kenyan HRVs clustered into three main species comprising HRV‐A (54%), HRV‐B (12%), and HRV‐C (35%). Overall, 20 different serotypes were identified. Intrastrain sequence homology among the Kenyan strains ranged from 58% to 100% at the nucleotide level and 55% to 100% at the amino acid level.

Conclusion

These results show that a wide range of HRV serotypes with different levels of nucleotide variation were present in Kenya. Furthermore, our data show that HRVs contributed substantially to influenza‐like illness in Kenya in 2008.

Absence of back to school peaks in human rhinovirus detections and respiratory symptoms in a cohort of children with asthma

Much of what is known about the seasonality of human rhinovirus (hRV) infections has been learned from the study of acute asthma exacerbations presenting to emergency care, including those among children at the start of the school term. Much less is known about the patterns of hRVs in the community. In this study, viruses and day-to-day symptoms of asthma and colds were monitored twice weekly in 67 children with asthma aged 5-12 years, over a 15 month period in Sydney, Australia. Overall hRV was detected in 314/1232 (25.5%) of nasal wash samples and 142/1231 (11.5%) of exhaled breath samples; of these, 231 and 24 respectively were genotyped. HRVs were detected with similar prevalence rate throughout the year, including no peak in hRV prevalence following return to school. No peaks were seen in asthma and cold symptoms using twice-weekly diary records. However, over the same period in the community, there were peaks in asthma emergency visits both at a large local hospital and in state-wide hospitalizations, following both return to school (February) and in late autumn (May) in children of the same age. This study suggests that hRV infections are common throughout the year among children, and differences in virus prevalence alone may not account for peaks in asthma symptoms.

Hospitalizations and outpatient visits for rhinovirus-associated acute respiratory illness in adults

BACKGROUND

Rhinovirus is linked to asthma exacerbations and chronic obstructive pulmonary disease exacerbations in adults. The severity and rates of rhinovirus acute respiratory illnesses (ARIs) in adults are uncertain.

OBJECTIVES

We sought to determine rhinovirus-associated ARI rates in adults presenting for care in multiple settings and identify factors associated with rhinovirus detection.

METHODS

This prospective, population-based cohort enrolled Tennessee residents 18 years or older in the emergency department (ED), outpatient clinics, or hospitalized for ARI from December 2008 to May 2010. Nasal/throat swabs were collected and tested for rhinovirus and other viruses by using RT-PCR. Rates of ED visits and hospitalizations were calculated and rhinovirus-positive and rhinovirus-negative patients were compared.

RESULTS

Among 2351 enrollees, rhinovirus was detected in 247 (11%). There were 7 rhinovirus-associated ED visits and 3 hospitalizations per 1000 adults annually. Patients with rhinovirus, compared with virus-negative ARI, were more likely to present with wheezing (odds ratio [OR], 1.7; 95% CI, 1.23-2.35; P < .001), to be a current smoker (OR, 2.31; 95% CI, 1.68-3.19) or live with a smoker (OR, 1.72; 95% CI, 1.10-2.67), have a history of chronic respiratory disease (OR, 1.61; 95% CI, 1.17-2.22), and were less likely to be hospitalized versus seen in the outpatient setting (OR, 0.58; 95% CI, 0.41-0.83).

CONCLUSIONS

Rhinovirus is associated with a substantial number of ED visits and hospitalizations for ARIs in adults. There may be modifiable factors that can reduce the likelihood of presenting with rhinovirus-associated ARIs.

Molecular evolution of the VP1, VP2, and VP3 genes in human rhinovirus species C

Human rhinovirus species C (HRV-C) was recently discovered, and this virus has been associated with various acute respiratory illnesses (ARI). However, the molecular evolution of the major antigens of this virus, including VP1, VP2, and VP3, is unknown. Thus, we performed complete VP1, VP2, and VP3 gene analyses of 139 clinical HRV-C strains using RT-PCR with newly designed primer sets and next-generation sequencing. We assessed the time-scale evolution and evolutionary rate of these genes using the Bayesian Markov chain Monte Carlo method. In addition, we calculated the pairwise distance and confirmed the positive/negative selection sites in these genes. The phylogenetic trees showed that the HRV-C strains analyzed using these genes could be dated back approximately 400 to 900 years, and these strains exhibited high evolutionary rates (1.35 to 3.74 × 10⁻³ substitutions/site/year). Many genotypes (>40) were confirmed in the phylogenetic trees. Furthermore, no positively selected site was found in the VP1, VP2, and VP3 protein. Molecular modeling analysis combined with variation analysis suggested that the exterior surfaces of the VP1, VP2 and VP3 proteins are rich in loops and are highly variable. These results suggested that HRV-C may have an old history and unique antigenicity as an agent of various ARI.

Molecular Epidemiology of the Human Rhinovirus Infection in Mongolia during 2008-2013

Rhinovirus infections are common in all age groups world-wide, and they occur throughout the year. In this study, we examined 2,689 nasopharyngeal swabs collected in Mongolia during 2008-2013. Human rhinoviruses (HRVs) were detected in 295 (11.0%) samples, and 85 (28.8%) patients were co-infected with other respiratory viruses. HRV was co-detected with bocavirus, human coronavirus, and respiratory syncytial virus in 21 (24.7%), 17 (20.0%), and 14 (16.5%), respectively. We tested 170 (57.6%) of the 295 HRV-positive samples: 117 HRV strains were typed by using the VP4/VP2 method and 53 by using 5' UTR method. We found HVR-A, HVR-C, and HVR-B infections in 80 (47.1%), 76 (44.7%), and 14 (8.2%) samples, respectively.

Human rhinovirus induced cytokine/chemokine responses in human airway epithelial and immune cells

Infections with human rhinovirus (HRV) are commonly associated with acute upper and lower respiratory tract disease and asthma exacerbations. The role that HRVs play in these diseases suggests it is important to understand host-specific or virus-specific factors that contribute to pathogenesis. Since species A HRVs are often associated with more serious HRV disease than species B HRVs, differences in immune responses they induce should inform disease pathogenesis. To identify species differences in induced responses, we evaluated 3 species A viruses, HRV 25, 31 and 36 and 3 species B viruses, HRV 4, 35 and 48 by exposing human PBMCs to HRV infected Calu-3 cells. To evaluate the potential effect of memory induced by previous HRV infection on study responses, we tested cord blood mononuclear cells that should be HRV naïve. There were HRV-associated increases (significant increase compared to mock-infected cells) for one or more HRVs for IP-10 and IL-15 that was unaffected by addition of PBMCs, for MIP-1α, MIP-1β, IFN-α, and HGF only with addition of PBMCs, and for ENA-78 only without addition of PBMCs. All three species B HRVs induced higher levels, compared to A HRVs, of MIP-1α and MIP-1β with PBMCs and ENA-78 without PBMCs. In contrast, addition of CBMCs had less effect and did not induce MIP-1α, MIP-1β, or IFN-α nor block ENA-78 production. Addition of CBMCs did, however, increase IP-10 levels for HRV 35 and HRV 36 infection. The presence of an effect with PBMCs and no effect with CBMCs for some responses suggest differences between the two types of cells possibly because of the presence of HRV memory responses in PBMCs and not CBMCs or limited response capacity for the immature CBMCs relative to PBMCs. Thus, our results indicate that different HRV strains can induce different patterns of cytokines and chemokines; some of these differences may be due to differences in memory responses induced by past HRV infections, and other differences related to virus factors that can inform disease pathogenesis.

Molecular evolution of VP3, VP1, 3C(pro) and 3D(pol) coding regions in coxsackievirus group A type 24 variant isolates from acute hemorrhagic conjunctivitis in 2011 in Okinawa, Japan

A large acute hemorrhagic conjunctivitis (AHC) outbreak occurred in 2011 in Okinawa Prefecture in Japan. Ten strains of coxsackievirus group A type 24 variant (CA24v) were isolated from patients with AHC and full sequence analysis of the VP3, VP1, 3C(pro) and 3D(pol) coding regions performed. To assess time-scale evolution, phylogenetic analysis was performed using the Bayesian Markov chain Monte Carlo method. In addition, similarity plots were constructed and pairwise distance (p-distance) and positive pressure analyses performed. A phylogenetic tree based on the VP1 coding region showed that the present strains belong to genotype 4 (G4). In addition, the present strains could have divided in about 2010 from the same lineages detected in other countries such as China, India and Australia. The mean rates of molecular evolution of four coding regions were estimated at about 6.15 to 7.86 × 10(-3) substitutions/site/year. Similarity plot analyses suggested that nucleotide similarities between the present strains and a prototype strain (EH24/70 strain) were 0.77-0.94. The p-distance of the present strains was relatively short (<0.01). Only one positive selected site (L25H) was identified in the VP1 protein. These findings suggest that the present CA24v strains causing AHC are genetically related to other AHC strains with rapid evolution and emerged in around 2010.

Molecular epidemiology of rhinoviruses in Cyprus over three consecutive seasons

Human rhinoviruses (HRVs) are widespread respiratory pathogens and a major cause of acute respiratory tract infections. The aim of this study was to investigate the molecular epidemiology of rhinovirus infections in children in Cyprus over three consecutive winter seasons. From a total of 116 rhinovirus-positive samples, 68 were sequenced in the 5'-UTR and VP4/VP2 regions. Thirty-six (52.9%) samples were identified as HRV-A and 27 (39.7%) as HRV-C, with only five (7.4%) samples belonging to the HRV-B species. Of these, a total of 46 different genotypes were identified. In the VP2/VP4 phylogenetic tree all strains clustered in three different well-defined clades, whereas the 5'-UTR tree exhibited clades with a mixed clustering of HRV-A and HRV-C strains reflecting the evolutionary history of recombination between HRV-A and HRV-C that has been observed previously. In summary, a high intra- and inter-season diversity of HRV types was observed. Despite its geographical isolation the frequency of HRV species in Cyprus is comparable to that reported in other regions of the world supporting the concept of an unrestricted global circulation. This study assesses, for the first time, the epidemiology of rhinovirus infections in Cypriot children and will be helpful to clinicians and researchers interested in the treatment and control of viral respiratory tract infections.

Molecular epidemiology of human rhinovirus in children with acute respiratory diseases in Chongqing, China

Human rhinovirus-C (HRV-C) has been increasingly detected in patients with acute respiratory diseases (ARDs). Prolonged surveillance was performed on children with ARD to investigate the molecular epidemiology and clinical characteristics of HRV in Chongqing, China. Nasopharyngeal aspirates (NPA) were collected from hospitalized children with ARD during 2009–2012. HRV-C was genotyped by sequencing the VP4/VP2 coding region. Among the 1,567 NPAs obtained, 223 (14.2%) were HRV positive, and 75.3% of these 223 NPAs were co-infected with other viruses. HRV-A (54.7%) and HRV-C (39.9%) accounted for the majority of HRV infections. Logistic regression models demonstrated significant associations between HRV-A, HRV-C, and asthma attacks, as well as between HRV-C and wheezing. A phylogenetic tree showed that HRV-C2 was the predominant type of HRV-C, followed by HRV-C43, HRV-C1, and HRV-C17. Three novel genotypes were proposed on the basis of a low identity with the known HRVs. Our results showed that HRV-A and HRV-C were the predominant types of HRV infection, and HRV-C showed a high genetic variation in Chongqing, China. HRV infection was associated with asthma attacks and wheezing; furthermore, HRV infections played a minor role in causing severe pneumonia. This knowledge provides information for the prevention and control of HRV associated with ARDs.

Emerging respiratory viruses other than influenza

Non-influenza respiratory virus infections are common worldwide and contribute to morbidity and mortality in all age groups. The recently identified Middle East respiratory syndrome coronavirus has been associated with rapidly progressive pneumonia and high mortality rate. Adenovirus 14 has been increasingly recognized in severe acute respiratory illness in both military and civilian individuals. Rhinovirus C and human bocavirus type 1 have been commonly detected in infants and young children with respiratory tract infection and studies have shown a positive correlation between respiratory illness and high viral loads, mono-infection, viremia, and/or serologically-confirmed primary infection.

Epidemiology of virus-induced asthma exacerbations: with special reference to the role of human rhinovirus

Viral respiratory infections may be associated with the virus-induced asthma in adults as well as children. Particularly, human rhinovirus is strongly suggested a major candidate for the associations of the virus-induced asthma. Thus, in this review, we reviewed and focused on the epidemiology, pathophysiology, and treatment of virus-induced asthma with special reference on human rhinovirus. Furthermore, we added our preliminary data regarding the clinical and virological findings in the present review.

The common cold: potential for future prevention or cure

The common cold is the most frequent, although generally mild, human disease. Human Rhinoviruses are the prevalent causative agents, but other viruses are also implicated. Being so common, viral colds, have significant implications on public health and quality of life, but may also be life-threatening for vulnerable groups of patients. Specific diagnosis and treatment of the common cold still remain unmet needs. Molecular diagnostic techniques allow specific detection of known pathogens as well as the identification of newly emerging viruses. Although a number of medications or natural treatments have been shown to have some effect, either on the number or on the severity of common colds, no single agent is considerably effective. Virus-specific management remains in most cases a challenging potential as many factors have to be taken into account, including the diversity of the viral genomes, the heterogeneity of affected individuals, as well as the complexity of this long standing host-virus relationship.

Phylogenetic analysis of human rhinovirus isolates collected from otherwise healthy children with community-acquired pneumonia during five successive years

In order to evaluate the circulation of the different human rhinovirus (HRV) species and genotypes in Italian children with radiographically confirmed community-acquired pneumonia (CAP), a nasopharyngeal swab was obtained from 643 children admitted to hospital because of CAP during five consecutive winter and early spring seasons (2007-2012). Real-time reverse transcriptase polymerase chain reaction (RT-PCR) was used to identify HRV, and the HRV-positive samples were used for sequencing analysis and to reconstruct the phylogenetic tree. HRV was identified in 198 samples (42.2%), and the VP4/VP2 region was successfully amplified in 151 (76.3%). HRV-A was identified in 78 samples (51.6%), HRV-B in 14 (9.3%) and HRV-C in 59 (39.1%). Forty-seven (31.1%) of the children with HRV infection were aged <1 year, 71 (47.0%) were aged 1-3 years, and 33 (21.9%) were aged ≥4 years. Blast and phylogenetic analyses showed that the HRV strains were closely related to a total of 66 reference genotypes, corresponding to 29 HRV-A, 9 HRV-B and 28 HRV-C strains. Nucleotide variability was 37% between HRV-A and HRV-B, 37.3% between HRV-A and HRV-C, and 39.9% between HRV-B and HRV-C. A number of sequences clustered with known serotypes and, within these clusters, there were strains circulating during several seasons. The most frequently detected genotypes were HRV-A78 (n=17), HRV-A12 (n=9) and HRV-C2 (n=5). This study shows that, although it is mainly associated with HRV-A, pediatric CAP can also be diagnosed in subjects infected by HRV-C and, more rarely, by HRV-B. Moreover, a large number of genotypes may be involved in causing pediatric CAP and can be different from year to year. Although the prolonged circulation of the same genotypes can sometimes be associated with a number of CAP episodes in different years.

Genetic analysis of human rhinovirus species A to C detected in patients with acute respiratory infection in Kumamoto prefecture, Japan 2011-2012

We performed detailed genetic analysis of the VP4/VP2 coding region in human rhinovirus species A to C (HRV-ABC) strains detected in patients with a variety of acute respiratory infections in Kumamoto, Japan in the period 2011-12. The phylogenetic tree and evolutionary timescale were obtained by the Bayesian Markov chain Monte Carlo method. Phylogenetic analyses showed that the present HRV-A, -B, and -C strains belonged to 25, 4, and 18 genotypes, respectively. Some new genotypes were confirmed as prevalent strains of HRV-C. An ancestor of the present HRV-ABCs could be dated back to about 20,000 years ago. The present HRV-A and -C strains have wide genetic divergence (pairwise distance >0.2) with rapid evolutionary rates (around 7 × 10(-4) to 4 × 10(-3)substitutions/site/year). Over 100 sites were found to be under negative selection, while no positively selected sites were found in the analyzed region. No evidence of recombination events was found in this region of the present strains. Our results indicate that the present HRV strains have rapidly evolved and subsequently diverged over a long period into multiple genotypes.

Molecular epidemiology of respiratory viruses in virus-induced asthma

Acute respiratory illness (ARI) due to various viruses is not only the most common cause of upper respiratory infection in humans but is also a major cause of morbidity and mortality, leading to diseases such as bronchiolitis and pneumonia. Previous studies have shown that respiratory syncytial virus (RSV), human rhinovirus (HRV), human metapneumovirus (HMPV), human parainfluenza virus (HPIV), and human enterovirus infections may be associated with virus-induced asthma. For example, it has been suggested that HRV infection is detected in the acute exacerbation of asthma and infection is prolonged. Thus it is believed that the main etiological cause of asthma is ARI viruses. Furthermore, the number of asthma patients in most industrial countries has greatly increased, resulting in a morbidity rate of around 10-15% of the population. However, the relationships between viral infections, host immune response, and host factors in the pathophysiology of asthma remain unclear. To gain a better understanding of the epidemiology of virus-induced asthma, it is important to assess both the characteristics of the viruses and the host defense mechanisms. Molecular epidemiology enables us to understand the pathogenesis of microorganisms by identifying specific pathways, molecules, and genes that influence the risk of developing a disease. However, the epidemiology of various respiratory viruses associated with virus-induced asthma is not fully understood. Therefore, in this article, we review molecular epidemiological studies of RSV, HRV, HPIV, and HMPV infection associated with virus-induced asthma.

From sneeze to wheeze: what we know about rhinovirus Cs

While the discovery of HRV-Cs is recent, there are no indications that they are new viruses, or that they are emerging in real-time. Genetically, HRV-Cs are most closely related to the members of HRV-A and HRV-B but even a small genetic difference can impart encompass significant changes to their clinical impact, complicated by a diverse human background of prior virus exposure and underlying host immune and disease variability. It is well known that HRVs are a major trigger of asthma exacerbations and HRV-Cs are now under investigation for their potential involvement in asthma inception. The newly described HRV-Cs account for a large proportion of HRV-related illness, including common colds and wheezing exacerbations. HRV-Cs are genetically diverse and appear to circulate with seasonal variation, exchanging dominance with HRV-A. Whether HRV-Cs are consistently more pathogenic or "asthmagenic" is unproven. Antigenic diversity complicates passive and active prophylactic interventions (i.e. antibodies or vaccines), so further identification and characterisation of individual types (and their neutralising antigens) is likely to inform future preventive strategies. In the meantime, new antivirals should benefit groups at risk of the most severe disease.

Molecular epidemiology and genetic diversity of human rhinovirus affecting hospitalized children in Rome

Human rhinoviruses (HRV) have been re-classified into three species (A-C), but the recently discovered HRV-C strains are not fully characterized yet. This study aimed to undertake a molecular and epidemiological characterization of HRV strains infecting children hospitalized over one year in two large research hospitals in Rome. Nasal washings from single HRV infections were retrospectively subjected to phylogenetic analysis on two genomic regions: the central part of the 5'Untranslated Region (5'UTR) and the Viral Protein (VP) 4 gene with the 5' portion of the VP2 gene (VP4/2). Forty-five different strains were identified in 73 HRV-positive children: 55 % of the cases were HRV-A, 38 % HRV-C and only 7 % HRV-B. HRV-C cases were less frequent than HRV-A during summer months and more frequent in cases presenting wheezing with respect to HRV-A. Species distribution was similar with respect to patient age, and seasonality differed during summer months with fewer HRV-C than HRV-A cases. On admission, a significantly higher number of HRV-C cases presented with wheezing with respect to HRV-A. The inter- and intra-genotype variability in VP4/2 was higher than in 5'UTR; in particular, HRV-A patient VP4/2 sequences were highly divergent (8-14 %) at the nucleotide level from those of their reference strains, but VP4 amino acid sequence was highly conserved. In HRV-C isolates, the region preceding the initiator AUG, the amino acids involved in VP4 myristoylation, the VP4-VP2 cleavage site and the cis-acting replication element were highly conserved. Differently, VP4 amino acid conservation was significantly lower in HRV-C than in HRV-A strains, especially in the transiently exposed VP4 N-terminus. This study confirmed the high number of different HRV genotypes infecting hospitalized children over one year and reveals a greater than expected variability in HRV-C VP4 protein, potentially suggestive of differences in replication.

[Epidemiological analysis and clinical study of pediatric human metapneumovirus detected in patients with acute respiratory infection]

We detected and isolated human metapneumovirus (HMPV) and isolated another respiratory virus in pharyngeal swab specimens from 502 pediatric patients with acute respiratory infection, seen at 3 Kyoto City sentinel hospitals from January to December 2011. Our prospective study detected 43 positive HMPV cases (8.6%). Phylogenetic analysis showed that subgroup A2 was most common, followed by B1 and B2, and that A1 was not detected. HMPV was detected mostly in specimens from patients less than 3 years old, and positive HMPV was identified most in spring, peaking in March. Our clinical study showed that positive HMPV patients had fever above 38 degrees (86%) and cough (65%). Among the 30 whose chest radiography was examined, radiological findings were recognized in 18 cases. We found inflammatory infiltrative shadows around the bronchus and peribronchus near the hilum of the lung. Lobar pneumonia and diffuse infiltrative shadows coinciding with peripheral alveolar involvement were not recognized. No difference affecting illness severity was seen among subgroups, viral isolation results, or mixed coxsackie virus or influenza virus infection. In hospitalization, mean disease lasted significantly longer in those with lower respiratory tract symptoms at first'examination than in those without such symptoms. We detected HMPV RNA in pharyngeal swabs and stool specimens from patients admitted to the hospital for rhabdomyolysis.

George K, Walsh TJ. Human rhinoviruses

Human rhinoviruses (HRVs), first discovered in the 1950s, are responsible for more than one-half of cold-like illnesses and cost billions of dollars annually in medical visits and missed days of work. Advances in molecular methods have enhanced our understanding of the genomic structure of HRV and have led to the characterization of three genetically distinct HRV groups, designated groups A, B, and C, within the genus Enterovirus and the family Picornaviridae. HRVs are traditionally associated with upper respiratory tract infection, otitis media, and sinusitis. In recent years, the increasing implementation of PCR assays for respiratory virus detection in clinical laboratories has facilitated the recognition of HRV as a lower respiratory tract pathogen, particularly in patients with asthma, infants, elderly patients, and immunocompromised hosts. Cultured isolates of HRV remain important for studies of viral characteristics and disease pathogenesis. Indeed, whether the clinical manifestations of HRV are related directly to viral pathogenicity or secondary to the host immune response is the subject of ongoing research. There are currently no approved antiviral therapies for HRVs, and treatment remains primarily supportive. This review provides a comprehensive, up-to-date assessment of the basic virology, pathogenesis, clinical epidemiology, and laboratory features of and treatment and prevention strategies for HRVs.

Spread of different rhinovirus B genotypes in hospitalized children in Spain

Please cite this paper as: Cuevas et al. (2013) Spread of different rhinovirus B genotypes in hospitalized children in Spain. Influenza and Other Respiratory Viruses 7(5), 623–628.

Human Rhinovirus (HRV) classification is an evolving process. New genotypes have been described within HRV‐A and HRV‐C species, but only one has been accepted related to HRV‐B. From 2003 to 2010, a total of 3987 nasopharyngeal aspirate samples were taken from pediatric patients admitted to the Severo Ochoa Hospital in Madrid (Spain). After viral analysis, 949 (23·8%) tested positive to HRV. A random selection of 397 (42%) positive samples showed that 39 (9·8%) were HRV‐B. The sequencing of partial VP4/VP2 coding region revealed the spread of 13 of 25 defined HRV‐B serotypes and three putative new genotypes. Such results remark the high diversity of HRV‐B.

Picornavirus and enterovirus diversity with associated human diseases

Members of the Picornaviridae family are non-enveloped, positive-stranded RNA viruses with a 30nm icosahedral capsid. This virus family exhibits a considerable amount of genetic variability driven both by mutation and recombination. Recently, three previously unknown human picornaviruses, namely the human Saffold cardiovirus, cosavirus and salivirus, have been identified in stools or respiratory samples from subjects presenting symptoms ranging from gastroenteritis to acute flaccid paralysis. However, these viruses were also frequently detected in asymptomatic subjects and their clinical relevance remains to be elucidated. The Enterovirus genus is a prototype example of the Picornaviridae heterogeneity at both genetic and phenotypic levels. This genus is divided into 10 species, seven of which contain human viruses, including three Rhinovirus species. Both human rhino- and enteroviruses are also characterized by high levels of genetic variability, as exemplified by the existence of over 250 different serotypes and the recent discovery of new enterovirus genotypes and the Rhinovirus C species. Despite their common genomic features, rhinoviruses are restricted to the respiratory tract, whereas the vast majority of enteroviruses infect the gastrointestinal tract and can spread to other organs, such as the heart or the central nervous system. Understanding the genetic determinants of such phenotypic diversity is an important challenge and a field for future investigation. Better characterization of these ubiquitous human pathogens may help to develop vaccines or antiviral treatments and to monitor the emergence of new strains.

Clinical and molecular features of human rhinovirus C

A newly discovered group of human rhinoviruses (HRVs) has been classified as the HRV-C species based on distinct genomic features. HRV-Cs circulate worldwide, and are important causes of upper and lower respiratory illnesses. Methods to culture and produce these viruses have recently been developed, and should enable identification of unique features of HRV-C replication and biology.