Human rhinovirus and human respiratory enterovirus (EV68 and EV104) infections in hospitalized patients in Italy, 2008-2009

Epidemiological and Clinical Insights into the Enterovirus D68 Upsurge in Europe 2021-2022 and Emergence of Novel B3-Derived Lineages, ENPEN Multicentre Study

Enterovirus D68 (EV-D68) infections are associated with severe respiratory disease and acute flaccid myelitis (AFM). The European Non-Polio Enterovirus Network (ENPEN) aimed to investigate the epidemiological and genetic characteristics of EV-D68 infections and its clinical impact during the fall-winter season of 2021-2022. From 19 European countries, 58 institutes reported 10 481 (6.8%) EV-positive samples of which 1004 (9.6%) were identified as EV-D68 (including 852 respiratory samples). Clinical data were reported for 969 cases; 78.9% of infections were reported in children (0-5 years); and 37.9% of cases were hospitalized. Acute respiratory distress was commonly noted (93.1%) followed by fever (49.4%). Neurological problems were observed in 6.4% of cases including 6 diagnosed with AFM. Phylodynamic/Nextstrain and phylogenetic analyses based on 694 sequences showed the emergence of 2 novel B3-derived lineages, with no regional clustering. In conclusion, we describe a large-scale European EV-D68 upsurge with severe clinical impact and the emergence of B3-derived lineages.

Persistence of RNA Viruses in the Respiratory Tract: An Overview

Respiratory RNA viruses are a major cause of acute lower respiratory tract infections and contribute substantially to hospitalization among infants, elderly, and immunocompromised. Complete viral clearance from acute infections is not always achieved, leading to persistence. Certain chronic respiratory diseases like asthma and chronic obstructive pulmonary disease have been associated with persistent infection by human respiratory syncytial virus and human rhinovirus, but it is still not clear whether RNA viruses really establish long-term infections as it has been recognized for DNA viruses as human bocavirus and adenoviruses. Herein, we summarize evidence of RNA virus persistence in the human respiratory tract, as well as in some animal models, to highlight how long-term infections might be related to development and/or maintenance of chronic respiratory symptoms.

Molecular Epidemiology of Rhinovirus/Enterovirus and Their Role on Cause Severe and Prolonged Infection in Hospitalized Patients

Rhinovirus is one of the most common respiratory viruses, causing both upper and lower respiratory tract infections. It affects mainly children and could cause prolonged infections, especially in immunocompromised patients. Here we report our data on a 15-month surveillance of Rhinovirus seasonality and circulation in Lombardy Region, Italy. All rhinovirus/enterovirus-positive samples were amplified with RT-PCR for the VP4-VP2 region to assign the correct genotype. The median age of RV/EV-positive patients is 9 years, with a range of 0–96. RV-A and RV-C were detected in the majority of cases, while RV-B accounted for less than 10% of cases. An enterovirus species was detected in 6.45% of the cases. A total of 7% of the patients included in this study had a prolonged infection with a median duration of 62 days. All these patients were immunocompromised and most of them were pediatric with an RV-A infection. Two outbreaks were identified, mainly in the neonatal intensive care unit (NICU) and Oncohematology Department, caused by RV A89 and C43, respectively. Nearly 4.5% of the patients were admitted to the ICU requiring mechanical ventilation; all of which had preexisting comorbidities.

Global prevalence and case fatality rate of Enterovirus D68 infections, a systematic review and meta-analysis

A substantial amount of epidemiological data has been reported on Enterovirus D68 (EV-D68) infections after the 2014 outbreak. Our goal was to map the case fatality rate (CFR) and prevalence of current and past EV-D68 infections. We conducted a systematic review (PROSPERO, CRD42021229255) with published articles on EV-68 infections in PubMed, Embase, Web of Science and Global Index Medicus up to January 2021. We determined prevalences using a model random effect. Of the 4,329 articles retrieved from the databases, 89 studies that met the inclusion criteria were from 39 different countries with apparently healthy individuals and patients with acute respiratory infections, acute flaccid myelitis and asthma-related diseases. The CFR estimate revealed occasional deaths (7/1353) related to EV-D68 infections in patients with severe acute respiratory infections. Analyses showed that the combined prevalence of current and past EV-D68 infections was 4% (95% CI = 3.1-5.0) and 66.3% (95% CI = 40.0-88.2), respectively. The highest prevalences were in hospital outbreaks, developed countries, children under 5, after 2014, and in patients with acute flaccid myelitis and asthma-related diseases. The present study shows sporadic deaths linked to severe respiratory EV-D68 infections. The study also highlights a low prevalence of current EV-D68 infections as opposed to the existence of EV-D68 antibodies in almost all participants of the included studies. These findings therefore highlight the need to implement and/or strengthen continuous surveillance of EV-D68 infections in hospitals and in the community for the anticipation of the response to future epidemics.

OUP accepted manuscript

Chronic enterovirus infections can cause significant morbidity, particularly in immunocompromised patients. This study describes a fatal case associated with a chronic untypeable enterovirus infection in an immunocompromised patient admitted to a Dutch university hospital over nine months. We aimed to identify the enterovirus genotype responsible for the infection and to determine potential evolutionary changes. Long-read sequencing was performed using viral targeted sequence capture on four respiratory and one faecal sample. Phylogenetic analysis was performed using a maximum likelihood method, along with a root-to-tip regression and time-scaled phylogenetic analysis to estimate evolutionary changes between sample dates. Intra-host variant detection, using a Fixed Ploidy algorithm, and selection pressure, using a Fixed Effect Likelihood and a Mixed Effects Model of Evolution, were also used to explore the patient samples. Near-complete genomes of enterovirus C104 (EV-C104) were recovered in all respiratory samples but not in the faecal sample. The recovered genomes clustered with a recently reported EV-C104 from Belgium in August 2018. Phylodynamic analysis including ten available EV-C104 genomes, along with the patient sequences, estimated the most recent common ancestor to occur in the middle of 2005 with an overall estimated evolution rate of 2.97 × 10⁻³ substitutions per year. Although positive selection pressure was identified in the EV-C104 reference sequences, the genomes recovered from the patient samples alone showed an overall negative selection pressure in multiple codon sites along the genome. A chronic infection resulting in respiratory failure from a relatively rare enterovirus was observed in a transplant recipient. We observed an increase in single-nucleotide variations between sample dates from a rapidly declining patient, suggesting mutations are weakly deleterious and have not been purged during selection. This is further supported by the persistence of EV-C104 in the patient, despite the clearance of other viral infections. Next-generation sequencing with viral enrichment could be used to detect and characterise challenging samples when conventional workflows are insufficient.

Essential Role of Non-Coding RNAs in Enterovirus Infection: From Basic Mechanisms to Clinical Prospects

Enteroviruses (EVs) are common RNA viruses that can cause various types of human diseases and conditions such as hand, foot, and mouth disease (HFMD), myocarditis, meningitis, sepsis, and respiratory disorders. Although EV infections in most patients are generally mild and self-limiting, a small number of young children can develop serious complications such as encephalitis, acute flaccid paralysis, myocarditis, and cardiorespiratory failure, resulting in fatalities. Established evidence has suggested that certain non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) are involved in the occurrence and progression of many human diseases. Recently, the involvement of ncRNAs in the course of EV infection has been reported. Herein, the authors focus on recent advances in the understanding of ncRNAs in EV infection from basic viral pathogenesis to clinical prospects, providing a reference basis and new ideas for disease prevention and research directions.

Frequent detection of enterovirus D68 and rhinovirus type C in children with acute respiratory infections

This study aimed to evaluate the prevalence of human rhinoviruses (HRVs) and the emergence of enterovirus D68 (EV-D68) in children. A total of 322 nasopharyngeal swab samples were provided from children with an initial diagnosis of upper and lower respiratory tract infections. A total of 34 and 70 cases were positive for EV-D68 and HRV, respectively. The phylogenetic analysis revealed that the clades A and B are the prevalent genotypes for EV-D68 and the HRV-positive samples belong to three types including HRV-A, HRV-B, and HRV-C. The results showed that EV-D68 and HRV-C are circulating in Iran especially in the winter.

Emergence of divergent enterovirus (EV) D68 sub-clade D1 strains, northern Italy, September to October 2018

Between September and October 2018, an enterovirus D68 (EV-D68) outbreak occurred in patients hospitalised with severe acute respiratory infection in northern Italy; 21 laboratory-confirmed cases were reported. Phylogenetic analysis revealed that 16/20 of the EV-D68 sequences belonged to a divergent group within the sub-clade D1. Since its upsurge, EV-D68 has undergone rapid evolution with the emergence of new viral variants, emphasising the need for molecular surveillance that include outpatients with respiratory illness.

Enterovirus-D68 (EV-D68) in pediatric patients with respiratory infection: The circulation of a new B3 clade in Italy

BACKGROUND

In recent years, several outbreaks due to Enterovirus D-68 (EV-D68) have been reported, and it was confirmed that the virus can cause upper and lower respiratory tract diseases and be associated with the development of neurological problems.

OBJECTIVES

The main aim of this research was to study the genetic characteristics of EV-D68 strains that were circulating in Italy identified during an outbreak of an EV-D68 infection that occurred in Italy during the period March-October 2016.

STUDY DESIGN

A retrospective study of the circulation of different types and subtypes of EV-D68 was performed. Nasopharyngeal swabs were collected from March 2016 through October 2016 in children admitted to the Emergency Room with respiratory diseases.

RESULTS

Among 390 children, 22 (59.1% males; mean age 47 months) were found to be infected by EV-D68 and most of them were immunocompetent (72.7%). Pneumonia was diagnosed in 12 (54.5%) children. Phylogenetic analysis of the VP1 region showed that all the strains identified in this study belonged to clade B3. Within B3 subclade, the Italian EV-D68 strains were most closely related to strains detected in Southern China in 2015 as well as to strains detected in US and the Netherlands in 2016.

CONCLUSIONS

These results showed that EV-D68 infections are a common cause of lower respiratory illness in pediatric age. The circulation of one EV-D68 lineage has been proven in Italy and in the European region during 2016. However, further studies are required to investigate whether some strains or lineages may possess a higher affinity for the lower airway or central nervous system.

Human enterovirus D68 in clinical and sewage samples in Israel

BACKGROUND

Since mid-August 2014, North America experienced a wide outbreak of Enterovirus D68 (EV-D68) associated with severe respiratory illness in children. Several other countries also reported cases of EV-D68 in 2014.

OBJECTIVES

The aim of this study was to determine whether EV-D68 circulated in Israel in 2014, caused severe respiratory illness in children and was the causative agent of Acute Flaccid Paralysis.

STUDY DESIGN

Archived clinical respiratory samples from a cohort of 710 hospitalized pediatric patient's (<10years old) with respiratory illness were screened for clade B specific EV-D68 by real-time PCR. The patients were seen at four medical centers covering the entire country between August and November 2014. We also evaluated 49 patient stool samples from 26 AFP cases during 2014 for presence of EV-D68. In addition, RNA from sewage samples collected throughout Israel during the same study period was also tested for EV-D68. Partial VP1 sequencing was performed on all positive samples.

RESULTS

Of the 710 clinical samples evaluated, 7 (1%) were positive for EV-D68. Two patients were from the central part of Israel, while the rest was from the southern part. The majority of the patients did not have any underlying disease. Not only that, but, none of the 26 suspected AFP cases had EV-D68 nucleic acid in their stool samples. EV-D68 RNA was detected in 9 out of 93 sewage samples, mainly from Southern Israel. Sequence analysis of EV-D68 VP1 gene from both sewage and clinical samples indicated that the Israeli EV-D68 RNA belonged to Clade B which was genetically similar to 2014 circulating European and North American EV-D68 virus.

CONCLUSIONS

EV-D68 circulated in Israel during the 2014 summer-fall season and caused hospitalization of a small percent of the patients with respiratory illness.

Respiratory infections associated with enterovirus D68 from 2011 to 2015 in Beijing, China

Enterovirus D68 (EV-D68) is an emergent viral pathogen associated with mild to severe respiratory infections. In this study, we describe respiratory infections associated with EV-D68 in Beijing over a 4 year period. Total nucleic acid was extracted from 7,945 clinical specimens collected between January 5, 2011 and July 30, 2015 in Beijing and used for detecting EV-D68 and other enteroviruses by real-time PCR. Overall, 555/7,945 (6.99%) specimens were enterovirus positive: 12/7,945 (0.2%) specimens were EV-D68 positive. Of these patients, 11 were pediatric patients and 1 was a 76-year-old man. The main symptoms for the 12 EV-D68 positive patients were fever (10/12, 83.3%) and cough (6/12, 50%). Ten EV-D68 infection cases were identified in autumn or winter season. The phylogenetic relationships of the 12 EV-D68 viral strains with other strains were analyzed based on the sequences of viral protein 1(VP1). The EV-D68 strains from 2011 to 2013 belonged to groups 1 or 3, while all strains in 2014 were clustered into group 1 together with the strains circulating in the USA. In conclusion, EV-D68 played a role in respiratory infections in Beijing during this period. In addition, the most common EV-D68 strain detected was similar to that circulating in the USA in 2014. J. Med. Virol. 88:1529-1534, 2016. © 2016 Wiley Periodicals, Inc.

Update on Human Rhinovirus and Coronavirus Infections

Human rhinovirus (HRV) and coronavirus (HCoV) infections are associated with both upper respiratory tract illness (“the common cold”) and lower respiratory tract illness (pneumonia). New species of HRVs and HCoVs have been diagnosed in the past decade. More sensitive diagnostic tests such as reverse transcription-polymerase chain reaction have expanded our understanding of the role these viruses play in both immunocompetent and immunosuppressed hosts. Recent identification of severe acute respiratory syndrome and Middle East respiratory syndrome viruses causing serious respiratory illnesses has led to renewed efforts for vaccine development. The role these viruses play in patients with chronic lung disease such as asthma makes the search for antiviral agents of increased importance.

Prevalence of rhinoviruses in young children of an unselected birth cohort from the Netherlands

Rhinovirus (RV) is a frequent pathogen in young children, eliciting symptoms ranging from common colds to wheezing illnesses and lower respiratory tract infections. The recently identified RV-C seems to be associated with asthma exacerbations and more severe disease, but results vary. We studied the prevalence and severity of infection with RV in an unselected birth cohort. Children with respiratory symptoms entered the symptomatic arm of the cohort and were compared with asymptomatic children. Severity of wheezing and other respiratory symptoms was registered. Respiratory viruses were evaluated using throat and nasopharyngeal swabs on first presentation and after recovery (wheezing children). RV genotyping was performed on RV-PCR positive samples. RV was the most prevalent respiratory virus and was found in 58/140 symptomatic children (41%), 24/96 (25%) control children and 19/74 (26%) wheezing symptomatic children after recovery (p <0.05) and did not differ between wheezing and non-wheezing symptomatic children—respectively, 42% (38/90) and 40% (20/50). RV-A was the most commonly detected species (40/68, 59%), followed by RV-C (22/68, 32%) and RV-B (6/68, 9%). RV-B was more frequently detected in asymptomatic children (5/6, p <0.05). There was no significant difference in the frequency of RV species between wheezing and non-wheezing symptomatic children. Children with RV mono-infection had more severe symptoms, but no association between RV species and severity of disease was seen. In an unselected birth cohort from the Netherlands with mild respiratory disease RV was the most prevalent respiratory virus. RV(-C) infection was not associated with more severe disease or wheezing.

Enteroviruses and Rhinoviruses: Molecular Epidemiology of the Most Influenza-Like Illness Associated Viruses in Senegal

Different viruses have been identified as etiologic agents of respiratory tract infections, including severe cases. Among these, human rhinoviruses (HRVs) and human enteroviruses (HEVs) are recognized as leading causes. The present study describes the molecular epidemiology of HRVs and HEVs in Senegal over a 3-year surveillance period. From January 2012 to December 2014, nasopharyngeal and oropharyngeal swabs specimen were collected from patients with influenza-like illness (ILI). A real-time reverse transcription polymerase chain reaction was performed for HRV and HEV detection using the RV16 kit. Two regions were targeted for the molecular characterization of RVs: 5' untranslated region (5'UTR) and viral protein 4/viral protein 2 (VP4/VP2) transition region. For enteroviruses (EVs) phylogeny, VP1 gene was targeted. A total of 4,194 samples were collected. Children up to 5 years accounted for 52.9%. Among them, 1,415 (33.7%) were positive for HRV, 857 (20.4%) for HEV, and 437 cases of dual infections HRV/HEV. HRVs and HEVs were identified significantly in children aged 5 years or less. Only cough and vomiting signs were observed with significant association with viral infection. Both viruses co-circulated all year long with a marked increase of activity during rainy and cold period. All HRV types circulate in Senegal. HRV-A and C groups were the most common. HEV serotyping identified coxsackie B viruses (CBV) only. VP1 region revealed different CBV (CBV1, CBV2, CBV3, CBV4, and CBV5), echoviruses, coxsackieviruses A4-like strains and a poliovirus 2. The results suggest strong year-round respiratory picornavirus activity in children up to 5 years of age. Molecular studies identified a wide variety of RVs along with diverse EVs in samples from patients with ILI.

Detection of enterovirus D68 in patients hospitalised in three tertiary university hospitals in Germany, 2013 to 2014

Enterovirus D68 (EV-D68) has been recognised as a worldwide emerging pathogen associated with severe respiratory symptoms since 2009. We here report EV-D68 detection in hospitalised patients with acute respiratory infection admitted to three tertiary hospitals in Germany between January 2013 and December 2014. From a total of 14,838 respiratory samples obtained during the study period, 246 (1.7%) tested enterovirus-positive and, among these, 39 (15.9%) were identified as EV-D68. Infection was observed in children and teenagers (0–19 years; n=31), the majority (n=22) being under five years-old, as well as in adults > 50 years of age (n=8). No significant difference in prevalence was observed between the 2013 and 2014 seasons. Phylogenetic analyses based on viral protein 1 (VP1) sequences showed co-circulation of different EV-D68 lineages in Germany. Sequence data encompassing the entire capsid region of the genome were analysed to gain information on amino acid changes possibly relevant for immunogenicity and revealed mutations in two recently described pleconaril binding sites.

Prevalence and phylogenetic characterization of human enterovirus D68 among children with respiratory infection in Hong Kong

This is the first report on the prevalence of human enterovirus D68 (EV-D68) among children with respiratory infection in Hong Kong. Among 1461 respiratory samples taken in 2014, EV-D68 was identified in 24 (1.64%) of them with a unusual seasonal pattern. Phylogenetic analysis indicated that all EV-D68 detected in this study belong to clade B.

Rhinovirus Disease in Children Seeking Care in a Tertiary Pediatric Emergency Department

BACKGROUND

Rhinovirus is the most common cause of viral respiratory tract infections in children. Virologic predictors of lower respiratory tract infection (LRTI), such as viral load and the presence of another respiratory virus (coinfection), are not well characterized in pediatric outpatients.

METHODS

Mid-nasal turbinate samples were collected from children presenting for care to the Seattle Children's Hospital emergency department (ED) or urgent care with a symptomatic respiratory infection between December 2011 and May 2013. A subset of samples was tested for rhinovirus viral load by real-time polymerase chain reaction. Clinical data were collected by chart reviews. Multivariate logistic regression was used to evaluate the relationship between viral load and coinfection and the risk for LRTI.

RESULTS

Rhinovirus was the most frequent respiratory virus detected in children younger than 3 years. Of 445 patients with rhinovirus infection, 262 (58.9%) had LRTIs, 231 (51.9%) required hospital admission and 52 (22.5%) were hospitalized for 3 days or longer. Children with no comorbidities accounted for 142 (54%) of 262 rhinovirus LRTIs. Higher viral load was significantly associated with LRTI among illness episodes with rhinovirus alone (OR, 2.11; 95% confidence interval [CI], 1.24-3.58). Coinfection increased the risk of LRTI (OR, 1.83; 95% CI, 1.01-3.32).

CONCLUSIONS

Rhinovirus was the most common pathogen detected among symptomatic young children in a pediatric ED who had respiratory viral testing performed, with the majority requiring hospitalization. Higher rhinovirus viral load and coinfection increased disease severity. Virologic data may assist clinical decision making for children with rhinovirus infections in the pediatric ED.

Analysis of Enterovirus 68 Strains from the 2014 North American Outbreak Reveals a New Clade, Indicating Viral Evolution

Enterovirus 68 (EVD68) causes respiratory illness, mostly in children. Despite a reported low-level of transmission, the occurrence of several recent outbreaks worldwide including the 2014 outbreak in North America has raised concerns regarding the pathogenesis and evolution of EVD68. To elucidate the phylogenetic features of EVD68 and possible causes for the 2014 outbreak, 216 EVD68 strain sequences were retrieved from Genbank, including 22 from the 2014 outbreak. Several geographic and genotypic origins were established for these 22 strains, 19 of which were classified as Clade B. Of these 19 strains, 17 exhibited subsequent clustering and variation in protein residues involved in host-receptor interaction and/or viral antigenicity. Approximately 18 inter-clade variations were detected in VP1, which led to the identification of a new Clade D in EVD68 strains. The classification of this new clade was also verified by the re-construction of a Neighbor-Joining tree during the phylogenetic analysis. In addition, our results indicate that members of Clade B containing highly specific alterations in VP1 protein residues were the foremost contributors to the 2014 outbreak in the US. Altered host-receptor interaction and/or host immune recognition may explain the evolution of EVD68 as well as the global emergence and ongoing adaptation of this virus.

Clinical, virological and epidemiological characteristics of rhinovirus infections in early childhood: A comparison between non-hospitalised and hospitalised children

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Rhinoviruses (RV) frequently cause respiratory tract infections in young children.

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We evaluated characteristics of RV infections in relation to clinical outcome.

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In young children clinical outcome was not related to RV species or types.

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Outcome of RV disease is more likely influenced by multiple (host-specific) factors.

Background

Several studies have been published regarding the epidemiology and clinical significance of the different rhinovirus (RV) species (-A, -B and -C). However, data on RV types and the associations with clinical outcome in young children are limited. Here, we investigated the clinical, virological and epidemiological characteristics of RV infections in young children with mild or asymptomatic infection (non-hospitalised children) and in symptomatic young children admitted to the hospital.

Objectives

The aim of this study was to evaluate associations between different characteristics of RV infections and clinical outcome in young children.

Study design

RV-infected children were retrospectively selected from a Dutch birth cohort (EUROPA-study) and from hospitalised children admitted to the hospital because of respiratory symptoms. In total 120 RV-typed samples could be selected from 65 non-hospitalised and 49 hospitalised children between November 2009 and December 2012.

Results

RV-A was the predominant species in both study populations, followed closely by RV-C. RV-B was observed only sporadically. The distribution of the RV species was comparable in non-hospitalised and hospitalised children. In children with respiratory distress who required ICU-admission the distribution of RV species did not differ significantly from the non-hospitalised children. No predominant RV type was present in non-hospitalised nor hospitalised children. However, hospitalised children were younger, had more often an underlying illness, a higher RV load and more frequently a bacterial co-infection.

Conclusions

Clinical outcome of RV infected young children was not related to RV species or types, but may more likely be influenced by multiple (host-specific) factors.

Enterovirus D-68: an emerging cause of infection

The outbreak of Enterovirus D-68 (EV-D68) in the United States in 2014 raised great interest due to it affecting large numbers of people and because patients presented with severe respiratory and/or central nervous system involvement. Many studies have tried to evaluate the biologic and genetic characteristics of this virus, its association with disease development and the possibility of infection prevention and therapy. The main aim of this paper is to discuss what is presently known and what might be expected in the future regarding EV-D68. We highlight that further studies are needed to precisely define the epidemiology and total burden of EV-D68, the real age prevalence, and the factors that may lead to negative outcomes in some patients and not in others. Moreover, if recently reported clinical data are confirmed, specific efficacious prophylactic and therapeutic measures should be urgently developed.

Impact of Human Rhinovirus Types and Viral Load on the Severity of Illness in Hospitalized Children With Lower Respiratory Tract Infections

BACKGROUND

Human rhinovirus (HRV) is not only responsible for at least one-half of all common colds but also associated with bronchitis, bronchiolitis, pneumonia and acute asthma exacerbation. However, the impact of different HRV types and viral load on disease severity has not been thoroughly elucidated.

METHODS

From January 2012 to September 2014, 1742 nasopharyngeal aspirate specimens from hospitalized children with lower respiratory tract infections were analyzed by quantitative HRV-specific real-time polymerase chain reaction.

RESULTS

Among these 1742 children, HRV (407/1742, 23%) was the second most common viral agent after respiratory syncytial virus. HRV-A, HRV-B, HRV-C and HRV untyped were detected in 229 (56%), 27 (7%), 100 (25%) and 51 (13%) specimens, respectively. Children except who experienced wheezing were more common in the HRV-C detection group than in the HRV-A detection group; there were no other significant differences between the 2 groups, including the percent of children diagnosed with severe diseases. Logistic regression models demonstrated that there was no difference in disease severity among HRV types. In HRV-A detection group, in children younger than 2 years, the viral load was higher in the severe group than in the nonsevere group; but in the HRV-C detection group, there was no difference.

CONCLUSIONS

HRV was frequently present in hospitalized children with lower respiratory tract infections in Chongqing, China. The disease severity for HRV-C and HRV-A was similar. A high load of HRV-A in the lower respiratory tract might be connected with disease severity in children younger than 2 years.

European surveillance for enterovirus D68 during the emerging North-American outbreak in 2014

BACKGROUND

In August and September 2014, unexpected clusters of enterovirus-D68 (EV-D68) infections associated with severe respiratory disease emerged from North-America. In September, the European Centre for Disease Prevention and Control (ECDC) asked European countries to strengthen respiratory sample screening for enterovirus detection and typing in cases with severe respiratory presentations.

OBJECTIVES

To provide a detailed picture of EV-D68 epidemiology in Europe by conducting a retrospective and prospective laboratory analysis of clinical specimens.

STUDY DESIGN

An initiative supported by the European Society for Clinical Virology (ESCV) and ECDC was launched to screen for EV-D68 in respiratory specimens between July 1st and December 1st 2014 in Europe and to sequence the VP1 region of detected viruses for phylogenetic analytic purposes.

RESULTS

Forty-two institutes, representing 51 laboratories from 17 European countries, analyzed 17,248 specimens yielding 389 EV-D68 positive samples (2.26%) in 14 countries. The proportion of positive samples ranged between 0 and 25% per country. These infections resulted primarily in mild respiratory disease, mainly detected in young children presenting with wheezing and in immuno-compromised adults. The viruses detected in Europe are genetically very similar to those of the North-American epidemic and the majority (83%) could be assigned to clade B. Except for 3 acute flaccid paralysis (AFP) cases, one death and limited ICU admissions, no severe cases were reported.

CONCLUSIONS

The European study showed that EV-D68 circulated in Europe during summer and fall of 2014 with a moderate disease burden and different pathogenic profile compared to the North-American epidemic.

Spread of infectious microbes during emergency medical response

Background

To our knowledge, no studies to date demonstrate potential spread of microbes during actual emergency medical service (EMS) activities. Our study introduces a novel approach to identification of contributors to EMS environment contamination and development of infection control strategies, using a bacteriophage surrogate for pathogenic organisms.

Methods

Bacteriophage ΦX174 was used to trace cross-contamination and evaluate current disinfection practices and a hydrogen peroxide (H₂O₂) wipe intervention within emergency response vehicles. Prior to EMS calls, 2 surfaces were seeded with ΦX174. On call completion, EMS vehicle and equipment surfaces were sampled before decontamination, after decontamination per current practices, and after implementation of the intervention.

Results

Current decontamination practices did not significantly reduce viral loads on surfaces (P = .3113), but H₂O₂ wipe intervention did (P = .0065). Bacteriophage spread to 56% (27/48) of sites and was reduced to 54% (26/48) and 40% (19/48) with current decontamination practices and intervention practices, respectively.

Conclusion

Results suggest firefighters' hands were the main vehicles of microbial transfer. Current practices were not consistently applied or standardized and minimally reduced prevalence and quantity of microbial contamination on EMS surfaces. Although use of a consistent protocol of H₂O₂ wipes significantly reduced percent prevalence and concentration of viruses, training and promotion of surface disinfection should be provided.

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We use bacteriophage as a human pathogen surrogate to trace surface transfer during emergency medical service calls.

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We quantify efficacy of current decontamination practice and hydrogen peroxide wipe intervention.

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Cross-contamination of emergency vehicle sites in 100% (15/15) of emergency medical service calls.

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Viral loads of seeded sites were not significantly reduced by current decontamination practices.

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Hydrogen peroxide wipe intervention significantly reduced viral loads on surfaces.

Persistent rhinovirus infection in pediatric hematopoietic stem cell transplant recipients with impaired cellular immunity

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Persistent rhinovirus infections are associated with impaired cellular immunity.

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The persistence of HRV infection is due to unrestricted replication of single virus strains rather than reinfections by different strains.

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The reconstitution of cell-mediated immunity might be crucial for complete virus clearance.

Background

HRV infections are generally self-limiting in healthy subjects, whereas in immunocompromised hosts HRV infections can lead to severe complications and persistent infections. The persistence of HRV shedding could be due to the inefficient immunological control of a single infectious episode.

Objectives

To investigate the clinical, virologic and immunologic characteristics of pediatric HSCT recipients with HRV-PI infection.

Study design

During the period 2006–2012, eight hematopoietic stem cell transplant (HSCT) recipients presented with persistent rhinovirus infection (HRV-PI, ≥30 days). Viral load and T-CD4⁺, T-CD8⁺, B and NK lymphocyte counts at the onset of infection were compared with those of fourteen HSCT recipients with acute HRV infection (HRV-AI, ≤15 days).

Results

The median duration of HRV positivity in patients with HRV-PI was 61 days (range 30–174 days) and phylogenetic analysis showed the persistence of a single HRV type in all patients (100%). In HSCT recipients with HRV-PI, T-CD4⁺, T-CD8⁺ and NK cell counts at the onset of infection were significantly lower than those observed in recipients with HRV-AI (p < 0.01), while B cell counts were similar in the two groups (p =  0.25). A decrease in HRV load was associated with a significant increase in T-CD4⁺, T-CD8⁺and NK lymphocyte counts in HRV-PI patients (p < 0.01).

Conclusions

This study suggests a role for cellular immunity in HRV clearance and highlights the importance of its recovery for the control of HRV infection in HSCT recipients.

A new real-time reverse transcription-PCR assay for detection of human enterovirus 68 in respiratory samples

A global reemergence of human enterovirus 68 (EV-D68) associated with severe respiratory illness occurred in 2014. We developed and validated an EV-D68-specific real-time reverse transcription-PCR (RT-PCR) for the detection of EV-D68 in respiratory samples. The rapid diagnosis of EV-D68 may contribute to better management of EV-D68 infections.

Circulation of two Enterovirus C105 (EV-C105) lineages in Europe and Africa

The coding sequences of five human enterovirus (HEV)-C genotype 105 strains recovered in Italy, Romania and Burundi from patients with upper and lower respiratory tract infections were analysed and phylogenetically compared with other circulating HEV-C strains. The EV-C105 was closely related to EV-C109 and EV-C118 strains. The European strains were similar to other circulating EV-C105 strains, while the two African EV-C105 clustered in separate bootstrap-supported (>0.90) branches of the P2 and P3 region trees. Minor inconsistencies in the clustering pattern of EV-C105 in the capsid region (P1) and non-capsid region (P3) suggest that recombination may have occurred in EV-C105 group B viruses. In conclusion, phylogenetic analysis revealed the circulation of two distinct EV-C105 lineages in Europe and Africa. A different pattern of evolution could be hypothesized for the two EV-C105 lineages.

Global reemergence of enterovirus D68 as an important pathogen for acute respiratory infections

We previously detected enterovirus D68 (EV-D68) in children with severe acute respiratory infections in the Philippines in 2008-2009. Since then, the detection frequency of EV-D68 has increased in different parts of the world, and EV-D68 is now recognized as a reemerging pathogen. However, the epidemiological profile and clinical significance of EV-D68 is yet to be defined, and the virological characteristics of EV-D68 are not fully understood. Recent studies have revealed that EV-D68 is detected among patients with acute respiratory infections of differing severities ranging from mild upper respiratory tract infections to severe pneumonia including fatal cases in pediatric and adult patients. In some study sites, the EV-D68 detection rate was higher among patients with lower respiratory tract infections than among those with upper respiratory tract infections, suggesting that EV-D68 infections are more likely to be associated with severe respiratory illnesses. EV-D68 strains circulating in recent years have been divided into three distinct genetic lineages with different antigenicity. However, the association between genetic differences and disease severity, as well as the occurrence of large-scale outbreaks, remains elusive. Previous studies have revealed that EV-D68 is acid sensitive and has an optimal growth temperature of 33 °C. EV-D68 binds to α2,6-linked sialic acids; hence, it is assumed that it has an affinity for the upper respiratory track where these glycans are present. However, the lack of suitable animal model constrains comprehensive understanding of the pathogenesis of EV-D68.

Genetic diversity of human enterovirus 68 strains isolated in Kenya using the hypervariable 3'-end of VP1 gene

Reports of increasing worldwide circulation of human enterovirus-68 (EV68) are well documented. Despite health concerns posed by resurgence of these viruses, little is known about EV68 strains circulating in Kenya. In this study, we characterized 13 EV68 strains isolated in Kenya between 2008 and 2011 based on the Hypervariable 3'-end of the VP1 gene. Viral RNA was extracted from the isolates and partial VP1 gene amplified by RT-PCR, followed by nucleotide sequencing. Alignment of deduced amino acid sequences revealed substitutions in Kenyan EV68 isolates absent in the prototype reference strain (Fermon). The majority of these changes were present in the BC and DE-loop regions, which are associated with viral antigenicity and virulence. The Kenyan strains exhibited high sequence homology with respect to those from other countries. Natural selection analysis based on the VP1 region showed that the Kenyan EV68 isolates were under purifying selection. Phylogenetic analysis revealed that majority (84.6%) of the Kenyan strains belonged to clade A, while a minority belonged to clades B and C. Overall, our results illustrate that although EV68 strains isolated in Kenya were genetically and antigenically divergent from the prototype strain (Fermon), they were closely related to those circulating in other countries, suggesting worldwide transmissibility. Further, the presence of shared mutations by Kenyan EV68 strains and those isolated in other countries, indicates evolution in the VP1 region may be contributing to increased worldwide detection of the viruses. This is the first study to document circulation of EV68 in Kenya.

Enterovirus 68 3C protease cleaves TRIF to attenuate antiviral responses mediated by Toll-like receptor 3

Human enterovirus 68 (EV68) is a member of the EV-D species, which belongs to the EV genus of the Picornaviridae family. Over the past several years, there have been increasingly documented outbreaks of respiratory disease associated with EV68. As a globally emerging pathogen, EV68 infects both adults and children. However, the molecular basis of EV68 pathogenesis is unknown. Here we report that EV68 inhibits Toll-like receptor 3 (TLR3)-mediated innate immune responses by targeting the TIR domain-containing adaptor inducing beta interferon (TRIF). In infected HeLa cells, EV68 inhibits poly(I·C)-induced interferon regulatory factor 3 (IRF3) activation and beta interferon (IFN-β) expression. Further investigations revealed that TRIF, a critical adaptor downstream of TLR3, is targeted by EV68. When expressed alone, 3C(pro), an EV68-encoded protease, cleaves TRIF. 3C(pro) mediates TRIF cleavage at Q312 and Q653, which are sites in the amino- and carboxyl-terminal domains, respectively. This cleavage relies on 3C(pro)'s cysteine protease activity. Cleavage of TRIF abolishes the capacity of TRIF to activate NF-κB and IFN-β signaling. These results suggest that control of TRIF by 3C(pro) may be a mechanism by which EV68 subverts host innate immune responses.

IMPORTANCE

EV68 is a globally emerging pathogen, but the molecular basis of EV68 pathogenesis is unclear. Here we report that EV68 inhibits TLR3-mediated innate immune responses by targeting TRIF. Further investigations revealed that TRIF is cleaved by 3C(pro). These results suggest that control of TRIF by 3C(pro) may be a mechanism by which EV68 impairs type I IFN production in response to TLR3 activation.

Interferon lambda 1-3 expression in infants hospitalized for RSV or HRV associated bronchiolitis

OBJECTIVES

The airway expression of type III interferons (IFNs) was evaluated in infants hospitalized for respiratory syncytial virus (RSV) or rhinovirus (HRV) bronchiolitis. As an additional objective we sought to determine whether a different expression of IFN lambda 1-3 was associated with different harboring viruses, the clinical course of bronchiolitis or with the levels of well established IFN stimulated genes (ISGs), such as mixovirus resistance A (MxA) and ISG56.

METHODS

The analysis was undertaken in 118 infants with RSV or HRV bronchiolitis. Nasopharyngeal washes were collected for virological studies and molecular analysis of type III IFN responses.

RESULTS

RSV elicited higher levels of IFN lambda subtypes when compared with HRV. A similar expression of type III IFN was found in RSVA or RSVB infected infants and in those infected with HRVA or HRVC viruses. Results also indicate that IFN lambda 1 and IFN lambda 2-3 levels were correlated with each other and with MxA and ISG56-mRNAs. In addition, a positive correlation exists between the IFN lambda1 levels and the clinical score index during RSV infection. In particular, higher IFN lambda 1 levels are associated to an increase of respiratory rate.

CONCLUSIONS

These findings show that differences in the IFN lambda 1-3 levels in infants with RSV or HRV infections are present and that the expression of IFN lambda 1 correlates with the severity of RSV bronchiolitis.

Major and minor group rhinoviruses elicit differential signaling and cytokine responses as a function of receptor-mediated signal transduction

Major- and minor-group human rhinoviruses (HRV) enter their host by binding to the cell surface molecules ICAM-1 and LDL-R, respectively, which are present on both macrophages and epithelial cells. Although epithelial cells are the primary site of productive HRV infection, previous studies have implicated macrophages in establishing the cytokine dysregulation that occurs during rhinovirus-induced asthma exacerbations. Analysis of the transcriptome of primary human macrophages exposed to major- and minor-group HRV demonstrated differential gene expression. Alterations in gene expression were traced to differential mitochondrial activity and signaling pathway activation between two rhinovirus serotypes, HRV16 (major-group) and HRV1A (minor-group), upon initial HRV binding. Variances in phosphorylation of kinases (p38, JNK, ERK5) and transcription factors (ATF-2, CREB, CEBP-alpha) were observed between the major- and minor-group HRV treatments. Differential activation of signaling pathways led to changes in the production of the asthma-relevant cytokines CCL20, CCL2, and IL-10. This is the first report of genetically similar viruses eliciting dissimilar cytokine release, transcription factor phosphorylation, and MAPK activation from macrophages, suggesting that receptor use is a mechanism for establishing the inflammatory microenvironment in the human airway upon exposure to rhinovirus.

Emerging and re-emerging virus infections in neonates and young pediatric patients

The epidemiology of virus infections has changed dramatically in Europe in recent years due to ecologic, anthropologic and biologic factors such as: i) climate modifications, ii) global exchange of goods and international travel, iii) increased immigration flux from Africa, South America, the Middle East and Asia, iv) reduction of cultivated areas, and v) emergence and re-emergence of human viruses from zoonotic reservoirs. In addition, recent technical advancements have allowed the identification of previously unrecognized autochthonous viral species. Thus, at present, the technical and cultural challenge is to recognize infections caused by viruses not normally circulating in our geographical region (both as imported cases or potential local outbreaks), sustained by recently discovered autochthonous viruses or due to recognized viruses which are no longer widespread in Western Europe due to past vaccination campaigns.

Molecular detection of human rhinoviruses in respiratory samples: a comparison of Taqman probe-, SYBR green I- and BOXTO-based real-time PCR assays

BACKGROUND

Human Rhinoviruses (HRV) are major causative agents of acute respiratory tract infections in all age group and important contributing factors of childhood morbidity and mortality. Clinical presentation is poorly specific and the great antigenic and genetic variability of HRVs renders the biological diagnosis complex. Here, we have evaluated several molecular diagnostic protocols, including Taqman probe-based and intercalating agent-based RT-PCR assays.

METHODS

5,627 respiratory samples sent to the laboratory of Virology of the University Hospitals of Marseille, France, from March 2011 to February 2012, were tested using a real-time RT-PCR assay in the 5'NCR of the rhinoviral genome that associated a Taqman probe and the detection of DNA-BOXTO-dye complexes. A sample of 500 BOXTO-positive samples were further tested using the same probe assay (without BOXTO), and a SYBR Green assay (using the same amplification primers). The specific amplification of HRV sequences was assessed by NGS amplicon sequencing.

RESULTS

The Taqman probe RT-PCR assay identified 696/5,627 samples (12,4%) as HRV-positive. BOXTO-positive samples included all probe-positive samples and 1,913 additional samples, of which only 24.3% were confirmed by sequencing. The SYBR Green assay was more specific (16/550 samples were probe-negative/SYBR Green-positive, all confirmed by 5'NCR sequencing), but 3/500 samples were probe-positive/SYBR Green-negative.

CONCLUSIONS

Our results highlight the difficulty in detecting HRVs in clinical samples using a single molecular detection system. Amongst the 3 systems tested, the best compromise was obtained with the SYBR Green assay, which, by comparison with our probe-based assay provided an improved sensitivity without altering the detection specificity. Interestingly, a majority of probe-negative/BOXTO- or SYBR Green-positive samples were not associated with mutations in the sequence targeted by the probe. Sequence-based modifications of the secondary structure of the HRV 5'NCR may be associated with a limited access to the probe hybridisation region. Further investigations may identify a test combining a probe based- and an intercalating agent-based detection, which will significantly improve the diagnosis of HRV infections.

Phylogenetic characterization of enterovirus 68 strains in patients with respiratory syndromes in Italy

Enterovirus 68 (EV‐D68) was associated with mild to severe respiratory infections. In the last 4 years, circulation of different EV‐D68 strains has been documented worldwide. In this study, the phylogenetic characterization of nine EV‐D68 strains identified in patients in the 2010–2012 period and 12 additional EV‐D68 Italian strains previously identified in 2008 in Italy was described. From January 2010 to December 2012, a total of 889 respiratory specimens from 588 patients stayed or visited at the Fondazione IRCCS Policlinico San Matteo were positive for HRV or HEV. Extracted nucleic acids were amplified by one‐step RT‐PCR with primer specific for VP1 region of EV‐D68 and purified positive PCR products were directly sequenced. Overall, 9/3736 (0.24%) patients were EV‐D68 positive. Of these, 7/9 (77.8%) were pediatric and two (22.2%) were adults. Five out of seven (71.4%) pediatric patients had lower respiratory tract infection with oxygen saturation <94%. Four cases were detected from August through October 2010, while five other cases from September through December 2012. The Italian EV‐D68 strains in 2008 belonged to clade A (n = 5) and clade C (n = 7). In 2010 all the Italian strains belonged to clade A (n = 4) and in 2012, four Italian strains belonged to clade B and one to clade A. In conclusion, we provide additional evidence supporting a role of EV‐D68 in severe respiratory infection in pediatric patients. In addition, all the three EV‐D68 clades circulating worldwide were identified in Italy in a 5‐year period of time. J. Med. Virol. 86:1590–1593, 2014. © 2013 Wiley Periodicals, Inc.

Complete genome characterization of enterovirus 104 circulating in Northern Italy shows recombinant origin of the P3 region

Human enterovirus 104 (EV-C104) is a member of the Human Enterovirus species C (Family Picornaviridae, Genus Enterovirus) and has been associated with mild respiratory syndromes. At present, only two EV-C104 complete genome sequences from strains detected in Switzerland and Japan have been deposited in GenBank. In this study a complete genome analysis of seven Italian EV-C104 strains was carried out. In addition, VP1 sequence analysis was performed in an additional 5 Italian strains (for a total of 12 strains). The genome length of the seven strains was 7406 nucleotides (nt). The seven genomes showed 91.0-96.9% nucleotide identity with respect to other available EV-C104 complete genomes. The P1 and P2 regions of the Italian strains were closely related to EV-C104 identified in Switzerland, while the P3 region was closely related to the EV-C117 strain. In addition, bootscan analysis showed the presence of one putative recombination breakpoint between the P2 and P3 regions. Based on the trees constructed with partial VP1/2A nucleotide sequences, as well as the 3D partial coding region tree, the Italian strains appear to form a single and independent cluster together with the EV-C104 Japanese strain. In conclusion, a complete phylogenetic analysis of the relationship between EV-C104 and other known HEV-C strains was achieved. In addition, the recombinant origin of EV-C104, which has circulated in Italy and Japan, was demonstrated.

Genomic analysis of coxsackieviruses A1, A19, A22, enteroviruses 113 and 104: viruses representing two clades with distinct tropism within enterovirus C

Coxsackieviruses (CV) A1, CV-A19 and CV-A22 have historically comprised a distinct phylogenetic clade within Enterovirus (EV) C. Several novel serotypes that are genetically similar to these three viruses have been recently discovered and characterized. Here, we report the coding sequence analysis of two genotypes of a previously uncharacterized serotype EV-C113 from Bangladesh and demonstrate that it is most similar to CV-A22 and EV-C116 within the capsid region. We sequenced novel genotypes of CV-A1, CV-A19 and CV-A22 from Bangladesh and observed a high rate of recombination within this group. We also report genomic analysis of the rarely reported EV-C104 circulating in the Gambia in 2009. All available EV-C104 sequences displayed a high degree of similarity within the structural genes but formed two clusters within the non-structural genes. One cluster included the recently reported EV-C117, suggesting an ancestral recombination between these two serotypes. Phylogenetic analysis of all available complete genome sequences indicated the existence of two subgroups within this distinct Enterovirus C clade: one has been exclusively recovered from gastrointestinal samples, while the other cluster has been implicated in respiratory disease.

Enteroviruses as major cause of microbiologically unexplained acute respiratory tract infections in hospitalized pediatric patients

OBJECTIVE

To assess the etiological role and the clinical characteristics of HRV and HEV infections in pediatric patients hospitalized for acute respiratory tract infections (ARTIs).

METHODS

RT-qPCR assays and molecular sequencing methods were used to identify HRV and HEV strains in nasopharyngeal aspirates of 309 hospitalized pediatric patients with microbiologically unexplained ARTIs and in 210 hospitalized pediatric patients without respiratory symptoms from September 2009 to June 2010 in France.

RESULTS

Among the 309 ARTI cases, 15 HEV and 172 HRV strains were identified whereas only 1 HEV and 37 HRV strains were observed in control patients (187 vs. 38: P < 10(-3)). HRV strains were identified in 150 of the 164 lower ARTIs whereas HEV strains were identified in only 14 of these cases. Among bronchiolitis and asthma exacerbation cases (n = 133), HEV infected cases were older (Median age (months) 36 vs. 11, P = 0.003) and were more frequently associated with a respiratory distress (P = 0.01) and a need for oxygen supply at the time of admission (P = 0.01) than cases infected by HRV strains.

CONCLUSION

HRV and HEV strains were identified as potential etiological causes of 60.5% of microbiologically unexplained ARTIs diagnosed in hospitalized pediatric cases. A higher clinical severity was observed in HEV infected bronchiolitis or asthma exacerbation cases in comparison to HRV infected cases.

Genome characterisation of enteroviruses 117 and 118: a new group within human enterovirus species C

The more than 120 genotypes of human enteroviruses (HEVs) reflect a wide range of evolutionary divergence, and there are 23 currently classified as human enterovirus C species (HEV-C). Two new HEV-C (EV-C117 and EV-C118) were identified in the Community-Acquired Pneumonia Pediatric Research Initiative (CAP-PRI) study, and the present paper describes the characterisation of the complete genome of one EV-C117 strain (LIT22) and two EV-C118 (ISR38 and ISR10) strains. The EV-C117 and EV-C118 5'UTR sequences were related to those of EV-C104, EV-C105 and EV-C109, and were slightly shorter than those of other HEV A-D species. Similarity plot analyses showed that EV-C117 and EV-C118 have a P1 region that is highly divergent from that of the other HEV-C, and phylogenetic analyses highly supported a monophyletic group consisting of EV-C117, EV-C118, EV-C104, EV-C105 and EV-C109 strains. Phylogenetic, Simplot and Bootscan analyses indicated that recombination was not the main mechanism of EV-C117 and EV-C118 evolution, thus strengthening the hypothesis of the monophyletic origin of the coding regions, as in the case of other HEV-C. Phylogenetic analysis also revealed the emergence of a new group within HEV-C that is divided into two subgroups. Nucleotide and amino acid identity in VP1 sequences have been established as useful criteria for assigning new HEV types, but analysis of the complete P1 region improves resolution.

Virus shedding after human rhinovirus infection in children, adults and patients with hypogammaglobulinaemia

The shedding of human rhinovirus (HRV) after an acute, naturally acquired infection has not been described in detail. We determined the duration of HRV shedding in immunocompetent children and adults, and in patients with primary hypogammaglobulinaemia. Subjects with symptoms of respiratory tract infection, and their household contacts, were screened for HRV by reverse transcription PCR. They were followed by serial, self-collected nasal swab specimens until negative for HRV or infected by another HRV type. We followed 62 HRV infections in 54 subjects. The mean (95% CI) duration of HRV shedding was 11.4 (8.2-14.7) days in children, 10.1 (7.4-12.9) days in adults, and 40.9 (26.4-55.4) days in patients with hypogammaglobulinaemia (p <0.001). The duration of respiratory tract symptoms correlated with the duration of virus shedding (p 0.002). A new infection by another HRV type soon after the first episode was common. We conclude that the shedding times of HRV are relatively short in otherwise healthy individuals. In contrast, prolonged shedding over 28 days is frequent in patients with hypogammaglobulinaemia despite immunoglobulin replacement therapy.

Prospective detection of respiratory pathogens in symptomatic children with cancer

BACKGROUND

: The data on human rhinovirus, coronavirus, bocavirus, metapneumovirus, Chlamydophila pneumoniae, Mycoplasma pneumoniae and Bordetella pertussis infections in children with cancer is limited.

METHODS

: We sought to determine prospectively the prevalence of respiratory pathogens in these children, using multiplexed-polymerase chain reaction.

RESULTS

: We enrolled 253 children with upper or lower respiratory tract infection (LRTI) during a 1-year period. A respiratory virus was detected in 193 (76%) patients; 156 (81%) patients had upper respiratory tract infection. Human rhinovirus was the most common virus detected in 97 (62%) and 24 (65%) patients with upper respiratory tract infection and LRTI, respectively. Leukemia or lymphoma was the most common underlying diagnosis in 95 (49%) patients followed by solid tumor 47 (24%), posthematopoietic stem cell transplant 28 (15%) and brain tumor in 23 (12%) patients. By multiple logistic regression analysis, human bocavirus was the most commonly detected respiratory virus in patients with LRTI (P = 0.008; odds ratio, 4.52; 95% confidence interval: 1.48-13.79). Coinfection with >1 virus was present in 47 (24%) patients, and did not increase the risk for LRTI. Two (0.7%) patients succumbed to LRTI from parainfluenza virus-3 and respiratory syncytial virus/human rhinovirus infection, respectively. C. pneumoniae and M. pneumoniae were detected in 4 and 3 patients, respectively.

CONCLUSIONS

: Human rhinovirus was the most common virus detected in children with cancer and posthematopoietic stem cell transplant hospitalized with an acute respiratory illness, and was not associated with increased morbidity. Prospective studies with viral load determination and asymptomatic controls are needed to study the association of these emerging respiratory viruses with LRTI in children with cancer and posthematopoietic stem cell transplant.

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.

Genomic analysis of two novel human enterovirus C genotypes found in respiratory samples from Peru

We report the discovery of two enteroviruses detected in nasopharyngeal samples obtained from subjects with respiratory disease in Peru. Phylogenetic analysis indicated that both viruses belong to a clade within the species Human enterovirus C, which includes the recently characterized human enteroviruses 109 and 104. Members of this clade have undergone significant genomic rearrangement, as indicated by deletions in the hypervariable region of the 5' UTR and the VP1 protein, as well as recombination within the non-structural genes. Our findings and review of published sequences suggests that several novel human enterovirus C serotypes are currently circulating worldwide.