Molecular assays for detection of human metapneumovirus

Review of new and newly discovered respiratory tract viruses in children

Respiratory tract viral infection continues to be among the most common reasons for emergency department visits and hospitalization of children, particularly infants younger than 1 year, in the United States. Throughout the years, clinicians have considered respiratory syncytial virus followed by influenza as the most common pathogens responsible. Over the past decade, new viruses have been discovered through both more specific testing and the finding of new agents causing infection. This includes human metapneumovirus, which leads to similar but often epidemiologically more severe clinical symptoms than respiratory syncytial virus. Other agents responsible for lower respiratory tract infection include Coronavirus (severe acute respiratory syndrome), Bocavirus, and others. This review serves to focus on some of the recent literature on these agents and the clinical impact they have on pediatric lung infection.

Novel respiratory virus infections in children, Brazil

Recently discovered respiratory viruses were detected in 19 (9.2%) of 205 nasal swab specimens from children in Brazil with respiratory illnesses. Five each were positive for human metapneumovirus (HMPV) alone and human bocavirus (HBoV) alone, 3 for human coronaviruses (HCoV-HKU1 or -NL63) alone, and 6 for more than 1 recently discovered virus.

Human metapneumovirus: a new respiratory pathogen

Human metapneumovirus is a recently recognized pathogen of acute respiratory tract infection (ARI) in children as well as elderly and immunocompromised adults.The virus belongs to the family Paramyxoviridae, sub family Pneumovirinae and genus Metapneumovirus. Through genetic analysis it has been characterized into two groups A and B which are further divided into four sub-lineages. The virus is difficult to grow in tissue culture and hence reverse transcriptase-polymerase chain reaction (RT-PCR) for N and L gene is the method of choice for diagnosis. The virus has been seen in all countries with seasonal distribution in winter months for temperate and spring/summer for tropical countries. F gene is the most conserved among different lineages and efforts are underway to design recombination vaccine using F gene.

The impact of viral respiratory infection on the severity and recovery from an asthma exacerbation

BACKGROUND

: Viral respiratory illness triggers asthma exacerbations, but the influence of respiratory illness on the acute severity and recovery of childhood asthma is unknown. Our objective was to evaluate the impact of a concurrent acute respiratory illness (based on a clinical definition and PCR detection of a panel of respiratory viruses, Mycoplasma pneumoniae and Chlamydia pneumoniae) on the severity and resolution of symptoms in children with a nonhospitalized exacerbation of asthma.

METHODS

: Subjects were children aged 2 to 15 years presenting to an emergency department for an acute asthma exacerbation and not hospitalized. Acute respiratory illness (ARI) was clinically defined. Nasopharyngeal aspirates (NPA) were examined for respiratory viruses, Chlamydia and Mycoplasma using PCR. The primary outcome was quality of life (QOL) on presentation, day 7 and day 14. Secondary outcomes were acute asthma severity score, asthma diary, and cough diary scores on days 5, 7, 10, and 14.

RESULTS

: On multivariate regression, presence of ARI was statistically but not clinically significantly associated with QOL score on presentation (B = -0.36, P = 0.025). By day 7 and 14, there was no difference between groups. Asthma diary score was significantly higher in children with ARI (B = 0.41, P = 0.039) on day 5 but not on presentation or subsequent days. Respiratory viruses were detected in 54% of the 78 NPAs obtained. There was no difference in the any of the asthma outcomes of children grouped by positive or negative NPA.

CONCLUSIONS

: The presence of a viral respiratory illness has a modest influence on asthma severity, and does not influence recovery from a nonhospitalized asthma exacerbation.

Comprehensive detection of causative pathogens using real-time PCR to diagnose pediatric community-acquired pneumonia

We have developed a real-time reverse transcription-PCR (RT-PCR) method to detect 13 respiratory viruses: influenza virus A and B; respiratory syncytial virus (RSV) subgroup A and B; parainfluenza virus (PIV) 1, 2, and 3; adenovirus; rhinovirus (RV); enterovirus; coronavirus (OC43); human metapneumovirus (hMPV); and human bocavirus (HBoV). The new method for detection of these viruses was applied simultaneously with real-time PCR for the detection of six bacterial pathogens in clinical samples from 1700 pediatric patients with community-acquired pneumonia (CAP). Of all the patients, 32.5% were suspected to have single bacterial infections; 1.9%, multiple bacterial infections; 15.2%, coinfections of bacteria and viruses; 25.8%, single viral infections; and 2.1%, multiple viral infections. In the remaining 22.6%, the etiology was unknown. The breakdown of suspected causative pathogens was as follows: 24.4% were Streptococcus pneumoniae, 14.8% were Mycoplasma pneumoniae, 11.3% were Haemophilus influenzae, and 1.4% were Chlamydophila pneumoniae. The breakdown of viruses was as follows: 14.5% were RV, 9.4% were RSV, 7.4% were hMPV, 7.2% were PIV, and 2.9% were HBoV. The new method will contribute to advances in the accuracy of diagnosis and should also result in the appropriate use of antimicrobials.

Detection of respiratory viruses by molecular methods

SUMMARY

Clinical laboratories historically diagnose seven or eight respiratory virus infections using a combination of techniques including enzyme immunoassay, direct fluorescent antibody staining, cell culture, and nucleic acid amplification tests. With the discovery of six new respiratory viruses since 2000, laboratories are faced with the challenge of detecting up to 19 different viruses that cause acute respiratory disease of both the upper and lower respiratory tracts. The application of nucleic acid amplification technology, particularly multiplex PCR coupled with fluidic or fixed microarrays, provides an important new approach for the detection of multiple respiratory viruses in a single test. These multiplex amplification tests provide a sensitive and comprehensive approach for the diagnosis of respiratory tract infections in individual hospitalized patients and the identification of the etiological agent in outbreaks of respiratory tract infection in the community. This review describes the molecular methods used to detect respiratory viruses and discusses the contribution that molecular testing, especially multiplex PCR, has made to our ability to detect respiratory viruses and to increase our understanding of the roles of various viral agents in acute respiratory disease.

A scoring system for management of acute pharyngo-tonsillitis in adults

Objectives

The aim of this study was to develop and evaluate a scoring system for the management of acute pharyngo-tonsillitis.

Methods

We conducted a prospective study between May 2004 and June 2005. Patients with acute pharyngo-tonsillitis were evaluated for causative pathogens and were assessed clinical symptoms and pharyngo-tonsillar finding by a clinical scoring system.

Results

A total 214 adult patients were enrolled in this study. Streptococcus pyogenes were identified at 13.6%. Thirty-one viruses were also identified by PCR. They were adenovirus (4.8%), influenza virus (1.0%), RS virus (6.3%), and human metapneumovirus (2.9%). Numbers of total white blood cells and levels of C-reactive protein showed a significant positive correlation with clinical scores (p < 0.001) and were also higher in cases with S. pyogenes. The clinical scores rapidly improved after the antimicrobial treatments in moderate cases and severe cases.

Conclusion

The current study strongly suggested that the clinical scoring system reflected disease severity well and would be very useful for evaluating clinical course and decision making for the antimicrobial treatment of acute pharyngo-tonisllitis.

Clinical and laboratory evaluation of upper respiratory symptoms in elite athletes

OBJECTIVE

To characterize the etiology of upper respiratory symptoms in elite athletes presenting to a sports physician for treatment.

DESIGN

Prospective clinical and laboratory investigations.

SETTING

Sports medicine clinic.

PARTICIPANTS

Seventy elite-level athletes.

MAIN OUTCOME MEASUREMENTS

Physician-recorded symptoms and diagnosis; health/training questionnaires; laboratory investigations of respiratory pathogens, white blood cell differential counts, and immune parameters.

RESULTS

Physicians characterized 89% of presentations as viral or bacterial upper respiratory tract infection. Only 57% of presentations were associated with an identified pathogen or other laboratory parameters indicative of infection. Demographic information, previous illness, and training history did not distinguish between presentations with or without objective measures of infection. Elevated white blood cell and neutrophil counts and lower vitamin D concentrations partially distinguished infectious episodes. The number of systemic symptoms/behaviors at presentation (cough, headache, earache, fatigue, fever/rigors, myalgia/arthralgia, or cessation of training before clinic attendance) had some predictive value for infection: odds ratio per symptom, 1.23 (90% confidence interval: 0.91 to 1.66); probability of infection, 48% with no symptoms to 77% with 6 symptoms. Laboratory investigation identified allergy in a considerable proportion of the cohort (39%).

CONCLUSIONS

The discrepancy between physician and laboratory diagnosed infection in elite athletes highlights the need for consideration of alternate diagnostic options when evaluating upper respiratory symptoms in athletes. A considerable proportion of episodes of respiratory symptoms in athletes were not associated with identification of a respiratory pathogen; other potentially treatable causes of upper respiratory symptoms should be considered, particularly in athletes with recurrent symptoms.

False-negative results in nucleic acid amplification tests-do we need to routinely use two genetic targets in all assays to overcome problems caused by sequence variation?

Nucleic acid amplification tests (NAATs) have numerous advantages over traditional diagnostic techniques and so are now widely used by diagnostic laboratories for routine detection of infectious agents. However, there is some concern over the increasing numbers of reports of NAAT false-negative results caused by sequence variation. Highly conserved NAAT target sequences have been reported for many organisms, yet sequence-related problems continue to be observed in commercial and in-house assays targeting a broad range of microbial pathogens. In light of these ongoing problems, it may be time to consider the use of two genetic targets in NAAT methods to reduce the potential for sequence-related false-negative results.

The emergence of human metapneumovirus

Until relatively recently there had been episodes when children had been admitted into hospitals with symptoms that were similar to those expected for human respiratory syncytial virus (HRSV), but the available diagnostic procedures failed to detect the presence of HRSV, and the causative disease agent remained unidentified. Dutch scientists examined nasopharyngeal aspirates from similar patients in Holland using advanced molecular biology and imaging techniques. The conclusions of this study were published in 2001, revealing that a previously unidentified paramyxovirus was responsible for these infections. This agent was grouped within the subfamily Pneumovirinae, genus metapneumovirus, and given the name human metapneumovirus (HMPV) to distinguish it from other members of the genus Metapneumovirus that are of avian origin. Although HMPV is associated with upper respiratory tract infection, it is now recognized as a major cause of lower respiratory infection (LRTI) in children in a variety of different geographical regions. Furthermore, retrospective studies have detected the presence of HMPV in archived clinical material dating from the 1950s, suggesting that this was not a new virus, but it had remained undetected for several decades until its ‘emergence’ in 2001. This review will discuss the increasing global importance of HMPV as a cause of LRTI among young children.

[Human metapneumovirus]

Le métapneumovirus humain (hMPV) est un nouveau Pneumovirinae apparenté au métapneumovirus aviaire du type C. Le génome du hMPV diffère de celui du virus respiratoire syncytial humain (RSV) par l’ordre des gènes et le manque des gènes non structuraux. Deux sous-groupes génétiques de hMPV et quatre sous-types ont été identifiés. Les infections à hMPV évoluent sous forme d’épidémies hivernales régulières, superposées à celle du RSV et d’importance à peu près égale d’une année sur l’autre. Chez les enfants hospitalisés à Caen, le hMPV est détecté dans 9,7 % des cas, après le RSV (37 %), les rhinovirus (18 %), les virus influenza (15,4 %), les adénovirus (9 %) et les virus parainfluenza (5 %). La plupart des infections à hMPV sont observées chez des enfants atteints de bronchiolites, mais par comparaison à l’infection à RSV, l’atteinte respiratoire basse et les signes de gravité sont moins fréquents. Le hMPV est très difficile à isoler en cultures des cellules. Le diagnostic a reposé jusqu’ici sur la détection moléculaire par RT–PCR. L’apparition récente des tests antigéniques permet de disposer aujourd’hui d’un test de diagnostic rapide, simple et économique.

Detection and characterisation of human metapneumovirus from children with acute respiratory symptoms in north-west England, UK

BACKGROUND

Human metapneumovirus (hMPV) causes a spectrum of respiratory disease ranging from trivial coryzal symptoms to fatal pneumonia, with a predilection for the very young, the immune suppressed and the frail elderly. Five distinct lineages of the virus genome have been described.

OBJECTIVES

To develop and evaluate a sensitive, real-time PCR (RT-PCR) assay capable of detecting all lineages of hMPV, suitable for use in a diagnostic laboratory.

STUDY DESIGN

An RT-PCR assay was developed using novel primers and dual-labelled minor-groove-binding (MGB) probes complementary to consensus sequences. The assay and two alternative assays were tested against external quality assurance (EQA) panels. 221 respiratory samples collected during 2003-2004 were screened using the new assay. hMPV positive samples were sequenced and phylogenetically analysed.

RESULTS

Three genetic lineages of hMPV were detected during 2003-2004. Incidence was low (2.3%) compared to previous years. All five lineages had been present in the same community within the past 3 years.

CONCLUSIONS

The new assay correctly identified more EQA samples, including those at greatest dilution, than the alternative assays and detected all five lineages. Seasonal circulation of hMPV in paediatric patients with acute respiratory symptoms is dynamic with respect to incidence and viral genotype.

Major histocompatibility complex class I cytotoxic T lymphocyte immunity to human metapneumovirus (hMPV) in individuals with previous hMPV infection and respiratory disease

Recently identified human metapneumovirus (hMPV) is an important respiratory pathogen in children and adults worldwide. Little is known about cytotoxic T lymphocyte (CTL) responses that may control hMPV infection in humans. To address this, we evaluated major histocompatibility complex (MHC) class I T cell immunity in 7 patients with previous hMPV respiratory disease. CTL responses were evident in most patients and to most proteins of hMPV. Individual patients had responses to at least 2 hMPV proteins (particularly the M protein) and had multiallele responses. In addition, we identified 9 CTL epitopes that are presented by human leukocyte antigen alleles of the most common MHC "supertypes." Many of these CTL epitopes are conserved across hMPV types, and there is epitope similarity between hMPV and human respiratory syncytial virus. This study provides the first report of MHC class I T cell immunity to hMPV in humans. These findings have significance for understanding cellular immunity to hMPV infection and for future vaccine development.

Clinical evaluation of NucliSENS magnetic extraction and NucliSENS analyte-specific reagents for real-time detection of human metapneumovirus in pediatric respiratory specimens

In this study, we evaluated the NucliSENS miniMAG (MM) and easyMAG (EM) nucleic acid extraction platforms (bioMérieux, Durham, NC) in combination with the NucliSENS EasyQ basic kit and analyte-specific reagents (ASRs) (bioMérieux) for the detection of human metapneumovirus (hMPV) in respiratory samples. Total nucleic acids from pediatric clinical samples (n = 653) and an hMPV-specific inhibition control (h-IC) were coextracted using the MM and/or the EM. Nucleic acid sequence-based amplification and real-time molecular beacon detection of hMPV were performed using a NucliSENS EasyQ analyzer (bioMérieux). Positive results were confirmed using an in-house-validated reverse transcriptase PCR ASR-based assay. The inclusion of the h-IC monitored the entire process, including the efficiency of nucleic acid extraction, amplification, and detection. The percentages of samples with inhibited amplification of the h-IC after initial NA extraction by EM and MM were 1.88% and 3.17%, respectively. After reprocessing of a new aliquot, the final h-IC inhibition rates were 0% (EM) and 1.06% (MM). The limit of detection of the assay was between 2 (EM extraction) and 10 (MM extraction) RNA copies/reaction, and specificity was 100% when testing viral respiratory isolates and clinical samples. hMPV was detected in 5.6% of pediatric samples tested and was also detected in three coinfections with respiratory syncytial virus (RSV). hMPV was the second most frequently detected respiratory virus in children of 0 to 2 years of age, after RSV. In summary, NucliSENS extraction and ASRs provided a sensitive and specific method for the detection of hMPV in respiratory samples.

Development of a microtiter plate hybridization-based PCR-enzyme-linked immunosorbent assay for identification of clinically relevant human group A rotavirus G and P genotypes

A microtiter plate hybridization-based PCR-enzyme-linked immunosorbent assay (PCR-ELISA) has been used for the detection and identification of a variety of microorganisms. Here, we report the development of a PCR-ELISA for the identification of clinically relevant human rotavirus VP7 (G1 to G6, G8 to G10, and G12) and VP4 (P[4], P[6], P[8], P[9], and P[14]) genotypes. The G and P types of reference human and animal rotavirus strains for which specific probes were available were correctly identified by the PCR-ELISA. In addition, reference strains bearing G or P genotypes for which specific probes were unavailable, such as G11, G14, P[3], P[10], and P[11], did not display any cross-reactivity to the probes. The usefulness of the assay was further evaluated by analyzing a total of 396 rotavirus-positive stool samples collected in four countries: Brazil, Ghana, Japan, and the United States. The results of this study showed that the PCR-ELISA was sensitive and easy to perform without the use of any expensive and sophisticated equipment, the reagents used are easy to obtain commercially and advantageous over multiplex PCR since more than one type-specific probe is used and the selection of probes is more flexible.

Infections respiratoires virales émergentes

Viral respiratory infections are very frequent diseases with variable degrees of severity. During the past few years, new respiratory viruses have been discovered by means of molecular biology techniques. In fact, these so far unidentified viruses have been present in humans for a long time but remained unidentified. These viruses are mainly represented by the human metapneumovirus (HMPV), the coronaviruses HCoV-NL63, HCoV-NH and HCoVHKU1, the human bocavirus (HBoV), and the newly described human polyomaviruses WU and KI. Beside these newly identified viruses, new respiratory viruses have emerged in humans within the last years. These viruses have been introduced from animal reservoirs and they generally present a high degree of pathogenicity with high level of mortality in humans. These emerging respiratory viruses are represented by the henipaviruses (Hendra and Nipah viruses), the New World hantaviruses associated with the Hantavirus Pulmonary Syndrome, the coronavirus responsible for the Severe Acute Respiratory Syndrome (SARS-CoV), and the avian influenza virus H5N1. This latter constitutes a major threat, with the risk of a murderous pandemic offering some parallels with the 1918-1919 Spanish flu which caused 20-50 millions deaths worldwide.

Currently used nucleic acid amplification tests for the detection of viruses and atypicals in acute respiratory infections

For the detection of respiratory viruses conventional culture techniques are still considered as the gold standard. However, results are mostly available too late to have an impact on patient management. The latest developments include appropriate DNA- and RNA-based amplification techniques (both NASBA and PCR) for the detection of an extended number of agents responsible for LRTI. Real time amplification, the latest technical progress, produces, within a considerable shorter time, results with a lower risk of false positives. As results can be obtained within the same day, patient management with appropriate therapy or reduction of unnecessary antibiotic therapy in LRTI will be possible. A number of technical aspects of these amplification assays, and their advantages are discussed.

The availability and use of these new diagnostic tools in virology has contributed to a better understanding of the role of respiratory viruses in LRTI. The increasing importance of the viral agents, Mycoplasma pneumoniae and Chlamydophila pneumoniae in ARI is illustrated. A great proportion of ARI are caused by viruses, but their relative importance depends on the spectrum of agents covered by the diagnostic techniques and on the populations studied, the geographical location and the season. The discovery of new viruses is ongoing; examples are the hMPV and the increasing number of coronaviruses. Indications for the use of these rapid techniques in different clinical situations are discussed. Depending on the possibilities, the laboratory could optimize its diagnostic strategy by applying a combination of immunofluorescence for the detection of RSV an IFL, and a combination of real-time amplification tests for other respiratory viruses and the atypical agents. When implementing a strategy, a compromise between sensitivity, clinical utility, turn around time and cost will have to be found.

Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein

Human metapneumovirus (hMPV), a newly discovered virus of the family Paramyxoviridae, has been associated with upper and lower respiratory tract infections in different age groups in many countries. The putative attachment (G) glycoprotein of this virus was previously reported to have shown more extensive nucleotide and deduced amino acid sequence polymorphism than any other genomic regions of this virus, leading to four sub-lineages. Using a maximum likelihood-based codon substitution model of sequence evolution, here we report that sequences of extracellular domain of 8 amino acid sites in lineage 1a, and 3 amino acid sites each in lineage 1b, 2a, and 2b have a higher rate of nonsynonymous substitutions (d(N)) than the synonymous substitutions (d(S)) with a posterior probability above 0.95, thus suggesting the evidence of adaptive evolution driven by Darwinian selection. Although it is unclear whether these amino acid adaptations are driven by differential immune pressure or some other factors, identification of these positively selected amino acid sites would help in better screening using epitope mapping technology to identify and localize the sites that can be recognized by the immune system. We also observed surprisingly higher nucleotide substitution rates per site, per year for each lineage of hMPV than the rates that were previously reported for the human respiratory syncytial virus, suggesting rapid evolutionary dynamics of hMPV.

Diagnosis and epidemiological studies of human metapneumovirus using real-time PCR

Background

Human metapneumovirus (hMPV) is prevalent in children, the elderly and immunocompromised individuals, but available epidemiological data is limited.

Objectives

(1) To develop and validate a real-time PCR method for hMPV diagnosis. (2) To determine the percentage of hMPV in respiratory specimens from the community and its association with outbreaks in our geographic area. (3) To provide epidemiological data in terms of age distribution, seasonality and co-infections.

Study design

A real-time PCR assay was designed for detection of hMPV lineages A and B. Prospective testing for hMPV over a 22-month period was then undertaken.

Results

The real-time PCR was sensitive and specific for detection of both lineages of hMPV. hMPV was detected in 9.5% (n = 8239) of the specimens and 25% of the outbreaks (n = 100) tested. The hMPV-positive patients ranged in age from 18 days to 99 years with a median age of 24 months. The number of positive samples peaked during the winter months of December, January and February. A high rate of co-infections was noted in the samples tested.

Conclusions

hMPV is common in the community and is associated with outbreaks. Including hMPV in routine testing improves etiological diagnosis of acute respiratory infections.

Incidence, etiology, and symptomatology of upper respiratory illness in elite athletes

PURPOSE

Upper respiratory illness (URI) is the most common medical condition affecting elite athletes. The aims of this study were to identify and evaluate the incidence, pathogenic etiology, and symptomatology of acute URI during a 5-month training and competition period.

METHODS

Thirty-two elite and 31 recreationally competitive triathletes and cyclists, and 20 sedentary controls (age range 18.0-34.1 yr) participated in a prospective surveillance study. Nasopharyngeal and throat swabs were collected from subjects presenting with two or more defined upper respiratory symptoms. Swabs were analyzed using microscopy, culture, and PCR testing for typical and atypical respiratory pathogens. The Wisconsin Upper Respiratory Symptom Survey (WURSS-44) was used to assess symptomatology and functional impairment.

RESULTS

Thirty-seven URI episodes were reported in 28 subjects. Incidence rate ratios for illness were higher in both the control subjects (1.93, 95% CI: 0.72-5.18) and elite athletes (4.50, 1.91-10.59) than in the recreationally competitive athletes. Infectious agents were identified in only 11 (two control, three recreationally competitive, and six elite) out of 37 illness episodes. Rhinovirus was the most common respiratory pathogen isolated. Symptom and functional impairment severity scores were higher in subjects with an infectious pathogen episode, particularly on illness days 3-4.

CONCLUSION

The results confirm a higher rate of URI among elite athletes than recreationally competitive athletes during this training and competition season. However, because pathogens were isolated in fewer than 30% of URI cases, further study is required to uncover the causes of unidentified but symptomatic URI in athletes. Despite the common perception that all URI are infections, physicians should consider both infectious and noninfectious causes when athletes present with symptoms.

Detection of respiratory viruses and subtype identification of influenza A viruses by GreeneChipResp oligonucleotide microarray

Acute respiratory infections are significant causes of morbidity, mortality, and economic burden worldwide. An accurate, early differential diagnosis may alter individual clinical management as well as facilitate the recognition of outbreaks that have implications for public health. Here we report on the establishment and validation of a comprehensive and sensitive microarray system for detection of respiratory viruses and subtyping of influenza viruses in clinical materials. Implementation of a set of influenza virus enrichment primers facilitated subtyping of influenza A viruses through the differential recognition of hemagglutinins 1 through 16 and neuraminidases 1 through 9. Twenty-one different respiratory virus species were accurately characterized, including a recently identified novel genetic clade of rhinovirus.

Detection of human metapneumovirus in hospitalized children with acute respiratory tract infection using real-time RT-PCR in a hospital in northern Taiwan

Background/purpose

Human metapneumovirus (hMPV) is a newly discovered respiratory pathogen. This prospective hospital-based study investigated the clinical role and features of hMPV in Taiwan.

Methods

Respiratory specimens collected from hospitalized children with acute respiratory tract infection between September 1, 2003 and April 10, 2005 were screened for metapneumovirus using real-time reverse transcription-polymerase chain reaction (RT-PCR).

Results

During the study period, 930 specimens were obtained from 926 hospitalized children. After exclusion of 200 cases due to lack of clinical evidence of airway infection or diseases with known etiology, 726 were included in the analysis. Among these, 33 children had a positive result for hMPV infection. The majority of these patients were admitted during spring and early summer. Twenty-one (63.6%) were younger than 2 years of age. hMPV accounted for 13.3% of respiratory infections occurring between the ages of 18 and 24 months and was as common a respiratory pathogen as respiratory syncytial virus (RSV) in that age group. The 11 patients (33.3%) with underlying diseases had a similar disease course to those without underlying diseases. A co-pathogen was found in 11 patients (33.3%). Infected children between 2 and 5 years of age had significantly higher titers of hMPV in their respiratory specimens (10^3.88 copies/mL) than children younger than 2 years (10^2.26 copies/mL) (p = 0.013) and children older than 5 years (10^2.25 copies/mL) (p = 0.005). hMPV positive cases were significantly older than those with RSV infection (p = 0.002) and had a shorter duration of hospitalization (p = 0.001), fewer days of oxygen use (p = 0.001) and higher levels of C-reactive protein (p = 0.004).

Conclusion

Metapneumovirus circulates in children in northern Taiwan during spring and early summer. hMPV was the most common respiratory pathogen in children aged between 18 and 24 months hospitalized with acute respiratory tract infection. Real-time RT-PCR is a sensitive method for investigating the epidemiology and diseases associated with hMPV. [J Formos Med Assoc 2007;106(1):16-24]

Human metapneumovirus induces more severe disease and stronger innate immune response in BALB/c mice as compared with respiratory syncytial virus

BACKGROUND

Human metapneumovirus (HMPV) and respiratory syncytial virus (RSV) are members of the Pneumovirinae subfamily of Paramyxoviridae and can cause severe respiratory disease, especially in infants and young children. Some differences in the clinical course of these infections have been described, but there are few comparative data on pathogenesis in humans and animal models. In this study, HMPV and RSV were compared for replication, pathogenesis and immune induction in BALB/c mice infected with equivalent inocula of either virus.

METHODS

Viral titers in the lungs and in the nasal turbinates of mice were determined by plaque assay. Histopathological changes in the lungs as well as weight loss and levels of airway obstruction were monitored in the infected mice to record the severity of illness. Inflammatory cells recruited to the lungs were characterized by flow cytometry and by differential staining. In the case of natural killer cells, cytotoxic activity was also measured. Cytokine levels in the BAL were determined by cytometric bead array.

RESULTS

RSV replicated to higher titers than HMPV in the lung and in the upper respiratory tract (URT), and virus elimination from the lungs was more rapid in HMPV-infected mice. Clinical illness as determined by airway obstruction, weight loss, and histopathology was significantly more severe after HMPV infection. A comparison of the cellular immune response revealed similar recruitment of T lymphocytes with a predominance of IFN-gamma-producing CD8+ T cells. By contrast, there were obvious differences in the innate immune response. After HMPV infection, more neutrophils could be detected in the airways and there were more activated NK cells than in RSV-infected mice. This correlated with higher levels of IL-6, TNF-alpha and MCP-1.

CONCLUSION

This study shows important differences in HMPV and RSV pathogenesis and suggests that the pronounced innate immune response observed after HMPV infection might be instrumental in the severe pathology.

Human metapneumovirus infection

Initially, human metapneumovirus (hMPV) was isolated from children with clinical symptoms of respiratory syncytial virus (RSV) infection in whom RSV could not be detected. Since then, numerous reports have described the detection of hMPV in clinical specimens from children, adults and the elderly (both immunocompetent and immunocompromised patients), diagnosed with an acute respiratory illness all over the world. hMPV is associated with a substantial number of respiratory tract infections in otherwise healthy children, with clinical illnesses similar to those associated with other common respiratory viruses. Serological surveys have shown that hMPV is a ubiquitous virus that infects all children by the age of 5–10 years and has been circulating in humans for at least 50 years. hMPV is a member of the Metapneumovirus genus of the Paramyxoviridae family, a group of negative-stranded RNA viruses. Genetic studies on hMPV have demonstrated the presence of two distinct hMPV serotypes each divided in two subgroups. Diagnosis is made by RT-PCR assays on respiratory secretions. Rapid antigen detection tests are not yet available and its growth in cell cultures is fastidious. No vaccines, antibodies (monoclonal or polyclonal), or chemotherapeutic agents are currently licensed for use to prevent or treat hMPV infections. The contribution of hMPV to pediatric respiratory tract infections suggests that it will be important to develop a vaccine against this virus in combination with those being developed for RSV and parainfluenza viruses. Reverse genetics technology is currently used to develop multivalent vaccines against hMPV and a variety of other important respiratory viruses such as RSV. Additional research to define the pathogenesis of this viral infection and the host’ specific immune response will enhance our knowledge to guide the search for preventive and therapeutical strategies.

Characterization of human metapneumovirus infections in Israel

Respiratory tract infections are a leading cause of morbidity and mortality worldwide. Even with the advancement of diagnostic tools, the causative agent of 20 to 30% of upper respiratory tract infections go undiagnosed. Recently, a newly identified human respiratory virus, human metapneumovirus (hMPV), was discovered in young children in The Netherlands. To study the prevalence of hMPV infections in Israeli children, respiratory specimens from 388 hospitalized children less than 5 years of age were evaluated for the presence of hMPV RNA, which was present in 42 (10.8%) of these samples. All hMPV-positive samples were negative for respiratory syncytial virus (RSV), influenza viruses (Flu) A and B, adenovirus, and parainfluenza viruses 1, 2, and 3. Conversely, hMPV RNA was not detected in 76 RSV-positive and 38 Flu A- or B-positive samples. Most hMPV activity was between the months February and April. Sequence analysis of 20 positive samples revealed that both of the hMPV genotypes (groups 1 and 2) have circulated in central Israel during the study period. Moreover, three of the four known hMPV subgroups (1A, 1B, and 2B) were detected among the tested samples. Seroprevalence of hMPV in 204 patients from the central part of Israel revealed that 100% of the children are hMPV seropositive by the age of 5 years old. We conclude that hMPV is a common respiratory pathogen in Israel, while mixed infections of hMPV with RSV or Flu in hospitalized children are apparently rare.

Human metapneumovirus infection in hospitalized children with acute respiratory disease in Korea

Human metapneumovirus (hMPV) is a recently isolated virus, mostly associated with acute lower respiratory infection in children, of which symptoms are similar to those of respiratory syncytial virus (RSV) infection. The aim of our study was to determine the frequency of hMPV in hospitalized children with acute respiratory tract disease in Korea. Nasal aspirates from hospitalized children with respiratory infections under 15 yr old between December 2003 and February 2005 were included in the study. Each sample was analyzed for RSV, adenovirus, influenza virus A and B, and parainfluenza virus by indirect fluorescent assay (IFA). F-gene sequences were used for PCR for the detection and sequencing of hMPV. In total 381 samples, negative samples in which any viral pathogen could not be identified by IFA were 231 cases. hMPV was detected using reverse transcriptase-PCR (RT-PCR) in 28 of 231 (12.1%) children who were not infected with another respiratory viruses. The hMPV-infected children were diagnosed as having pneumonia, bronchiolitis, bronchial asthma exacerbation, croup, and upper respiratory tract infection. Most of the RT-PCR positive samples for hMPV were collected in winter season. These results suggest that hMPV may be a responsible pathogen causing acute respiratory tract infection in Korean children.

The cell biology of acute childhood respiratory disease: therapeutic implications

Respiratory syncytial virus (RSV), the recently identified human metapneumovirus (HMPV), and the human parainfluenza viruses (HPIVs), cause most cases of childhood croup, bronchiolitis, and pneumonia. Influenza virus also causes a significant burden of disease in young children, although its significance in children was not fully recognized until recently. This article discusses pathogens that have been studied for several decades, including RSV and HPIVs, and also explores the newly identified viral pathogens HMPV and human coronavirus NL63. The escalating rate of emergence of new infectious agents, fortunately meeting with equally rapid advancements in molecular methods of surveillance and pathogen discovery, means that new organisms will soon be added to the list. A section on therapies for bronchiolitis addresses the final common pathways that can result from infection with diverse pathogens, highlighting the mechanisms that may be amenable to therapeutic approaches. The article concludes with a discussion of the overarching impact of new diagnostic strategies.

Multi-year study of human metapneumovirus infection at a large US Midwestern Medical Referral Center

BACKGROUND

Because of its recent identification, few multi-year epidemiologic studies of hMPV infection have been reported.

OBJECTIVE

We sought to retrospectively describe hMPV infections among patients evaluated by a large US Midwestern referral laboratory.

STUDY DESIGN

Clinical specimens were submitted to a large US Midwest referral hospital from 1 October 2001 to 18 May 2004. RT-PCR was used to retrospectively screen the clinical specimens for human metapneumovirus. Demographic and clinical data were retrieved.

RESULTS

34 (2.6%) of 1294 specimens were hMPV positive. Among these, 21 (62%) were culture positive and available for genetic typing. A previously considered rare genotype of hMPV, B1, was the most common single genotype identified, comprising 9 (43%) of the 21 isolates. Multivariate logistic regression modeling identified patients aged 0.4-9 years (OR=8.9; 95% CI=2.0-38.5) and those under intensive care (OR=3.2; 95% CI=1.1-8.7) as more likely to have hMPV infection than their peers.

CONCLUSION

In this large referral hospital viral assays more often had evidence of hMPV when they were collected from children receiving intensive care.

Human metapneumovirus in paediatric patients

Acute respiratory tract infections (ARTIs) are a leading cause of morbidity and mortality in children worldwide, but the aetiology of many ARTIs is still unknown. In 2001, researchers in The Netherlands reported the discovery of a previously unidentified pathogen called human metapneumovirus (hMPV). Since its initial description, hMPV has been associated with ARTI in Europe (Italy, France, Spain, the UK, Germany, Denmark, Finland and Norway), America (the USA, Canada, Argentina and Brazil), Asia (India, Japan, China and Singapore), Australia and South Africa in individuals of all ages. The incidence of infection varies from 1.5% to 25%, indicating that hMPV is a ubiquitous virus with a worldwide distribution. hMPV seems to play an important role as a cause of paediatric upper and lower respiratory tract infection, with similar, but not identical, epidemiological and clinical features to those of respiratory syncytial virus and influenza virus. Moreover, the socio‐economic impact of hMPV‐infected children on their families seems to be considerable, which suggests that, like influenza virus, hMPV infection may be a substantial public health problem for the community. It may be associated with significant morbidity and mortality in pre‐term infants and children with underlying clinical conditions, although more adequately controlled studies are needed to confirm its importance in such patients. Many fundamental questions concerning the pathogenesis of hMPV disease and the host's specific immune response remain to be answered. Further studies are also required to properly define hMPV diagnosis, treatment and prevention strategies.

Human metapneumovirus, Peru

We retrospectively studied 420 pharyngeal swab specimens collected from Peruvian and Argentinean patients with influenzalike illness in 2002 and 2003 for evidence of human metapneumovirus (HMPV). Twelve specimens (2.3%) were positive by multiple assays. Six specimens yielded HMPV isolates. Four of the 6 isolates were of the uncommon B1 genotype.

Human metapneumovirus infection in young children hospitalized with respiratory tract disease

BACKGROUND

Human metapneumovirus (hMPV) is a newly recognized pathogen associated with respiratory tract disease (RTD).

OBJECTIVES

To evaluate the incidence of hMPV infection in children hospitalized with RTD and to analyze the virologic and clinical features of hMPV infection.

STUDY DESIGN

All children younger than 5 years of age hospitalized for RTD were included in this 1-year prospective study. hMPV was detected in nasopharyngeal secretions by reverse transcription polymerase chain reaction. The hMPV F gene amplification products were sequenced, and a phylogenetic tree was constructed. Samples were also tested for other respiratory viruses by both direct immunofluorescence assay and virus culture.

RESULTS

hMPV, detected in 50 of 589 (8.5%) children, represented the second leading cause of RTD after respiratory syncytial virus (RSV). Infections with hMPV occurred mainly between December and April. hMPV isolates clustered into the 4 subgroups (A1, A2, B1 and B2) currently recognized; the majority (72%) of hMPV isolates belonged to subgroup A1. Among the 35 children infected with hMPV alone, 23 (65.7%) had bronchiolitis, 5 (14.3%) had pneumonia, 2 (5.7%) had asthma exacerbation and 5 (14.3%) had a limited upper RTD. Fifteen (30%) of the hMPV-infected children were coinfected with RSV. As compared with children infected with hMPV or RSV alone, duration of hospitalization and requirement for supplemental oxygen were increased in the hMPV/RSV-coinfected children.

CONCLUSIONS

hMPV is a frequent cause of RTD in young children. hMPV/RSV coinfection is frequent and could be more severe than a single hMPV or RSV infection.

Detection and monitoring of virus infections by real-time PCR

The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.

Cytotoxic T-lymphocyte epitope vaccination protects against human metapneumovirus infection and disease in mice

Human metapneumovirus (hMPV) has emerged as an important human respiratory pathogen causing upper and lower respiratory tract infections in young children and older adults. In addition, hMPV infection is associated with asthma exacerbation in young children. Recent epidemiological evidence indicates that hMPV may cocirculate with human respiratory syncytial virus (hRSV) and mediate clinical disease similar to that seen with hRSV. Therefore, a vaccine for hMPV is highly desirable. In the present study, we used predictive bioinformatics, peptide immunization, and functional T-cell assays to define hMPV cytotoxic T-lymphocyte (CTL) epitopes recognized by mouse T cells restricted through several major histocompatibility complex class I alleles, including HLA-A*0201. We demonstrate that peptide immunization with hMPV CTL epitopes reduces viral load and immunopathology in the lungs of hMPV-challenged mice and enhances the expression of Th1-type cytokines (gamma interferon and interleukin-12 [IL-12]) in lungs and regional lymph nodes. In addition, we show that levels of Th2-type cytokines (IL-10 and IL-4) are significantly lower in hMPV CTL epitope-vaccinated mice challenged with hMPV. These results demonstrate for the first time the efficacy of an hMPV CTL epitope vaccine in the control of hMPV infection in a murine model.

Detection and monitoring of virus infections by real-time PCR

The employment of polymerase chain reaction (PCR) techniques for virus detection and quantification offers the advantages of high sensitivity and reproducibility, combined with an extremely broad dynamic range. A number of qualitative and quantitative PCR virus assays have been described, but commercial PCR kits are available for quantitative analysis of a limited number of clinically important viruses only. In addition to permitting the assessment of viral load at a given time point, quantitative PCR tests offer the possibility of determining the dynamics of virus proliferation, monitoring of the response to treatment and, in viruses displaying persistence in defined cell types, distinction between latent and active infection. Moreover, from a technical point of view, the employment of sequential quantitative PCR assays in virus monitoring helps identifying false positive results caused by inadvertent contamination of samples with traces of viral nucleic acids or PCR products. In this review, we provide a survey of the current state-of-the-art in the application of the real-time PCR technology to virus analysis. Advantages and limitations of the RQ-PCR methodology, and quality control issues related to standardization and validation of diagnostic assays are discussed.

Real-time PCR in clinical microbiology: applications for routine laboratory testing

Real-time PCR has revolutionized the way clinical microbiology laboratories diagnose many human microbial infections. This testing method combines PCR chemistry with fluorescent probe detection of amplified product in the same reaction vessel. In general, both PCR and amplified product detection are completed in an hour or less, which is considerably faster than conventional PCR detection methods. Real-time PCR assays provide sensitivity and specificity equivalent to that of conventional PCR combined with Southern blot analysis, and since amplification and detection steps are performed in the same closed vessel, the risk of releasing amplified nucleic acids into the environment is negligible. The combination of excellent sensitivity and specificity, low contamination risk, and speed has made real-time PCR technology an appealing alternative to culture- or immunoassay-based testing methods for diagnosing many infectious diseases. This review focuses on the application of real-time PCR in the clinical microbiology laboratory.

Two RT-PCR based assays to detect human metapneumovirus in nasopharyngeal aspirates

Two sensitive and specific RT-PCR assays were standardised for testing the presence of human metapneumovirus. A total of 300 nasopharyngeal aspirates collected from infants suffering from bronchiolitis since October 2000 to June 2003 and shown previously as negative to common respiratory viruses were examined. Matrix and polymerase viral genes, which show a low rate of variation, were chosen to design amplification assays to ensure that any genotype of the human metapneumovirus could be detected. A RT-PCR followed by a reverse line blotting hybridisation was developed for viral polymerase gene. For the matrix gene, after the RT-PCR assay, a subsequent nested PCR was carried out. Both assays had similar sensitivity, equivalent to 0.1 TCID₅₀ of human metapneumovirus strain NL/1/99 which was used as the positive control. The human metapneumovirus was present in 16.6% of the specimens studied. The approaches described below are not only a robust method for rapid diagnosis of the human metapneumovirus, but also to establish an etiological surveillance tool for epidemiological studies. Based on the results obtained, human metapneumovirus infections in Madrid followed a seasonal pattern, with most of the infections occurring between February and April.

Production and characterization of neutralizing monoclonal antibodies against human metapneumovirus F protein

Human metapneumovirus (hMPV) F protein promotes fusion of viral and cell membranes, and is thought to be a major antigenic determinant that mediates effective neutralization and protection against hMPV infection. In this paper, the development of two mouse monoclonal antibodies (MAbs) by immunization with hMPVinfected cells is described. Immunofluorescence assay (IFA) using hMPV F protein-expressing cells indicated that two MAbs, designated 1G3 and 9B10, recognized hMPV F protein. Both MAbs were found to be reactive to two groups of hMPV by an IFA using two groups of hMPV-infected cells. The 9B10 mAb had strong neutralizing activity against both groups of hMPV, while the 1G3 MAb had only weak neutralization activity. These results indicate that the hMPV F protein is a major antigenic determinant that mediates extensive cross-lineage neutralization and protection. Production of MAbs to the hMPV F protein is critical for development of diagnostic techniques, vaccine research, and studies on viral pathogenesis.

Human metapneumovirus: a ubiquitous and long-standing respiratory pathogen

BACKGROUND

Human metapneumovirus (hMPV) is a recently described human pathogen first identified in respiratory specimens of young children suffering from respiratory syndromes ranging from mild to severe.

METHODS AND RESULTS

Virological studies have reported the presence of hMPV infections in many countries from all continents. Seroprevalence studies have indicated that the virus has been circulating in humans for more than 50 years and that it infects virtually all children by the ages of 5-10 years. In young children, hMPV has been mainly associated with bronchiolitis but also with pneumonitis, otitis media and acute exacerbation of asthma. The contribution of hMPV in respiratory syndromes of adults has been studied considerably less; initial studies have indicated a role for this pathogen in flu-like syndromes and in significant percentages of chronic obstructive pulmonary disease exacerbations and cases of community-acquired pneumonia during the winter-spring period. Both primate and rodent experimental models have been used to characterize the pathogenesis of this respiratory virus. In some of these models, intranasal hMPV inoculation has elicited not only important viral replication but also significant pulmonary inflammation and clinical disease. Recently a few groups have developed reverse genetic systems for hMPV, allowing a better understanding of viral pathogenesis and generation of attenuated viral strains for immunization.

CONCLUSIONS

Recent studies on hMPV have provided a better understanding of the epidemiology and pathogenesis associated with this viral infection, and have enhanced the prospect of developing efficient therapeutic agents and vaccine candidates.

Human metapneumovirus infections in Mexico: epidemiological and clinical characteristics

The human metapneumovirus (hMPV) is a recently described respiratory RNA virus that mainly affects children. To date there has not been a report that describes the detection of this virus in Mexico. This study was performed to detect hMPV in hospitalized Mexican children with respiratory infections, and describe their epidemiological and clinical characteristics. Nasal wash samples from 558 children younger than 3 years of age with the admission diagnosis of a respiratory tract infection were evaluated. Respiratory viruses were detected in 221 children [respiratory syncytial virus (RSV), 193 (34.6 %); influenza virus, 13 (2.3 %); parainfluenza viruses, 15 (2.7 %)]. Respiratory secretions of 323 children in whom the presence of these viruses was excluded (131 admitted during the 2002-2003 respiratory season and 192 during the 2003-2004 season) were tested for hMPV infection. The hMPV genome was detected in 34 specimens by amplification using real-time RT-PCR. Sequencing of amplicons and phylogenetic analysis indicated the predominance of genotype A hMPV. The months with the highest number of hMPV detections were February and March. During the 2002-2003 season hMPV activity peaked after the RSV season. During the 2003-2004 season hMPV and RSV epidemics occurred simultaneously. The clinical presentation of an hMPV infection was indistinguishable from other respiratory infections. Except for one death, the outcomes of the hMPV infections were good. In this study, among the viruses routinely tested for, hMPV was the second most common agent, after RSV, in children younger than 3 years of age hospitalized with respiratory tract infections.

Diagnosis of human metapneumovirus and rhinovirus in patients with respiratory tract infections by an internally controlled multiplex real-time RNA PCR

Background:

Adequate laboratory diagnosis of human rhinoviruses (hRV) and human metapneumoviruses (hMPV) requires molecular methods as viral culture lacks sensitivity. However, setting up individual PCRs for all respiratory viruses is not practical so preferentially multiplex PCRs are used.

Objectives:

To develop for routine diagnosis a rapid real-time PCR assay for detection of hRV and hMPV including an internal control in a single tube multiplex reaction using probes carrying different fluorophores to discriminate targets.

Study design:

The multiplex real-time RNA PCR was optimized to include the internal control virus and a total of 358 respiratory samples from 239 patients taken over a one-year period were analyzed by the multiplex assay.

Results:

The multiplex assay with co-amplification of the internal control was as sensitive and specific as the individual assays. Application of this assay on clinical samples from 239 patients in a one-year period resulted in an incidence of hRV and hMPV of 41/239 (17.1%) and 6/239 (2.5%), respectively. Inhibition, defined as poor internal control amplification, was detected in 8 (2.2%) samples. Culture was performed on these samples and only four hRV were detected.

Conclusions:

This real-time PCR method enables sensitive diagnosis of these two respiratory pathogens with the potential to expand the assay as part of a full molecular respiratory viral screen.