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

Human Metapneumovirus: Etiological Agent of Severe Acute Respiratory Infections in Hospitalized and Deceased Patients with a Negative Diagnosis of Influenza

Human metapneumovirus (HMPV) is one of the four major viral pathogens associated with acute respiratory tract infections (ARI) and creates a substantial burden of disease, particularly in young children (<5 years) and older individuals (≥65 years). The objective of this study was to determine the epidemiological behavior of HMPV in Mexico. This retrospective study was conducted over a nine-year period and used 7283 influenza-negative respiratory samples from hospitalized and deceased patients who presented Severe Acute Respiratory Infection (SARI). The samples were processed with the help of qualitative multiplex RT-PCR for simultaneous detection of 14 respiratory viruses (xTAG^® RVP FAST v2). 40.8% of the samples were positive for respiratory viruses, mainly rhinovirus/enterovirus (47.6%), respiratory syncytial virus (15.9%), HMPV (11.1%) and parainfluenza virus (8.9%). Other respiratory viruses and co-infections accounted for 16.5%. HMPV infects all age groups, but the most affected group was infants between 29 days and 9 years of age (65.6%) and adults who are 40 years and older (25.7%). HMPV circulates every year from November to April, and the highest circulation was observed in late winter. The results of this study aim to raise awareness among clinicians about the high epidemiological impact of HMPV in young children and older individuals in order to reduce the economic burden in terms of health care costs.

Viruses in bronchiectasis: a pilot study to explore the presence of community acquired respiratory viruses in stable patients and during acute exacerbations

Background

Bronchiectasis is a chronic respiratory condition. Persistent bacterial colonisation in the stable state with increased and sometimes altered bacterial burden during exacerbations are accepted as key features in the pathophysiology. The extent to which respiratory viruses are present during stable periods and in exacerbations is less well understood.

Methods

This study aimed to determine the incidence of respiratory viruses within a cohort of bronchiectasis patients with acute exacerbations at a teaching hospital and, separately, in a group of patients with stable bronchiectasis. In the group of stable patients, a panel of respiratory viruses were assayed for using real time quantitative PCR in respiratory secretions and exhaled breath. The Impact of virus detection on exacerbation rates and development of symptomatic infection was evaluated.

Results

Routine hospital-based viral PCR testing was only requested in 28% of admissions for an exacerbation. In our cohort of stable bronchiectasis patients, viruses were detected in 92% of patients during the winter season, and 33% of patients during the summer season. In the 2-month follow up period, 2 of 27 patients presented with an exacerbation.

Conclusions

This pilot study demonstrated that respiratory viruses are commonly detected in patients with stable bronchiectasis. They are frequently detected during asymptomatic viral periods, and multiple viruses are often present concurrently.

A one-step duplex rRT-PCR assay for the simultaneous detection of duck hepatitis A virus genotypes 1 and 3

Duck hepatitis A virus (DHAV) is a highly infectious pathogen that causes significant bleeding lesions in the viscera of ducklings less than 3 weeks old. There are three serotypes of DHAV: serotype 1 (DHAV-1), serotype 2 (DHAV-2) and serotype 3 (DHAV-3). These serotypes have no cross-antigenicity with each other. To establish an rRT-PCR assay for the rapid detection of a mixed infection of DHAV-1 and DHAV-3, two pairs of primers and a pair of matching TaqMan probes were designed based on conserved regions of DHAV-1 VP0 and DHAV-3 VP3. Finally, we established a one-step duplex rRT-PCR assay with high specificity and sensitivity for the simultaneous detection of DHAV-1 and DHAV-3. This method showed no cross-antigenicity with the other pathogens tested, including duck plague virus, Muscovy duck parvovirus, Riemerella anatipestifer, and pathogenic E. coli from ducks. Sensitivity tests identified the minimum detection limits of this method as 98 (DHAV-1) and 10 (DHAV-3) copies/reaction. To validate the method, thirty-eight clinical samples and thirty artificially infected samples collected from dead duck embryos were studied. Thirty-seven samples were positive for DHAV-1, seventeen samples were positive for DHAV-3, and fourteen samples were positive for a mixed infection using the duplex rRT-PCR method. The method established in this study is specific, sensitive, convenient and timesaving and is a powerful tool for detecting DHAV-1, DHAV-3, and their mixed infection and for conducting surveys of pandemic virus strains.

Development of real-time RT-PCR for detection of human metapneumovirus and genetic analysis of circulating strains (2009-2011) in Pune, India

Human metapneumovirus (HMPV) is an important respiratory virus implicated in respiratory infections. The purpose of this study was to develop a one-step real-time RT-PCR assay that can detect all four lineages of HMPV and to identify the HMPV lineages circulating in Pune, India. Conserved regions of the nucleoprotein gene were used to design real-time primers and a probe. A total of 224 clinical samples that were positive for different respiratory viruses (including 51 samples that were positive for HMPV) were tested using the real time RT-PCR assay, and the specificity of the assay was observed to be 100 %. Using in vitro-synthesized RNA, the sensitivity of the assay was ascertained to be 100 copies of the target gene per reaction. Phylogenetic analysis of the nucleoprotein (N) and attachment glycoprotein (G) genes confirmed that this assay detected all lineages of HMPV. A2, B1 and B2 strains were observed during the study period. Our assay is highly sensitive and specific for all known lineages of HMPV, making it a valuable tool for rapid detection of the virus. A2 and B2 were the predominant subtypes circulating in Pune, Western India.

Use of an innovative web-based laboratory surveillance platform to analyze mixed infections between human metapneumovirus (hMPV) and other respiratory viruses circulating in Alberta (AB), Canada (2009-2012)

We investigated the proportions of mono vs. mixed infections for human metapneumovirus (hMPV) as compared to adenovirus (ADV), four types of coronavirus (CRV), parainfluenza virus (PIV), RSV, and enterovirus/rhinovirus (ERV) in Alberta, Canada. Using the Data Integration for Alberta Laboratories (DIAL) platform, 26,226 respiratory specimens at ProvLab between 1 July 2009 and 30 June 2012 were selected and included in the study. Using the Respiratory Virus Panel these specimens tested positive for one or more respiratory virus and negative for influenza A and B. From our subset hMPV was the fourth most common virus (n=2,561) with 373 (15%) identified as mixed infection using DIAL. Mixed infection with hMPV was most commonly found in infants less than 6 months old and ERV was most commonly found in mixed infection with hMPV (230/373, 56%) across all age groups. The proportion of mixed-infection vs. mono-infection was highest for ADV (46%), followed by CRV 229E (32%), CRV HKU1 (31%), CRV NL63 (28%), CRV OC43 (23%), PIV (20%), RSV (17%), hMPV (15%) and ERV (13%). hMPV was significantly more likely to be identified in mono infection as compared with ADV, CRV, PIV, and RSV with the exception of ERV [p < 0.05].

Rates of hospitalizations for respiratory syncytial virus, human metapneumovirus, and influenza virus in older adults

BACKGROUND

We performed a prospective study to determine the disease burden of respiratory syncytial virus (RSV) and human metapneumovirus (HMPV) in older adults in comparison with influenza virus.

METHODS

During 3 consecutive winters, we enrolled Davidson County (Nashville, TN) residents aged ≥ 50 years admitted to 1 of 4 hospitals with acute respiratory illness (ARI). Nasal/throat swabs were tested for influenza, RSV, and HMPV with reverse-transcriptase polymerase chain reaction. Hospitalization rates were calculated.

RESULTS

Of 1042 eligible patients, 508 consented to testing. Respiratory syncytial virus was detected in 31 participants (6.1%); HMPV was detected in 23 (4.5%) patients; and influenza was detected in 33 (6.5%) patients. Of those subjects aged ≥ 65 years, 78% received influenza vaccination. Compared with patients with confirmed influenza, patients with RSV were older and more immunocompromised; patients with HMPV were older, had more cardiovascular disease, were more likely to have received the influenza vaccination, and were less likely to report fever than those with influenza. Over 3 years, average annual rates of hospitalization were 15.01, 9.82, and 11.81 per 10,000 county residents due to RSV, HMPV, and influenza, respectively.

CONCLUSIONS

In adults aged ≥ 50 years, hospitalization rates for RSV and HMPV were similar to those associated with influenza.

Increase human metapneumovirus mediated morbidity following pandemic influenza infection

Human metapneumovirus (hMPV) is a recently discovered respiratory pathogen, infecting mainly young children. The infected patients suffer from influenza like symptoms (ILS). In Israel the virus is mainly circulating in February to March. Here we report on an increased rate of hMPV infection in the winter season of 2009–10. The 2009–10 infection had several unique characteristics when compared to previous seasons; it started around January and a large number of infants were infected by the virus. Genetic analysis based on the viral L and F genes of hMPV showed that only subtypes A2 and B2 circulated in Israel. Additionally, we have identified a novel variant of hMPV within subgroup A2b, which subdivide it into A2b1 and A2b2. Finally, we showed that the hMPV infection was detected in the country soon after the infection with the pandemic influenza virus had declined, that infection with the pandemic influenza virus was dominant and that it interfered with the infection of other respiratory viruses. Thus, we suggest that the unusual increase in hMPV infection observed in 2009–10 was due to the appearance of the pandemic influenza virus in the winter season prior to 2009–10.

Evaluation of xTAG Respiratory Viral Panel FAST and xTAG Human Parainfluenza Virus Analyte-Specific Reagents for detection of human parainfluenza viruses in respiratory specimens

The multiplex xTAG^® Respiratory Viral Panel FAST (RVP FAST) research-use-only assay and xTAG^® Human Parainfluenza Virus Analyte-Specific Reagent (HPIV-ASR) assay were evaluated with 99 culture-confirmed human parainfluenza virus (HPIV)–positive and –negative specimens and found to have analytical sensitivities of 95.2% and 100% and specificities of 98.3% and 96.6%, respectively. Since the in vitro diagnostic (IVD) version of the RVP FAST assay does not include HPIVs, the HPIV-ASR assay can be tested in parallel with RVP FAST-IVD for optimal detection of HPIVs.

Comparison of the Luminex xTAG respiratory viral panel with xTAG respiratory viral panel fast for diagnosis of respiratory virus infections

Nucleic acid tests are sensitive and specific and provide a rapid diagnosis, making them invaluable for patient and outbreak management. Multiplex PCR assays have additional advantages in providing an economical and comprehensive panel for many common respiratory viruses. Previous reports have shown the utility of the xTAG respiratory viral panel (RVP) assay manufactured by Luminex Molecular Diagnostics for this purpose. A newer generation of this kit, released in Canada in early 2010, is designed to simplify the procedure and reduce the turnaround time by about 24 h. The assay methodology and targets included in this version of the kit are different; consequently, the objective of this study was to compare the detection of a panel of respiratory viral targets using the older Luminex xTAG RVP (RVP Classic) assay with that using the newer xTAG RVP Fast assay. This study included 334 respiratory specimens that had been characterized for a variety of respiratory viral targets; all samples were tested by both versions of the RVP assay in parallel. Overall, the RVP Classic assay was more sensitive than the RVP Fast assay (88.6% and 77.5% sensitivities, respectively) for all the viral targets combined. Targets not detected by the RVP Fast assay included primarily influenza B virus, parainfluenza virus type 2, and human coronavirus 229E. A small number of samples positive for influenza A virus, respiratory syncytial virus B, human metapneumovirus, and parainfluenza virus type 1 were not detected by the RVP Classic assay and in general had low viral loads.

Viral etiology of influenza-like illnesses in Antananarivo, Madagascar, July 2008 to June 2009

BACKGROUND

In Madagascar, despite an influenza surveillance established since 1978, little is known about the etiology and prevalence of viruses other than influenza causing influenza-like illnesses (ILIs).

METHODOLOGY/PRINCIPAL FINDINGS

From July 2008 to June 2009, we collected respiratory specimens from patients who presented ILIs symptoms in public and private clinics in Antananarivo (the capital city of Madagascar). ILIs were defined as body temperature ≥38°C and cough and at least two of the following symptoms: sore throat, rhinorrhea, headache and muscular pain, for a maximum duration of 3 days. We screened these specimens using five multiplex real time Reverse Transcription and/or Polymerase Chain Reaction assays for detection of 14 respiratory viruses. We detected respiratory viruses in 235/313 (75.1%) samples. Overall influenza virus A (27.3%) was the most common virus followed by rhinovirus (24.8%), RSV (21.2%), adenovirus (6.1%), coronavirus OC43 (6.1%), influenza virus B (3.9%), parainfluenza virus-3 (2.9%), and parainfluenza virus-1 (2.3%). Co-infections occurred in 29.4% (69/235) of infected patients and rhinovirus was the most detected virus (27.5%). Children under 5 years were more likely to have one or more detectable virus associated with their ILI. In this age group, compared to those ≥5 years, the risk of detecting more than one virus was higher (OR = 1.9), as was the risk of detecting of RSV (OR = 10.1) and adenovirus (OR = 4.7). While rhinovirus and adenovirus infections occurred year round, RSV, influenza virus A and coronavirus OC43 had defined period of circulation.

CONCLUSIONS

In our study, we found that respiratory viruses play an important role in ILIs in the Malagasy community, particularly in children under 5 years old. These data provide a better understanding of the viral etiology of outpatients with ILI and describe for the first time importance of these viruses in different age group and their period of circulation.

Evaluation of commercial ResPlex II v2.0, MultiCode-PLx, and xTAG respiratory viral panels for the diagnosis of respiratory viral infections in adults

Background

Commercial multiplex PCR panels for respiratory viruses (PRV) have been recently developed. ResPlex II Panel v2.0 (Qiagen), MultiCode^®-PLx (EraGen Biosciences), and xTAG^® (Luminex) PRV's were studied. All assays detect influenza A and B, adenovirus, parainfluenza 1–3, respiratory syncytial virus A and B, human metapneumovirus and human rhinovirus. The ResPlex II additionally detects coronavirus (229E, OC43, NL63, HKU1), coxsackie/echo virus, bocavirus and differentiates adenoviruses (B, E). The MultiCode-PLX assay detects 229E, OC43, and NL63, differentiates parainfluenza 4a, 4b and adenoviruses (B, C, E). The xTAG additionally subtypes influenza A as seasonal H1 and H3.

Study design

202 specimens collected from adult patients with signs of respiratory infection from November, 2008 to May, 2009 were used for evaluating the performance of the three commercial PRV assays. Viral culture and xTAG were used as the standards to assess sensitivity and specificity.

Results

The PRV assays detected more viruses than culture. When compared to culture, the xTAG PRV showed a sensitivity and specificity of 100% and 91%, compared to MultiCode-PLx with 89% and 87%, and ResPlex II with 89% and 94%, respectively. Co-infection was detected in a small subset of patient specimens. Each panel showed differences in sensitivities for individual viruses.

Conclusions

While the ResPlex II and MultiCode-PLx offer a broader virus detection range and greater ease of use, the xTAG PRV showed increased sensitivity to common viral targets represented in the assays, and also had the ability to differentiate human from non-human influenza A H1.

High seroprevalence of neutralizing capacity against human metapneumovirus in all age groups studied in Bonn, Germany

Human metapneumovirus (hMPV) infections occur frequently despite high rates of perpetual seroprevalence for all age groups. Analyses of approximately 2,000 archived, randomly selected serum samples demonstrated that neutralizing capacities remain high, with a minor decrease for individuals over 69 years of age, leading to the hypothesis that reinfections occur because humoral immune responses play minor roles in the clearance of hMPV infections.

Enhanced viral etiological diagnosis of respiratory system infection outbreaks by use of a multitarget nucleic acid amplification assay

A study was undertaken to assess the utility of the xTAG respiratory viral panel (RVP) for enhanced laboratory investigation of respiratory outbreaks. Specimens (n = 1,108) from 244 suspected respiratory virus outbreaks in 2006 and 2007 in Alberta, Canada, were included in the study. Testing by direct fluorescent antigen detection (DFA) and various in-house nucleic acid amplification tests (NATs) for common respiratory viruses provided an etiological diagnosis in 177 outbreaks (72.5%), with 524 samples testing positive (47.3%) for a respiratory virus. Two hundred samples from 51 unresolved outbreaks were further tested by RVP retrospectively. Fifty-eight samples from 30 unresolved outbreaks had a respiratory virus detected by RVP (47 picornavirus-positive, 9 coronavirus-positive, and 2 influenza virus A-positive samples). Overall, detection of a viral etiological agent was achieved in 90.8% of outbreaks using a combination of DFA, NATs, and RVP. Use of RVP enhances the laboratory investigation of respiratory virus outbreaks and facilitates appropriate patient and outbreak management.

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.

[Application of molecular methods in the diagnosis and epidemiological study of viral respiratory infections]

Hasta la fecha se han identificado más de 200 virus pertenecientes a 6 familias taxonómicas diferentes asociados con la infección del tracto respiratorio humano. La utilización generalizada de métodos moleculares en los laboratorios de microbiología clínica no sólo ha aportado grandes ventajas al diagnóstico de estas infecciones, sino también está permitiendo profundizar en el conocimiento de la enfermedad y el comportamiento epidemiológico de los virus causantes. Esta tecnología incrementa de manera notable el rendimiento de detección de virus en las muestras respiratorias, debido a su elevada sensibilidad en comparación con las técnicas clásicas y a la posibilidad de identificar virus no cultivables o de crecimiento fastidioso en las líneas celulares habituales, lo que permite realizar el diagnóstico etiológico con mayor rapidez. Sin embargo, también comporta algunos inconvenientes, como son detectar virus que se encuentran colonizando la mucosa respiratoria de personas asintomáticas, o en secreciones de pacientes que ya se han recuperado de una infección pasada, a consecuencia de excreción prolongada de éstos. La secuenciación de los productos obtenidos en la reacción de amplificación genómica permite caracterizar de forma adicional los virus detectados mediante su genotipado, realizar estudios de epidemiología molecular e identificar resistencias a determinados antivirales, por citar sólo algunos ejemplos.

Using multiplex real time PCR in order to streamline a routine diagnostic service

An increasing number of virology laboratories are now utilising in house real time PCR assays as the frontline diagnostic tests. As the number of tests on offer increases the natural progression from this will be to rationalise their service via multiplexing. Since 2003 we have introduced a large number of qualitative and quantitative multiplex real time PCR assays into our routine testing service. This paper describes the development of the multiplex assays, the problems encountered and the resultant benefits to the routine service.

Viral infection in adults hospitalized with community-acquired pneumonia: prevalence, pathogens, and presentation

Background

The potential role of respiratory viruses in the natural history of community-acquired pneumonia (CAP) in adults has not been well described since the advent of nucleic amplification tests (NATs).

Methods

From 2004 to 2006, adults with CAP who were admitted to five hospitals were prospectively enrolled in the study, and clinical data, cultures, serology, and nasopharyngeal swabs were obtained. NATs from swabs were tested for influenza, human metapneumovirus (hMPV), respiratory syncytial virus (RSV), rhinovirus, parainfluenza virus 1–4, coronaviruses (OC43, 229E, and NL63), and adenovirus.

Results

A total of 193 patients were included; the median age was 71 years, 51% of patients were male, and 47% of patients had severe CAP. Overall, 75 patients (39%) had a pathogen identified. Of these pathogens, 29 were viruses (15%), 38 were bacteria (20%), 8 were mixed (4%), and the rest were “unknown.” Influenza (n = 7), hMPV (n = 7), and RSV (n = 5) accounted for most viral infections; other infections included rhinovirus (n = 4), parainfluenza (n = 3), coronavirus (n = 4), and adenovirus (n = 2). Streptococcus pneumoniae was the most common bacterial infection (37%). Compared with bacterial infection, patients with viral infection were older (76 vs 64 years, respectively; p = 0.01), were more likely to have cardiac disease (66% vs 32%, respectively; p = 0.006), and were more frail (eg, 48% with limited ambulation vs 21% of bacterial infections; p = 0.02). There were few clinically meaningful differences in presentation and no differences in outcomes according to the presence or absence of viral infection.

Conclusions

Viral infections are common in adults with pneumonia. Easily transmissible viruses such as influenza, hMPV, and RSV were the most common, raising concerns about infection control. Routine testing for respiratory viruses may be warranted for adults who have been hospitalized with pneumonia.

Development and application of a one-step real-time Taqman RT-PCR assay for detection of Duck hepatitis virus type1

A one-step real-time RT-PCR assay (rRT-PCR) was developed for efficient detection of Duck hepatitis virus type1 (DHV-1). A pair of specific primers was designed against the conserved region in the 3D gene that encodes the RNA dependent RNA polymerase with a single conserved TaqMan probe. The detection limit of this assay was 10 viral genomic copies per reaction and it was highly specific to DHV-1. The rRT-PCR assay was used to determine the distribution and concentration of DHV-1 virulent strain in duck embryos as well as the DHV-1 attenuated vaccine strain in chicken embryos. The results revealed that the copy numbers of DHV-1 reached a peak in duck embryos and chicken embryos at 28-40h, 44-56h postinoculation respectively. The comparative tests for ducklings infected artificially and clinical samples between neutralization test and rRT-PCR showed that the positive results of infected samples were the same, while the rRT-PCR method was more sensitive than neutralization test for detection of clinical samples. The rapid, sensitive and specific rRT-PCR assay will be a powerful tool for detection of suspected cases of DHV-1, distribution pattern of DHV-1 in vivo and molecular epidemiological screening.

Comparison of the Luminex xTAG respiratory viral panel with in-house nucleic acid amplification tests for diagnosis of respiratory virus infections

Detection of respiratory viruses using sensitive real-time nucleic acid amplification tests (NATs) is invaluable for patient and outbreak management. However, the wide range of potential respiratory virus pathogens makes testing using individual real-time NATs expensive and laborious. The objective of this study was to compare the detection of respiratory virus targets using the Luminex xTAG respiratory viral panel (RVP) assay with individual real-time NATs used at the Provincial Laboratory of Public Health, Calgary, Alberta, Canada. The study included 1,530 specimens submitted for diagnosis of respiratory infections from December 2006 to May 2007. Direct-fluorescent-antigen-positive nasopharyngeal samples were excluded from this study. A total of 690 and 643 positives were detected by RVP and in-house NATs, respectively. Kappa correlation between in-house NATs and RVP for all targets ranged from 0.721 to 1.000. The majority of specimens missed by in-house NATs (96.7%) were positive for picornaviruses. Samples missed by RVP were mainly positive for adenovirus (51.7%) or respiratory syncytial virus (27.5%) by in-house NATs and in general had low viral loads. RVP allows for multiplex detection of 20 (and differentiation between 19) respiratory virus targets with considerable time and cost savings compared with alternative NATs. Although this first version of the RVP assay has lower sensitivity than in-house NATs for detection of adenovirus, it has good sensitivity for other targets. The identification of picornaviruses and coronaviruses and concurrent typing of influenza A virus by RVP, which are not currently included in our diagnostic testing algorithm, will improve our diagnosis of respiratory tract infections.

Respiratory failure associated with human metapneumovirus infection in an infant posthepatic transplant

This is the first reported case of respiratory failure associated with human metapneumovirus (hMPV) infection in a liver transplant recipient or in a pediatric solid transplant recipient. A 9-month-old female developed respiratory distress 8 days following a liver transplant. hMPV was detected and she required intubation followed by extracorporeal membrane oxygenation for 26 days. Immunosuppressive medications were stopped during the acute infection except for methylprednisolone as treatment for acute respiratory distress. Serial Doppler ultrasounds were used to monitor for hepatic vessel thromboses and serum liver function tests to assess for hepatic dysfunction and there was no evidence of allograft rejection. The patient recovered from the nosocomial hMPV infection with satisfactory pulmonary function and possible mild developmental delay.

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.

Respiratory virus surveillance and outbreak investigation

Sensitive, rapid detection of respiratory viruses is needed for surveillance and for investigation of epidemiologically linked cases. The utility of rapid antigen-based methods for detection of common respiratory viruses and to confirm the cause of outbreaks is well established. However, nucleic acid amplification tests (NATs) offer some benefits above antigen or culture-based procedures, with the main advantages being sensitivity and range of pathogens detectable. It is important to understand how changes in our testing methodology alter respiratory virus detection and information for epidemiological studies. For viruses such as influenza A, influenza B and respiratory syncytial virus, NATs offer enhanced sensitivity above antigen assays but still identify the seasonal peaks important for predicting disease and managing time-sensitive prophylaxis. For other viruses, such as rhinoviruses, coronaviruses, human bocavirus and parainfluenza virus type 4, culture and antigen-based procedures are not available and/or lack sensitivity. Thus such targets would be missed if NATs were not included in testing for surveillance and outbreak investigation. As more respiratory viruses are identified there is a need to expand surveillance and further evaluate new technologies and automation beyond currently-available diagnostics to address detection of a broad range of potential pathogens.