Antigenic and genetic variability of human metapneumoviruses

Residues of the human metapneumovirus fusion (F) protein critical for its strain-related fusion phenotype: implications for the virus replication cycle

The paramyxovirus F protein promotes fusion of the viral and cell membranes for virus entry, as well as cell-cell fusion for syncytium formation. Most paramyxovirus F proteins are triggered at neutral pH to initiate membrane fusion. Previous studies, however, demonstrated that human metapneumovirus (hMPV) F proteins are triggered at neutral or acidic pH in transfected cells, depending on the strain origin of the F sequences (S. Herfst et al., J. Virol. 82:8891-8895, 2008). We now report an extensive mutational analysis which identifies four variable residues (294, 296, 396, and 404) as the main determinants of the different syncytial phenotypes found among hMPV F proteins. These residues lie near two conserved histidines (H368 and H435) in a three-dimensional (3D) model of the pretriggered hMPV F trimer. Mutagenesis of H368 and H435 indicates that protonation of these histidines (particularly His435) is a key event to destabilize the hMPV F proteins that require low pH for cell-cell fusion. The syncytial phenotypes were reproduced in cells infected with the corresponding hMPV strains. However, the low-pH dependency for syncytium formation could not be related with a virus entry pathway dependent on an acidic environment. It is postulated that low pH may be acting for some hMPV strains as certain destabilizing mutations found in unusual strains of other paramyxoviruses. In any case, the results presented here and those reported by Schowalter et al. (J. Virol. 83:1511-1522, 2009) highlight the relevance of certain residues in the linker region and domain II of the pretriggered hMPV F protein for the process of membrane fusion.

Genomic analysis of four human metapneumovirus prototypes

Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in children. We determined the complete genome sequence of four strains of HMPV representing each of the four lineages. These sequences were compared with published HMPV genome sequences. Most genes were conserved between the genetic lineages (79.5-99.6%), though nucleotide diversity was greater than amino acid diversity, suggesting functional constraints on mutation. However, the SH and G open reading frames were more variable (mean 76.4% and 59.0% aa identity, respectively), with mostly nonsynonymous changes, suggesting selective pressure on the SH and G proteins. Gene-start regions were largely conserved between genes and viruses, while gene-end sequences were conserved between viruses but not between genes. The SH-G and G-L intergenic regions were extremely long (∼200 nt) and have no defined function, yet were highly conserved within major groups. These findings highlight broadly conserved regions of the HMPV genome and suggest unidentified biological roles for SH and G.

Usefulness of two new methods for diagnosing metapneumovirus infections in children

Human metapneumovirus (hMPV) is associated with acute respiratory tract infections, mainly in paediatric patients. The aim of this study was to evaluate the usefulness of two new commercial techniques available for the detection of hMPV in clinical samples from children: an enzyme immunoassay, hMPV EIA (Biotrin International Ltd), and a molecular assay, real-time RT-PCR (Pro hMPV Real Time Assay Kit; Prodesse). A total of 184 nasopharyngeal aspirate specimens from 173 children aged less than 5 years who were hospitalized with acute wheezing were analysed. Respiratory syncytial virus was detected in 27% of the samples, followed by influenza A virus (6%), parainfluenza virus (PIV)3 (2.2%), adenovirus (2%), PIV1 (1.1%), PIV2 (1.1%), and influenza B virus (0.5%). The presence of hMPV was tested in all samples, using the real-time RT-PCR and EIA. Real-time RT-PCR detected 13 hMPV-positive samples (8%), and EIA detected 17 (9.3%). When the EIA results were compared with those of real-time RT-PCR for the detection of hMPV, a good correlation was found (94%). A relatively low co-infection rate (15%) was observed in our patients. RT-PCR and EIA provide robust methods for the diagnosis of hMPV infection in children.

Co-circulation of genetically distinct human metapneumovirus and human bocavirus strains in young children with respiratory tract infections in Italy

The discovery of human Metapneumovirus (hMPV) and human Bocavirus (hBoV) identified the etiological causes of several cases of acute respiratory tract infections in children. This report describes the molecular epidemiology of hMPV and hBoV infections observed following viral surveillance of children hospitalized for acute respiratory tract infections in Milan, Italy. Pharyngeal swabs were collected from 240 children ≤3 years of age (130 males, 110 females; median age, 5.0 months; IQR, 2.0–12.5 months) and tested for respiratory viruses, including hMPV and hBoV, by molecular methods. hMPV‐RNA and hBoV‐DNA positive samples were characterized molecularly and a phylogenetical analysis was performed. PCR analysis identified 131/240 (54.6%) samples positive for at least one virus. The frequency of hMPV and hBoV infections was similar (8.3% and 12.1%, respectively). Both infections were associated with lower respiratory tract infections: hMPV was present as a single infectious agent in 7.2% of children with bronchiolitis, hBoV was associated with 18.5% of pediatric pneumonias and identified frequently as a single etiological agent. Genetically distinct hMPV and hBoV strains were identified in children examined with respiratory tract infections. Phylogenetic analysis showed an increased prevalence of hMPV genotype A (A2b sublineage) compared to genotype B (80% vs. 20%, respectively) and of the hBoV genotype St2 compared to genotype St1 (71.4% vs. 28.6%, respectively). Interestingly, a shift in hMPV infections resulting from A2 strains has been observed in recent years. In addition, the occurrence of recombination events between two hBoV strains with a breakpoint located in the VP1/VP2 region was identified. J. Med. Virol. 83:156–164, 2011. © 2010 Wiley‐Liss, Inc.

Genetic variability of attachment (G) and Fusion (F) protein genes of human metapneumovirus strains circulating during 2006-2009 in Kolkata, Eastern India

Background

Human metapneumovirus (hMPV) is associated with the acute respiratory tract infection (ARTI) in all the age groups. However, there is limited information on prevalence and genetic diversity of human metapneumovirus (hMPV) strains circulating in India.

Objective

To study prevalence and genomic diversity of hMPV strains among ARTI patients reporting in outpatient departments of hospitals in Kolkata, Eastern India.

Methods

Nasal and/or throat swabs from 2309 patients during January 2006 to December 2009, were screened for the presence of hMPV by RT-PCR of nucleocapsid (N) gene. The G and F genes of representative hMPV positive samples were sequenced.

Results

118 of 2309 (5.11%) clinical samples were positive for hMPV. The majority (≈80%) of the positive cases were detected during July−November all through the study period. Genetic analysis revealed that 77% strains belong to A2 subgroup whereas rest clustered in B1 subgroup. G sequences showed higher diversity at the nucleotide and amino acid level. In contrast, less than 10% variation was observed in F gene of representative strains of all four years. Sequence analysis also revealed changes in the position of stop codon in G protein, which resulted in variable length (217-231 aa) polypeptides.

Conclusion

The study suggests that approximately 5% of ARTI in the region were caused by hMPV. This is the first report on the genetic variability of G and F gene of hMPV strains from India which clearly shows that the G protein of hMPV is continuously evolving. Though the study partially fulfills lacunae of information, further studies from other regions are necessary for better understanding of prevalence, epidemiology and virus evolution in Indian subcontinent.

Genetic variability of human metapneumovirus amongst an all ages population in Cambodia between 2007 and 2009

First identified in 2001, human metapneumovirus (HMPV) is a novel pathogen and causative agent of acute respiratory tract infection. Re-infection with HMPV is common, and currently there is no available vaccine against HMPV infection. Two genotypes of HMPV have been identified, A and B, both of which can be divided further into at least two distinct sub-genotypes. Here we report the results of the first study to investigate the genetic variability of HMPV strains circulating within Cambodia. The overall incidence of HMPV infection amongst an all-ages population of patients hospitalised with ALRI in Cambodia during 3 consecutive years, between 2007 and 2009, was 1.7%. The incidence of HMPV infection was highest amongst children less than 5 years of age, with pneumonia or bronchopneumonia the most frequent clinical diagnoses across all age groups. The incidence of HMPV infection varied annually. As anticipated, genetic diversity was low amongst the conserved F gene sequences but very high amongst G gene sequences, some strains sharing as little as 56.3% and 34.2% homology at the nucleotide and amino acid levels, respectively. Simultaneous co-circulation of strains belonging to the HMPV sub-genotypes B1, B2 and lineage A2b, amongst patients recruited at 2 geographically distinct provincial hospitals, was detected. Sub-genotype B2 strains were responsible for the majority of the infections detected, and a significant (p  =  0.013) association between infection with lineage A2b strains and disease severity was observed.

Human metapneumovirus subgroup changes and seasonality during epidemics

BACKGROUND

Human metapneumovirus (HMPV) is a major cause of respiratory tract illness in young children and causes annual outbreaks in winter and spring seasons. We evaluated the subgroups of HMPV that caused annual outbreaks and its seasonal occurrence during a 21-year period.

METHODS

Real-time PCR was used for detection of HMPV in 3576 nasopharyngeal aspirates that had been continuously collected year-round for the years 1987 to 2008 from infants hospitalized with acute respiratory tract illness. Phylogenetic analysis was used to assess HMPV subgroups.

RESULTS

Of the 3576 samples obtained, 202 (5.6%) tested positive for HMPV. All known HMPV subgroups (A1, A2a, A2b, B1, B2) could be identified as important respiratory tract pathogens in infants. We found that one HMPV subgroup predominated each year, and it was displaced by another subgroup every 1 to 3 years. Besides the frequent change in predominant HMPV subgroups, we observed a yearly shift in the seasonal occurrence, with a strong peak of HMPV activity in late spring-summer months every second year.

CONCLUSION

HMPV activity is characterized by a periodic change in the predominant subgroup and it shows a stable seasonal rhythm of alternating winter and spring activity.

The distinguishing features of human metapneumovirus and respiratory syncytial virus

Acute respiratory tract infections (RTIs) are a leading cause of morbidity and mortality worldwide. Human Metapneumovirus (hMPV) is a member of the Metapneumovirus genus within the Pneumovirinae subfamily of the Paramyxoviridae family. Though hMPV was only discovered in 2001, a large body of work has already shown that it is the aetiologic agent of a substantial proportion of upper and lower RTIs across all age groups in both healthy and immunocompromised hosts throughout the world. RSV, also a pneumovirus, is the human pathogen most closely related to hMPV. RSV is the leading cause of pneumonia and bronchiolitis in infants and young children, but can also cause respiratory tract disease in all age groups. In this paper, we will review the salient features of the virology, epidemiology, pathogenesis, host immune responses, clinical manifestations and diagnostic modalities of hMPV, using RSV as a comparison. In addition, we will show how immunoprophylactic and therapeutic strategies studied and used in clinical practice for RSV-some with great success, and others tragic failure-have led to promising areas of research for the prevention and treatment of the significant burden of disease caused by hMPV.

Molecular monitoring of causative viruses in child acute respiratory infection in endemo-epidemic situations in Shanghai

BACKGROUND

Numerous viruses are responsible for respiratory infections; however, both their distribution and genetic diversity, in a limited area and a population subgroup, have been studied only rarely during a sustained period of time.

METHODS

A 2-year surveillance program of children presenting with acute respiratory infections (ARIs) was carried out to characterize the viral etiology and to assess whether using gene amplification and sequencing could be a reliable approach to monitor virus introduction and spread in a population subgroup.

RESULTS

Using multiplex RT-PCR, 15 different respiratory viruses were detected within the 486 nasopharyngeal positive samples collected among 817 children aged <9-year old who presented with ARI during October 2006 to September 2008. A single virus was detected in 373 patients (45.7%), and two to four viruses in 113 patients (13.8%). The most frequent causative viruses were respiratory syncytial virus (RSV) (24.7%), human bocavirus (24.5%), and human rhinovirus (HRV) (15%). RSV was more prevalent in winter and among young infants. Cases of seasonal influenza A and B viruses were reported mainly in January and August. An increase in adenovirus infection was observed during the spring of the second year of the study. Sequence analyses showed multiple introductions of different virus subtypes and identified a high prevalence of the newly defined HRV-C species. A higher viral incidence was observed during the winter of 2008, which was unusually cold.

CONCLUSIONS

This study supports the usefulness of multiplex RT-PCR for virus detection and co-infection, and for implementation of a molecular monitoring system for endemic and epidemic viral respiratory infections.

Complete nucleotide sequences of avian metapneumovirus subtype B genome

Complete nucleotide sequences were determined for subtype B avian metapneumovirus (aMPV), the attenuated vaccine strain VCO3/50 and its parental pathogenic strain VCO3/60616. The genomes of both strains comprised 13,508 nucleotides (nt), with a 42-nt leader at the 3'-end and a 46-nt trailer at the 5'-end. The genome contains eight genes in the order 3'-N-P-M-F-M2-SH-G-L-5', which is the same order shown in the other metapneumoviruses. The genes are flanked on either side by conserved transcriptional start and stop signals and have intergenic sequences varying in length from 1 to 88 nt. Comparison of nt and predicted amino acid (aa) sequences of VCO3/60616 with those of other metapneumoviruses revealed higher homology with aMPV subtype A virus than with other metapneumoviruses. A total of 18 nt and 10 deduced aa differences were seen between the strains, and one or a combination of several differences could be associated with attenuation of VCO3/50.

Detection of novel respiratory viruses from influenza-like illness in the Philippines

Several novel viruses have been recently identified in respiratory samples. However, the epidemiology of these viruses in tropical countries remains unclear. The aim of the present study was to provide an overview of the epidemiology of novel respiratory viruses, including human metapneumovirus, human bocavirus, new subtypes of human coronavirus (NL63 and HKU1), KI virus, WU virus, and Melaka virus in the Philippines, a tropical country. Nasopharyngeal aspirates from 465 patients with influenza‐like illness were collected in 2006 and 2007. Reverse transcription polymerase chain reaction (RT‐PCR) and PCR were performed to detect viruses from culture‐negative specimens. Human metapneumovirus, human bocavirus, human coronavirus HKU1, KI virus, and WU virus were detected for the first time in the Philippines; Melaka virus was not found. J. Med. Virol. 82:1071–1074, 2010. © 2010 Wiley‐Liss, Inc.

Studies of culture conditions and environmental stability of human metapneumovirus

Human metapneumovirus (HMPV) is a paramyxovirus that is a leading cause of acute respiratory disease. HMPV is difficult to cultivate and limited published data describe the in vitro growth characteristics of the virus and its ability to replicate in different cell lines. Stability of HMPV to different temperatures or environmental conditions has not been described. Nosocomial infections due to HMPV have been reported, and thus the survival of infectious particles on environmental surfaces is important. We tested multiple cell lines for the ability to support HMPV replication both in the presence and absence of exogenous trypsin. The most permissive monkey kidney epithelial cells were LLC-MK2 and Vero, while the most permissive human airway epithelial cell line was BEAS-2B. LLC-MK2 cells were tolerant of trypsin and thus remain an ideal cell line for HMPV cultivation. Spinoculation significantly increased the infectivity of HMPV for cells in monolayer culture. Infectious virus was very stable to repeat freeze-thaw cycles, ambient room temperature, or 4 degrees C, while incubation at 37 degrees C led to degradation of virus titer. Finally, nonporous materials such as metal or plastic retained infectious virus for prolonged periods, while virus deposited on tissue and fabric rapidly lost infectivity. These findings provide guidance for laboratories attempting to culture HMPV and relevant information for infection control policies.

Population-based incidence of human metapneumovirus infection among hospitalized children

Background. Human metapneumovirus (HMPV) is a leading cause of acute respiratory illness (ARI) in children. Population-based incidence rates and comprehensive clinical characterizations of disease have not been established.

Methods. We conducted population-based prospective surveillance for 2 years in 2 US counties of HMPV infection among children <5 years old who were hospitalized with ARI or fever. Nasal and throat specimens obtained with swabs were tested for HMPV by real-time reverse-transcription polymerase chain reaction and genotyped.

Results. Forty-two (3.8%) of 1104 children tested positive for HMPV. The overall annual rate of HMPVassociated hospitalizations per 1000 children <5 years old was 1.2 (95% confidence interval [CI], 0.9–1.6). This rate was highest among infants 0–5 months old (4.9 per 1000 [95% CI, 2.9–7.2]), followed by children 6–11 months old (2.9 per 1000 [95% CI, 1.4–4.7]). The annual rate of hospitalization for HMPV infection was less than that for respiratory syncytial virus infection but similar to that for influenza and parainfluenza virus 3 infection in all age groups. The mean age of children hospitalized with HMPV infection was 6 months. Bronchiolitis, pneumonia, and asthma were the most common diagnoses among children with HMPV infection. All 4 HMPV subgroups were detected during both years at both sites. HPMV infection was most prominent from March through May.

Conclusion. HMPV was detected in 3.8% of children hospitalized with ARI or fever, with a population incidence similar to that of influenza virus and parainfluenza virus 3.

Soluble recombinant human metapneumovirus G protein is immunogenic but not protective

Human metapneumovirus (HMPV) expresses the major surface glycoproteins F and G. We evaluated the protective efficacy of immunization with G. We generated a recombinant form of G ectodomain (GDeltaTM) that was secreted from mammalian cells and purified by affinity chromatography. We tested the immunogenicity of GDeltaTM in cotton rats. Animals were immunized with PBS, GDeltaTM alone or adjuvanted, or were infected once with HMPV, and challenged with live HMPV at 28 days. Animals vaccinated with adjuvanted and non-adjuvanted GDeltaTM developed high levels of serum antibodies to both recombinant and native G protein; however, vaccinated animals did not develop neutralizing antibodies and were not protected against virus challenge. Unlike the analogous non-fusion glycoproteins of other human paramyxoviruses, HMPV G does not appear to be a protective antigen. This represents an unusual feature of HMPV.

Hematopoietic cell transplantation and emerging viral infections

Viral infections remain important causes of morbidity and mortality in hematopoietic cell transplant recipients. More recent developments in preparative regimens and graft manipulations, as well as the control of well-recognized post-transplant infections by the introduction of prophylaxis and preemptive strategies, have influenced the timing and the epidemiology of infections. As new pathogens, such as human metapneumovirus (HMPV), human bocavirus, human coronaviruses HCoV-NL63 and HCoV-HKU1, human herpesviruses HHV-6 and HHV-7, and polyomaviruses, have emerged, it is fundamental to determine the significance of the newly discovered viruses and their role in the transplantation field. This article summarizes recent data on epidemiology and laboratory diagnosis of new pathogens, as well as clinical features and management of the associated infectious complications. J. Med. Virol. 82:528-538, 2010. (c) 2010 Wiley-Liss, Inc.

Cell type-specific recognition of human metapneumoviruses (HMPVs) by retinoic acid-inducible gene I (RIG-I) and TLR7 and viral interference of RIG-I ligand recognition by HMPV-B1 phosphoprotein

Human metapneumoviruses (HMPVs) are recently identified Paramyxoviridae that contribute to respiratory tract infections in children. No effective treatments or vaccines are available. Successful defense against virus infection relies on early detection by germ line-encoded pattern recognition receptors and activation of cytokine and type I IFN genes. Recently, the RNA helicase retinoic acid-inducible gene I (RIG-I) has been shown to sense HMPV. In this study, we investigated the abilities of two prototype strains of HMPV (A1 [NL\1\00] and B1 [NL\1\99]) to activate RIG-I and induce type I IFNs. Despite the abilities of both HMPV-A1 and HMPV-B1 to infect and replicate in cell lines and primary cells, only the HMPV-A1 strain triggered RIG-I to induce IFNA/B gene transcription. The failure of the HMPV-B1 strain to elicit type I IFN production was dependent on the B1 phosphoprotein, which specifically prevented RIG-I-mediated sensing of HMPV viral 5' triphosphate RNA. In contrast to most cell types, plasmacytoid dendritic cells displayed a unique ability to sense both HMPV-A1 and HMPV-B1 and in this case sensing was via TLR7 rather than RIG-I. Collectively, these data reveal differential mechanisms of sensing for two closely related viruses, which operate in cell type-specific manners.

Prevalence and clinical and molecular characterization of human metapneumovirus in children with acute respiratory infection in China

BACKGROUND

Human metapneumovirus (HMPV), a newly discovered paramyxovirus, has been associated with acute respiratory tract infections (ARTIs). However, the prevalence and molecular characteristics of HMPV in China are still unclear.

METHODS

A total of 661 nasopharyngeal aspirates (NPA) specimens were collected from 661 children with ARTIs between December 2006 and November 2008. Specimens were screened for HMPV by reverse transcription-polymerase reaction. All positive amplification products were confirmed by sequencing.

RESULTS

HMPV was detected in 45 patients (6.80%) of the 661 children. The HMPV-infected patients were from 29 days to 9 years of age. A high incidence of HMPV infection (84.4%) was observed during the winter-spring season. Of the 45 HMPV-positive patients, 25 (55.6%) were co-infected with other respiratory viruses, and respiratory syncytial virus (RSV) was the most common additional respiratory virus. The most common clinical diagnosis was bronchopneumonia (57.8%) and cough (88.9%) was the most common clinical symptom. Phylogenetic analysis of the F gene revealed that 80% of the HMPV detected were A2, 2.2% were A1, and 17.8% were B1. Statistical analyses showed that sex, ages, seasons, and severity of the disease did not correlate with HMPV genotype (P = 0.986, 0.347, 0.660, 0.252), but viral coinfection with HMPV increased hospitalization rates (P = 0.005).

CONCLUSIONS

HMPV was frequently detected in the pediatric patients with ARTI in China. RSV was the most common coinfection virus and coinfection increased hospitalization rates. All HMPV subgroups except B2 cocirculated and there was no association found between HMPV genotypes and severity of disease.

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.

Microneutralization assay for the measurement of neutralizing antibodies to human metapneumovirus

BACKGROUND

Human metapneumovirus (hMPV) is a newly discovered virus which causes respiratory illness in persons of all ages.

OBJECTIVE

A simple and rapid method to determine neutralizing antibody titers against hMPV is needed to facilitate the development of vaccines and therapeutics for hMPV. Therefore, we sought to adapt the methodology used for RSV microneutralization assay (MNA) to measure neutralizing antibody titers against hMPV.

STUDY DESIGN

Serial 2-fold dilutions of serum were made in 96 well microtiter plates and incubated with approximately 50pfu of hMPV A or B strain for 60min at room temperature. LLC-MK2 cells were added to the serum-virus mixtures and plates incubated at 35 degrees C in CO(2) for 5 days. Plates were fixed with acetone; air dried, blocked and then developed with monoclonal antibody to the hMPV N protein followed by horse radish peroxidase labeled antibody and substrate. Neutralization titer was defined as the titer of serum that reduced color development by 50% compared to the positive control wells.

RESULTS

Titers measured by MNA correlated well with those determined by standard plaque reduction assay (R=0.77). Neutralization titers determined by MNA demonstrated excellent inter-assay variability (coefficient of variance=7%). In addition, there was good correlation of antibody titers from 10 hMPV infected adults measured by MNA using either group A or group B hMPV (R=0.87).

CONCLUSION

MNA is a simple and reproducible method for the measurement of serum neutralizing antibody against hMPV.

Prevalence of human metapneumovirus in hospitalized children with respiratory tract infections in Tianjin, China

Human metapneumovirus (hMPV) has recently been recognized as an important respiratory pathogen, especially in children. At present, our understanding of the characteristics of hMPV from China is very limited. Nasopharyngeal aspirates were taken from 310 hospitalized pediatric patients. Twenty (6.5%) of them were infected with hMPV, and they all developed pneumonia. Sixty five percent (13/20) of the cases were under 12 months. Phylogenetic analysis of F gene fragments indicated that three sub-genotypes of hMPV(A2a/A2b, B1,B2) circulated in Tianjin and A2b was the predominant subtype. The Vero-E6 cell line was better than LLC-MK2 for hMPV isolation. Three hMPV strains were successfully isolated using the Vero-E6 cell line.

Genetic diversity and evolution of human metapneumovirus fusion protein over twenty years

BACKGROUND

Human metapneumovirus (HMPV) is an important cause of acute respiratory illness in children. We examined the diversity and molecular evolution of HMPV using 85 full-length F (fusion) gene sequences collected over a 20-year period.

RESULTS

The F gene sequences fell into two major groups, each with two subgroups, which exhibited a mean of 96% identity by predicted amino acid sequences. Amino acid identity within and between subgroups was higher than nucleotide identity, suggesting structural or functional constraints on F protein diversity. There was minimal progressive drift over time, and the genetic lineages were stable over the 20-year period. Several canonical amino acid differences discriminated between major subgroups, and polymorphic variations tended to cluster in discrete regions. The estimated rate of mutation was 7.12 x 10(-4) substitutions/site/year and the estimated time to most recent common HMPV ancestor was 97 years (95% likelihood range 66-194 years). Analysis suggested that HMPV diverged from avian metapneumovirus type C (AMPV-C) 269 years ago (95% likelihood range 106-382 years).

CONCLUSION

HMPV F protein remains conserved over decades. HMPV appears to have diverged from AMPV-C fairly recently.

Limited inter- and intra-patient sequence diversity of the genetic lineage A human metapneumovirus fusion gene

Human metapneumovirus (hMPV) is associated with respiratory tract illness especially in young children. Two hMPV genetic lineages, A and B, and four sublineages A1, A2 and B1, B2 have been defined. Infection with hMPV occurs through membrane fusion mediated by the hMPV fusion (F) protein. In this study, the inter- and intra-patient genetic diversity of the lineage A hMPV F gene was investigated. Ten isolates were collected from 10 hMPV infected children. Viral RNA was isolated and amplified, and approximately 10 clones from each isolate were sequenced. Altogether 108 clones were successfully sequenced. The average interpatient sequence diversity was 1.68% and 1.64% at nucleotide and amino acid levels, respectively. The samples were divisible into two groups on the basis of intrapatient sequence diversity. In group 1 (4 children) the intra-patient sequence diversity was low (nt: 0.26-0.39%, aa: 0.51-0.94%) whereas group 2 (6 children) had a higher intra-patient sequence diversity (nt: 0.85-1.98%, aa: 1.08-2.22%). Phylogenetic analyses showed that the group 1 children harboured sublineage Al only, but interestingly group 2 children harboured both sublineages Al and A2, indicating they had been infected with at least two viruses. Several independent viruses contained premature stop codons in exactly identical positions resulting in truncated fusion proteins. Possibly this is a mechanism for immune system evasion. The F protein is a major antigenic determinant, and the limited sequence diversity observed lay emphasis on the hMPV F gene as a putative target for future vaccine development.

RNA viruses in community-acquired childhood pneumonia in semi-urban Nepal; a cross-sectional study

BACKGROUND

Pneumonia is among the main causes of illness and death in children <5 years of age. There is a need to better describe the epidemiology of viral community-acquired pneumonia (CAP) in developing countries.

METHODS

From July 2004 to June 2007, we examined nasopharyngeal aspirates (NPA) from 2,230 cases of pneumonia (World Health Organization criteria) in children 2 to 35 months old recruited in a randomized trial of zinc supplementation at a field clinic in Bhaktapur, Nepal. The specimens were examined for respiratory syncytial virus (RSV), influenza virus type A (InfA) and B (InfB), parainfluenza virus types 1, 2 and 3 (PIV1, PIV2, and PIV3), and human metapneumovirus (hMPV) using a multiplex reverse transcriptase polymerase chain reaction (PCR) assay.

RESULTS

We identified 919 virus isolates in 887 (40.0%) of the 2,219 NPA specimens with a valid PCR result, of which 334 (15.1%) yielded RSV, 164 (7.4%) InfA, 129 (5.8%) PIV3, 98 (4.4%) PIV1, 93 (4.2%) hMPV, 84 (3.8%) InfB, and 17 (0.8%) PIV2. CAP occurred in an epidemic pattern with substantial temporal variation during the three years of study. The largest peaks of pneumonia occurrence coincided with peaks of RSV infection, which occurred in epidemics during the rainy season and in winter. The monthly number of RSV infections was positively correlated with relative humidity (rs = 0.40, P = 0.01), but not with temperature or rainfall. An hMPV epidemic occurred during one of the three winter seasons and the monthly number of hMPV cases was also associated with relative humidity (rs = 0.55, P = 0.0005).

CONCLUSION

Respiratory RNA viruses were detected from NPA in 40% of CAP cases in our study. The most commonly isolated viruses were RSV, InfA, and PIV3. RSV infections contributed substantially to the observed CAP epidemics. The occurrence of viral CAP in this community seemed to reflect more or less overlapping micro-epidemics with several respiratory viruses, highlighting the challenges of developing and implementing effective public health control measures.

Human metapneumovirus and respiratory syncytial virus in hospitalized danish children with acute respiratory tract infection

The newly discovered human metapneumovirus (hMPV) has been shown to be associated with respiratory illness. We determined the frequencies and clinical features of hMPV and respiratory syncytial virus (RSV) infections in 374 Danish children with 383 episodes of acute respiratory tract infection (ARTI). Study material comprised routine nasopharyngeal aspirates obtained during 2 winter seasons (November-May) 1999-2000 and 2001-2002 from children hospitalized at the Departments of Paediatrics, Hvidovre Hospital and Amager Hospital, Denmark. hMPV was detected in 11 (2.9%) and RSV in 190 (49.6%) ARTI episodes by real-time reverse transcription-polymerase chain reaction using primers targeting the hMPV N gene and the RSV L gene. Two children were co-infected with hMPV and RSV. They were excluded from statistical analysis. Hospitalization for ARTI caused by hMPV was restricted to very young children 1-6 months of age. Asthmatic bronchitis was diagnosed in 66.7% of hMPV and 10.6% of RSV-infected children (p < 0.001). Overall symptoms and clinical findings were similar among hMPV and RSV positive episodes, but more RSV-infected children required respiratory support. hMPV is present in young Danish children hospitalized with ARTI although less frequent than RSV and with a tendency to a milder clinical course.

Epidemiology and genetic variability of human metapneumovirus during a 4-year-long study in Southeastern Brazil

Epidemiological and molecular characteristics of human metapneumovirus (hMPV) were compared with human respiratory syncytial virus (hRSV) in infants and young children admitted for acute lower respiratory tract infections in a prospective study during four consecutive years in subtropical Brazil. GeneScan polymerase chain assays (GeneScan RT-PCR) were used to detect hMPV and hRSV in nasopharyngeal aspirates of 1,670 children during January 2003 to December 2006. hMPV and hRSV were detected, respectively, in 191 (11.4%) and in 702 (42%) of the children admitted with acute lower respiratory tract infections at the Sao Paulo University Hospital. Sequencing data of the hMPV F gene revealed that two groups of the virus, each divided into two subgroups, co-circulated during three consecutive years. It was also shown that a clear dominance of genotype B1 occurred during the years 2004 and 2005, followed by genotype A2 during 2006.

Human metapneumovirus and human bocavirus in children

Several new viruses have recently been described in children, including human metapneumovirus (hMPV) and human bocavirus (HBoV). hMPV has been established as a common cause of upper and lower respiratory tract infections in children, often second only to respiratory syncytial virus as a cause of bronchiolitis in infants. Diagnostic tools have been developed for the clinician and effective treatment and prevention strategies are being investigated. HBoV was more recently identified. Although it was initially identified in the airway of children, high rates of codetection of other viral pathogens and detection of the virus in the stool have raised questions about the true role of HBoV as a cause of respiratory infections. A focus on epidemiology, pathogenesis, clinical features, and diagnostic techniques for hMPV and HBoV is presented.

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.

Molecular epidemiological investigation of a nosocomial outbreak of human metapneumovirus infection in a pediatric hemato-oncology patient population

We report the first nosocomial outbreak of human metapneumovirus (hMPV) infection in a pediatric patient population. Among 15 pediatric hMPV infections from March to May 2007, there was a nosocomial outbreak involving two patients sharing a room in a hemato-oncology ward with a patient with a community-acquired case of hMPV infection. The estimated incubation period was 7 to 9 days for a symptomatic nosocomial case. Sequencing of fusion genes of 15 isolates revealed two clusters belonging to subgroup A2 and one cluster belonging to subgroup B2. Three isolates from the outbreak had sequences identical to those of samples in the A2 cluster. There was also a separate nosocomial case represented by the B2 cluster.

[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.

Integrin alphavbeta1 promotes infection by human metapneumovirus

Human metapneumovirus (hMPV) is a recently described paramyxovirus that causes lower respiratory infections in children and adults worldwide. The hMPV fusion (F) protein is a membrane-anchored glycoprotein and major protective antigen. All hMPV F protein sequences determined to date contain an Arg-Gly-Asp (RGD) sequence, suggesting that F engages RGD-binding integrins to mediate cell entry. The divalent cation chelator EDTA, which disrupts heterodimeric integrin interactions, inhibits infectivity of hMPV but not the closely related respiratory syncytial virus (RSV), which lacks an RGD motif. Function-blocking antibodies specific for alphavbeta1 integrin inhibit infectivity of hMPV but not RSV. Transfection of nonpermissive cells with alphav or beta1 cDNAs confers hMPV infectivity, whereas reduction of alphav and beta1 integrin expression by siRNA inhibits hMPV infection. Recombinant hMPV F protein binds to cells, whereas Arg-Gly-Glu (RGE)-mutant F protein does not. These data suggest that alphavbeta1 integrin is a functional receptor for hMPV.

Evolutionary dynamics of human and avian metapneumoviruses

Human (HMPV) and avian (AMPV) metapneumoviruses are closely related viruses that cause respiratory tract illnesses in humans and birds, respectively. Although HMPV was first discovered in 2001, retrospective studies have shown that HMPV has been circulating in humans for at least 50 years. AMPV was first isolated in the 1970s, and can be classified into four subgroups, A-D. AMPV subgroup C is more closely related to HMPV than to any other AMPV subgroup, suggesting that HMPV has emerged from AMPV-C upon zoonosis. Presently, at least four genetic lineages of HMPV circulate in human populations - A1, A2, B1 and B2 - of which lineages A and B are antigenically distinct. We used a Bayesian Markov Chain Monte Carlo (MCMC) framework to determine the evolutionary and epidemiological dynamics of HMPV and AMPV-C. The rates of nucleotide substitution, relative genetic diversity and time to the most recent common ancestor (TMRCA) were estimated using large sets of sequences of the nucleoprotein, the fusion protein and attachment protein genes. The sampled genetic diversity of HMPV was found to have arisen within the past 119-133 years, with consistent results across all three genes, while the TMRCA for HMPV and AMPV-C was estimated to have existed around 200 years ago. The relative genetic diversity observed in the four HMPV lineages was low, most likely reflecting continual population bottlenecks, with only limited evidence for positive selection.

Identification of antibody neutralization epitopes on the fusion protein of human metapneumovirus

Human metapneumovirus (hMPV) is genetically related to respiratory syncytial virus (RSV); both cause respiratory tract illnesses ranging from a mild cough to bronchiolitis and pneumonia. The F protein-directed monoclonal antibody (mAb) palivizumab has been shown to prevent severe lower respiratory tract RSV infection in animals and humans. We have previously reported on a panel of mAbs against the hMPV F protein that neutralize hMPV in vitro and, in two cases, in vivo. Here we describe the generation of hMPV mAb-resistant mutants (MARMs) to these neutralizing antibodies. Sequencing the F proteins of the hMPV MARMs identified several neutralizing epitopes. Interestingly, some of the epitopes mapped on the hMPV F protein coincide with homologous regions mapped previously on the RSV F protein, including the site against which the broadly protective mAb palivizumab is directed. This suggests that these homologous regions play important, conserved functions in both viruses.

Low-pH triggering of human metapneumovirus fusion: essential residues and importance in entry

Human metapneumovirus (HMPV) is a significant respiratory pathogen classified in the Pneumovirinae subfamily of the paramyxovirus family. Recently, we demonstrated that HMPV F protein-promoted cell-cell fusion is stimulated by exposure to low pH, in contrast to what is observed for other paramyxovirus F proteins. In the present study, we examined the potential role of histidine protonation in HMPV F fusion and investigated the role of low pH in HMPV viral entry. Mutagenesis of the three ectodomain histidine residues of the HMPV F protein demonstrated that the mutation of a histidine in the heptad repeat B linker domain (H435) ablated fusion activity without altering cell surface expression or proteolytic processing significantly. Modeling of the HMPV F protein revealed several basic residues surrounding this histidine residue, and the mutation of these residues also reduced fusion activity. These results suggest that electrostatic repulsion in the heptad repeat B linker region may contribute to the triggering of HMPV F. In addition, we examined the effect of inhibitors of endosomal acidification or endocytosis on the entry of a recombinant green fluorescent protein-expressing HMPV. Interestingly, chemicals that raise the pH of endocytic vesicles resulted in a 30 to 50% decrease in HMPV infection, while the inhibitors of endocytosis reduced infection by as much as 90%. These data suggest that HMPV utilizes an endocytic entry mechanism, in contrast to what has been hypothesized for most paramyxoviruses. In addition, our results indicate that HMPV uses the low pH of the endocytic pathway to enhance infectivity, though the role of low pH likely differs from classically described mechanisms.

Human metapneumovirus reinfection among children in Thailand determined by ELISA using purified soluble fusion protein

BACKGROUND

Human metapneumovirus (hMPV) is a newly discovered paramyxovirus that causes acute respiratory illness. Despite apparent near-universal exposure during early childhood, immunity is transient.

METHODS

An indirect screening enzyme-linked immunosorbent assay using a recombinant soluble fusion (F) glycoprotein derived from hMPV was used to test for anti-F IgG in 1,380 pairs of acute- and convalescent-stage serum samples collected from children in Kamphaeng Phet, Thailand.

RESULTS

Of the 1,380 serum sample pairs tested, 1,376 (99.7%) showed evidence of prior infection with hMPV. Sixty-six paired specimens demonstrated a >or=4-fold rise in titer, for an overall reinfection rate of 4.9%. Two children demonstrated evidence of an initial infection. Forty-eight of the 68 new infections or reinfections occurred in 2000, accounting for 13.2% of all nonflaviviral febrile illnesses in the study population in that year. Of 68 positive cases, 85.3% complained of cough and 66.2% complained of rhinorrhea, compared with 61.4% and 49.0% of negative cases, respectively (P < .01). All positive samples were also tested for an increase in titer of antibodies to respiratory syncytial virus F, and 27% exhibited a >or=4-fold rise.

CONCLUSION

These results demonstrate that hMPV reinfections cause illness at a rate equal to that seen for initial infections. hMPV may have a more significant impact in older children than previously realized and may be the cause of significant outbreaks in this population.

Co-circulating genetically divergent A2 human metapneumovirus strains among children in southern Taiwan

An outbreak of human metapneumovirus (hMPV) among children in southern Taiwan in 2004 prompted the investigation of the molecular epidemiology of hMPV from September 2003 to August 2005. Respiratory specimens that were culture negative for a panel of respiratory viruses were examined for the presence of hMPV by RT-PCR. The results indicated that 59 out of 546 (10.8%) children were hMPV-positive. The majority of these hMPV-positive children were less than 2 years old (59.4%), females (61%), and inpatients (67.8%). Infections occurred throughout the year, but peaked during the spring and/or summer months. Sequence analysis of the fusion gene from the isolates revealed two phylogenetic groups with five possible lineages (A1, A2a/A2b, B1, and B2). Among these co-circulating strains, A2 strains were most frequently observed and demonstrated the greatest divergence. Deduced amino acid sequence analysis identified several variant amino acids specific to the A2 lineage. Lineage-specific amino acid substitutions were noted at aa233, aa286, aa312, aa348, and aa296. This study indicated that genetically divergent strains of hMPV which caused respiratory disease and hospitalization were circulating among children in Taiwan.

An alphavirus replicon-based human metapneumovirus vaccine is immunogenic and protective in mice and cotton rats

Human metapneumovirus (hMPV) is a recently discovered paramyxovirus that causes upper and lower respiratory tract infections in infants, the elderly, and immunocompromised individuals worldwide. Here, we developed Venezuelan equine encephalitis virus replicon particles (VRPs) encoding hMPV fusion (F) or attachment (G) glycoproteins and evaluated the immunogenicity and protective efficacy of these vaccine candidates in mice and cotton rats. VRPs encoding hMPV F protein, when administered intranasally, induced F-specific virus-neutralizing antibodies in serum and immunoglobulin A (IgA) antibodies in secretions at the respiratory mucosa. Challenge virus replication was reduced significantly in both the upper and lower respiratory tracts following intranasal hMPV challenge in these animals. However, vaccination with hMPV G protein VRPs did not induce neutralizing antibodies or protect animals from hMPV challenge. Close examination of the histopathology of the lungs of VRP-MPV F-vaccinated animals following hMPV challenge revealed no enhancement of inflammation or mucus production. Aberrant cytokine gene expression was not detected in these animals. Together, these results represent an important first step toward the use of VRPs encoding hMPV F proteins as a prophylactic vaccine for hMPV.

Antiviral therapy for respiratory tract infections

Viruses are important pathogens causing respiratory tract infections both in the community and health-care facility settings. They are extremely common causes of morbidity in the competent hosts and some are associated with significant mortality in the compromised individuals. With wider application of molecular techniques, novel viruses are being described and old viruses are found to have new significance in different epidemiological and clinical settings. Some of these emerging pathogens may have the potential to cause pandemics or global spread of a severe disease, as exemplified by severe acute respiratory syndrome and avian influenza. Antiviral therapy of viral respiratory infections is often unnecessary in the competent hosts because most of them are selflimiting and effective agents are not always available. In the immunocompromised individuals or for infections caused by highly pathogenic viruses, such as avian influenza viruses (AIV), antiviral treatment is highly desirable, despite the fact that many of the agents may not have undergone stringent clinical trials. In immunocompetent hosts, antiviral therapy can be stopped early because adaptive immune response can usually be mounted within 5-14 days. However, the duration of antiviral therapy in immunosuppressed hosts depends on clinical and radiological resolution, the degree and duration of immunosuppression, and therefore maintenance therapy is sometimes needed after the initial response. Immunotherapy and immunoprophylaxis appear to be promising directions for future research. Appropriate and targeted immunomodulation may play an important adjunctive role in some of these infections by limiting the extent of end-organ damage and multi-organ failure in some fulminant infections.

New respiratory viruses of humans

Acute respiratory viruses are a major cause of morbidity and mortality in humans worldwide and most acute respiratory infections are caused by viruses. Many of these viruses cause the highest burden of disease in specific risk groups such as young infants, the elderly, and immune-compromised individuals. Although the most important respiratory viruses of humans have been identified in the last century, in the past decade about a dozen "new" viruses have been discovered that may cause a high burden of acute respiratory disease in humans. Not only viruses were discovered that must have been with humans for many decades or centuries, such as human metapneumovirus and 2 different human coronaviruses, but also viruses that are truly new for humans and have emerged as a result of recent interspecies transmissions from other mammalian or avian reservoirs. The latter include highly pathogenic avian influenza viruses, severe acute respiratory syndrome (SARS) coronavirus, and Nipah virus. The discovery, etiologic role, and burden of disease caused by these infections are described.

Human metapneumovirus infection in adults

Human metapneumovirus (hMPV) was first identified in 2001 in Dutch children with bronchiolitis. The virus is an RNA virus in the Pneumovirinae subfamily and is most closely related to respiratory syncytial virus. hMPV has been shown to have worldwide circulation with nearly universal infection by age 5. Similar to influenza and respiratory syncytial virus, activity is greatest during the winter in temperate climates. Most of the available data on the clinical manifestations of hMPV infection are from studies of children where the virus causes upper respiratory tract infections, bronchiolitis, and pneumonia. Reinfections with hMPV occur throughout adult life and hMPV infection has been documented in 1-9% of adults each year using RT-PCR and serology for diagnosis. Illness is generally mild in young adults with serologic evidence of asymptomatic infection in many cases. Adults at highest risk of serious sequelae as a result of hMPV include the elderly, adults with underlying pulmonary disease, and those who are immunocompromised. Outbreaks of hMPV have been documented in long term care facilities with mortality of up to 50% in frail elderly residents. In addition, 6-12% of exacerbations of chronic obstructive pulmonary disease have been associated with hMPV and underlying lung disease is common in patients hospitalized with hMPV. Lastly, hMPV has been linked with severe idiopathic pneumonia in recipients of hematopoietic stem cell transplants. Although the true spectrum of adult hMPV remains to be defined, it is clear that hMPV can result in severe illness the frail elderly and adults with underlying diseases.

Detection of four genetic subgroup-specific antibodies to human metapneumovirus attachment (G) protein in human serum

Human metapneumovirus (hMPV) strains are classified into two genetic groups, A and B, each of which is further divided in two genetic subgroups, A1, A2, B1 and B2. hMPV encodes two major surface glycoproteins, the fusion (F) and attachment (G) proteins, which may be immunogenic and protective antigens. Although the amino acid sequences of hMPV F protein are highly conserved, those of the G protein are highly variable with low amino acid identity between the two groups. To address the antigenic variation between the genetic subgroups, we developed an immunofluorescence assay (IFA) method using Trichoplusia ni (Tn5) insect cells infected with each recombinant baculovirus-expressed hMPV G (Bac-G) protein of the four genetic subgroups. The titre of each antibody to the four Bac-G proteins was measured by the IFA in 12 paired serum samples obtained from children infected with hMPV of each genetic subgroup. Although 11 of the 12 acute-phase serum samples in paired samples were negative for the antibody to any Bac-G proteins, all of the convalescent-phase serum samples in those paired samples were positive for the antibody to only one of the four Bac-G proteins of the infecting genotype of hMPV. Since the antibody response to hMPV G protein was transient and genetic subgroup-specific without cross-reactivity, four genetic subgroups on the basis of hMPV G protein could be identified as different serotypes. This assay may be useful for the study of immune responses of humans to different hMPV strains, especially for clarifying the risk of reinfection with hMPV.