Detection of human bocavirus and human metapneumovirus by real-time PCR from patients with respiratory symptoms in Southern Brazil

The introduction of newer molecular methods has led to the discovery of new respiratory viruses, such as human metapneumovirus (hMPV) and human bocavirus (hBoV), in respiratory tract specimens. We have studied the occurrence of hMPV and hBoV in the Porto Alegre (PA) metropolitan area, one of the southernmost cities of Brazil, evaluating children with suspected lower respiratory tract infection from May 2007-June 2008. A real-time polymerase chain reaction method was used for amplification and detection of hMPV and hBoV and to evaluate coinfections with respiratory syncytial virus (RSV), influenza A and B, parainfluenza 1, 2 and 3, human rhinovirus and human adenovirus. Of the 455 nasopharyngeal aspirates tested, hMPV was detected in 14.5% of samples and hBoV in 13.2%. A unique causative viral agent was identified in 46.2% samples and the coinfection rate was 43.7%. For hBoV, 98.3% of all positive samples were from patients with mixed infections. Similarly, 84.8% of all hMPV-positive results were also observed in mixed infections. Both hBoV and hMPV usually appeared with RSV. In summary, this is the first confirmation that hMPV and hBoV circulate in PA; this provides evidence of frequent involvement of both viruses in children with clinical signs of acute viral respiratory tract infection, although they mainly appeared as coinfection agents.     

First detection of human metapneumovirus in children with respiratory infections in Romania

The human metapneumovirus (hMPV) was first isolated in 2001 in the Netherlands (Van der Hoogen and collaborators) from a nasopharyngeal aspirate sampled from an infant. Based on the morphological, biochemical and genetic characteristics, the hMPV was initially classified in the genus Metapneumovirus with the avian metapneumovirus (APV), the agent causing the respiratory infections of the upper tract in turkeys and other birds. Subsequently, together with the respiratory syncytial virus (RSV), it was classified in the Pneumovirus genus which is a part of the Pneumovirinae subfamily, the Paramyxoviridae family. The aim of the present study was to optimize hMPV molecular detection and to detect the virus in samples form children with respiratory infections in Romania. Two types of RTPCR commercial kits were evaluated for the detection of hMPV. Tests were performed on 28 pharyngeal exudates from children aged from 9 months to 6 years, which were negative for influenza viruses and for Respiratory Syncytial Virus (RSV). Among the tested samples 7 (25%) have been positive for hMPV by RT-PCR. These results document for the first time that hMPV is circulating in Romania and causes respiratory infections, especially in newborns and children under 6 years old.     

Viral and Atypical Bacterial Etiology of Acute Respiratory Infections in Children under 5 Years Old Living in a Rural Tropical Area of Madagascar

Background

In Madagascar, very little is known about the etiology and prevalence of acute respiratory infections (ARIs) in a rural tropical area. Recent data are needed to determine the viral and atypical bacterial etiologies in children with defined clinical manifestations of ARIs.

Methods

During one year, we conducted a prospective study on ARIs in children between 2 to 59 months in the community hospital of Ampasimanjeva, located in the south-east of Madagascar. Respiratory samples were analyzed by multiplex real-time RT-PCR, including 18 viruses and 2 atypical bacteria. The various episodes of ARI were grouped into four clinical manifestations with well-documented diagnosis: “Community Acquired Pneumonia”(CAP, group I), “Other acute lower respiratory infections (Other ALRIs, group II)”, “Upper respiratory tract infections with cough (URTIs with cough, group III)”and “Upper respiratory tract infections without cough (URTIs without cough, group IV)”.

Results

295 children were included in the study between February 2010 and February 2011. Viruses and/or atypical bacteria respiratory pathogens were detected in 74.6% of samples, the rate of co-infection was 27.3%. Human rhinovirus (HRV; 20.5%), metapneumovirus (HMPV A/B, 13.8%), coronaviruses (HCoV, 12.5%), parainfluenza virus (HPIV, 11.8%) and respiratory syncytial virus A and B (RSV A/B, 11.8%) were the most detected. HRV was predominantly single detected (23.8%) in all the clinical groups while HMPV A/B (23.9%) was mainly related to CAP (group I), HPIV (17.3%) to the “Other ALRIs” (group II), RSV A/B (19.5%) predominated in the group “URTIs with cough” (group III) and Adenovirus (HAdV, 17.8%) was mainly detected in the “without cough” (group IV).

Interpretation

This study describes for the first time the etiology of respiratory infections in febrile children under 5 years in a malaria rural area of Madagascar and highlights the role of respiratory viruses in a well clinically defined population of ARIs.     

Molecular Characterization of Circulating Respiratory Syncytial Virus (RSV) Genotypes in Gilgit Baltistan Province of Pakistan during 2011-2012 Winter Season

Respiratory syncytial virus (RSV) is the major cause of acute lower respiratory tract infections in young children, but very little is known about its epidemiology and circulating genotypes in Pakistan. This study analyzed the epidemiological and molecular characteristics of RSV genotypes detected in Pakistani children less than 2 years of age with acute respiratory tract infections (ARIs) in a tertiary care hospital in Gilgit Baltistan (GB) province during 2011-12 winter season. RSV was detected in 75 out of 105 children presenting with acute respiratory infection. Male infants between 2-6 months age made up the highest percentage of RSV positive cases. Epidemiological factors such as pre-maturity, mean weight, clinical features and diagnosis when compared between RSV positive and negative groups were found to be statistically insignificant. Phylogenetic analysis classified all 75 of the RSV strains into 71 strains of subgroups A and 4 strains of subgroup B, respectively. Strains belonging to subgroups A and B were further subdivided into NA1/GA2 and BA, respectively. The nucleotide and deduced amino acid sequence identities were relatively high among these strains (>90%). Both RSV-A and RSV-B isolates had two potential N-glycosylation sites in HVR2 of G protein and with heavy O-glycosylation of serine and threonine residues (G scores of 0.5-0.7). This report highlights the significance of RSV as a dominant viral etiologic agent of pediatric ARIs, and need for continued molecular epidemiological surveys for early detection of prevalent strains and newly emerging genotypes to understand epidemiology of RSV infections in various regions of Pakistan.     

Respiratory viruses in children younger than five years old with acute respiratory disease from 2001 to 2004 in Uberlândia, MG, Brazil

The main viruses involved in acute respiratory diseases among children are: respiratory syncytial virus (RSV), influenzavirus (FLU), parainfluenzavirus (PIV), adenovirus (AdV), human rhinovirus (HRV), and the human metapneumovirus (hMPV). The purpose of the present study was to identify respiratory viruses that affected children younger than five years old in Uberlandia, Midwestern Brazil. Nasopharyngeal aspirates from 379 children attended at Hospital de Clínicas (HC/UFU), from 2001 to 2004, with acute respiratory disease, were collected and tested by immunofluorescence assay (IFA) to detect RSV, FLU A and B, PIV 1, 2, and 3 and AdV, and RT-PCR to detect HRV. RSV was detected in 26.4% (100/379) of samples, FLU A and B in 9.5% (36/379), PIV 1, 2 and 3 in 6.3% (24/379) and AdV in 3.7% (14/379). HRV were detected in 29.6% (112/379) of the negative and indeterminate samples tested by IFI. RSV, particularly among children less than six months of life, and HRV cases showed highest incidence. Negative samples by both IFA and RT-PCR might reflect the presence of other pathogens, such as hMPV, coronavirus, and bacteria. Laboratorial diagnosis constituted an essential instrument to determine the incidence of the most common viruses in respiratory infections among children in this region.     

Aetiology of Acute Respiratory Tract Infections in Hospitalised Children in Cyprus

In order to improve clinical management and prevention of viral infections in hospitalised children improved etiological insight is needed. The aim of the present study was to assess the spectrum of respiratory viral pathogens in children admitted to hospital with acute respiratory tract infections in Cyprus. For this purpose nasopharyngeal swab samples from 424 children less than 12 years of age with acute respiratory tract infections were collected over three epidemic seasons and were analysed for the presence of the most common 15 respiratory viruses. A viral pathogen was identified in 86% of the samples, with multiple infections being observed in almost 20% of the samples. The most frequently detected viruses were RSV (30.4%) and Rhinovirus (27.4%). RSV exhibited a clear seasonality with marked peaks in January/February, while rhinovirus infections did not exhibit a pronounced seasonality being detected almost throughout the year. While RSV and PIV3 incidence decreased significantly with age, the opposite was observed for influenza A and B as well as adenovirus infections. The data presented expand our understanding of the epidemiology of viral respiratory tract infections in Cypriot children and will be helpful to the clinicians and researchers interested in the treatment and control of viral respiratory tract infections.     

Detection of KI polyomavirus and WU polyomavirus DNA by real-time polymerase chain reaction in nasopharyngeal swabs and in normal lung and lung adenocarcinoma tissues

Polyomaviruses KI (KIPyV) and WU (WUPyV) were detected from 7 (3.0%) and 38 (16.4%) of 232 children with respiratory tract infections by real-time PCR. The rates of infection by KIPyV and WUPyV alone were 3 of 7 (42.9%) and 20 of 38 (52.6%), respectively. In the other samples, various viruses (human respiratory syncytial virus, human metapneumovirus, human rhinovirus, parainfluenza virus 1 and human bocavirus) were detected simultaneously. One case was positive for KIPyV, WUPyV and hMPV. There was no obvious difference in clinical symptoms between KIPyV-positive and WUPyV-positive patients with or without coinfection. KIPyV was detected in one of 30 specimens of lung tissue (3.3%). Neither of the viruses was detected in 30 samples of lung adenocarcinoma tissue.     

北京地区成人呼吸道感染病人中人偏肺病毒感染情况的初步分析

目的:了解北京地区成人呼吸道感染患者中人偏肺病毒(hMPV)的感染情况、流行分布和临床表现特点。方法:采集2010年5月至2011年4月北京地区成人呼吸道感染患者鼻咽拭子标本413份,利用巢式PCR法进行hMPV筛查,对PCR阳性片段进行核酸序列测定,确定hMPV感染基因型别;同时,分析hMPV感染的流行病学特点,并对感染阳性患者进行临床表现的初步分析。结果:413份鼻咽拭子标本中检出hMPV阳性4份(0.97%),分别存在于2010年8月、10月和2011年2月、4月,其中1例合并鼻病毒感染;感染患者临床表现主要是发热、鼻塞、流涕、头痛、咳嗽,有1例出现呕吐和腹泻;hMPV阳性片段系统进化分析发现这4例感染中的3例为B2型,1例为A2b型。结论:北京地区成人呼吸道感染患者中存在hMPV感染,其基因型为B2和A2b型。     

569例呼吸道感染住院儿童7种常见呼吸道病毒病原学分析

目的了解呼吸道感染住院患儿呼吸道病毒的分布情况。方法选取2015年7月至2016年6月呼吸道感染的住院患儿病例,抽取鼻咽分泌物,采用直接免疫荧光法检测常见的7种病毒,即呼吸道合胞病毒(RSV)、甲型流感病毒(IVA)、乙型流感病毒(IVB)、副流感病毒1型(PIV1)、副流感病毒2型(PIV2)、副流感病毒3型(PIV3)、腺病毒(IVD)。结果共有569例样本送检,193例病毒检测阳性(33.92%),其中有3例为2种病毒的混合感染。男性共369例,女性共200例。其中RSV、PIV3、ADV的感染率居前三位。呼吸道病毒的感染率随着患儿年龄的增长逐渐下降,除新生儿外,6个月内的婴幼儿呼吸道病毒检出率最高。RSV检测阳性率自11月开始呈增高趋势,12月最高,达55.86%。PIV3的检出高峰出现在7月,达13.64%。结论 RSV是本地区儿童呼吸道感染最常见的病毒。呼吸道病毒的检出率与年龄、季节等因素有关。     

High Human Bocavirus Viral Load Is Associated with Disease Severity in Children under Five Years of Age

Human bocavirus (HBoV) is a parvovirus and detected worldwide in lower respiratory tract infections (LRTIs), but its pathogenic role in respiratory illness is still debatable due to high incidence of co-infection with other respiratory viruses. To determine the prevalence of HBoV infection in patients with LRTI in Shanghai and its correlation with disease severity, we performed a 3-year prospective study of HBoV in healthy controls, outpatients and inpatients under five years of age with X-ray diagnosed LRTIs. Nasopharyngeal aspirates were tested by PCR for common respiratory viruses and by real time PCR for HBoV subtypes 1–4. Nasopharyngeal swabs from healthy controls and serum samples and stools from inpatients were also tested for HBoV1-4 by real time PCR. Viral loads were determined by quantitative real time PCR in all HBoV positive samples. HBoV1 was detected in 7.0% of inpatients, with annual rates of 5.1%, 8.0% and 4.8% in 2010, 2011 and 2012, respectively. Respiratory syncytial virus (RSV) subtype A was the most frequent co-infection detected; HBoV1 and RSVA appeared to co-circulate with similar seasonal variations. High HBoV viral loads (>10⁶ copies/ml) were significantly more frequent in inpatients and outpatients than in healthy controls. There was a direct correlation of high viral load with increasing disease severity in patients co-infected with HBoV1 and at least one other respiratory virus. In summary, our data suggest that HBoV1 can cause LRTIs, but symptomatic HBoV infection is only observed in the context of high viral load.     

Co-infection of human metapneumovirus with adenovirus or respiratory syncytial virus among children in Japan

Human metapneumovirus (hMPV) is one of the etiological agents of acute respiratory tract infections. From June 2005 to May 2006, we collected 185 clinical specimens from children in Osaka City, Japan, and detected 41 hMPV RNA. Of the 41 specimens, four (9.8%) also contained other viruses (3 with adenovirus [AdV] and 1 with respiratory syncytial virus [RSV]). The clinical symptoms of patients coinfected with AdV were indistinct from those of patients mono-infected with hMPV. The symptoms of the one patient co-infected with RSV were clinically severe. Further research is needed to clarify the effect of hMPV on other respiratory viruses or vice versa.     

280例呼吸道感染儿童呼吸道病毒病原学检出情况及流行规律分析

目的:了解呼吸道感染儿童呼吸道病毒病原学检出情况及其流行规律,为儿童呼吸道感染的预防、诊断及治疗提供病原学依据。方法:选取2016年1月-2017年12月期间中国人民解放军中部战区总医院收治的280例呼吸道感染患儿为研究对象,分析患儿呼吸道分泌物中呼吸道病毒的检出情况,并分析呼吸道感染儿童呼吸道病毒感染与年龄、季节、疾病类型的关系。结果:280例呼吸道感染患儿中共检出98份阳性标本,阳性率为35.00%,其中有2份标本中检出2种病毒感染,混合感染阳性率为0.71%;在所有病毒类型中,呼吸道合胞病毒(RSV)病毒感染阳性率最高。1岁患儿的病毒感染阳性率最高,与其他年龄段病毒感染阳性率比较差异有统计学意义(P0.05)。呼吸道感染患儿春季、冬季的病毒感染阳性率明显高于夏季、秋季(P0.05)。不同呼吸道感染疾病类型患儿病毒感染阳性率比较差异有统计学意义(P0.05),以喘息性肺炎、毛细支气管炎、肺炎患儿病毒感染阳性率较高。结论:RSV是呼吸道感染儿童呼吸道病毒感染的主要致病病原体,1岁的婴幼儿较易感染,春季、冬季为其高发季节,且以肺炎、毛细支气管炎、喘息性肺炎患儿的病毒感染阳性率较高。     

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.     

Isolation and characterization of monoclonal antibodies which neutralize human metapneumovirus in vitro and in vivo

Human metapneumovirus (hMPV) is a recently described member of the Paramyxoviridae family/Pneumovirinae subfamily and shares many common features with respiratory syncytial virus (RSV), another member of the same subfamily. hMPV causes respiratory tract illnesses that, similar to human RSV, occur predominantly during the winter months and have symptoms that range from mild to severe cough, bronchiolitis, and pneumonia. Like RSV, the hMPV virus can be subdivided into two genetic subgroups, A and B. With RSV, a single monoclonal antibody directed at the fusion (F) protein can prevent severe lower respiratory tract RSV infection. Because of the high level of sequence conservation of the F protein across all the hMPV subgroups, this protein is likely to be the preferred antigenic target for the generation of cross-subgroup neutralizing antibodies. Here we describe the generation of a panel of neutralizing monoclonal antibodies that bind to the hMPV F protein. A subset of these antibodies has the ability to neutralize prototypic strains of both the A and B hMPV subgroups in vitro. Two of these antibodies exhibited high-affinity binding to the F protein and were shown to protect hamsters against infection with hMPV. The data suggest that a monoclonal antibody could be used prophylactically to prevent lower respiratory tract disease caused by hMPV.     

近年北京人偏肺病毒基质蛋白、小疏水蛋白和粘附糖蛋白的遗传变异特征分析

为了探讨北京地区儿童中流行的人偏肺病毒(Human metapneumovirus,hMPV)结构蛋白基因特征,本研究着重对hMPV北京地区地方株的基质蛋白(Matrix protein,M)、小疏水蛋白(Small hydrophobic protein,SH)和粘附蛋白(Attachment protein,G)基因进行了基因特征的分析。本研究对2006年至2010年42株hMPV的M蛋白、49株SH蛋白和55株G蛋白基因特征进行了分析,进化分析显示北京地区流行的hMPV的这3个编码蛋白基因分别属于A2、B1和B2基因亚型。地方株M基因高度保守,A和B基因型之间存在7个氨基酸位点的变异(型内高度保守)。不同基因型(A和B)和不同基因亚型(A2和B1、A2和B2)之间的SH基因的氨基酸同源性在60.7%～64.4%之间,而同一基因亚型内的氨基酸同源性则在93.3%～100%之间;同一基因型不同基因亚型之间(B1和B2)的氨基酸同源性在84.7%～88.7%之间。不同年份不同基因亚型G蛋白具有遗传多样性,使用不同的终止密码、核苷酸缺失和插入导致其核苷酸长度不同,变异程度相当高。不同基因型和不同基因亚型之间的G基因的氨基酸同源性在34.0%～38.6%之间,同一基因亚型内的氨基酸同源性在81.5%～100%之间;同一基因型不同基因亚型之间的氨基酸同源性在64.3%～69.2%之间。2008年至2010年的B2基因亚型的毒株大多数在多个位点出现了相同的氨基酸突变,同时出现了2个氨基酸的插入或重复插入,这些毒株在B2基因亚型内形成了一个新的进化簇。抗原位点预测分析显示不同基因亚型的SH和G蛋白的抗原位点均存在差异。     

Genetic variability and circulation pattern of human metapneumovirus isolated in Italy over five epidemic seasons

Human metapneumovirus (hMPV) is an important aetiological agent of respiratory tract infection (RTI) in infants. Based on genetic differences, hMPVs are separated into two main groups, A and B, and two subgroups 1 and 2. To better understand the genetic diversity of hMPV, we analyzed 435 bp fragments of the F gene from 49 isolates obtained from a paediatric clinical centre in Northern Italy from 2005 to 2009. The phylogenetic analysis showed that our hMPV sequences clustered into five main clades (A1, A2a, A2b, B1, B2) statistically supported. Most of the strains belong to A2 (49%) and to B1 (28.5%) lineages. The intermixing in the phylogenetic tree showed no seasonal distribution between samples collected over a 5 year period. Mean genetic distances showed that clade A2 was more heterogeneous than others. In our F glycoprotein dataset we observed only two positively selected sites with an w value of 1.408 and 1.429, respectively, and 27 negatively selected sites. The two positively selected sites could be considered evolutionary "hot spots" because they were under positive selection and/or relaxed selective constraints. The abundant negatively selected sites reflect a high degree of conservation of F protein, probably necessary for viral infection.     

实时荧光PCR技术诊断人偏肺病毒检测效果分析

目的：比较实时荧光PCR检测技术与直接免疫荧光检测技术及间接免疫荧光检测技术在呼吸道人偏肺病毒（hMPV）的检测效果,探讨实时荧光PCR检测技术的应用前景。方法：选取2010年4月至2013年1月因呼吸道感染在我院儿科门诊和住院部接受治疗的患儿鼻咽分泌物标本,共831份（男523例,女308例）。标本按年龄分0~6月龄（68例）、6月~1周岁（153例）、1~3周岁（281例）、3~6周岁（198例）、〉6周岁（131例）五组。采用实时荧光PCR检测技术与直接免疫荧光检测技术及间接免疫荧光检测技术进行检测与分析。结果：采用实时荧光PCR法共检测出221例hMPV阳性（26.6%）,直接免疫荧光法检出121例hMPV阳性（14.6%）,二者相比有统计学意义（X2=5.19,P〈0.05）;间接免疫荧光法检测出103例HMPV阳性（12.4%）与实时荧光PCR法相比有统计学差异（X2=7.17,P〈0.05）;1~3周岁组hMPV感染率与其它组相比差异有统计学意义（X2=12.89,P=0.01）。结论：实时免疫荧光技术hMPV的检测率明显高于直接免疫荧光法和间接免疫荧光法,对hMPV具有很高的临床诊断价值。