Phylogenetic analysis of human metapneumovirus from New York State patients during February through April 2010

Background

Human metapneumovirus (hMPV) is the second leading cause of lower respiratory infection (LRI) in children around the world and has been linked to LRI in multiple studies. Currently, hMPV is classified into 2 major subtypes (A and B), each with 2 subgroups (1 and 2).

Objective

To determine which hMPV genotypes were present in NYS patients with influenza-like illness (ILI) from February through April 2010, during a period of unusually heightened activity.

Study design

Specimens were collected from February through April of 2010 from patients presenting with ILI who were previously confirmed as positive for hMPV by real-time RT-PCR. A 700 base pair region of the hMPV fusion (F) gene was amplified, sequenced and resulting sequences aligned. A phylogenic tree was constructed based on prototype strains, and the partial F gene sequences obtained in this study.

Results

Bi-directional sequence was obtained from 30 patient samples and included in the phylogenic analysis. Specimen sequences grouped into hMPV genotype A2a (16), A2b (9), B2 (4) and B1 (1). No A1 genotypes were found.

Conclusion

Previously, reports have demonstrated that genotypes A1, A2, B1 and B2 circulate every season, usually with one dominant strain. In contrast, late in the 2009-2010 respiratory season, 4 of the 5 recognized genotypes of hMPV were isolated from NYS ILI patients, and by sequencing a larger portion of the fusion gene, we were able to identify the A2a and A2b genotypes.     

Genetic diversity of group a rotavirus isolates found in Western Siberia in 2007–2011

Genetic analysis of group A rotavirus isolates detected in the feces of children admitted to hospitals in Novosibirsk and Omsk within four epidemic seasons—2007, 2007–2008, 2009–2010, and 2010–2011—was carried out. 1416 Group A rotavirus isolates were genotyped by the multiplex PCR method. It is shown that, in 2007–2011 in Western Siberia, isolates of the widespread genotypes G1P[8], G4P[8], G2P[4], and G3P[8] cocirculated. In a few cases, genotypes G9P[8], G2P[8], G3P[9], and G4P[6] have been determined. In 2008 in Omsk and in 2009 in Novosibirsk, dominant genotype G1P[8] was replaced by genotype G4P[8]. The occurrence and spectrum of circulating genotypes differed and changed every epidemic season in both cities. Phylogenetic analysis of nucleotide sequences of three genome fragments that encode proteins VP4 (VP8*), VP7, and VP6 showed that most of the Novosibirsk and Omsk isolates clustered together and exhibited a high degree of homology with isolates identified in other regions of Eurasia. In addition, for the first time in Novosibirsk, 14 rotavirus isolates (genotypes G9, G1 and G4) related to the rare subline P[8]b (OP354-like) of the gene encoding the protein VP4 were detected, while in Omsk only the isolate Omsk08-381/G9P[8]b was found. The results obtained in this study indicate the need for long-term monitoring of rotavirus isolates circulating in Western Siberia, which is important when choosing a rotavirus vaccine to immunize young children and to improve the diagnostic kits for the infection, as well as to understand the epidemiology and evolution of group A rotaviruses.     

2007—2011年长沙地区急性下呼吸道感染住院儿童人偏肺病毒的流行状况

目的了解人偏肺病毒（hMPV）在长沙地区急性下呼吸道感染住院患儿中的流行病学特点。方法收集2007年9月至2011年2月因急性下呼吸道感染在湖南省人民医院儿科医学中心住院儿童的鼻咽抽吸物（nasopharyngealaspirates,NPA）样本2613份,采用逆转录聚合酶链反应法（RT—PCR）检测hMPVM基因,将阳性PCR扩增产物测序并与GenBank中已知的hMPV参考株进行比对、分析。结果2613份标本中hMPV阳性检出数135例,检出率为5．2％,男女之间的检出率比较有统计学差异（x2=8．007,P=0．003）,hMPV阳性检出患儿的年龄以1岁以内多见（63．2％）。hMPV阳性检出率在春季呈现高峰,从检出季节分布显示A2b型主要在冬春季节流行,而B2型主要在春夏季流行。135例hMPV长沙株分为A型和B型两个主要的基因型,其中A2b亚型在2007--2008年为优势流行型别,2009--2010年A2b和B2型共同流行,B2亚型在2011年呈优势流行型别。135例hMPV检出阳性患儿中有66例（48．9％）存在混合病毒感染,其中与HBoV混合检出率最高。结论长沙地区部分儿童的急性下呼吸道感染与hMPV有关,且阳性检出患儿年龄主要集中在1岁以下,男多于女,主要流行季节在春季,A2b型和B2型优势基因型在长沙地区共同流行,与其他病毒混合检出率较高。     

Prevalence of human rotavirus genotypes in Wuhan, China, during 2008-2011: changing trend of predominant genotypes and emergence of strains with the P[8]b subtype of the VP4 gene

Hospital-based surveillance of rotavirus genotypes was conducted in Wuhan, China, between March 2008 and May 2011. The detection rates of group A rotavirus were 24.6% (458/1859) and 12.1% (96/795) in children and adults, respectively, with diarrhea. Among the 554 positive specimens, the most frequent genotype was G3P[8] (57.9%), followed by G1P[8] (29.4%). Compared with previous studies in Wuhan (2000-2008), the relative frequency of G3P[8] has been decreasing year by year, while the predominant genotype G3 shifted to G1 in 2011. In the present study, a rare P[8]b subtype of the VP4 gene (OP354-like P[8]) was identified in nine strains. Full-length sequences of VP7, VP4, VP6 and NSP4 genes of two G9P[8]b strains (RVA/Human-wt/CHN/E1545/2009/G9P[8]b and RVA/Human-wt/CHN/Z1108/2008/G9P[8]b) were determined for phylogenetic analysis. The four genes of these strains were closely related to one another, and the G9-VP7 genes of these strains belonged to lineage III, which contains globally spreading G9 rotaviruses. The full-length sequence of VP4 gene segments of the P[8]b strains in Wuhan clustered with those of P[8]b strains in Vietnam, Russia and Belgium, while they were distinct from those of the OP354 strain from Malawi and Bangladeshi strains. The VP6 and NSP4 genes of two P[8]b strains belonged to the I1 and E1 genotype, respectively, and clustered with those of strains belonging to Wa-like human rotaviruses from various Asian countries. These findings indicate the changing epidemiologic trend of rotavirus genotypes in Wuhan, i.e., the shift of the predominant type from G3 to G1 and the emergence of P[8]b strains genetically related to those distributed in other Asian countries.     

人偏肺病毒感染住院儿童的临床特征及病毒基因特性分析

目的 了解急性呼吸道感染住院儿童中人偏肺病毒(hMPV)的感染情况、临床特征及人偏肺病毒基因特性.方法 对2006年2月至5月、2008年3月至4月及2008年9月至2009年2月收集的天津市儿童医院急性呼吸道感染住院儿童的310份鼻咽吸取物标本进行巢式PCR检测hMPV N基因片段,并对其中17株N基因片段进行序列测定,分析序列特征并绘制种系发生树.收集所有阳性患者的临床资料.同时采用多重PCR对N基因阳性标本进行其他常见呼吸道病毒的检测.结果 310份标本中共检出20份(6.5%)hMPV.hMPV阳性患儿的年龄中位数为15.0个月(16天～9岁),其中≤2岁患儿占90.0%(18/20).男性占60.0%(12/20).17株N基因种系发生树分析显示,11株为A2b亚型.20例hMPV阳性患儿的临床诊断均为支气管肺炎,占所有采集的肺炎患儿标本的7.1%(20/282),其临床症状以咳嗽、喘息、呼吸急促、发烧等常见.35%(7/20)需要重症监护,15%(3/20)需要吸氧治疗.平均住院时间为(11.9±4.8)d.A、B型间临床特征未见明显差别.hMPV无明显流行高峰.2例hMPV阳性患儿分别与腺病毒和鼻病毒混合感染.结论 hMPV可引起婴幼儿肺炎等严重疾病.天津地区流行的hMPV以A2b为优势流行型.     

南京地区儿童人偏肺病毒感染的流行病学及临床特征分析

目的了解南京地区儿童人偏肺病毒（hMPV）感染的流行病学特点及临床特征。方法收集2009年8月至2010年7月南京医科大学附属南京儿童医院住院及门诊呼吸道感染患儿的鼻咽抽吸物（NPA）及咽拭子（NPS）共642例,采用逆转录聚合酶链反应法（RT—PCR）检测hMPVM基因,将阳性PCR扩增产物进行测序、同源性和进化分析。结果642例标本中共检出hMPV阳性扩增产物35份,检出率为5．5％。系统进化分析显示南京地区hMPVB1型占51．4％,A2b型占31．4％。hMPV的发病高峰在4月份。其致呼吸道感染以1岁以内多见（71．4％）。35例hMPV感染患儿中有15例（42．8％）存在混合感染,其中与HRV的混合感染检出率最高。临床诊断以肺炎（17例,48．6％）最为常见。结论人偏肺病毒是南京地区儿童急性呼吸道感染的重要病原之一,该年度其优势流行型别为B1型,南京地区A、B两型hMPV感染患儿临床特征无明显差异。     

Influenza virus infections from 0 to 2 years of age: A birth cohort study

Background/purposeInfluenza vaccine has been recommended in Finland since 2007 for all children of 6–35 months of age and in 2009 for those ≥6 months against pandemic influenza. We investigated the incidence of influenza and vaccine effectiveness in a birth cohort of children in 2008–2011.MethodsWe followed 923 children from birth to 2 years of age for respiratory tract infections. A nasal swab sample for PCR for influenza A and B viruses was taken at the onset of acute respiratory infections. Samples were collected either at the study clinic or at home by parents. Vaccination data was retrieved from the health registries.ResultsVaccination coverage of children aged 6–23 months was 22–47% against seasonal influenza and 80% against the A(H1N1)pdm09 virus in the pandemic season 2009–2010. During 3 influenza seasons, 1607 nasal swab samples were collected. Influenza was confirmed in 56 (6.1%) of 923 children (16 A(H1N1), 14 A(H3N2), and 26 B viruses). The incidence of influenza was 5.1% in 2008–2009, 2.7% in 2009–2010, and 5.0% in 2010–2011. Effectiveness of the adjuvanted vaccine against the pandemic influenza A(H1N1)pdm09 was 97% (95% confidence interval, 76–100%). Three children with influenza were hospitalized.ConclusionThe yearly incidence of seasonal influenza was 5% in this cohort of very young children with variable influenza vaccine coverage. Adjuvanted vaccine against the pandemic influenza was highly effective. Both seasonal and pandemic influenza cases were mostly non-severe.     

Clinical impact of human metapneumovirus genotypes and genotype-specific seroprevalence in Yamagata, Japan

The clinical impact of human metapneumovirus (hMPV) genotypes and the relation between the hMPV genotype in circulation and genotype-specific seroprevalence are yet to be clarified. We determined the genotypes of 93 hMPV strains that were isolated between 2004 and 2006 in Yamagata, Japan, and identified 35 genotype A2, 14 genotype B1, and 44 genotype B2 isolates. Children infected with genotype A2 hMPV were significantly older than those infected with genotype B1 hMPV. Diagnosis of laryngitis was more common in children with genotype B1 hMPV infection and wheezing was more prevalent in children with genotype B1 and B2 hMPV infection than in those with genotype A2 hMPV infection. We then examined genotype-specific seroprevalence by neutralization assay. The higher seropositive rate for the B2 genotype among the children aged 1-2 years is likely to reflect the outbreak of B2 genotype strains in the previous year in this community. The low seropositive rate for the B1 genotype among children aged 1-2 years appears to be associated with a finding that more than 70% of children infected with the B1 genotype were less than 3 years old. In conclusion, we found that the different clinical characteristics of hMPV infection may be associated with hMPV genotype, and the predominant genotype during a season and the affecting age may be closely related to genotype-specific immune status within a community.     

Human metapneumovirus and human bocavirus associated with respiratory infection in Apulian population

We have studied the occurrence of hBoV, hMPV and InfA-B in an Apulian population with respiratory tract infections. During influenza season 2008-2009, 116 oropharingeal swabs were collected from patients affected by Influenza-Like Illness (ILI). The PCR products of hMPV M and HBoV NP-1 genes were sequenced. 78 out of 116 samples were positive for at least one respiratory virus; hBoV was detected in 53, hMPV in 22 and InfA-B in 41 out of 116 swabs. A high rate of hBoV infection in adult (18.9%) and elderly (26.4%) subjects was found. The co-infection rate was higher for hMPV (18/22 cases, 81.8%) compared to hBoV (26/53 cases, 49.1%), and InfA-B (25/41 cases, 61.0%). Co-infections were common in children. hBoV positive samples shared a high level of genetic similarity with the hBoV1 genotype, and hMPV positive samples clustered with A2 subgroup. Our results suggest that hBoV and hMPV play a role in ILI.     

Prevalence and genetic characterization of respiratory syncytial virus (RSV) in hospitalized children in Korea

Human respiratory syncytial virus (HRSV) is the most common respiratory pathogen among infants and young children. To investigate the prevalence and genetic characteristics of HRSVs circulating in South Korea, we analyzed medical records of patients and performed molecular analysis of the G-protein gene of viruses detected from nasopharyngeal aspirates (NPA) of admitted patients at the Pediatrics Department of Chungbuk National University Hospital from April 2008 to April 2010. Epidemiological data revealed that the prevalence of HRSV infection was high during both winter seasons (October 2008 to February 2009 and November 2009 to February 2010). Of the 297 positive NPA specimens from infants or children tested, 67% were identified as HRSV-A while 33% were HRSV-B. The HRSV subgroup B was the most dominant in December 2008, but its dominance was dramatically replaced by HRSV subgroup A strains by February 2009. Phylogenetic analysis of the G protein sequences of HRSVs revealed novel genotypes within the HRSV-A (genotype CB-A) and B (genotypes BA11 and CB-B) subgroups in South Korea in addition to other strains identified in other countries. Molecular analysis also revealed genetic variability at the C-terminal end of the G proteins of the two HRSV subgroups, suggesting selection pressure in this region, which may potentially impact immune recognition. This is the first report of these HRSV variants in South Korea, indicating active genetic evolution of HRSV strains. Therefore, this study provides information on the molecular epidemiology of current HRSVs in the country and presents data for comparative analysis with other HRSV strains circulating worldwide.     

Molecular epidemiology of human respiratory syncytial virus subgroups A and B identified in adults with hematological malignancy attending an Irish hospital between 2004 and 2009

Human respiratory syncytial virus (HRSV) is an important cause of respiratory infection in patients with hematological malignancy, particularly hematopoietic stem cell transplant recipients. This study investigated the genetic variability of the attachment (G) protein gene among HRSV isolates collected from adult patients with hematological malignancy. Between December 2004 and March 2009, 60 samples collected from 58 adults attending an Irish hospital were positive for HRSV by direct immunofluorescence. Nucleotide sequence analysis of the G gene showed a slightly higher frequency of HRSV subgroup A (52%) than HRSV subgroup B (48%). Genetic variability was higher among subgroup A viruses (up to 13% at nucleotide level) than among subgroup B viruses (up to 4%). Phylogenetic analysis revealed two genotypes of HRSV subgroup A, GA2 and GA5, which cocirculated between 2004/2005 and 2007/2008, although GA2 alone was identified in season 2008/2009. Genotype BA was the only genotype of HRSV subgroup B identified. Genotype-specific amino acid substitutions were identified, with two and seven changes for GA2 and GA5, respectively. Furthermore, one to four potential N-glycosylation sites were found among HRSV subgroup A isolates while two to three were identified in HRSV B isolates. Predicted O-glycosylation sites included 25-34 and 40-43 in HRSV subgroups A and B, respectively. The average synonymous mutation-to-non-synonymous mutation ratios (dS/dN) implied neutral selection pressure on both HRSV subgroup isolates. This study provides data for the first time on the molecular epidemiology of HRSV isolates over five successive epidemic seasons among patients attending an Irish hospital.     

Genetic variation in the VP7 gene of rotavirus G1P[8] strains isolated in Vietnam, 1998-2009

Group A rotavirus genotype G1P[8] is the most common strain affecting humans around the world over the past few decades. In this study, we examined genetic variation in the VP7 gene of rotavirus G1P[8] strains, detected in children of four major cities of Vietnam during three different rotavirus seasons: 1998-1999, 2007-2008 and 2008-2009 in order to assess the evolution of the virus over 11 years. Fecal samples (n=73) from children hospitalized for gastroenteritis caused by G1P[8] rotavirus were analyzed by DNA sequencing of gene 9 encoding the VP7 capsid protein. Phylogenetic analyses indicated that VP7 gene of the G1 strains from 1999 contained a lineage I, while rotaviruses from 2009 clustered in lineage II. Both of these lineages were found co-circulating in 2007-2008 season. While different sublineages of lineage I and II co-circulated in the 1998-1999 and 2007-2008 seasons, almost all strains in 2009 belonged to sub-lineage II-C. In the analysis using selected 10 strains, the VP4 genes of these 2 VP7-G1 lineages were all grouped in F45-like cluster. Deduced amino acid analyses indicated that there were thirteen amino acid substitutions between strains of two lineages. Of those, two were found in antigenic regions A and C, implying possible antigenic differences between these two lineages. The G1P[8] strains in Vietnam are very genetically diverse and dynamic, implying the frequent monitoring on evolution of rotavirus will be important to assess efficacy of rotavirus vaccine in Vietnam.     

Genotype variability of human metapneumovirus, South Korea

Human metapneumovirus (hMPV), a virus causing lower respiratory tract infections in children, is classified two major groups or genotypes of hMPV and recently existence of multiple lineages has been suggested. The purpose of this study was to examine the extent of genetic variation and circulation pattern of hMPV in Korea. Between January 2005 and April 2007, nasopharyngeal aspirates were collected from 1,214 children <16 years of age hospitalized with acute respiratory tract infection at Sanggyepaik Hospital. Nasopharyngeal aspirates were tested for common respiratory pathogens using immunofluorescence or multiplex RT-PCR. RT-PCR was used to detect hMPV. The PCR products were purified and subsequently sequenced directly on both strands. hMPV was detected in 8.4% (102/1,214) of nasopharyngeal aspirates from children with acute respiratory tract infection. The 102 hMPV strains detected in this study were classified into two distinct F lineages, 87 strains belonged to genogroup A2 (A2a in 42, A2b in 45) and 15 strains to genogroup B. All hMPV subtypes except A1 co-circulated in Korean population. Although alternating predominance of hMPV subtypes from year to year could not be found, the changing predominance of sublineage A2a and A2b was demonstrated.     

Monitoring progress toward measles elimination by genetic diversity analysis of measles viruses in China 2009–2010

With the achievement of high coverage for routine immunization and supplementary immunization activities (SIAs), measles incidence in mainland China reached its lowest level in 2010. The proportion of measles cases in the vaccination-targeted population decreased during 2007–2010 after the SIAs. More than 60% of measles cases were in adults or infants, especially in the coastal and eastern provinces during 2009 and 2010. A total 567 isolates of measles virus were obtained from clinical specimens from 27 of 31 provinces in mainland China during 2009 and 2010. Except for two vaccine-associated cases, one genotype D4 strain, two genotype D9 strains, and four genotype D11 strains, the other 558 strains were genotype H1 cluster H1a. Genotype H1 has been the only endemic genotype detected in China since surveillance began in 1993. Only genotype H1 was found in mainland China during 1993–2008, except for one detection of genotype H2. More recently, multiple genotypes of imported measles were detected even with the background of endemic genetotype H1 viruses. Analysis of the 450-nucleotide sequencing window of the measles virus N gene showed that the overall genetic diversity of the recent geneotype H1 strains decreased between 2008 and 2010. The lower genetic diversity of H1 strains suggested that enhanced vaccination may have reduced the co-circulating lineages of endemic genotype H1 strains in mainland China.