Human infection with avian influenza A（H7N9） virus in Shanghai： current status and future trends

Avian influenza A（H7N9） virus is one subgroup among the larger group of H7 viruses,which normally circulate among birds.The H7N9 subtype of avian influenza viruses has not been known to infect humans until only recently.On March 31,2013,China confirmed the first three human cases of novel avian influenza A（H7N9）infection in Shanghai and Anhui,two of these patients died.1 As of February 27,2014,367 laboratory-confirmed human cases have been reported from 15 provinces/municipalities in mainland China,     

A Novel Reassortant H2N3 Influenza Virus Lsolated from China

Objective To analyze the genetic composition of a novel H2N3 virus isolate identified from a duck cage swab in a live poultry market （LPM） in 2009 in Guangdong province of China. Methods PCR-positive specimens were inoculated into embryonated chicken eggs and subtyped by conventional RT-PCR. All segments of the virus A/environment/Guangdong/2/2009 were sequenced, and phylogenetic trees were constructed and analyzed. Results The genes of this virus belong to Eurasian-lineage avian viruses. The virus is a reassortant with the HA gene from an H2N2 virus and the NA gene from an H5N3 virus. The PB1, PB2, and NP genes were from an H4N6 virus, the PA was from an H3N8 virus, the M gene was from an H1N3 virus, and the NS gene was from an H10N6 virus. Conclusion market. Its A novel avian-origin reassortant H2N3 influenza virus was detected in a live poultry potential impacts and evolution should be closely monitored.     

568份疑似甲型H1N1流感病例标本病原学检测结果分析

目的对河池市568份疑似甲型H1N1流感病例标本进行核酸检测,为甲型H1N1流感疫情的防控提供依据。方法对疑似甲型H1N1流感病例标本用实时荧光定量RT-PCR法（Real-time RT-PCR）检测,检测项目为A型流感病毒核酸、B型流感病毒核酸和甲型H1N1流感病毒核酸,对A型流感病毒核酸阳性而B型流感病毒核酸和甲型H1N1流感病毒核酸均阴性标本再进行季节性流感病毒H1N1、H3N2亚型流感病毒核酸检测。结果检测疑似病例标本568份,其中甲型H1N1流感病毒核酸阳性334份,季节性流感病毒H1N1亚型核酸阳性14份,季节性流感病毒H3N2亚型核酸阳性25份,A未分型流感病毒核酸阳性40份。结论实验室检测为甲型H1N1流感疫情的确认、防控以及病人的处理提供了依据,对提高实验室检测技术的敏感性、特异性和实效性具有重要的意义。     

广州地区新型甲型H1N1流感患者病毒RNA检出率与病程关系的研究

目的 探讨2009年新型甲型H1N1流感患者病毒RNA检出率与人群年龄分布和病程变化的关系.方法 选取广州地区新型甲型H1N1临床病例共248例,对151例进行病程动态咽拭子采样833份,统计分析患病人群年龄分布和采用荧光定量RT-PCR方法对不同病程的患者咽拭子标本进行甲型HINl流感病毒RNA的检测,并采用趋势x~2检验探讨标本阳性率与不同发病时间的关系.结果 发病人群以青壮年为主,主要集中在10～20岁(57.26%)和20～30岁(22.18%)两个年龄段.对咽拭子标本阳性率随发病时间的变化进行趋势x~2结果显示标本阳性率随着病程的延长而下降(x~2=9.784,P=0.002).讨论此次研究表明新型H1N1流感患者主要集中在青壮年人群中,且有最长可达10天以上的病程,标本阳性率随着病程的延长而下降.

Abstract：

Objective To study the relation of the detection rates of the novel influenza virus A/H1N1 RNA in clinically confirmed patients in the 2009 pandemic with the age distribution of the patients and the disease course. Methods A total of 151 clinical patients with H1N1 infection were enrolled in this study, from whom 833 dynamic throat swab samples were obtained for detecting the H1N1 RNA using real-time PCR. A statistical analysis of the age distribution was performed among the patients with different disease courses. Chi-square for trend test was used to study the correlation between the detection rates of H1N1 RNA and the time of disease onset. Results The majority of patients were young with their ages ranging from 10 to 20 years (57.26%) and 20 to 30 years (22.18%). Chi-square for trend test revealed that the positivity rates of the throat swabs in the patients decreased with the prolongation of the disease course (x~2=9.784, P=0.002). Conclusion Most of the H1N1 patients are young within the age range of 10-30 years, and the longest disease course can exceed 10 days. The positivity rates of throat swabs from the H1N1 patients decreases with the prolongation of the disease course.     

Effect of human rhinovirus infection in pediatric patients with influenza-like illness on the 2009 pandemic influenza A（H1N1） virus

Background Some research groups have hypothesized that human rhinoviruses （HRVs） delayed the circulation of the 2009 pandemic influenza A（H1N1） virus （A（H1N1）pdm09） at the beginning of Autumn 2009 in France.This study aimed to evaluate the relationship between HRV and A（H1N1）pdm09 in pediatric patients with influenza-like illness in Beijing,China.Methods A systematic analysis to detect A（H1N1）pdm09 and seasonal influenza A virus （FLU A） was performed on 4 349 clinical samples from pediatric patients with influenza-like illness during the period June 1,2009 to February 28,2010,while a one-step real-time RT-PCR （rRT-PCR） assay was used to detect HRV in 1 146 clinical specimens selected from those 4 349 specimens.Results During the survey period,only one wave of A（H1N1）pdm09 was observed.The percentage of positive cases for A（H1N1）pdm09 increased sharply in September with a peak in November 2009 and then declined in February 2010.Data on the monthly distribution of HRVs indicated that more HRV-positive samples were detected in September （2.2％） and October （3.3％）,revealing that the peak of HRV infection in 2009 was similar to that of other years.Among the 1 146 specimens examined for HRVs,21 （1.8％） were HRV-positive,which was significantly lower than that reported previously in Beijing （15.4％ to 19.2％） （P ＜0.01）.Overall,6 samples were positive for both A（H1N1）pdm09 and HRV,which represented a positive relative frequency of 1.60％ and 2.08％ HRV,considering the A（H1N1）pdm09-positive and-negative specimens,respectively.The odds ratio was 0.87 （95％ CI 0.32; 2.44,P=0.80）.Conclusions HRVs and A （H1N1）pdm09 co-circulated in this Chinese population during September and October 2009,and the HRV epidemic in 2009 did not affect A（H1N1）pdm09 infection rates in Beijing,China as suggested by other studies.However,the presence of A（H1N1）pdm09 might explain the unexpected reduction in the percentage of HRV positive cases during the period studied.     

H5N1 Avian Influenza Pre-pandemic Vaccine Strains in China

Objective To prepare the 4 candidate vaccine strains of H5N1 avian influenza virus isolated in China Methods Recombinant viruses were rescued using reverse genetics. Neuraminidase （NA） and hemagglutinin （HA） segments of the A/Xinjiang/1/2006, A/Guangxi/1/2009, A/Hubei/1/2010, and A/Guangdong/1/2011 viruses were amplified by RT-PCR. Multibasic amino acid cleavage site of HA was removed and ligated into the pCIpoll vector for virus rescue. The recombinant viruses were evaluated by trypsin dependent assays. Their embnjonate survival and antigenicity were compared with those of the respective wild-type viruses. Results The 4 recombinant viruses showed similar antigenicity compared with wild-type viruses, chicken embryo survival and trypsin-dependent characteristics. Conclusion The 4 recombinant viruses rescued using reverse genetics meet the criteria for classification of low pathogenic avian influenza strains, thus supporting the use of them for the development of seeds and production of pre-pandemic vaccines.     

Emergence of truncated PB1-F2 protein of H3N2 influenza virus during its epidemic period in Jiangsu Province, China

Background PB1-F2 protein has been proven to increase the pathogenicity of influenza A virus （IAV） strains in primary infection and in secondary bacterial infection. It can also regulate the activity of viral polymerase. However, it was shown in another retrospective study that a portion of IAVs do not express full-length PB1-F2 protein during virus development; different kinds of stop codons cause exits in the open reading frames and form PB1-F2 gene products with the corresponding genotypes. Truncated PB1-F2 in human H3N2 IAVs has long been detected in North America but its evolution in China is still unclear. Methods Influenza-like illnesses （ILls） from the whole of Jiangsu Province were collected and inspected to determine the type and subtype of the viruses. A portion of isolates collected in the epidemic period were selected as samples for later whole-genome sequencing, and the exact sequences were determined and analyzed. Results H3N2 influenza virus was one of the epidemical strains which had been prevalent during 2009-2010, in Jiangsu. Five H3N2 isolates with truncated PB1-F2 protein （25aa） were detected in influenza samples from Nanjing and Xuzhou, while seven similar H3N2 isolates were also reported in Niigata, Japan. Conclusion This emergence indicates the possibility that there has been transmission of the H3N2 virus between the two countries.     

Phylogenetic and Molecular Analysis of an H7N7 Avian Influenza Virus Isolated in East Dongting Lake in 2012

Objective In March 2012, an H7N7 subtype avian influenza virus (AIV) named A/wild goose/Dongting/PC0360/2012 (H7N7) (DT/PC0360) was recovered from a wild goose in East Dongting Lake. We performed whole-genome sequencing of the isolate, and analyzed the phylogenetic and molecular characterization.
Methods RNA was extracted from environment samples (including fecal samples from wild bird or domestic ducks, and water samples) for detecting the presence of Influenza A Virus targeting Matrix gene, using realtime RT-PCR assay. The positive samples were performed virus isolation with embryonated eggs. The subtype of the isolates were identified by RT-PCR assay with the H1-H16 and N1-N9 primer set. The whole-genome sequencing of isolates were performed. Phylogenetic and molecular characterizations of the eight genes of the isolates were analyzed.
Results Our results suggested that all the eight gene segments of DT/PC0360 belonged to the Eurasian gene pool, and the HA gene were belonged to distinct sublineage with H7N9 AIV which caused outbreaks in Mainland China in 2013. The hemagglutinin cleavage site of HA of DT/PC0360 showed characterization of low pathogenic avian influenza virus.
Conclusion Strengthening the surveillance of AIVs of wild waterfowl and poultry in this region is vital for our knowledge of the ecology and mechanism of transmission to prevent an influenza pandemic.     

甲型H1N1流感病毒神经氨酸酶基因遗传进化分析

【目的】 了解季节性H1N1流感病毒与2009年新型H1N1流感病毒神经氨酸酶(NA)基因的遗传进化关系,探讨甲型H1N1流感病毒的遗传变异规律｡【方法】 分别从2006年和2009年流感病人标本中分离并鉴定出季节性HIN1流感病毒和新型H1N1流感病毒,用RT-PCR技术扩增了病毒NA基因全序列,并对其分子进化和重要功能位点的遗传变异进行了分析｡ 【结果】 2009年新型H1N1流感病毒与2006年季节性HIN1流感病毒比较,NA基因的同源性较低(77.9% ~ 78.8 %),与世界各地不同年代代表株及WHO推荐的1979 ~ 2010年季节性流感疫苗株比较,NA基因的同源性也较低(78.1% ~ 79.3%),但与WHO推荐的2009年新型H1N1流感疫苗株比较同源性则高达99%以上;系统进化分析结果表明,2009年新型H1N1流感病毒NA基因与欧亚猪流感病毒株A/swine/Belgium/1/1983的亲缘关系最近;并发现自2005年以来季节性H1N1流感病毒NA基因的某些抗原位点和神经氨酸酶活性位点已发生了变异｡【结论】 2009年新型H1N1流感病毒NA基因可能来源于欧亚猪流感病毒;接种季节性流感疫苗不能对本次流行的新型流感产生有效的免疫保护作用;季节性H1N1流感病毒在流行过程中NA基因已发生了一定的变异,有必要持续跟踪和监测病毒的变异情况｡     

2009年新型甲型H1N1流感病毒神经氨酸酶基因进化分析

目的:探讨2009年新型甲型H1N1流感病毒神经氨酸酶(NA)基因的进化及NA基因编码蛋白抗原性、酶活性位点、糖基化位点变异情况。方法:从NCBI基因库检索获得43株不同年代不同地域甲型流感病毒NA基因序列,用Molecular Evolutionary Genetics Analysis version 4.0（MEGA 4.0）软件进行基因进化分析和氨基酸序列分析。结果:2009年新型甲型H1N1流感病毒与禽H5N1流感病毒NA基因的同源性达到85％,潜在抗原位点氨基酸分布相同;所有毒株的酶活性中心位点高度保守,但糖基化位点有变异。结论:2009年新型甲型H1N1流感病毒的NA基因可能来源于禽H5N1流感病毒;神经氨酸酶抑制剂治疗有效。     

2009年新型甲型H1N1流感病毒血凝素基因进化分析

目的:探讨2009年新型甲（A）型H1N1流感病毒血凝素（HA）基因与世界各地不同年代分离的A/H1N1代表株HA基因的进化关系。方法:从NCBI数据库下载2009年新型A/H1N1亚型流感病毒的HA基因序列以及以往流行的人、猪和禽的A/H1N1亚型流感病毒参考序列,采用Molecular Evolutionary Genetics Analysis version 4.0（MEGA4.0）软件进行序列比对和构建系统进化树,并分别比较2009年新型甲型H1N1流感病毒HA基因与北美地区、欧洲地区、亚洲地区A/H1N1流感病毒HA基因编码蛋白的氨基酸序列。结果:不同时期人A/H1N1亚型流感病毒代表株HA基因进化分析显示：2009年新型A/H1N1流感病毒HA基因与1976~2007年北美地区分离的7株人A/H1N1亚型流感病毒具有较高的同源性,与欧洲和亚洲地区的同源性较低。不同种属间A/H1N1亚型流感病毒HA基因进化分析显示：2009年新型A/H1N1流感病毒HA基因与1998和2007年北美地区分离的A/H1N1猪流感病毒的HA基因进化关系较近,与欧洲及亚洲地区分离的A/H1N1猪流感病毒及A/H1N1禽流感病毒进化关系较远。氨基酸比对结果显示2009年新型A/H1N1流感病毒HA基因的重要抗原位点与北美地区分离的A/H1N1猪流感病毒相近,与欧洲和亚洲地区分离的A/H1N1猪流感病毒及人类流感病毒疫苗株相比变化较大。结论:2009年新型甲型H1N1流感病毒HA基因可能是北美地区甲型H1N1猪流感病毒长期进化并与该地区人A/H1N1流感病毒部分基因片段重排的结果,对人H1N1甲型流感病毒疫苗可能并不敏感。     

2009年新型甲型H1N1流感病毒全基因组序列重组分析

目的:分析2009年流行的新型甲型流感病毒（A/H1N1）全序列的基因重组现象。方法:从NCBI基因数据库下载2009年新型甲型流感病毒（A/H1N1）全基因组序列,采用Molecular Evolutionary Genetics Analysis version 4.0（MEGA 4.0）软件对8条基因序列进行拼接和比对,分析2009年爆发株与历史流行株序列间的同源性;同时采用Simplot 3.5.1软件分析新型流感病毒A/H1N1基因重组现象。结果:2009年3月以来爆发的新型A/H1N1病毒株聚合酶B1(polymerase B1,PB1)基因来自于人H3N2,其同源性为93.7%;聚合酶B2 (polymerase B2,PB2)和聚合酶A (polymerase A,PA)与禽H5N1同源性较高,同源性分别为89.0%、89.9%;血凝素(hemagglutinin,HA)、核蛋白(nucleoprotein,NP)和非结构蛋白(non-structural protein,NS)与北美地区猪H1N1同源性较高,同源性分别为91.7%、93.1%和93.1%;神经氨酸酶(neuraminidase,NA)和基质蛋白(matrix protein,MP)与欧洲地区猪H1N1同源性较高,同源性分别为90.5%、95.5%。全基因序列同源性分析发现2009年新型A/H1N1病毒与北美地区猪H1N1病毒同源性最高,为83.9%。结论:2009年新型甲型H1N1流感病毒可能是人H3N2、北美地区猪H1N1、欧洲地区猪H1N1、禽H5N1的基因重排病毒。     

检测甲型H1N1流感病毒富集方法的初步探索

目的探索甲型H1N1流感病毒的富集方法,提高流感病毒核酸检测的灵敏度。方法分别用ProteinA/G及H1N1特异性血清处理流感病毒样品,根据国家流感中心设计的H1N1亚型检测通用引物,采用反转录-聚合酶链反应（RT-PCR）方法,扩增产物为527bp,来评价病毒的富集效果。结果两种富集方法均能提高检测灵敏度,用ProteinA/G富集处理后检测灵敏度可达10-6,用H1N1特异性血清沉淀富集处理后灵敏度为10-5。结论初步建立的富集甲型H1N1流感病毒方法,有效提高了流感病毒RT-PCR检测的灵敏度,可用于甲型H1N1流感病毒的检测。     

2009年新型甲型H1N1流感病毒聚合酶编码基因进化分析

目的:探讨2009年新型甲型流感病毒(A/H1N1)聚合酶PA、PB1和PB2编码基因的进化规律。方法:从NCBI流感病毒基因数据库下载2009年新型甲型H1N1流行株的PA、PB1和PB2聚合酶编码基因序列以及人、猪和禽流感病毒相应的参考序列,采用Molecular Evolutionary Genetics Analysis version 4.0（MEGA4.0）软件比对和修剪此次流行株的代表序列及所有参考株序列并构建系统树,再比对和修剪此次流行株的代表序列及人A/H1N1病毒各年代(1918~2008年)参考序列并构建系统树,同时比对此次流行株的代表序列及人A/H1N1各年代(1918~2008年)参考序列编码PB2蛋白的氨基酸序列。结果:不同地区分离的2009年新型甲型H1N1流感病毒的聚合酶PA、PB1和PB2编码基因均具有高度同源性,并聚集在一个独特的进化支上,与猪流感病毒对应基因接近。三者均与2005年美国爱荷华州分离的人A/H1N1病毒基因(A/Iowa/CEID23/2005/H1N1)具有高度的相似性。2009年新型甲型H1N1流感病毒、2005年美国爱荷华州流行的H1N1 (DQ889682)病毒PB2蛋白第627位氨基酸与禽类流感病毒相同,均为谷氨酸,而与其他人A/H1N1 (1918~2008年)病毒的赖氨酸不同。结论:2009年新型甲型H1N1流感病毒聚合酶基因可能来源于2005年美国爱荷华州分离的人A/H1N1病毒,禽流感病毒可能参与了聚合酶基因的重排过程。     

2009年新型甲型H1N1流感病毒基质蛋白及核蛋白基因进化分析

目的:探讨2009年新型甲型流感病毒(A/H1N1)基质蛋白(M)及核蛋白(NP)基因的进化规律。方法:从NCBI数据库下载147条甲型H1N1流感病毒M基因及NP基因序列,采用Molecular Evolutionary Genetics Analysis version 4.0(MEGA4.0)软件对M基因和NP基因序列进行比对,并用NJ法构建进化树,同时采用Epi Info软件分析1918~2009年人H1N1病毒的M基因和NP基因序列进化距离的线性趋势。采用MEGA4.0软件对M2蛋白氨基酸序列进行比对。结果:不同地区的2009年新型甲型H1N1流感病毒M基因、NP基因同源性高,但与历史上流行的H1N1流感病毒M基因、NP基因差异较大,且M基因进化距离随分离年限变化的趋势性检验结果有统计学意义(Ptrend=0.001)。2009年新型甲型A/H1N1流感病毒M2蛋白与1918~2008年人A/H1N1病毒M2蛋白氨基酸序列进行比对,结果显示在第11、43、54、57、77、78氨基酸位点发生了改变;与猪、禽A/H1N1的M2蛋白氨基酸序列进行比对,结果显示仅在第43、77位氨基酸位点发生改变。结论:2009年新型甲型A/H1N1流感病毒NP基因片段较以往流行的人H1N1流感病毒NP基因发生了改变;M2蛋白位于胞外编码区的第11位氨基酸、位于TM结构域的第43位氨基酸突变可能导致了新型甲型A/H1N1流感病毒对金刚烷胺类特异性抗病毒药物产生耐药。     

2009年新型甲型H1N1流感病毒非结构蛋白基因进化分析

目的:探讨2009年新型甲型H1N1流感病毒的非结构蛋白(NS)基因进化规律。方法:从NCBI下载2009年新型甲型H1N1流感病毒以及北美、欧洲、亚洲地区以往流行的甲型H1N1流感病毒NS基因序列,利用Molecular Evolutionary Genetics Analysis version 4.0(MEGA 4.0)软件对所选序列进行基因进化分析,并用NJ法构建进化树;对2009年新型甲型H1N1流感病毒NS基因核苷酸序列同源性及编码蛋白氨基酸序列进行分析。结果:2009年新型甲型H1N1流感病毒NS基因来源于猪A/H1N1流感病毒,与2005~2007年猪A/H1N1流感病毒具有较高的同源性(97.5％~97.6％),与1930~2007年猪A/H1N1流感病毒具有明显的时间进化关系;其重要抗原及拮抗宿主抗病毒能力的氨基酸位点基本没有变异。结论:2009年新型甲型H1N1流感病毒NS基因来源于猪A/H1N1流感病毒,NS基因编码蛋白拮抗宿主抗病毒能力并没有改变。     

双重荧光定量RT-PCR快速检测流感病毒H1、H3亚型的研究

目的 利用荧光定量RT-PCR技术建立一种快速检测流感病毒H1、H3亚型的方法.方法 根据H1、H3亚型流感病毒HA基因的相对保守序列,设计两对引物及其相应的Taqman探针,利用一步法RT-PCR试剂盒建立优化反应体系后,将荧光定量RT-PCR的产物采用10倍稀释法,即107～100 copies/μl,再次用荧光定量PCR方法检验建立体系的灵敏度和重复性,并建立相对定量标准曲线;利用多种流感病毒和具有相似临床症状的呼吸道病毒检验建立体系的特异性.结果 H1和H3亚型流感病毒的检测灵敏度为102 copies/μl,扩增效率分别为101.35％和113.28％,标准曲线相关系数大于99％,重复性良好,特异度实验未发现有非特异性扩增.结论 本研究建立的双重荧光定量RT-PCR技术可以快速、准确地检测H1、H3亚型流感病毒.