长白县黑线姬鼠携带汉坦病毒的S基因特征研究

为了解长白县黑线姬鼠中汉坦病毒流行情况及病毒型别,采用巢式RT-PCR方法筛查鼠肺RNA,并对PCR阳性样本进行全S基因的扩增、克隆及测序;构建系统发生树并进行分子进化分析。结果显示:共捕获黑线姬鼠58只,共检测出4份阳性标本,阳性率6.90%。经过序列测定及进化分析显示黑线姬鼠所携带的病毒与汉滩病毒第6基因亚型标准株核苷酸的同源性为95.8%～96.3%,氨基酸同源性为98.6%～99.5%。同时发现,长白县黑线姬鼠携带的汉滩病毒的NP蛋白共有1个特异性氨基酸位点为S387。     

2004年冬至2005年春引起北京地区儿童肺炎的腺病毒基因特点分析

为了解北京地区腺病毒的流行毒株,从北京儿童医院收集25份儿童肺炎患者的痰洗液标本(2004年冬到2005年春),患者的年龄在2个月到2岁,临床表现以持续高热、咳喘和气促为主。对25份标本分别用Hep-2细胞进行了病毒分离培养、腺病毒属特异性引物PCR扩增以及PCR产物的序列测定分析。结果发现25份标本中有9份PCR扩增阳性,其中2份病毒培养物观察到典型的细胞病变;将9份PCR阳性产物纯化后进行序列测定,结果7份标本核苷酸序列完全一致,同源性100%,并与GenBank发表的序列相比较,发现与腺病毒7型最为接近,同源性皆为99.7%;2份与腺病毒3型最接近,同源性为99.6%。结果表明,此次病毒分离株为腺病毒B亚群。北京儿童医院2004年12月至2005年3月腺病毒引起的肺炎主要以7型和3型为主,7型占优势,与国内其它地区的情况相似。     

2012年大连市流行性角结膜炎疫情的病原鉴定与基因特征分析

目的 鉴定一起大连市流行性角结膜炎疫情的病原体及型别.方法 采用荧光PCR方法针对30份眼拭标本进行检测,确定病原,并针对特定片段扩增产物测序进行分子定型.结果 21份标本荧光PCR检测结果为腺病毒阳性,核苷酸序列与人腺病毒15、29、56及其重组型高度同源,多重序列比对后构建的系统进化树上与人腺病毒56及其重组型位于同一分支.结论 本次疫情的致病病原为D亚属人腺病毒,疑为人腺病毒56型或其重组型.后续需要开展对五邻体(Penton)及纤突(Fi-ber)基因的全核苷酸序列测定及生物信息学分析最终确定型别.     

安阳地区2013年手足口病柯萨奇病毒A6 VP1基因特征研究

为了解2013年安阳地区手足口病病原谱组成特点及柯萨奇病毒A6(CV-A6)VP1基因特征,采用实时荧光逆转录PCR方法对全年采集的临床手足口病例的479份粪便标本进行检测和分型,统计各型肠道病毒阳性标本数量及比例。对10份CV-A6阳性标本VP1基因进行扩增测序以获得全序列。使用BIOEDIT 7.2和MEGA 5.1软件对获得序列和NCBI数据库中检索到的参考序列进行VP1基因核苷酸、氨基酸相似性及系统发育分析。研究结果显示,检出肠道病毒阳性标本共429份,其中CV-A6阳性标本为90份,占全部阳性标本的比例为20.98%,这是安阳地区首次记录非CV-A16和EV-A71型肠道病毒列居手足口病病原谱第二位,成为手足口病主要病原之一。将成功获得的10条VP1序列与CV-A6原型株Gdula比较,发现安阳序列与Gdula VP1基因的核苷酸、氨基酸序列差异皆较大。与河南历史株HN421(2011)比较,发现有4条本地序列与HN421的核苷酸、氨基酸序列差异较大,其余6条与HN421差异较小。系统发育树显示,全部49条CV-A6序列共形成A、B、C、D四个分支。其中D分支可进一步分为D1和D2两个亚分支。安阳地区获得的10条CV-A6序列中,有6条属于D1亚分支,4条属于D2亚分支。     

甘肃省瓜州县一起由埃可病毒30引致的无菌性脑炎疫情病原学分析

对2015年6~8月发生在中国甘肃省瓜州县一起病毒性脑炎疫情进行病原学诊断及其分子特征研究。采集74例病例样本132份(脑脊液14份,咽拭子25份,血清66份以及粪便27份)。对血清与脑脊液标本经ELISA IgM检测初步排除乙脑病毒、单纯疱疹病毒、流行性腮腺炎病毒和腺病毒感染之后,采用实时荧光PCR法对所有标本进行人类肠道病毒核酸检测,阳性者使用HEp-2和RD细胞进行病毒分离,并对分离株进行全长VP1区核苷酸序列测定及其分子特征分析。结果发现:132份标本中人类肠道病毒核酸检测阳性72份,71份分子定型结果为埃克病毒30(E-30);从29例病例的46份样本分离到E-30;甘肃瓜州E-30的全长VP1区核苷酸序列的同源性高达99.2%~100.0%,进化树图显示其与中国2011年以后的E-30分离株属同一个分支。E-30是引起本次甘肃省瓜州县局部地区病毒性脑炎暴发的病原,且属于中国正在流行的ECHO30进化分支中近期流行簇。     

抗—HCV阴性献血员中丙型肝炎病毒RNA检测及序列分析

对95份抗—HCVIgG阴性献血员采用逆转录聚合酶链反应法（PCR）检测丙型肝炎病毒RNA,结果8次中有6次其检测出17份阳性标本（17／95,17．9％）,复查抗—HCVIgG仍为阴性。对其中8份阳性产物中高变区1的序列分析结果表明均为不同株HCV序列．排除了PCR污染的可能性。对其中2份阳性产物测定了全序列并与HCV各基因型代表株的相应序列比较,与HCVⅡ型相应序列的核苷酸同源性为77％～79％。而与HCVⅠ、Ⅲ、Ⅳ相应序列间的同源性为62％～69％,表明为HCVⅡ型序列。结果提示献血员抗—HCVIgG筛选不能完全排除HCV感染者,漏检不是由于HCV基因序列变异．而是检测方法本身缺陷所致。     

吉林地区HFRS病原体基因型分析

为调查吉林地区褐家鼠中汉坦病毒病原体基因型及其分布情况,采用免疫荧光法检测吉林市区及吉林市所属各县市收集的鼠肺标本,对汉坦病毒抗原阳性标本以巢式RT-PCR法扩增S基因片段上的核苷酸序列并测序,将扩增片段的核苷酸序列与已知病毒序列进行同源性分析及系统进化树分析.序列分析发现吉林地区褐家鼠携带的汉坦病毒均为汉城病毒,S3...     

HIV-1抗体阳性血浆中HIV-1病毒基因分型研究

为了解HIV抗体阳性血浆中的HIV-1病毒基因亚型的情况,应用逆转录PCR和DNA序列测定技术,对6份获自高危人群的抗HIV-1阳性血浆进行序列分析和基因亚型分型的研究,结果表明均属HIV-1B亚型.V3环氨基酸序列分析指出这些HIV-1B亚型病毒株与泰国HIV-1B亚型病毒株核苷酸和氨基酸序列相似;同时发现HIV-1 cDNA和氨基酸序列均相同,推测这6份标本可能来自同时感染同一株HIV病毒的感染者.本研究对了解高危人群中HIV-1流行的遗传变异和HIV-1亚型病毒株的分子流行病分析具有一定的意义.     

在传染性非典型肺炎患者组织和血液中发现冠状病毒

用RT-PCR从广东两例传染性非典型肺炎(非典型肺炎)死亡病例的肺和脾标本中,以及北京、辽宁和宁夏非典型肺炎患者血清中,扩增出冠状病毒核苷酸序列。这些PCR产物为冠状病毒RNA聚合酶基因部分片段,所有测定的序列和国内外SARS病毒序列相同。这些发现提示,冠状病毒和非典型肺炎关系密切,有助于确定我国非典型肺炎的病因。所建立的套式PCR方法可以用于检测临床标本。由于血液中存在SARS病毒,进行血清操作时需要注意安全保护。     

湖州市GⅡ.P16-GⅡ.2型诺如病毒胃肠炎疫情的病原分子特征分析

鉴定湖州市2017年11月3起急性胃肠炎疫情的病原,并对病原进行基因特征研究。收集3起疫情中采集的患者粪便标本,采用荧光定量RT-PCR方法对其进行诺如病毒核酸检测,并对核酸阳性标本进行多聚酶和衣壳蛋白部分区域的RT-PCR扩增。选取阳性扩增产物进行序列测定和分子特征分析。同时收集疫情的相关流行病学资料。3起暴发疫情中15份标本经荧光PCR检测为GII型诺如病毒核酸阳性,其中9份标本成功测序。在线分型、系统进化和重组分析判定3起均是GII.P16-GII.2型重组株引起的诺如病毒感染聚集性疫情。系统进化分析显示,本研究中检出的GII.P16-GII.2与2016年底中国各地以及德国、法国检出的GII.P16-GII.2相聚在一起并区别于2016年以前的GII.P16-GII.2形成了一个相对独立的进化分支。提示2016年新出现的GII.P16-GII.2在多聚酶区和衣壳蛋白区都各自经历了一定进化获得了在人群中广泛流行的能力,具体机制有待进一步的研究。这也是首次在本地的诺如病毒胃肠炎疫情中检出GII.P16-GII.2重组株。     

A novel hantavirus associated with an outbreak of fatal respiratory disease in the southwestern United States: evolutionary relationships to known hantaviruses.

Four Corners hantavirus (FCV) is the tentative name of the suspected etiologic agent of the newly identified hantavirus-associated respiratory distress syndrome (HARDS). The identification in HARDS patients of serum immunoglobulin M and immunoglobulin G antibodies that cross-reacted with Hantaan, Seoul, and Puumala virus antigens first suggested that FCV is a hantavirus. Limited nucleotide sequence data from the FCV glycoprotein-2 (G2) confirmed that FCV is a hantavirus and showed that it is most closely related to Prospect Hill and Puumala viruses. We have molecularly cloned approximately 95% of the sequences of the M and S segments of the FCV genome encoding the envelope glycoproteins and nucleocapsid protein N from the lungs of a patient with HARDS. The nucleotide sequence has been determined for 2,632 bases. The nucleotide sequence data show that FCV is a new member of the Puumala virus and Prospect Hill virus division of the hantavirus genus. Phylogenetic tree analyses indicate that the M and S segments have evolved in parallel. Therefore, the novel pathogenic activity of FCV is not likely to be the result of recent reassortment of segments from less pathogenic viruses.     

我国肾综合征出血热疫苗生产株LR1株的全基因组序列分析

为测定我国肾综合征出血热疫苗生产株LR1株的全基因组序列 ,了解该株分子基础 ,从提取的细胞总RNA逆转录PCR扩增 ,产物纯化后克隆T载体纯化后测序 ,结果证明 ,LR1株全基因组序列由L6 5 33、M36 16、S片段的16 92个核苷酸组成 ,依各自读码框架分别编码 2 15 1、1135、42 9个氨基酸。序列同源比较分析表明 ,LR1毒株与国外HTN型毒株高度同源 ,属同一亚型 ,尤其与HTN代表株 76 - 1183个片段同源率高达 99 3%～ 99 8% ,而与国内的HTN型病毒差异较大 ,同源率仅为 79 4%～ 84 6 %。氨基酸比较也显示了同样的结果。     

Molecular Evolution and Spatial Transmission of Severe Fever with Thrombocytopenia Syndrome Virus Based on Complete Genome Sequences

Severe fever with thrombocytopenia syndrome virus (SFTSV) was a novel tick-borne bunyavirus that caused hemorrhagic fever with a high fatality rate in East Asia. In this study we analyzed the complete genome sequences of 122 SFTSV strains to determine the phylogeny, evolution and reassortment of the virus. We revealed that the evolutionary rate of three genome segments were different, with highest in the S segment and lowest in the L segment. The SFTSV strains were phylogenetically classified into 5 lineages (A, B, C, D and E) with each genome segment. SFTSV strains from China were classified in all 5 lineages, strains from South Korea were classified into 3 lineages (A, D, and E), and all strains from Japan were classified in only linage E. Using the average evolutionary rate of the three genome segments, we found that the extant SFTSV originated 20–87 years ago in the Dabie Mountain area in central China. The viruses were then transmitted to other areas of China, Japan and South Korea. We also found that six SFTSV strains were reassortants. Selection pressure analysis suggested that SFTSV was under purifying selection according to the four genes (RNA-dependent RNA polymerase, glycoprotein, nucleocapsid protein, non-structural protein), and two sites (37, 1033) of glycoproteins were identified as being under strong positive selection. We concluded that SFTSV originated in central China and spread to other places recently and the virus was under purifying selection with high frequency of reassortment.     

A novel mosquito-borne reassortant orbivirus isolated from Xishuangbanna,China

<正>Dear Editor,The genus Orbivirus,within the family Reoviridae,includes 22 virus species(King et al.,2011).They are distributed globally,but are particularly prevalent in Europe,Asia,and Africa.In addition,they can be transmitted by ticks or other hematophagous insect vectors,including Culicoides,mosquitoes,and sandflies(Belaga-     

用SARS冠状病毒全基因组芯片杂交方法分析SARS-CoV

为从临床样品中检测和分析SARSCoV病毒打基础,并为分析SARSCoV病毒的复制和转录等机理提供一种有效方法。以SARS冠状病毒TOR2株序列作为标准设计和制备一种覆盖SARS冠状病毒全基因组的寡聚核苷酸芯片,探针长度为70nt,每相邻的探针序列重复25nt,共660条。用该芯片分析了细胞培养的SARSCoV病毒总RNA、7个SARSCoV病毒的基因克隆片段。对RNA样品用随机引物进行反转录PCR获得cDNA。对DNA用随机引物扩增和dUTPcy3标记。结果用这种芯片杂交检测SARSCoV病毒RNA可见阳性信号呈全基因组分布,并且有多处连续的阳性信号点;用正常人的白细胞RNA为对照,杂交未出现明显阳性信号。检测7个SARSCoV病毒基因克隆片段,在该片段相应的探针区段出现连续阳性信号点。这种方法可有效地检测和分析样品中SARS冠状病毒全基因组的信息。     

斑点杂交生物素法检测流行性出血热病毒RNA

为寻找一种用于检测流行性出血热病毒的分子杂交方法,以生物素-7-dATP标记流行性出血热病毒(EHFV)R_(22)株M片段的cDNAR_3克隆作探针,与人源性的EHFVH-114、H-435株RNA基因组进行斑点杂交,得到阳性结果,可检出5pg的cDNA或RNA。此探针与疱疹病毒DNA不出现杂交信号。以上结果说明这种标记探针具有EHFV特异性,可以扩大应用范围,结果还表明动物源性和人源性EHFV均具有共同的保守核苷酸序列。     

Cell culture adaptation of Puumala hantavirus changes the infectivity for its natural reservoir, Clethrionomys glareolus, and leads to accumulation of mutants with altered genomic RNA S segment.

This paper reports the establishment of a model for hantavirus host adaptation. Wild-type (wt) (bank vole-passaged) and Vero E6 cell-cultured variants of Puumala virus strain Kazan were analyzed for their virologic and genetic properties. The wt variant was well adapted for reproduction in bank voles but not in cell culture, while the Vero E6 strains replicated to much higher efficiency in cell culture but did not reproducibly infect bank voles. Comparison of the consensus sequences of the respective viral genomes revealed no differences in the coding region of the S gene. However, the noncoding regions of the S gene were found to be different at positions 26 and 1577. In one additional and independent adaptation experiment, all analyzed cDNA clones from the Vero E6-adapted variant were found to carry substitutions at position 1580 of the S segment, just 3 nucleotides downstream of the mutation observed in the first adaptation. No differences were found in the consensus sequences of the entire M segments from the wt and the Vero E6-adapted variants. The results indicated different impacts of the S and the M genomic segments for the adaptation process and selective advantages for the variants that carried altered noncoding sequences of the S segment. We conclude that the isolation in cell culture resulted in a phenotypically and genotypically altered hantavirus.     

中国分离巴泰病毒基因组全编码区序列测定和分析

采用RT-PCR和TAIL-PCR方法,首次对我国分离的巴泰病毒(YN92-4株)基因组的全编码区进行序列测定和分析。结果显示,YN92-4株病毒基因组由S、M、L三个片段组成,长度分别为947、4 371、6 860个核苷酸。其中,S片段基因编码由234个氨基酸残基组成的核衣壳蛋白和由102个氨基酸残基组成的非结构蛋白,M片段基因编码由1 435个氨基酸残基组成的前体蛋白,L片段基因编码由2 239个氨基酸残基组成的RNA聚合酶。与国外其它地区的巴泰病毒分离株进行基因组全编码区序列比较后发现,YN92-4株与日本牛血清分离株(ON-7/B/01株)在S、M片段核苷酸(氨基酸)的同源性最高,分别为97.7%(100%)和95.7%(98%);由于本研究首次开展对巴泰病毒L基因片段核苷酸序列的研究,因此国际基因库尚无可参考的序列信息,本研究比较了我国分离的巴泰病毒与同一血清组的代表病毒Bunyamwera病毒L片段的核苷酸和氨基酸序列同源性,分别为73.5%和81.6%。系统进化分析显示,YN92-4株基因组与其它巴泰病毒分离株在各自分支下形成独立分支。本研究提示我国分离的巴泰病毒YN92-4株未发生基因重配(...     

Molecular and genetic analysis of influenza A viruses isolated in Russia, based on the neuraminidase and M2 protein gene sequence

The results of molecular analysis of 15 influenza A(H3N2) and 17-A(H1N1) epidemic strains isolated in the Russian Federation in 1995-2007 are described. The analysis on the M2 and neuraminidase influenza A virus genes was performed. The M2 sequences analysis among the remantadin resistant viruses demonstrated the S31N substitution in all strains. Besides S31N substitution, additional mutations were detected in both proteins. Mutations associated with S31N substitution were detected in each virus subtype, which may be considered as new markers for the identification of remantadin-resistant strains. The sequencing of the NA segments from all viruses showed no amino acid substitutions known to cause resistance to neuraminidase inhibitors, which indicates susceptibility to NA inhibitors among the strains.     

A comparison of complete genome sequences of a rabies virus chinese isolate SH06 with the vaccine strains

In this study, we determined the complete nucleotide and deduced amino acid sequence of a primary isolate of rabies virus (SH06) obtained from the brain of a rabid dog. The overall length of the genome was 11 924 nucleotides. Comparison of the genomic sequence showed the homology of SH06 at nucleotide level with full-length genomes of reference vaccine strains ranged from 82.2% with the PV strain to 86.9% with the CTN strain. A full-length genome-based phylogenetic analysis was performed with sequences available from GenBank. Phylogenetic analysis of the complete genome sequences indicated that the SH06 exhibited the highest homology with rabies street virus BD06 and CTN vaccine strain originated from China.