Standardization of rabies virus genome amplification for its use in molecular epidemiology studies

In order to improve the diagnosis and typification of rabies viruses at the Instituto Nacional de Salud National Reference Laboratory for rabies, we standardized techniques for the amplification of a 902 nucleotide DNA fragment, complementary to a selected region of the rabies virus genomic RNA. This region codes for a segment of both the glycoprotein and protein L, and contains the G-L intergenic noncoding region known as Pseudogen Psi. The standardized techniques included: 1) biological amplification of rabies viruses by intracerebral mouse inoculation; 2) total RNA extraction from the brains of infected mice, 3) RT-PCR amplification of a 902 nucleotide DNA fragment complementary to the selected RNA region. The study sample consisted of 30 rabies virus strains isolated from dogs and selected from the virus bank of the Virology Laboratory. Due to their simplicity the methods described have several advantages when compared to methods reported in previous papers. The technology proposed is a precise complement to rabies diagnosis techniques, and can be applied to the identification of phylogenetic relations among rabies isolates, and, therefore, it is also used to identify rabies transmission dynamics and geographical distribution.     

Phylogenetic relationship of street rabies virus strains and their antigenic reactivity with antibodies induced by vaccine strains. I. Analysis of phylogenetic relationship of street rabies virus strains isolated in Poland

The aims of these studies were: genetic characteristic of street rabies virus strains isolated from different animal species in Poland and determination of phylogenetic relationships to reference laboratory strains of the street rabies viruses belonging to genotype 1 and 5. The variability of rabies isolates and their phylogenetic relationship were studied by comparing the nucleotide sequence of the virus genome fragment. The Polish strains of genotype 1 belong to four phylogenetic groups (NE, CE, NEE, EE) corresponding to four variants: fox-racoon dog (F-RD); European fox 1 (F1); European fox 2 (F2) and European fox 3 (F3). On the Polish territories there are no rabies strains representing the variant dog-wolf and typical for arctic fox variant. The similarity of nucleotide and amino acid sequences of street rabies strains belonging to genotype 1 and laboratory strain CVS is very high. It is about 91% similarity at nucleotide level and 95% at amino acid level. Rabies strain CVS is similar to genotype 5 bat strains (EBL 1) only in about 69% and 74% at nucleotide and amino acid level, respectively. The genetic divergence of rabies strains circulating in Poland raised the need of permanent epidemiological and virological surveillance. The genotype and variant of isolated strains should be determined (using PCR and RLFP methods).     

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.     

贵州省25株狂犬病病毒核蛋白基因序列分析

分析贵州省25株狂犬病病毒的核蛋白基因(N基因)序列,探讨贵州省狂犬病流行特征与狂犬病病毒变异情况。以RT-nested PCR检测来自贵州省2005年至2010年不同地区的病人脑组织、病人唾液以及犬脑组织标本狂犬病病毒RNA,经测序与拼接后得到25条N基因全长序列,采用生物信息学软件对N基因序列进行分析。25株狂犬病病毒核蛋白在核苷酸及氨基酸水平上彼此的同源性分别为89.3%～100%和98.%～100%;与国内其他省已发表基因1型狂犬病病毒核苷酸和氨基酸序列同源性分别为88%～99.1%和88%～99.7%,与已知的基因1型狂犬病病毒比较,25株病毒核蛋白氨基酸序列发生了若干位点的取代。进化树分析显示,同一地区内与相邻地区,以及同一时间段与相邻时间段内狂犬病病毒N基因进化亲缘关系相近。25株贵州省狂犬病病毒流行毒株均属基因1型,其核蛋白在基因的核苷酸及推导的氨基酸水平上均有变异,且这些变异具有地域和时间分布特性。     

Molecular epidemiology of rabies epizootics in Colombia, 1994-2002: evidence of human and canine rabies associated with chiroptera

Three urban rabies outbreaks have been reported in Colombia during the last two decades, one of which is ongoing in the Caribbean region (northern Colombia). The earlier outbreaks occurred almost simultaneously in Arauca (eastern Colombia) and in the Central region, ending in 1997. Phylogenetic relationships among rabies viruses isolated from the three areas were based on a comparison of cDNA fragments coding for the endodomain of protein G and a fragment of L protein obtained by RT-PCR. The sequenced amplicons which included the G-L intergenic region contained 902 base pairs. Phylogenetic analysis showed three distinct groups of viruses. Colombian genetic variant I viruses were isolated only from Arauca and the Central region, but are now apparently extinct. Colombian genetic variant II viruses were isolated in the Caribbean region and are still being transmitted in that area. The third group of bat rabies variants were isolated from two insectivorous bats, three domestic dogs and a human. This associates bat rabies virus with rabies in Colombian dogs and humans, and indicates bats to be a rabies reservoir of public health significance.     

Genetic analysis of rabies virus isolates in the Philippines

To determine the genetic characteristics of the rabies virus in the Philippines, 59 rabies virus isolates were obtained from domestic rabid dogs and their partial nucleotide sequences of nucleoprotein (N) gene were compared. Based on comparison with reported sequences, phylogenetic analysis revealed that all isolates from the Philippines had close genetic relations and formed two subgroups. The Philippines isolates belonged to a different lineage from other Asian isolates but were closer to them than to terrestrial isolates and laboratory strains. Several specific nucleotide and amino acid substitutions were observed among the Philippines isolates. Our results suggest that rabies viruses in the Philippines might have a characteristic evolution.     

浙江地区鼬獾和犬源狂犬病病毒分离株全基因组测序与分析

测定浙江地区狂犬病病毒分离株(鼬獾和犬)全基因组序列,从分子水平对病毒进行遗传变异特征分析,了解狂犬病病毒在浙江的流行和变异情况以及目前浙江流行株的遗传学背景,以丰富中国狂犬病病毒街毒流行株的全基因组信息。脑内接种1~2日乳鼠分离狂犬病病毒,RT-PCR反应测定浙江地区狂犬病病毒分离株全基因组核苷酸序列,并进行编码蛋白和序列相似性比较及种系发生分析。测序获得狂犬病病毒浙江淳安鼬獾分离株F02、F04和松阳犬分离株D01、D02全基因组核苷酸序列信息:基因组全长11 923和11 925 nts,前导序列Leader长58nts,5个ORF为:NP(1 353 nts);PP(894 nts);MP(609 nts);GP(1 575 nts);LP(6 386 nts),N-P-M-G间隔序列长2、5、5 nts;G-L基因间的伪基因Ψ长423 nts;Trailer尾长70 nts。核酸BLAST及多重序列比对分析显示浙江地区4个狂犬病病毒分离株的全基因组序列的组成和结构符合弹状病毒科狂犬病病毒属的特征;中国毒株之间特别是浙江同种动物狂犬病病毒之间各个基因区域核苷酸与氨基酸序列相似性最高,浙江病毒全基因组序列编码蛋白氨基酸序列相似性高于核苷酸序列相似性,说明蛋白质编码基因的核苷酸变异大多属于同义突变;浙江病毒负链RNA基因组5个基因编码氨基酸的长度没有变异,5个编码蛋白仅表现较少的序列变化;浙江病毒与本研究选择的代表性引用街毒株或者来自街毒的减毒株的变异位点和变异类型相似,多重序列相似性的比较和种系发生分析显示所分离的狂犬病病毒浙江街毒株均属于基因1型,具有较独特的中国地域性特点,故本研究中的浙江地区分离株极有可能是自然界中固有的街毒株。     

Detection and genetic characterization of rabies virus from human patients

Saliva and blood were collected from two patients who had not received post exposure prophylaxis in the cities of Wenzhou and Xinning respectively. Both patients were confirmed as positive for rabies by detection of rabies virus specific nucleoprotein antibodies in the sera by Western Blot. However, rabies virus specific RNA was only identified in the saliva collected from the patient in Wenzhou. Furthermore, the isolate Zhejiang Wz0 (H) was obtained by inoculating one-day-old suckling mice. Both nucleoprotein (N) and glycoprotein (G) genes from the isolate were amplified by RT-PCR and sequenced. Phylogenetic analysis indicated that the isolate belonged to classic rabies virus, and shared a higher homology with the street viruses from dogs in the main endemic areas in China and the street virus from dogs in Indonesia than with other known strains. Further comparison of the deduced amino acid sequences between the isolate and the vaccine strains used in China showed that the virus had a higher level of homology with the vaccine strain CTN than with the other vaccine strains (3aG, PV, PM and ERA). In particular, amino acid residues substitutions located in antigenic site III in the G protein, which could react with the neutralizing antibodies, were observed. These results suggested that the virus belonged to the classic rabies virus, and both N and G genes diverged from the current vaccine strains used in China at either the nucleotide or the amino acid level. Foundation items: The project was supported by the Grants (2003BA712A08-02 and 2004BA718B03) from the Chinese Ministry of Science and Technology.     

中国19个狂犬病病毒街毒分离株N基因的序列分析

测定了30年来从不同动物中分离的19个中国狂犬病病毒街毒株N基因的部分核酸序列,并对其核苷酸差异做了比较分析.可将中国狂犬病病毒街毒株分为4个组群,各组间的同源性为83.45%～88.62%.除广西地区分离的狂犬病病毒街毒株彼此差异较大外,其余街毒株的地理分布与其N基因核酸序列差异的距离是密切相关的,基本上可按其地理分布分为东、西二大组.     

Molecular Epidemiology of Japanese Encephalitis Virus in Okinawa

In order to elucidate the molecular characteristics of Japanese encephalitis (JE) virus in Okinawa, 23 strains of JE virus isolated in a 25-year span were sequenced for the 240 nucleotides of the C-preM junction region and 111 nucleotides of the E gene region and compared with those of reference strains isolated in mainland Japan. The results of phylogenic analysis showed that although all the Okinawan isolates showed more than 96% homology in the nucleotide sequence in each region, they were chronologically divided into two groups: the old group (nine strains) and a new group (14 strains). On the other hand, in a comparison with reference strains in mainland Japan, the Okinawan isolates showed more than 94% nucleotide sequence homology in both regions, indicating that the Okinawan strains belong to the same genotype as that of JE strains in mainland Japan. The nucleotide homology of the old group was relatively higher than that of the new group. Among the 14 strains in the new group, 13 strains were isolated from mosquitoes collected from a pig farm from 1986 through 1992. These strains showed higher nucleotide divergence than the old group strains, isolated from mosquitoes and swine sera collected at several sites, in both regions. A nucleotide substitution at the position 1920 in the E gene was identified in three isolates. This substitution generated an asparagine-proline-threonine sequence capable of serving as an attachment site of carbohydrate.     

1株梅花鹿源狂犬病街毒株全基因组测序与分析

对1株梅花鹿源性狂犬病街毒株(DRV)进行全基因组克隆,对全长cDNA进行测序分析.RT-PCR扩增克隆覆盖全基因组9个重叠基因片段,基因组3'和5'末端采取3,-RACE和5'-RACE方法,9个重叠基因片段序列拼接得到DRV全基因组cDNA序列,共11 863个核苷酸.DRV毒株全基因组构成与其他狂犬病毒基因组构成相似,由5个编码区组成,基因起始位点和终止位点高度保守,在核蛋白和糖蛋白的重要抗原位点有个别氨基酸发生变异,对已完成全基因组测序的几个基因1型毒株分别进行了N、P、M、G、L基因核苷酸及氨基酸的同源性比较.与其他具有代表性的毒株进行N基因序列比较建立的系统进化树表明,DRV毒株属于基因1型,与中国人用疫苗株3aG同源性最高为94%,与分类位置未确定的北高加索毒株(WCBV)的同源性最低为71%.本研究结果可为狂犬病毒各项分子生物学研究提供理论参考.     

家养犬、猫及野生动物中狂犬病病毒流行病学调查及我国不同类型狂犬病疫苗免疫效果观测研究

选择我国狂犬病高发地区(湖南、贵州)、低发地区(江苏、武汉)和无狂犬病报告地区(沈阳)等三种不同类型的地区,开展针对家养犬、猫和啮齿类动物,以及蝙蝠等野生动物的狂犬病病毒带毒率的流行病学调查,对分离到的病毒株在抗原型别、基因变异以及与现行疫苗是否匹配等方面进行分析、比较研究。结果显示:我国狂犬病的主要宿主动物为犬,捕获犬总带毒率为2.56%;犬中狂犬病病毒的监测点最高阳性检出率达到20.0%;啮齿类动物及蝙蝠等野生动物在本次研究未检测到狂犬病病毒。我国自主研制成功的以aG株和CTN株为毒种的现行人用狂犬病疫苗,经应用研究发现,CTN株的糖蛋白基因与本研究分离到的街毒核酸序列更接近。为进一步评价现行疫苗的有效性,在5个观察点分别以aG株和CTN株毒种生产的疫苗接种两组人群(每组各约50人),结果显示均未出现中、强度反应,疫苗免疫后第7d和14d产生的中和抗体分别达到0.49IU/mL~0.52IU/mL和6.7IU/mL~7.53IU/mL;抗体阳转率分别为45.1%~47.9%和100%,表明这些疫苗具有良好的安全性和保护效果。     

Phylogenetic relationships of aquatic birnaviruses based on deduced amino acid sequences of genome segment A cDNA.

Aquatic birnaviruses, such as infectious pancreatic necrosis virus (IPNV), cause serious diseases in a variety of fish species used worldwide in aquaculture and have also been isolated from a variety of healthy fish and shellfish species. These viruses exhibit a high degree of antigenic heterogeneity and variation in biological properties such as pathogenicity, host range, and temperature of replication. To better understand genetic and biological diversity among these viruses, the nucleotide and deduced amino acid sequences were determined from cDNA of the large open reading frame (ORF) of genome segment A of the 9 type strains of Serogroup A and 4 other representative strains of Serotype A1, the predominant serotype in the United States. In addition, nucleotide and deduced amino acid sequences were determined for the VP2 coding region of a variety of isolates representing 5 of the 9 serotypes. VP2 is the major outer capsid protein of aquatic birnaviruses. RT-PCR was used to amplify a 2904 bp cDNA fragment including all but a few bp of the large ORF of genome segment A or a 1611 bp fragment representing the entire VP2 coding region. Nucleotide and deduced amino acid sequences were determined from the PCR products. Pairwise comparisons were made among our data and 2 other aquatic birnavirus sequences previously published. Several hypervariable regions were identified within the large ORF. The most divergent pair of viruses exhibited a similarity of 80.1% in the deduced amino acid sequence encoded by the large ORF. Genomic relationships revealed in a phylogenetic tree constructed from comparison of the deduced amino acid sequences of the large ORF demonstrated that these viruses were clustered into several genogroups. Phylogenetic comparison of the deduced amino acid sequences of the VP2 coding region of 28 aquatic birnavirus isolates, including the type strains of all 9 serotypes, demonstrated 6 genogroups, some of which were comprised of several genotypes. The most divergent pair of viruses exhibited a similarity of 81.2% in the deduced amino acid sequence from the VP2 coding region. In contrast to previous studies of much shorter genomic sequences within the C-terminus-pVP2/NS junction coding region, these genogroups based on the entire large ORF or the VP2 coding region generally correlated with geographical origin and serological classification. Isolates from the major Canadian serotypes were more closely related to the European isolates than to isolates from the United States.     

2001～2011年上海市风疹病毒分子流行病学研究

本研究对2001～2011年本实验室保存的血清标本检测结果为麻疹IgM阴性,风疹IgM阳性病例相对应的咽拭子标本进行风疹病毒（Rubella virus,RV）分离,用RT-PCR方法对细胞培养产物鉴定后扩增病毒E1基因,扩增产物用于核苷酸序列测定,并进行分子流行病学分析。结果表明,60份咽拭子标本共分离到31株RV,获得27株RV的739nt（nt8 731～nt9 469）核苷酸序列,系统同源性分析表明,27株RV分离株分别属于两个不同的基因型,除分离自2011年的11009株、11052株和11106株为2B基因型外,其他分离株均为1E基因型。27株RV分离株大部分的核苷酸突变为无义突变,氨基酸序列高度保守。24株1E基因型分离株中大部分毒株氨基酸序列完全一致,自2001年以来可能有来自同一传播链的RV在持续传播。本研究首次监测到2B基因型RV2011年开始在上海流行,经GenBank核苷酸序列比对发现,其与越南、日本、阿根廷等国家近几年的RV分离株核苷酸序列同源性达99%。由于以前对风疹的监测较少,尚不能证明其来源。     

The full-length genome analysis of a street rabies virus strain isolated in Yunnan province of China

The epidemic of rabies has rapidly increased and expanded in Yunnan province in recent years.In order to further analyze and understand the etiological reasons for the rapid expansion of rabies in Yunn...     

Molecular characterization of viral G gene in emerging and Re-emerging areas of rabies in China, 2007 to 2011

In recent years (2007 to 2011),although the overall number of rabies cases in China has decreased,there is evidence of emerging or re-emerging cases in regions without previous rabies cases or with low...     

广西不同时期IBV分离株S1基因高变区Ⅰ的遗传变异分析

对广西1985-2007年间分离到的22株传染性支气管炎病毒（IBV）的S1基因高变区I（HVRI）进行序列测定,并与发表的其他IBV参考株及鸽子分离的冠状病毒株的基因序列进行比较和分析。系统进化关系显示毒株可分为5个基因群,其中有16个广西分离株属第1群,它们与鸽子冠状病毒分离株的氨基酸序列同源性较高,与Massachusetts（Mass）型疫苗株的同源性较低。有15个分离株在33-34位和34～35之间分别有4个和3个氨基酸残基的插入,GX-NN6在33～34位和34～35位之间则均有4个氨基酸残基的插入;GX-YL1、GX-NN2与常用的Mass型疫苗株的亲缘关系最近,同属于第Ⅱ群;GX-G、GX-XD与日本同一时期分离的毒株JP Miyazaki 89亲缘关系最近,属于第Ⅲ群;GX-YL6、GX-NN7与欧洲毒株4／91亲缘关系较近,属于第V群。结果表明广西存在着多种类型IBV毒株的流行,毒株S1基因HVRI碱基的突变或插入比较普遍,可导致其氨基酸序列的变化,绝大部分毒株与目前常用的Mass型疫苗株的亲缘关系较低。同一时期的分离株同源性较高,但无明显的地域性差异。     

Variability of human immunodeficiency virus type 1 group O strains isolated from Cameroonian patients living in France.

Human immunodeficiency virus type 1 (HIV-1) nucleotide sequences encoding p24Gag and the Env C2V3 region were obtained from seven patients who were selected on the basis of having paradoxical seronegativity on a subset of HIV enzyme-linked immunosorbent assay detection kits and having atypical Western blot (immunoblot) reactivity. Sequence analyses showed that all of these strains were more closely related to the recently described Cameroonian HIV isolates of group O (HIV-1 outlier) than to group M (HIV-1 major). All seven patients had Cameroonian origins but were living in France at the time the blood samples were taken. Characterization of a large number of group M strains has to date revealed eight distinct genetic subtypes (A to H). Genetic distances between sequences from available group O isolates were generally comparable to those observed in M intersubtype sequence comparisons, showing that the group O viruses are genetically very diverse. Analysis of sequences from these seven new viral strains, combined with the three previously characterized group O strains, revealed few discernable phylogenetic clustering patterns among the 10 patients' viral sequences. The level of diversity among group O sequences suggests that they may have a comparable (or greater) age than the M group sequences, although for unknown reasons, the latter group dispersed first and is the dominant lineage in the pandemic.     

Size and Sequence Polymorphism in the Isocitrate Dehydrogenase Kinase/Phosphatase Gene (Acek) and Flanking Regions in Salmonella Enterica and Escherichia Coli

The sequence of aceK, which codes for the regulatory catalytic enzyme isocitrate dehydrogenase kinase/phosphatase (IDH K/P), and sequences of the 5' flanking region and part or all of the 3' flanking region were determined for 32 strains of Salmonella enterica and Escherichia coli. In E. coli, the aceK gene was 1734 bp long in 13 strains, but in three strains it was 12 bp shorter and the stop codon was TAA rather than TGA. Strains with the shorter aceK lacked an open reading frame (f728) downstream between aceK and iclR that was present, in variable length, in the other strains. Among the 72 ECOR strains, the truncated aceK gene was present in all isolates of the B2 group and half of those of the D group. Other variant conditions included the presence of IS1 elements in two strains and large deletions in two strains. The aceK-aceA intergenic region varied in length from 48 to 280 bp in E. coli, depending largely on the number of repetitive extragenic palindromic (REP) sequences present. Among the ECOR strains, the number of REP elements showed a high degree of phylogenetic association, and sequencing of the region in the ECOR strains permitted partial reconstruction of its evolutionary history. In S. enterica, the normal length of aceK was 1752 bp, but three other length variants, ranging from 1746 to 1785 bp, were represented in five of the 16 strains examined. The flanking intergenic regions showed relatively minor variation in length and sequence. The occurrence of several nonrandom patterns of distribution of polymorphic synonymous nucleotide sites indicated that intragenic recombination of horizontally exchanged DNA has contributed to the generation of allelic diversity at the aceK locus in both species.     

重组人抗狂犬病病毒单抗SO57、SOJB对不同狂犬病病毒毒株中和作用的研究

用不同的动物模型研究了具有专利的重组人抗狂犬病病毒单克隆抗体SO57、SOJB对不同狂犬病病毒株的中和作用,100IU/kg的SO57能100%保护被中国街毒株SBD攻击的中国仓鼠;首次用小鼠模型模拟人体被狂犬病病毒攻击后的治疗情况,在小鼠被CVS及中国街毒代表株攻击后,SO57与HRIG具有相近的对小鼠的暴露后保护作用;同时结果显示HRIG对SBD株攻击的保护率不能到达100%,仅使用疫苗是不能对感染病毒的小鼠百分之百的保护;SOJB与SO57 1:1联合使用未显示比SO57单独使用更好的保护效果。SO57极有可能在中国代替HRIG用于狂犬病病毒暴露后治疗。