浙江省基因Ⅰ型乙脑病毒全基因序列的测定及分析

目的 为了获得浙江省乙脑病毒基因组详尽的资料,研究基因Ⅰ型乙脑病毒的分子特征及变异程度,为乙脑病毒分子流行病学及其基因研究提供科学依据.方法 设计特异性引物、RT-PCR分段扩增XJ69和XJP613株全基因,PER产物纯化后克隆于T载体并进行序列测定.通过生物学软件进行核苷酸序列和氨基酸序列分析和病毒的系统进化分析.结果 新分离乙脑病毒XJ69和NJP613株全基因组全长均为10 964个核苷酸,含有一个开放阅读框架,编码3432个氨基酸.与GenBank中选择的32株乙脑病毒全基因序列比较发现,其核苷酸同源为83.5%～99.2%,氨基酸总体同源性为97.5%～99.7%.通过PrM/C区段、E区段及全基因序列进行系统进化分析均显示该毒株属于基因Ⅰ型乙脑病毒.结论 新分离的乙脑病毒XJ69和XJP613株属于基因Ⅰ型,与上海三带喙库蚊分离株SH17M-07关系最为接近.     

我国新分离乙脑病毒02-76株的全基因序列特征

目的对我国新分离乙脑病毒02-76株进行全基因序列测定和分析，了解乙脑病毒基因组结构及毒力特性。方法设计乙脑病毒全基因组扩增引物，RT-PCR扩增片段，PCR产物直接测序，拼接后获得全基因序列。通过Clustal X（1．8）、DNASTAR、GENEDOC（3．2）等生物学软件进行核苷酸序列及氨基酸序列分析和病毒的系统进化分析。结果新分离乙脑病毒02．76株全基因组全长10977个核苷酸，从96位到10391位，共10296个核苷酸编码一个开放阅读框，编码3432个氨基酸。与我国1949年分离的Beijing-1株相比较共存在248个核苷酸差异，16个氨基酸差异。与GenBank中选择的29株乙脑病毒全基因序列比较发现，其核苷酸总体差异率为0．6％-15．1％，氨基酸总体差异率为0．2％-4．6％。通过PrM／C区段、E区段、3’NTR区段及全基因序列进行系统进化分析均显示该毒株属于基因3型乙脑病毒。结论新分离的乙脑病毒02-76株属于基因3型，与中国分离株SA-14进化关系最接近。     

Genomic changes in an attenuated genotype I Japanese encephalitis virus and comparison with virulent parental strain

Genotype I Japanese encephalitis virus (JEV) strain SCYA201201 was previously isolated from brain tissues of aborted piglets. In this study, we obtained an attenuated SCYA201201-0901 strain by serial passage of strain SCYA201201-1 in Syrian baby hamster kidney cells, combined with multiple plaque purifications and selection for virulence in mice. We investigated the genetic changes associated with attenuation by comparing the entire genomes of SCYA201201-0901 and SCYA201201-1. Sequence comparisons identified 14 common amino acid substitutions in the coding region, with two nucleotide point mutations in the 5′-untranslated region (UTR) and another three in the 3′-UTR, which differed between the attenuated and virulent strains. In addition, a total of 13 silent nucleotide mutations were found after attenuation. These substitutions, alone or in combination, may be responsible for the attenuated phenotype of the SCYA201201-0901 strain in mice. This information will contribute to our understanding of attenuation and of the molecular basis of virulence in genotype I strains such as SCYA201201-0901, as well as aiding the development of safer JEV vaccines.     

山东省新分离乙脑病毒(SD08-10株)全基因组序列特征

目的 对山东省新分离乙脑病毒SD08-10株进行全基因组序列测定和分析,全面了解其基因组特征.方法 设计乙脑病毒全基因组序列扩增引物,RT-PCR扩增片段,PCR产物直接测序,拼接后获得全基因组序列.采用Clestal X(1.8)、DNAStar、GENEDOC(3.2)、Mega(4.0)等生物学软件进行核苷酸序列及氨基酸序列分析和病毒的系统进化分析.结果 新分离乙脑病毒SD08-10株基因组全长10 965个核苷酸,从97位到10 392位,共10 296个核苷酸编码一个开放阅读框,编码3432个氨基酸.与GenBank登录的所有59株乙脑病毒全基因组序列比较发现,其核苷酸总体差异率为0.7%～18.9%,氨基酸总体差异率为0.1%～5.2%.与目前使用的减毒活疫苗株SA-14-14-2株相比较,全基因组共存在1253个核苷酸差异,82个氨基酸差异.全基因组序列系统进化分析显示SD08-10属于基因Ⅰ型乙脑病毒.结论 新分离的乙脑病毒SD08-10株属于基因Ⅰ型,与2007年中国分离株SH17M-07进化关系最接近.     

流行性乙型脑炎病毒脑脊液分离株"47株"全基因组特征分析

目的 对1950年分离自我国黑龙江省患者脑脊液的乙脑病毒"47株"进行全基因组序列的测定和分析,全面了解其全基因组特征.方法 复苏毒种提取病毒RNA,使用自行设计的乙脑病毒全基因组扩增测序引物,完成对病毒全基因组序列的测定.采用DNAStar、Modeltest、Phylip等生物软件完成全基因组核苷酸、氨基酸序列差异分析和乙脑病毒全基因组的系统进化分析.结果 乙脑病毒"47株"全长10 977个核苷酸.96至10 391位为开放读码框ORF,共10 296个核苷酸,编码3432个氨基酸."47株"与5株疫苗株在全基因组水平的核苷酸差异在2.4%～4.4%之间,氨基酸差异在0.3%～1.1%之间.乙脑病毒全基因组最适进化模型为GTR+I+G.全基因组进化分析显示"47株"属于基因Ⅲ型乙脑病毒.结论 "47株"全基因组核苷酸和氨基酸高度保守,属于基因Ⅲ型乙脑病毒.     

2008年辽宁省乙脑病毒分离株全基因组特征分析

目的 对2008年分离自辽宁蚊虫的乙脑病毒株进行全基因组序列测定和分析,了解其全基因组特征.方法 使用针对乙脑病毒全基因组测序引物,RT-PCR扩增片段,完成对病毒全基因组序列的测定.应用Chstal X(1.83)、ATGC(V4)、DNAStar、GENEDOC(3.2)、Mega(4.0)等生物学软件完成全基因组核苷酸和氨基酸序列分析及病毒的系统进化分析.结果 乙脑病毒LN0828株基因组全长10 965个核苷酸,其中从97位到10 392位为开放读码框,编码3432个氨基酸.与GenBank中的32株乙脑病毒在全基因组水平的核苷酸总体差异率为1.6%～16.4%,氨基酸总体差异率为0.3%～5.1%.与减毒活疫苗株SA14-14-2相比,编码区共存在1186个核苷酸差异,86个氨基酸差异.全基因组序列系统进化分析显示LN0828株属于基因Ⅰ型乙脑病毒.结论 与该地区2002年和2007年乙脑病毒分离株高度同源,关键位点氨基酸未见变异.     

Genetic characterization and pathogenicity assessment of Newcastle disease virus isolated from wild peacock

The continued spread and occurrence of Newcastle disease virus (NDV) has posed potential threat to domestic poultry industry around the globe. Mainly, wild avian species has always been implicated for the natural reservoir for virus and spread of the disease. In the present study, we report the isolation of Newcastle disease virus (NDV/Peacock/India/2012) in necropsy brain tissue sample of wild peacock from North India. Complete genome of the virus was found to be 15,186 nucleotides (nts) with six genes in order of 3′-N–P-M-F-HN-L-5′, which was limited by 55-nts leader region at the 3′ end and a 114-nts trailer sequence at 5′ end. Sequence analysis of fusion protein revealed the dibasic amino acid cleavage site ¹¹²R-R-Q-K-R-F¹¹⁷, a characteristic motif of virulent virus. Phylogenetic analysis placed the isolate in genotype II of Newcastle disease virus showing the lowest mean percent divergence (6 %) with other genotype II counterparts. The isolate was characterized as mesogenic (intermediate pathotype) based on the mean death time (63 h) in embryonated chicken eggs and the intra-cerebral pathogenicity index (1.40) in day-old chicks. The report emphasizes the dynamic ecology of NDV strains circulating in a wild avian host during the outbreak of 2012 in North India. Further the genotypic and pathotypical characterizations of the isolate could help in development of homologous vaccine against NDV strain circulating in avian population.     

Molecular phylogenetic and positive selection analysis of Japanese encephalitis virus strains isolated from pigs in China

Japanese encephalitis virus (JEV) is one of the most important virus which causes encephalitis. This disease is most prevalent in the south, southeast and the east region of Asia. In this study, two JEV strains, named JEV/SW/GD/01/2009 and JEV/SW/GZ/09/2004, were isolated from aborted fetuses and seminal fluid of pigs in China. To determine the characteristic of these virus isolates, the virulence of two newly JEV isolates was investigated, the result evidenced that the JEV/SW/GD/01/2009 did not kill mice, while the JEV/SW/GZ/09/2004 displayed neurovirulence with 0.925 log₁₀ p.f.u./LD50. Additionally, the full genome sequences of JEV were determined and compared with other known JEV strains. Results demonstrated that the genome of two JEV isolates was 10,976 nucleotides (nt) in length. As compared to the Chinese vaccine strain SA14-14-2, the JEV/SW/GD/01/2009 and the JEV/SW/GZ/09/2004 showed 99.7% and 97.5% identity at the nucleotide level, 99.6% and 96.7% identity at the amino acid level, respectively. Phylogenetic analysis, based on the full-length genome revealed that two JEV isolates were all clustered into genotype III compared to the reference strains. Furthermore, selection analyses revealed that dominant selective pressure acting on the JEV genome was purifying selection. Four sites under positive selection were identified: codon 521 (amino acid E-227), 2296 (amino acid NS4b-24), 3048 (amino acid NS5-521) and 3055 (amino acid NS5-528). Amino acid E-227 was proved to be related to neurovirulence. Taken together, the molecular epidemiology and functional of positively selected amino acid sites of two newly JEV isolates were fully understood, which might be helpful to predict possible changes in virulence.     

Analysis of the complete genome sequence and capsid region of black queen cell viruses from infected honeybees (Apis mellifera) in Korea

Black queen cell virus (BQCV) infection is one of the most common viral infections in honeybees (Apis mellifera). A phylogenetic tree was constructed for 19 partial nucleotide sequences for the capsid region of South Korean BQCV, which were also compared with 10 previously reported BQCV sequences derived from different countries. The Korean BQCV genomes were highly conserved and showed 97–100 % identity. They also showed 92–99 % similarity with other country genotypes and showed no significant clustering in the phylogenetic tree. In order to investigate this phenomenon in more detail, the complete genome sequence of the Korean BQCV strain was determined and aligned with those from a South African reference strain and European genotypes, Poland4–6 and Hungary10. A phylogenetic tree was then constructed. The Korean BQCV strain showed a high level of similarity (92 %) with Hungary10, but low similarity (86 %) with the South African reference genotype. Comparison of the Korean and other sequences across different genome regions revealed that the 5′-UTR, the intergenic region, and the capsid regions of the BQCV genome were highly conserved. ORF1 (a non-structural protein coding region) was more variable than ORF2 (a structural protein coding region). The 5′-proximal third of ORF1 was particularly variable and contained several insertions/deletions. This phenomenon may be explained by intra-molecular recombination between the Korean and other BQCV genotypes; this appeared to have happened more with the South African reference strain than with the European genotypes.     

Molecular characterisation of novel mitoviruses associated with Sclerotinia sclerotiorum

Seven putative mitoviral genomes, representing four species from three Sclerotinia sclerotiorum isolates, were fully sequenced. The genome lengths ranged from 2438 to 2815 nucleotides. The RNA-dependent RNA polymerase (RdRp) of one genome shared high amino acid (aa) sequence identity (98.5 %) with the previously described Sclerotinia sclerotiorum mitovirus 2 (SsMV2/NZ1) and was provisionally assigned the name SsMV2/14563. The RdRps of three of the genomes with closest aa sequence identity of 78.8-79.3 % to Sclerotinia sclerotiorum mitovirus 1 (SsMV1/KL1) were provisionally considered to represent a new species, and the corresponding virus was named Sclerotinia sclerotiorum mitovirus 5 (SsMV5/11691, SsMV5/14563 and SsMV5/Lu471). The remaining two novel genomes, for which the viruses were provisionally named Sclerotinia sclerotiorum mitovirus 6 (SsMV6/14563 and SsMV6/Lu471) and Sclerotinia sclerotiorum mitovirus 7 (SsMV7/Lu471), showed closest aa sequence identities to Sclerotinia sclerotiorum mitovirus 3 (SsMV3/NZ1; 57.5-57.8 %) and Cryphonectria cubensis mitovirus 1a (CcMV1a; 32 %), respectively. The RdRp proteins of all seven genomes contained the conserved aa sequence motifs (I-IV) previously reported for mitoviruses, and their 5′ and 3′ untranslated regions (UTRs) have the potential to fold into stem-loop secondary structures.     

从病毒性脑炎患者标本分离的基因I型乙脑病毒全基因组序列特征研究

目的通过现代分子生物学理论与技术测定和分析了从脑炎患者脑脊液标本分离的基因I型乙脑病毒（GZ56株）全基因组序列特征,以了解其致病性的分子基础。方法采用RT．PCR法和核酸序列测定法获得病毒基因组全序列,并利用DNASTAR、ClustalX version2．0．9及MEGAversion4．1等生物学软件分析该乙型脑炎病毒核苷酸序列、氨基酸序列及系统进化等。结果研究结果表明从病毒性脑炎患者脑脊液标本分离的基因I型乙脑病毒（GZ56株）基因组全长为10965nt,编码3432个氨基酸。病毒全基因组分子进化分析显示GZ56株全基因组与国际上第一株从蚊虫分离的基因I型乙脑病毒（M-28株）处于同一进化分支。GZ56株与其他基因I型乙脑病毒核昔酸和氨基酸序列同源性分别为96．2％～98．6％和98．2％～99．7％。病毒E基因与乙脑病毒灭活疫苗株P3相比存在11个氨基酸差异位点,而与乙脑病毒减毒活疫苗株SA14-14-2相比,在E蛋白上存在14个氨基酸差异位点。结论本研究提示,从病毒性脑炎患者标本分离的基因I型乙脑病毒全基因组未见明显变化,从基因组水平可以推测该病毒可以被现行的乙脑疫苗所保护。     

Identification of mutations that occurred on the genome of Japanese encephalitis virus during the attenuation process

The total nucleotide sequences of the genomes of two Japanese encephalitis virus (JEV) strains, the attenuated vaccine strain SA₁₄-14-2 and its parental virulent strain SA₁₄, were determined by using the molecular cloning technique. The sequence analysis revealed that both virion RNA molecules were 10,976 nucleotides long with 95 and 585 flanking bases at the 5 and 3 untranslated sequences, respectively. A single, long open reading frame spanning 10,296 nucleotides was observed to encode a polyprotein of 3432 amino acid residues. When these sequences were compared with each other, 57 nucleotide substitutions were found to be scattered all over the genome. Of these, 24 resulted in amino acid changes within viral proteins. Structural proteins C and E contain one and eight amino acid changes, respectively. Of the nonstructural proteins, NS1 contains three, NS2a two, NS2b two, NS3 four, NS4a one, NS4b one, and NS5 two amino acid substitutions. The 5- and 3-terminal untranslated regions contain one- and two-point mutations, respectively. These data and comparative studies with other JEV strain genomes provide a molecular basis for investigating attenuation mechanisms of JEV.     

Molecular characterization of the full-length genome of the Japanese encephalitis viral strain K87P39

We have determined the complete nucleotide and deduced amino acid sequences of the Japanese encephalitis virus (JEV) strain K87P39, isolated from a pool of circulating Culex tritaeniorhynchus mosquitoes in Korea. In comparison with 27 fully sequenced JEV genomes currently available, we found that the 10968-nucleotide RNA genome of K87P39 has a nine-nucleotide deletion in the 3' nontranslated variable region and that its single open reading frame has a total of eight amino acid substitutions. The K87P39 isolate is highly similar to other JEV isolates, and homology ranges from 97.9 to 89.0% at the nucleotide level, and 99.1 to 96.7% at the deduced amino acid level. Phylogenetic analyses using the full-length sequence of the 27 available JEV genomes showed that the K87P39 strain is most closely related to six Chinese SA14 derivatives and that it is distantly related to the Australian FU, Korean K94P05 and Japanese Ishikawa strains. In addition, we also found that phylogenetic relationships based on the full-length genome are highly similar to those based on the E gene, indicating that phylogenetic analysis of the E gene will be useful for studying the genetic relationships among JEV isolates. We therefore performed a more extensive E gene-based phylogenetic analysis on a selection of 70 JEV isolates available from GenBank, which represent a temporally and geographically wide variety of JEV strains.     

Isolation and genome characterization of a novel duck Tembusu virus with a 74 nucleotide insertion in the 3′ non-translated region

During investigations into the outbreak of duck Tembusu virus (DTMUV) infection in 2011 in China, a DTMUV strain (DTMUV-AH2011) was isolated from the affected ducks. The length of the genome of the DTMUV-AH2011 strain was found to be 11,064 nucleotides and to possess 10,278 nucleotides of one open reading frame (ORF), flanked by 94 nucleotides of the 5′ non-translated region (NTR) and 692 nucleotides of the 3′ NTR. In comparison with five fully sequenced TMUV genomes, the genome of DTMUV-AH2011 had a 74 nucleotide insertion in the 3′ NTR. Comparison of the DTMUV-AH2011 fully deduced amino acid sequences with those of other Tembusu virus strains reported recently in China showed they had a highly conserved polyprotein precursor, sharing 98.9% amino acid identities, at least. The overall divergences of amino acid substitutions were randomly distributed among viral proteins except for the protein NS4B, the protein NS4B was unchanged. Knowledge of the biological characters of DTMUV and the potential role of the insertion in the 3′ NTR in RNA replication will be useful for further studies of the mechanisms of virus replication and pathogenesis.     

2010年福建省流行性乙型脑炎病毒监测

目的掌握福建省自然界蚊虫中乙型脑炎病毒感染率及基因型别特征。方法2010年在福建省三明市、建阳市和福州市采集蚊虫标本,研磨处理后采用乙脑病毒特异性检测引物进行分子筛查。PCR产物直接进行双向测序,应用ATGC、ClustalX（1．83）、MegAlign、GeneDoc3．2和Mega4等生物学软件完成全基因组序列拼接、比对和核苷酸与氨基酸同源性分析、系统进化分析。结果共采集6987只蚊虫标本,主要是三带喙库蚊和中华按蚊。3个监测点均检测到乙脑病毒核酸序列,三明市、建阳市和福州市蚊虫中乙脑病毒带毒率分别为1．25％、1．76％和0．65％。从建阳市采集的三带喙库蚊中扩增出1株乙脑病毒全基因序列,经鉴定所有检测到的乙脑病毒序列均属于基因I型。结论福建省自然界蚊虫中以基因I型乙脑病毒为主。     

Recombination and positive selection identified in complete genome sequences of Japanese encephalitis virus

The mosquito-borne Japanese encephalitis virus (JEV) causes encephalitis in man but not in pigs. Complete genomes of a human, mosquito and pig isolate from outbreaks in 1982 and 1985 in Thailand were sequenced with the aim of identifying determinants of virulence that may explain the differences in outcomes of JEV infection between pigs and man. Phylogenetic analysis revealed that five of these isolates belonged to genotype I, but the 1982 mosquito isolate belonged to genotype III. There was no evidence of recombination among the Thai isolates, but there were phylogenetic signals suggestive of recombination in a 1994 Korean isolate (K94P05). Two sites of the genome under positive selection were identified: codons 996 and 2296 (amino acids 175 of the non-structural protein NS1 and 24 of NS4B, respectively). A structurally significant substitution was seen at NS4B position 24 of the human isolate compared with the mosquito and pig isolates from the 1985 outbreak in Thailand. The potential importance of the two sites in the evolution and ecology of JEV merits further investigation.     

Analysis of a QX-like avian infectious bronchitis virus genome identified recombination in the region containing the ORF 5a, ORF 5b, and nucleocapsid protein gene sequences

The complete genome of a QX-like infectious bronchitis virus (IBV) strain Sczy3 isolated recently in Sichuan was sequenced. The genome contains 27,695 nucleotides (nt), and possesses a genomic structure similar to other IBV strains. Sequence comparisons demonstrated that the Sczy3 genome had the highest nt sequence identity with QX-like IBVs and was most dissimilar to the Massachusetts type IBV. Differences in the sequences of genes present in the Sczy3 genome and other IBVs gene sequences were also identified. Phylogenic analysis showed that the entire genome and most of the Sczy3 genes were located in the same cluster as LX4. Recombination analysis showed that Sczy3 is a chimeric strain derived from LX4 (major parental sequence) and H120 (minor parental sequence) suggesting that recombination occurred in a region containing the 3′ terminal 5a sequence (83 nt), the 5′ terminal 5b sequence (222 nt), and the 5′ terminal nucleocapsid protein gene sequence (132 nt). Mutations and intergenic recombination may have played an important role in the evolution of IBVs.     

新分离登革2型病毒福建株基因组全序列的测定

目的 对新近分离的导致1999年福建省登热流行的登革2型病毒FJ－10株进行基因组全序列测定及系统发生树分析。方法 利用RT－PCR和5′、3′RACE法扩增FJ－10株cDNA,并进行克隆测序,利用DNASTAR折Clustal方法绘制系统发生树。结果 JF－10株基因组全长10723个核苷酸,有1个单一开放读码框架（ORF,第97－10269nt）,编码3391个氨基酸,5′和3′非编码区长度分别为96和454个核苷酸,通过与标准株NGC株和我国其他地区分离株DEN2－04、43、44株比较,核苷酸同源性分别为94.0%、92.8%、93.9%和93.9%,氨基酸同源性分别为97.9%、97.2%、97.7%和97.9%。以47株登革2型病毒E／NS1连接区240个核苷酸序列进行发生树分析,福建株与印度尼西亚和斯里兰卡分离株亲缘关系较近,同属第Ⅳ基因型。结论 FJ－10株基因组全序列一级结构与其他登革2型病毒类似,其基因型不同于我国其他地区分离株DEN2－04、43和44株。     

Molecular characterization of KGH, the first human isolate of rabies virus in Korea

The complete genome sequence of the KGH strain of the first human rabies virus, which was isolated from a skin biopsy of a patient with rabies, whose symptoms developed due to bites from a raccoon dog in 2001. The size of the KGH strain genome was determined to be 11,928 nucleotides (nt) with a leader sequence of 58 nt, nucleoprotein gene of 1,353 nt, phosphoprotein gene of 894 nt, matrix protein gene of 609 nt, glycoprotein gene of 1,575 nt, RNA-dependent RNA polymerase gene of 6,384 nt, and trailer region of 69 nt. Sequence similarity was compared with 39 fully sequenced rabies virus genomes currently available, and the result showed 70.6–91.6 % at the nucleotide level, and 82.8–97.9 % at the amino acid level. The deduced amino acids in the viral protein were compared with those of other rabies viruses, and various functional regions were investigated. As a result, we found that the KGH strain only had a unique amino acid substitution that was identified to be associated either with host immune response and pathogenicity in the N protein, or with a related region regulating STAT1 in the P protein, and related to pathogenicity in G protein. Based on phylogenetic analyses using the complete genome of 39 rabies viruses, the KGH strain was determined to be closely related with the NNV-RAB-H strain and transplant rabies virus serotype 1, which are Indian isolates, and was confirmed to belong to the Arctic-like 2 clade. The KGH strain was most closely related to the SKRRD0204HC and SKRRD0205HC strain when compared with Korean animal isolates, which was separated around the same time and place, and belonged to the Gangwon III subgroup.     

Genomic analysis of a Canadian equine rhinitis A virus reveals low diversity among field isolates

Equine rhinitis A virus (ERAV) is an ubiquitous virus, routinely identified in equine respiratory infections; however, its role in disease and genetic features are not well defined due to a lack of genomic characterization of the recovered isolates. Therefore, we sequenced the full-length genome of a Canadian ERAV (ERAV/ON/05) and compared it with other ERAV sequences currently available in GenBank. The ERAV/ON/05 genome is 7,839 nucleotides (nts) in length with a variable 5′UTR and a more conserved 3′UTR. When ERAV/ON/05 was compared to other reported ERAV isolates, an insertion of 13 nt in the 5′UTR was identified. Further phylogenetic analysis demonstrated that ERAV/ON/05 is closely related to the ERAV/PERV isolate, which was isolated in 1962 in the United Kingdom. The polyprotein of ERAV/ON/05 had a 96 % nucleotide and amino acid sequence identity to reported ERAVs, and it appears that, despite the high error rate of RNA-dependent RNA polymerase, this isolate has retained high sequence identity to the strain first described by Plummer in 1962.