应用两种基因组快速扩增方法进行病毒芯片杂交鉴定

为了摸索均衡的病毒基因组扩增方法,建立高通量的病毒检测基因芯片技术平台,本研究以甲病毒属的辛德比斯病毒作为检测模型,分别以随机PCR扩增法和MDA( Multiple Displacement Amplification)扩增法扩增病毒基因组,并以两种扩增产物作为模板,扩增辛德比斯病毒的特异基因片段以验证基因组扩增的均衡性;然后将两种基因组扩增产物标记荧光染料后与基因芯片进行杂交;结果表明从两种基因组扩增产物中正确扩增出了辛德比斯的特定基因片段,作为探针可与基因芯片上的靶标基因特异性结合;基因组扩增产物与基因芯片进行杂交,可成功检测到甲病毒属的特异性信号,充分说明随机PCR扩增法和MDA扩增法用于扩增病毒基因组均具有良好的均衡性,扩增产物可用于病毒性病原体的基因芯片检测。     

First complete genome sequence of garlic virus X infecting Allium sativum- G282 from India

The present report communicates the first full genome sequencing of the Garlic virus X from northern India. The total genome size of Garlic virus X (MK503771) reported in this study is 8458 bp ssRNA. The full genome sequence analysis showed the close relationship of Garlic virus X from India to that of from China, Korea, Australia and Spain. The full genome sequence based study of Indian Garlic virus X reveals the geographical relationship of this virus in India and global origin which may assists in development of control strategy for this virus.     

Characterization of the genome of the murine papovavirus K.

The DNA genome of the murine papovavirus K virus (KV) was characterized and compared with the genome of polyoma virus. A physical map of the KV genome was constructed by analysis of the size of DNA fragments generated by sequential cleavage with combinations of restriction endonucleases. By using one of the three EcoRI sites in the KV genome as the 0 map position, the KV physical map was then oriented to the polyoma virus genome. Of 42 restriction sites mapped within the KV genome, 7 were localized within 0.01 map unit of their respective sites in the polyoma virus genome; an eighth site mapped within 0.02 map unit. KV replication was examined and found to be bidirectional, initiating at approximately 0.70 map unit. This corresponds well to the origin of replication within the polyoma virus genome and further supports the orientation of the KV physical map.     

Analysis of the myeloproliferative sarcoma virus genome: limited changes in the prototype lead to altered target cell specificity.

The myeloproliferative sarcoma virus (MPSV) derived from Moloney sarcoma virus (MSV-Mol) is a unique sarcoma virus which causes expansion of the hematopoietic stem cell compartment as well as the erythroid and myeloid cell lineages. MPSV also induces spleen focus formation in adult mice as do Friend and Rauscher viruses. Analysis of the MPSV genome on methyl mercury gels showed that the genome size is 7.0 kilobases, which is larger than the defective genome of any known MSV-Mol isolate. Hybridization analysis with specific cDNA probes showed that MPSV is a modified sarcoma virus with no sequences in the unique region of the defective sarcoma genome related to unique Friend virus sequences. The only viral sequences in the defective genome other than helper virus-related sequences are derived from the Moloney sarcoma virus genome with no new cellular sequences added. There was no evidence for induction of xenotropic virus sequences in MPSV-infected spleens of DBA/2J mice, indicating that spleen focus formation can be obtained by different mechanisms.     

Identification of nucleotide sequences which may encode the oncogenic capacity of avian retrovirus MC29.

The retrovirus strain MC29 induces a variety of tumors in chickens, including myelocytomatosis and carcinomas of the kidney and liver. In addition, the virus can transform cultures of embryonic avian macrophages and fibroblasts. We have characterized the genome of MC29 virus and have identified nucleotide sequences that may encode the oncogenic potential ofthe virus. MC29 virus can replicate only with the assistance of a related helper virus. The defect in replication is apparently a consequence of a deletion in one or more viral genes: the haploid genome of the MC29 virus has a molecular weight of ca. 1.7 X 10(6), whereas the genome of the helper virus MCAV has a molecular weight of ca. 3.1 X 10(6). Although MC29 virus transforms fibroblasts in culture, its genome has no detectable homology with the gene src that is responsible for transformation of fibroblasts by avian sarcoma viruses. We prepared radioactive single-stranded DNA complementary to nucleotide sequences present in the genome of MC29 virus but not in the genome of MCAV (cDNA(MC29)). If they are contiguous, these sequences (ca. 1,500 nucleotides) are sufficiently complex to encode at least one protein. Homologous sequences were not detectable in several strains of avian sarcoma viruses or in an endogenous virus of chickens. Our findings confirm and extend recent reports from other laboratories and lead to the conclusion that MC29 virus may contain a previously unidentified gene(s) that is capable of transforming several distinct target cells. The evolutionary origins of this putative gene and its location on the viral genome can be explored with cDNA(MC29).     

Adeno-associated virus vectors.

Adeno-associated virus is a human parvovirus that integrates its DNA genome into host cell chromosomes with very high efficiency. This suggests that adeno-associated virus may be a useful vector for human gene therapy. Interest in adeno-associated virus vectors increased greatly in the last year following reports that adeno-associated virus genome integration may be site specific and occur at preferred sites in the human genome. Several genes relevant to the treatment of genetic or infectious diseases have been expressed in adeno-associated virus vectors in vitro.     

Structure and origin of a novel class of defective interfering particle of vesicular stomatitis virus

The genome structure and terminal sequences of a 'copyback' defective interfering (DI) particle ST1, and a novel complexly rearranged 'snapback' DI particle ST2 of vesicular stomatitis virus have been determined. The ST1 DI genome RNA possesses 54 base long inverted complementary termini, the 5' end of which is homologous to the standard virus genome 5' end. Following this region of inverted complementarity the DI RNA 5' end continues to be homologous to standard virus RNA 5' sequences, whereas the 3' end diverges into sequences within the virus L gene internal sequences. ST2 DI genome RNA does not contain colinear covalently linked plus and minus sense RNA copies of the standard infectious virus RNA 5' terminus as predicted from the prototype snapback DI structure, but instead appears to be a hairpin copy of the ST1 DI RNA genome. This is the first evidence suggesting that DI particles may be generated from RNA templates other than the standard virus RNA. Generation models and the implications of these findings for RNA virus evolution are discussed.     

流感病毒的分子生物学研究进展

流感病毒是分节段的负链RNA病毒,由RNA依赖的RNA聚合酶起始病毒的复制。流感病毒的特殊基因组结构和病毒蛋白的功能使其极易发生抗原转换和抗原漂移,这使得病毒能够逃避多种宿主的长效中和性免疫反应。本文从病毒结构、基因组及其编码蛋白质、病毒复制过程和病毒的易感宿主等几方面论述了流感病毒的分子生物学研究进展。     

传染性法氏囊病病毒多聚蛋白基因在家蚕中的表达

将传染性法氏囊病病毒(IBDV)细胞致弱株(JD1株)的基因组A节段基因重组于家蚕杆状病毒转移载体pAcHLT-C中,获得的重组转移载体pAcHLT-C-A与线性化病毒Bm-BacPAK6 DNA共转染家蚕培养细胞,获得重组病毒BacPAK-A。DIG标记的DNA点杂交证实重组病毒基因组中含有A节段基因,重组病毒感染家蚕5龄幼虫进行表达, ELISA和Western blotting等结果表明多聚蛋白基因在蚕体内得到了表达,表达产物具有免疫反应性,表达量在感染后5～6 d达到最高。家蚕生物反应器表达IBDV多聚蛋白具有我国的资源优势,为今后研制低成本、实用化的IBDV基因工程疫苗打下基础。     

Cloning of infectious adeno-associated virus genomes in bacterial plasmids

We describe the construction of two Escherichia coli hybrid plasmids, each of which contains the entire 4.7-kb DNA genome of the human parvovirus, adeno-associated virus (AAV) type 2. Because the AAV genome was inserted into the plasmid DNA using BglII linkers the entire virus genome can be recovered by in vitro cleavage of the purified recombinant plasmid. Transfection of these recombinant DNAs into an adenovirus-transformed human cell line in the presence of helper adenovirus resulted in efficient rescue and replication of the AAV genome and production of fully infectious virus particles. These AAV-plasmid recombinant DNA molecules should be useful both for site-specific mutagenesis of the viral genome and to study the potential of AAV as a eukaryotic vector.     

Herpes simplex virus co-infection facilitates rolling circle replication of the adeno-associated virus genome

Adeno-associated virus (AAV) genome replication only occurs in the presence of a co-infecting helper virus such as adenovirus type 5 (AdV5) or herpes simplex virus type 1 (HSV-1). AdV5-supported replication of the AAV genome has been described to occur in a strand-displacement rolling hairpin replication (RHR) mechanism initiated at the AAV 3’ inverted terminal repeat (ITR) end. It has been assumed that the same mechanism applies to HSV-1-supported AAV genome replication. Using Southern analysis and nanopore sequencing as a novel, high-throughput approach to study viral genome replication we demonstrate the formation of double-stranded head-to-tail concatemers of AAV genomes in the presence of HSV-1, thus providing evidence for an unequivocal rolling circle replication (RCR) mechanism. This stands in contrast to the textbook model of AAV genome replication when HSV-1 is the helper virus.     

一株重组乙型肝炎病毒的全基因克隆和序列分析

通过血清学和PCR方法对广西地区乙型肝炎病毒感染者样本进行检测,发现一株乙型肝炎病毒基因序列与其余病毒差异较大,利用PCR的方法,扩增出该株病毒的全长cDNA序列,并将其克隆到T载体,进行序列测定,结果显示基因全长为3 215bp,血清型为adr.将测定序列与网上公布的标准基因序列进行比对分析,发现该株病毒全基因组序列进化分析结果与C型基因比较接近,而对其全基因组进行分析时发现1 630bp～2 880bp间基因起源与和C型基因最为接近,而其余基因序列则与A型基因更接近,提示这是一株C型和A型重组的乙型肝炎病毒,首次在国内发现这种类型的基因重组病毒,丰富了我国乙型肝炎病毒研究内容,并对基因型别研究和病毒进化研究提供了参考.     

Deep sequencing of small RNAs in tomato for virus and viroid identification and strain differentiation

Small RNAs (sRNA), including microRNAs (miRNA) and small interfering RNAs (siRNA), are produced abundantly in plants and animals and function in regulating gene expression or in defense against virus or viroid infection. Analysis of siRNA profiles upon virus infection in plant may allow for virus identification, strain differentiation, and de novo assembly of virus genomes. In the present study, four suspected virus-infected tomato samples collected in the U.S. and Mexico were used for sRNA library construction and deep sequencing. Each library generated between 5-7 million sRNA reads, of which more than 90% were from the tomato genome. Upon in-silico subtraction of the tomato sRNAs, the remaining highly enriched, virus-like siRNA pools were assembled with or without reference virus or viroid genomes. A complete genome was assembled for Potato spindle tuber viroid (PSTVd) using siRNA alone. In addition, a near complete virus genome (98%) also was assembled for Pepino mosaic virus (PepMV). A common mixed infection of two strains of PepMV (EU and US1), which shared 82% of genome nucleotide sequence identity, also could be differentially assembled into their respective genomes. Using de novo assembly, a novel potyvirus with less than 60% overall genome nucleotide sequence identity to other known viruses was discovered and its full genome sequence obtained. Taken together, these data suggest that the sRNA deep sequencing technology will likely become an efficient and powerful generic tool for virus identification in plants and animals.     

黄病毒基因组非编码区的结构与功能研究进展

黄病毒科黄病毒属是由一组含单股正链RNA基因组的囊膜病毒组成,包括登革病毒、流行性乙型脑炎病毒、寨卡病毒、西尼罗病毒、黄热病病毒等,经由虫媒传播,可引起人类和动物的严重虫媒病毒病。黄病毒基因组由1个开放阅读框、5′非编码区和3′非编码区三部分组成。5′和3′非编码区含有病毒基因组复制所必需的启动元件;高度结构化的3′非编码区负责黄病毒亚基因组RNA的产生,从而有助于病毒逃避宿主免疫反应;此外3′非编码区还可作为疫苗研究的靶标。鉴于非编码区在黄病毒的蛋白翻译、基因组复制和免疫调节中发挥的重要作用,本文就黄病毒基因组非编码区的结构与功能最新研究进展作一简要综述。     

中国小反刍兽疫病毒分离株China/Tib/07全基因组序列测定与分析

小反刍兽疫病毒属于副黏病毒科麻疹病毒属成员。本研究对我国首次分离的小反刍兽疫病毒株China/Ti-bet/07进行了全基因组序列测定及分子生物学特征分析。根据GenBank公布的小反刍兽疫病毒基因组序列设计引物通过RT-PCR扩增病毒基因组内部序列,通过3′和5′-RACE获得病毒基因组末端序列。序列测定与分析的结果表明,China/Tib/07株全长15948bp,预测编码6种结构蛋白和2种非结构蛋白,与已发表小反刍兽疫病毒基因组的长度和结构相似;在系统进化上与西南亚流行毒株有很高的同源性(91.6%～98.1%);与麻疹病毒属的其它成员相比,与牛瘟病毒的同源性最高(64.3%)。     

The impact of temperature on the inactivation of enteric viruses in food and water: a review

Temperature is considered as the major factor determining virus inactivation in the environment. Food industries, therefore, widely apply temperature as virus inactivating parameter. This review encompasses an overview of viral inactivation and virus genome degradation data from published literature as well as a statistical analysis and the development of empirical formulae to predict virus inactivation. A total of 658 data (time to obtain a first log(10) reduction) were collected from 76 published studies with 563 data on virus infectivity and 95 data on genome degradation. Linear model fitting was applied to analyse the effects of temperature, virus species, detection method (cell culture or molecular methods), matrix (simple or complex) and temperature category (<50 and ≥50°C). As expected, virus inactivation was found to be faster at temperatures ≥50°C than at temperatures <50°C, but there was also a significant temperature-matrix effect. Virus inactivation appeared to occur faster in complex than in simple matrices. In general, bacteriophages PRD1 and PhiX174 appeared to be highly persistent whatever the matrix or the temperature, which makes them useful indicators for virus inactivation studies. The virus genome was shown to be more resistant than infectious virus. Simple empirical formulas were developed that can be used to predict virus inactivation and genome degradation for untested temperatures, time points or even virus strains.