犬圆环病毒全基因组克隆与序列分析

犬圆环病毒(Dog circovirus,DogCV)是近年来新发现的一种哺乳动物圆环病毒。为研究DogCV中国流行毒株基因组特性和遗传进化,以犬血清样品提取的DNA为模板,采用重叠PCR技术首次获得DogCV中国流行毒株的全基因组序列,命名为JZ98/2014。序列分析表明JZ98/2014全基因组长度为2063nt,编码3个主要开放阅读框:ORF V1(Rep蛋白,303个氨基酸)、ORF C1(Cap蛋白,270个氨基酸)和ORF C2(106个氨基酸)。同源性比较显示JZ98/2014与美国、欧洲流行毒株的全基因组序列同源性为82.1%-89.5%,而Rep和Cap基因同源性分别为82.1%-89.5%和84.6%-89.1%。遗传进化树分析显示,目前世界流行的DogCV存在多个分支,而JZ98/2014与美国、欧洲流行毒株处于不同分支。     

牛病毒性腹泻病毒基因组快速进化表现出来的遗传多样性

牛病毒性腹泻病毒（Bovine viral diarrhea virus, BVDV）基因组的高突变性和同源/异源重组性导致其成为一种较难防控的家畜病原体。目前普遍接受的两种基因型是BVDV-1和BVDV-2，其中基因1型含有21个亚型而基因2型含有4个亚型。在流行态势上，BVDV-1无论在遗传多样性还是分离毒株的数量上均高于BVDV-2。虽然BVDV-1和BVDV-2在基因组遗传特征上存在明显的遗传差异，但是其基因组内部特定区域在遗传进化上存在着密切关联。除了病毒基因组自身高变异的特性外，同源/异源RNA重组在BVDV遗传变异进程中也发挥着重要的作用。借助这些遗传进化的途径，BVDV在世界各地的流行传播可以用“随心所欲”来形容。BVDV的流行特征总体表现为基因1型的毒株为主要流行毒株，各基因亚型之间交替更迭并呈现遗传多样性。鉴于BVDV遗传进化的多变性和复杂性，紧密追踪主要流行基因亚型的更迭以及收集不同基因亚型的特征性遗传信息对于制定切实有效的BVDV防控措施具有实际意义。     

猪繁殖与呼吸综合征病毒S1株基因组序列测定和分析

应用RT-PCR方法分段扩增出PRRSV上海分离株S1毒株的4条基因大片段,扩增后的产物分别克隆于pCR-XL-TOPO载体鉴定后测序,同时应用RACE方法对S1毒株的3'和5'基因末端进行了成功的扩增并克隆于pMD-18T载体进行测序,按顺序将这些序列进行拼接得到PRRSV S1株全基因组cDNA序列.测序结果表明PRRSV S1株基因组全长15441 bp,包含9个开放式阅读框,5'UTR含有189nt,3'端UTR含有181nt,其中包含30nt Poly (A).基因组序列分析结果显示该病毒与ATCC VR-2332和BJ-4分离株的核苷酸同源性分别99.5%和99.6%.与另一国内分离株CH-1a的核苷酸同源性为90.8%.     

福建一例HAstV-5型星状病毒的全基因组测序与重组分析

为了探究一例福建省检出的HAstV-5型星状病毒2013/Fuzhou/85毒株基因组分子结构特点,本研究采用PCR分段扩增、测序、拼接的方法,获得2013/Fuzhou/85毒株基因组序列全长6 803bp:5’端和3’端均有85bp非编码区;中间3个开放阅读框:ORF1a长2 802bp(86～2 887nt),编码非结构蛋白丝氨酸蛋白酶;ORF1b长1 548bp(2 827～4 374nt),编码非结构蛋白RNA聚合酶;ORF2长2 352bp(4 367～6 718nt),编码结构蛋白衣壳蛋白前体。目前,GenBank中仅有两株HAstV-5型星状病毒全基因组序列:中国辽宁毒株(JQ403108)和巴西哥亚尼亚毒株(DQ028633),2013/Fuzhou/85毒株和中国辽宁毒株核苷酸相似度最高,达94.4%。对该HAstV-5型星状病毒3个开放阅读框分别构建系统进化树,发现ORF1a与HAstV-1(JF327666)相似度最高,ORF1b和ORF2与HAstV-5(JQ403108)相似度最高,提示其有可能存在重组,用Simplot软件进行重组分析,重组位点位于2 741bp,在ORF1a和ORF1b重叠区的上游。本研究中对2013/Fuzhou/85毒株的全基因组测序和重组分析,可以为星状病毒的重组和遗传进化规律研究提供参考。     

猪瘟弱毒C81株全基因组测序及分子结构预测

参照已发表的猪瘟病毒弱毒株的序列,设计7对覆盖全长基因组的引物,通过RT-PCR从感染猪瘟病毒弱毒株的PK-15细胞中扩增得到7个cDNA片段,分别克隆到pMD18-T载体并测序,利用DNASIS软件获得猪瘟病毒C81株全基因组序列(GenBankAY663656).C81株基因组全长12310nt,只有一个大的开放阅读框,编码3898个氨基酸的聚蛋白.序列分析表明,C81株开放阅读框与其它各毒株核苷酸和氨基酸序列的同源性变化较大,分别为84.4%～99.6%和91.6%～99.4%.同时,我们绘制了26株CSFV ORF的进化树,比较了CSFV 5'非翻译区核苷酸序列并推测其二级结构,发现不同毒株之间存在较大的差异,另外对C81株聚蛋白的功能域和三维结构进行了预测.     

Asia1型口蹄疫病毒第V群猪源和牛源毒株全基因组比较分析

为了查明Asia1型FMDV第Ⅴ群猪源和牛源毒株的序列差异, 采用RT-PCR方法, 对Asia1型FMDV第Ⅴ群猪源分离毒株Asia1/HN/06的基因组全序列进行了扩增和测序, 并与第Ⅴ群牛源和猪源参考毒株基因组进行比较分析。结果表明, Asia1/HN/06毒株全基因组序列长约8236 nt [含38个A的poly(A)尾], 其中5'NCR长1116 nt, 前导蛋白(L)编码区长603 nt, 结构蛋白与非结构蛋白编码区的核苷酸序列为6990 nt, 3'NCR长93 nt, 3￠端是至少含有38个A的poly(A)尾巴。猪源毒株和牛源毒株的全基因比较分析表明, 属于第Ⅴ群, 全基因编码区核苷酸和氨基酸的同源性均为98.0%, 主要差别是猪源毒株Asia1/HN/06在细胞受体结合位点变为RDD和155位置的N变为S或D, 该群毒株3A更具有猪源毒株特征, 有4个特异性氨基酸变异。明确了Asia1型FMDV第Ⅴ群猪源和牛源毒株的序列差异, 为进一步利用反向遗传技术研究猪源和牛源毒株差异位点或基因在病毒表型变异中的作用奠定基础。     

猪瘟弱毒C81株全基因组测序及分子结构预测

参照已发表的猪瘟病毒弱毒株的序列,设计7对覆盖全长基因组的引物,通过RT-PCR从感染猪瘟病毒弱毒株的PK-15细胞中扩增得到7个cDNA片段,分别克隆到pMD18-T载体并测序,利用DNASIS软件获得猪瘟病毒C81株全基因组序列(GenBank:AY663656)。C81株基因组全长12310nt,只有一个大的开放阅读框,编码3898个氨基酸的聚蛋白。序列分析表明,C81株开放阅读框与其它各毒株核苷酸和氨基酸序列的同源性变化较大,分别为84.4%~99.6%和91.6%~99.4%。同时,我们绘制了26株CSFVORF的进化树,比较了CSFV5'非翻译区核苷酸序列并推测其二级结构,发现不同毒株之间存在较大的差异,另外对C81株聚蛋白的功能域和三维结构进行了预测。     

系统发生分析发现牛病毒性腹泻病病毒新基因亚型

本研究对我国首次分离获得的牛源牛病毒性腹泻病毒(BVDV)毒株Changchun 184(CC-184)和猪源牛病毒性腹泻病毒ZM-95进行了遗传衍化关系研究.选择主要抗原E2基因为研究对象,首先应用RT-PCR及套式PCR克隆得到CC-184和ZM-95的E2片段,通过序列测定发现CC-184和ZM-95 E2基因长度分别为1,122bp和1,125bp,各自编码374和375个氨基酸残基.核酸序列同源性比较和系统发生分析表明2株病毒均属于BVDV-1,CC-184与Osloss亲缘关系最近,都属于已有的b基因亚型,其E2基因同源性达91.8%.而ZM-95的E2基因有一个特征性的变异区,包含一个密码子序列插入,这一变异区编码了一段有别于其他瘟病毒的五肽氨基酸序列HYKKK.结果还表明ZM-95与BVDV-1现有的5个基因亚型的亲缘关系均较远,E2基因同源性最高(与Oregonc24v)只有72.4%.而BVDV 1亚型内毒株间的同源性大于85%,亚型间的同源性在69%～75%之间,充分说明ZM-95是BVDV-1中一个新发现的基因亚型.通常认为猪源BVDV来源于牛,应该与牛源BVDV有十分近的遗传关系,但是本研究发现ZM-95与其他已知牛源BVDV较低的基因同源性说明猪源BVDV还具有独立的遗传衍化与传播来源的可能性.     

我国登革 4型病毒 B5株基因组全序列的测定及分析(英文)

 对我国登革 4型病毒 B5株 (D4- B5)基因组进行全序列测定及分析 ,为研究病毒基因组结构与功能的关系及研制新型登革疫苗奠定基础 .根据登革 4型病毒 81 4669株的序列设计特异引物 ,通过 RT- PCR扩增出 D4- B5株不同长度的片段 ,分别克隆到 p GEM- T载体 ,将挑取的阳性克隆进行 PCR、酶切鉴定及序列测定 .结果显示 ,D4- B5株的基因组全长 1 0 665nt,5′和 3′非编码区分别为 1 0 1 nt和 40 3nt,中间一个长 1 0 1 61 nt的开放读码框架 ,编码 3387个氨基酸 .与 D4- 81 4669株比较 ,两者核苷酸序列同源性为 93.0 8% ,氨基酸序列同源性为 96.58% .D4- B5株的基因组全序列与 D4- 81 4669株类似 ,但也有较大差异 .同源进化分析表明 ,D4- B5株的基因型为 型 ,与登革 4型病毒菲律宾分离株亲缘关系较近 .这是首次报道的我国登革 4型病毒分离株基因组全序列 ,对研究病毒基因组结构与功能的关系 ,探讨我国毒株的地理来源及研制适合我国人群的新型登革疫苗具有一定的意义 .     

新异养硝化菌Colloides sp.JZ1-1的鉴定及其硝化性能

从驯化后的活性污泥中筛分、诱变出一株性能较好的异养硝化菌JZ1-1.经形态及生理生化特性分析,鉴定菌株JZ1-1为胶样菌属(Colloides sp.).分别考察了碳源、C/N、pH、溶解氧、温度和铵态氮初始浓度对JZ1-1硝化性能的影响.结果表明:菌株对柠檬酸钠的利用较好;C/N为10 ～14、30℃、pH 6-9和转速150 r·min-1以上有利于铵态氮的降解;菌株对中高浓度铵态氮废水(100 mg·L-1≤铵态氮浓度≤500 mg·L-1)的降解效果显著.经5次继代培养,菌株的稳定性较好.     

新异养硝化菌Colloidessp. JZ1-1的鉴定及其硝化性能

从驯化后的活性污泥中筛分、诱变出一株性能较好的异养硝化菌JZ1-1.经形态及生理生化特性分析,鉴定菌株JZ1-1为胶样菌属(Colloides sp.).分别考察了碳源、C/N、pH、溶解氧、温度和铵态氮初始浓度对JZ1-1硝化性能的影响.结果表明: 菌株对柠檬酸钠的利用较好;C/N为10～14、30 ℃、pH 6-9和转速150 r·min^-1以上有利于铵态氮的降解;菌株对中高浓度铵态氮废水（100 mg·L^-1≤铵态氮浓度≤500 mg·L^-1）的降解效果显著.经5次继代培养,菌株的稳定性较好.     

Viremia and virus shedding in elk infected with type 1 and virulent type 2 bovine viral diarrhea virus

In order to determine whether elk (Cervus elaphus) could be infected with and shed bovine viral diarrhea virus (BVDV) and to determine whether BVDV could cause disease in elk, two groups of five yearling elk each and two control cattle were experimentally inoculated intranasally with type 1 Singer strain or a virulent type 2 isolate of BVDV, strain 24515. Virulence of the type 2 isolate was confirmed by inoculation of a control bovine cow which developed diarrhea, dehydration, severe thrombocytopenia, hemorrhages, and enteritis with intestinal necrosis. None of the elk inoculated with type 1 or type 2 BVDV developed clinical signs of illness. However, all elk became infected as demonstrated by viremia, nasal shedding, and/or seroconversion. One uninoculated, in-contact elk contracted type 1 BVDV and seroconverted. Thus, although BVDV does not appear capable of producing disease in nonpregnant elk, the species is susceptible to infection and can shed and transmit BVDV.     

The impact of BVDV infection on adaptive immunity

Bovine viral diarrhea virus (BVDV) causes immunosuppression of the adaptive immune response. The level of suppression of the adaptive immune response is strain dependent. The early events of antigen presentation require activation of toll-like receptors that results in the release of pro-inflammatory cytokines. Non-cytopathic (ncp) BVDV infection stimulates cytokines from macrophages in vitro but the effect of BVDV infection in vivo on macrophages or in vitro with monocytes is not clear. Antigen presentation is decreased and co-stimulatory molecules are down regulated. T-lymphocytes numbers are reduced following BVDV infection in a strain dependent manner. There is recruitment of lymphocytes to the bronchial alveolar space following cytopathic (cp) BVDV infection. Depletion of T-lymphocytes occurs in the lymphoid tissue and is strain dependent. BVDV cp T-lymphocyte responses appear to be primarily a T helper 1 response while the response following ncp BVDV induces a T helper 2 response. Cytotoxic T-lymphocytes (CTL), an important BVDV defense mechanism are compromised. The major neutralizing antigens are well characterized but cross-protection between strains is variable. PI animals have normal adaptive immune responses with the exception of the PI strain immunotolerance and mucosal disease may be a function of the level of gamma delta T cells.     

Cytopathogenicity of a pestivirus correlates with a 27-nucleotide insertion.

Cytopathogenic (cp) bovine viral diarrhea virus (BVDV) strains are generated in cattle persistently infected with noncytopathogenic (noncp) BVDV.cp BVDV strains are considered crucial for the development of fatal mucosal disease. Comparative analysis of cp and noncp BVDV strains isolated from one animal suffering from mucosal disease revealed that the genomes of the cp BVDV strain (CP7) and the corresponding noncp BVDV strain (NCP7) are highly homologous. However, only the genome of CP7 contains an insertion of 27 nucleotides in the NS2 coding region. The inserted sequence represents a duplication of bases 4064 to 4090 of the viral genome, located between the formerly neighboring nucleotides 4353 and 4354. Parts of the viral polyproteins of CP7 and NCP7 were expressed in the T7 vaccinia virus system. These studies revealed that the insertion identified in the CP7 genome is necessary and sufficient for the induction of NS2-3 cleavage. Since the expression of NS3 is strictly correlated to cp BVDV, the insertion identified in the genome of BVDV CP7 represents most likely the relevant mutation leading to the evolvement of CP7 from NCP7.     

Maternal antibody blocks humoral but not T cell responses to BVDV.

Bovine viral diarrhoea virus (BVDV) contributes significantly to health-related economic losses in the beef and dairy industry. Antibodies of maternal origin can be protective against BVDV infection, however, calves with low titres of maternal antibody or that do not receive colostrum may be at risk for acute BVDV infection. Interference by high titres of maternal antibodies prevents the development of an antibody response following vaccination with either a killed or attenuated BVDV vaccine. However, the T cell mediated immune response to BVDV may be generated in the absence of a detectable serum neutralizing antibody response. Two trials were conducted to evaluate the potential to elicit T cell mediated immune responses to BVDV in calves with circulating maternal antibody to BVDV. In the first trial, calves with high levels of circulating maternal antibody to BVDV 1 and BVDV 2 were experimentally infected with BVDV 2 (strain 1373) at two to five weeks of age. The T-cell mediated immune responses of the experimentally infected calves and non-infected calves were monitored monthly until circulating maternal antibody was no longer detectable in either treatment group. Calves experimentally infected with BVDV developed BVDV specific CD4(+), CD8(+), and delta T cell responses while high levels of maternal antibody were circulating. A second challenge with BVDV 2 (strain 1373) was performed in the experimentally infected and control calves once maternal antibody could no longer be detected. Previous exposure to BVDV in the presence of maternal antibody protected calves from clinical signs of acute BVDV infection compared to the control calves. In the second trial, three groups of calves with circulating maternal antibody to BVDV were given either a modified live vaccine (MLV) containing BVDV 1 and BVDV 2, a killed vaccine containing BVDV 1 and BVDV 2, or no vaccine, at seven weeks of age. Serum neutralizing antibody levels and antigen specific T cell responses were monitored for 14 weeks following vaccination. Calves vaccinated with MLV BVDV developed BVDV 1 and BVDV 2 specific CD4(+)T cell responses, and BVDV 2 specific gammadelta T cell responses, in the presence of maternal antibody. Vaccination with killed BVDV did not result in the generation of measurable antigen specific T cell immune responses. In this trial, a second vaccination was performed at 14 weeks to determine whether an anamnestic antibody response could be generated when calves were vaccinated in the presence of maternal antibody. Calves vaccinated with either a MLV or killed BVDV vaccine while they had maternal antibody developed an anamnestic antibody response to BVDV 2 upon subsequent vaccination. The results of these trials indicate that vaccinating young calves against BVD while maternal antibody is present may generate BVDV specific memory T and B cells. The data also demonstrated that seronegative calves with memory T and B cells specific for BVDV may be immune to challenge with virulent BVDV.     

Bovine Viral Diarrhea Virus Strain Oregon: a Novel Mechanism for Processing of NS2-3 Based on Point Mutations

Bovine viral diarrhea virus (BVDV) isolates can either be cytopathogenic (cp) or noncytopathogenic (noncp). While both biotypes express the nonstructural protein NS2-3, generation of NS3 strictly correlates with the cp phenotype. The production of NS3 is usually caused by cp specific genome alterations, which were found to be due to RNA recombination. Molecular analyses of the cp BVDV strain Oregon revealed that it does not possess such genome alterations but nevertheless is able to generate NS3 via processing of NS2-3. The NS3 serine protease is not involved in this cleavage, which, according to protein sequencing, occurs between amino acids 1589 and 1590 of the BVDV Oregon polyprotein. Transient-expression studies indicated that important information for the cleavage of NS2-3 is located within NS2. This was verified by expression of chimeric constructs containing cDNA fragments derived from BVDV Oregon and a noncp BVDV. It could be shown that the C-terminal part of NS2 plays a crucial role in NS2-3 cleavage. These data, together with results obtained by site-specific exchanges in this region, revealed a new mechanism for NS2-3 processing which is based on point mutations within NS2.