Complete Genome Sequence of the First Chinese Virulent Infectious Laryngotracheitis Virus

Infectious laryngotracheitis (ILT) is an acute respiratory disease caused by infectious laryngotracheitis virus (ILTV). The complete genome sequences of five attenuated ILTV vaccine strains and six virulent ILTV strains as well as two Australian ILTV field strains have been published in Australia and the USA so far. To provide the complete genome sequence information of ILTVs from different geographic regions, the whole genome of ILTV LJS09 isolated in China was sequenced. The genome of ILTV LJS09 was 153,201 bp in length, and contained 79 ORFs. Most of the ORFs had high sequence identity with homologous ORFs of reference strains. There was a large fragment deletion within the noncoding region of unique long region (U_L) of ILTV LJS09 compared with SA2 and A20 strains. Though the origin binding protein of ILTV LJS09 existed, there was no AT-rich region in strain LJS09. Alignments of the amino acid sequences revealed seven mutations at amino acids 71 (Arg → Lys), 116 (Ala → Val), 207 (Thr → Ile) and 644 (Thr → Ile) on glycoprotein B, 155 (Phe → Ser) and 376 (Arg → His) on glycoprotein D and 8 (Gln→Pro) on glycoprotein L of ILTV LJS09 compared to those of virulent strain (USDA) as ILTV LJS09 did not grow on chicken embryo fibroblasts, suggesting the role of the key seven amino acids in determination of the cell tropism of ILTV LJS09. This is the first complete genome sequence of the virulent strain of ILTV in Asia using the conventional PCR method, which will help to facilitate the future molecular biological research of ILTVs.     

伪狂犬病病毒Ea株基因组UL区的克隆与序列分析

从伪狂犬病病毒Ea株基因组DNA中扩增到3.76 kb的基因组片段,该片段包含UL31、UL32、UL33和UL34基因完整编码区,以及UL30和UL35基因部分序列.UL31、UL32、UL33和UL34基因G+C含量为69.5%~73.4%,偏向于使用富含GC特别是第三密码子位置上核苷酸是C或G的密码子,Ala、Leu、Arg的利用率最高,占氨基酸残基总数的36.4%.PRV Ea株UL31和UL32基因与PRV Ka株核苷酸与氨基酸序列同源性都很高,在98%以上;而UL33和UL34基因与Ka株的氨基酸序列同源性较低,分别为95.7%和94.8%.UL31基因在疱疹病毒α-亚科所有成员之间都很保守,并且UL31基因与马疱疹病毒IV型同源程度最高.UL32、UL33和UL34基因均与牛疱疹病毒I型同源程度最高.UL31、UL32、UL33与UL34基因产物均有酪蛋白激酶2磷酸化位点和蛋白激酶C磷酸化位点,表明UL31、UL32、UL33、UL34蛋白质可能都是磷酸化蛋白质.     

伪狂犬病病毒Ea株基因组UL区的克隆与序列分析

从伪狂犬病病毒Ea株基因组DNA中扩增到3．76kb的基因组片段,该片段包含UL31、UL32、UL33和UL34基因完整编码区,以及UL30和UL35基因部分序列。UL31、UL32、UL33和UL34基因G C含量为69．5％～73．4％,偏向于使用富含GC特别是第三密码子位置上核苷酸是C或G的密码子,Ala、Leu、Arg的利用率最高,占氨基酸残基总数的36．4％。PRV Ea株UL31和UL32基因与PRV Ka株核苷酸与氨基酸序列同源性都很高,在98％以上;而UL33和UL34基因与Ka株的氨基酸序列同源性较低,分别为95．7％和94．8％。UL31基因在疱疹病毒α—亚科所有成员之间都很保守,并且UL31基因与马疱疹病毒IV型同源程度最高。UL32、UL33和UL34基因均与牛疱疹病毒I型同源程度最高。UL31、UL32、UL33与UL34基因产物均有酪蛋白激酶2磷酸化位点和蛋白激酶C磷酸化位点,表明UL31、UL32、UL33、UL34蛋白质可能都是磷酸化蛋白质。     

Full Genome Sequence-Based Comparative Study of Wild-Type and Vaccine Strains of Infectious Laryngotracheitis Virus from Italy

Infectious laryngotracheitis (ILT) is an acute and highly contagious respiratory disease of chickens caused by an alphaherpesvirus, infectious laryngotracheitis virus (ILTV). Recently, full genome sequences of wild-type and vaccine strains have been determined worldwide, but none was from Europe. The aim of this study was to determine and analyse the complete genome sequences of five ILTV strains. Sequences were also compared to reveal the similarity of strains across time and to discriminate between wild-type and vaccine strains. Genomes of three ILTV field isolates from outbreaks occurred in Italy in 1980, 2007 and 2011, and two commercial chicken embryo origin (CEO) vaccines were sequenced using the 454 Life Sciences technology. The comparison with the Serva genome showed that 35 open reading frames (ORFs) differed across the five genomes. Overall, 54 single nucleotide polymorphisms (SNPs) and 27 amino acid differences in 19 ORFs and two insertions in the UL52 and ORFC genes were identified. Similarity among the field strains and between the field and the vaccine strains ranged from 99.96% to 99.99%. Phylogenetic analysis revealed a close relationship among them, as well. This study generated data on genomic variation among Italian ILTV strains revealing that, even though the genetic variability of the genome is well conserved across time and between wild-type and vaccine strains, some mutations may help in differentiating among them and may be involved in ILTV virulence/attenuation. The results of this study can contribute to the understanding of the molecular bases of ILTV pathogenicity and provide genetic markers to differentiate between wild-type and vaccine strains.     

鸡传染性喉气管炎病毒gB基因的克隆及其在耻垢分枝杆菌中的表达

以ILTV基因组为模板 ,利用PCR特异扩增出gB基因 ,定向克隆到中间质粒载体pY_α ,构建了中间质粒pY_α_gB。然后以中间质粒pY_α_gB为模板 ,扩增出含有人结核分枝杆菌启动子hsp70基因和堪萨斯分枝杆菌α信号肽基因的hsp_α_gB片段 ,回收补平后与穿梭表达载体pRR3平端连接 ,从而构建大肠杆菌_分枝杆菌穿梭表达质粒pR_α_gB。再将其电转化至耻垢分枝杆菌M .smegmatismc2 15 5 ,ELISA检测表明重组菌株M .smegmatismc2 15 5 (pR_α_gB)的表达产物具有很好的反应原性。Westernblot检测说明gB基因在分枝杆菌中获得了表达并具有良好的免疫原性。鸡胚中和试验结果表明该重组菌株可以中和 1个剂量EID50 的ILTV强毒 ,能够保护SPF鸡胚抵抗强毒攻击     

Ilarviruses Encode a Cucumovirus-Like 2b Gene That Is Absent in Other Genera within the Bromoviridae

We found that RNA 2 of the four ilarviruses sequenced to date encodes an additional conserved open reading frame (ORF), 2b, that overlaps the 3′ end of the previously known ORF, 2a. A novel RNA species of 851 nucleotides was found to accumulate to high levels in plants infected with spinach latent virus (SpLV). Further analysis showed that RNA 4A is a subgenomic RNA of RNA 2 and encodes all of ORF 2b. Moreover, a protein species of the size expected for SpLV ORF 2b was translated in vitro from the RNA 4A-containing virion RNAs. The data support the suggestion that the SpLV 2b protein is translated in vivo. The 2b gene of ilarviruses, which is not encoded by alfamoviruses and bromoviruses, shares several features with the previously reported cucumovirus 2b gene; however, their encoded proteins share no detectable sequence similarities. The evolutionary origin of the 2b gene is discussed.     

Comparison of the Pseudorabies Virus Us9 Protein with Homologs from Other Veterinary and Human Alphaherpesviruses

Pseudorabies virus (PRV) Us9 is a small, tail-anchored (TA) membrane protein that is essential for axonal sorting of viral structural proteins and is highly conserved among other members of the alphaherpesvirus subfamily. We cloned the Us9 homologs from two human pathogens, varicella-zoster virus (VZV) and herpes simplex virus type 1 (HSV-1), as well as two veterinary pathogens, equine herpesvirus type 1 (EHV-1) and bovine herpesvirus type 1 (BHV-1), and fused them to enhanced green fluorescent protein to examine their subcellular localization and membrane topology. Akin to PRV Us9, all of the Us9 homologs localized to the trans-Golgi network and had a type II membrane topology (typical of TA proteins). Furthermore, we examined whether any of the Us9 homologs could compensate for the loss of PRV Us9 in anterograde, neuron-to-cell spread of infection in a compartmented chamber system. EHV-1 and BHV-1 Us9 were able to fully compensate for the loss of PRV Us9, whereas VZV and HSV-1 Us9 proteins were unable to functionally replace PRV Us9 when they were expressed in a PRV background.Alphaherpesviruses are classified by their variable host range, short reproductive cycle, and ability to establish latency in the peripheral nervous system (PNS) (36, 37). Commonly studied pathogens of this subfamily include herpes simplex virus (HSV) and varicella-zoster virus (VZV), as well as the veterinary pathogens pseudorabies virus (PRV), equine herpesvirus (EHV), and bovine herpesvirus (BHV). Initial infection begins with the virus entering the host mucosal surfaces and spreading between cells of the mucosal epithelium. Invariably, virus enters the PNS through the infection of peripheral nerves that innervate this region. The virus establishes a latent infection in PNS neurons that can be reactivated and that persists for the life of the host (36). In most natural infections, virus replication in the PNS never spreads to the central nervous system (CNS). However, on rare occasions, invasion of the CNS does occur, resulting in devastating encephalitis (46). Trafficking of virus particles from infected epithelial cells into the axon and subsequent transport to neuronal cell bodies is known as retrograde spread of infection. Trafficking of virus particles that are assembled in the neuronal cell body and subsequently sorted into axons for transport to epithelial cells at the initial site of infection (upon reactivation from latency) is known as anterograde spread of infection.Though the natural host of PRV is swine, the virus infects a wide variety of animals, including rodents, cats, dogs, rabbits, cattle, and chicken embryos, but not higher primates (1, 30, 47). In contrast to the well-contained spread of PRV within its natural host, infection of other mammals is usually lethal. Instead of stopping in the PNS, infection continues on to second-order and third-order neurons in the CNS (reviewed in reference 35). This facet of PRV infection makes it a useful tracer of neuronal connections (18). Work in our lab has identified three PRV proteins, Us9 and the gE/gI heterodimer, which are critical for efficient anterograde spread of infection in vivo (i.e., spread from presynaptic to postsynaptic neurons) (6, 45). The molecular mechanism by which these proteins function has been further elucidated in vitro using primary neuronal cultures of superior cervical ganglion (SCG) harvested from embryonic rat pups. PRV Us9 and, to a lesser extent, gE/gI are required for efficient axonal targeting of viral structural proteins, a necessary step for subsequent anterograde, transneuronal spread (10, 11, 27, 28, 42).PRV Us9 is a type II, tail-anchored (TA) membrane protein that is highly enriched in lipid raft microdomains and resides predominantly in or near the trans-Golgi network (TGN) inside infected cells (5-7, 27). It has homologs in most of the alphaherpesviruses, including VZV (16), HSV-1 (22), HSV-2 (17), EHV-1 (21, 40), EHV-4 (41), BHV-1 (25), and BHV-5 (14). Though several studies have examined individually the Us9 proteins encoded by VZV (16), HSV-1 (4, 22, 34, 39), BHV-1 (13), and BHV-5 (14), several gaps in our understanding of Us9 biology remain, namely, whether all of the PRV Us9 homologs are type II membrane proteins, if the proteins localize to similar subcellular compartments within different cell types, and if they can functionally substitute for the loss of PRV Us9 in axonal sorting and anterograde spread of infection. The aim of this study is to examine PRV Us9 in parallel assays with its homologs from VZV, HSV-1, EHV-1, and BHV-1 to identify potential similarities and differences between these highly conserved alphaherpesvirus proteins.     

Caprine Arthritis-Encephalitis Virus Is Distinct from Visna and Progressive Pneumonia Viruses as Measured by Genome Sequence Homology

Competitive inhibition of hybridization between ¹²⁵I-labeled caprine arthritis-encephalitis viral RNA and homologous cDNA by heterologous viral RNA shows that the caprine retrovirus shares <20% genome sequence homology with visna and progressive pneumonia viruses. These viruses, however, are indistinguishable in immunodiffusion reactions involving the major structural protein (p28).     

In Situ Hybridization for the Detection of Infectious Laryngotracheitis Virus in Sections of Trachea from Experimentally Infected Chickens

An in situ hybridization procedure for the detection of infectious laryngotracheitis virus (ILTV) in experimentally infected chickens is described. Formalin-fixed, paraffin-embedded sections of trachea, taken from chickens on days 3–10 post-inoculation (p.i.) with ILTV were hybridized with a mixture of 2 biotinylated, polymerase chain reaction-generated DNA fragments. The fragments correspond to sequences of the ILTV glycoprotein C and thymidine kinase genes. In situ hybridization was seen in 7 out of 7 chickens examined on day 3 p.i., 2 out of 2 examined on day 4 p.i. and 3 out of 3 examined on day 5 p.i. No hybridization was observed in 3 out of 3 chickens examined on day 10 p.i. ILTV nucleic acid was detected in nuclei of degenerated tracheal epithelial cells and in intranuclear inclusion bodies of syncytia.     

Sequence and Genetic Arrangement of the US Region of the Monkey B Virus (Cercopithecine Herpesvirus 1) Genome and Comparison with the US Regions of Other Primate Herpesviruses

The sequence of the unique short (U(S)) region of monkey B virus (BV) was determined. The 13 genes identified are arranged in the same order and orientation as in herpes simplex virus (HSV). These results demonstrate that the BV U(S) region is entirely colinear with that of HSV type 1 (HSV-1), HSV-2, and simian agent 8 virus.     

The Replicase Gene of Avian Coronavirus Infectious Bronchitis Virus Is a Determinant of Pathogenicity

We have previously demonstrated that the replacement of the S gene from an avirulent strain (Beaudette) of infectious bronchitis virus (IBV) with an S gene from a virulent strain (M41) resulted in a recombinant virus (BeauR-M41(S)) with the in vitro cell tropism of the virulent virus but that was still avirulent. In order to investigate whether any of the other structural or accessory genes played a role in pathogenicity we have now replaced these from the Beaudette strain with those from M41. The recombinant IBV was in effect a chimaeric virus with the replicase gene derived from Beaudette and the rest of the genome from M41. This demonstrated that it is possible to exchange a large region of the IBV genome, approximately 8.4 kb, using our transient dominant selection method. Recovery of a viable recombinant IBV also demonstrated that it is possible to interchange a complete replicase gene as we had in effect replaced the M41 replicase gene with the Beaudette derived gene. Analysis of the chimaeric virus showed that it was avirulent indicating that none of the structural or accessory genes derived from a virulent isolate of IBV were able to restore virulence and that therefore, the loss of virulence associated with the Beaudette strain resides in the replicase gene.     

The N-terminal Helical Region of the Hepatitis C Virus p7 Ion Channel Protein Is Critical for Infectious Virus Production

The hepatitis C virus (HCV) p7 protein is required for infectious virus production via its role in assembly and ion channel activity. Although NMR structures of p7 have been reported, the location of secondary structural elements and orientation of the p7 transmembrane domains differ among models. Furthermore, the p7 structure-function relationship remains unclear. Here, extensive mutagenesis, coupled with infectious virus production phenotyping and molecular modeling, demonstrates that the N-terminal helical region plays a previously underappreciated yet critical functional role, especially with respect to E2/p7 cleavage efficiency. Interrogation of specific N-terminal helix residues identified as having p7-specific defects and predicted to point toward the channel pore, in a context of independent E2/p7 cleavage, further supports p7 as a structurally plastic, minimalist ion channel. Together, our findings indicate that the p7 N-terminal helical region is critical for E2/p7 processing, protein-protein interactions, ion channel activity, and infectious HCV production.     

IBDVvp2基因高变区序列测定与进化分析

本实验采用来源于江苏地区的六株不同鸡传染性法氏囊病病毒(Infectious bursal disease virus,IBDV)毒株,应用RT-PCR法对vp2基因高变区进行了扩增,构建重组质粒pMD18T-vp2,测序。与有代表性的IBDV毒株VP2基因高变区序列进行比较分析,以ClustalX软件进行序列比对,得到基因序列及氨基酸序列同源性,IBDV Y3、P2G、P8G、SZ、Y5和W04(6株)IBDV与D6984(荷兰)的同源性达到99．0％以上,与其它一些超强毒株(very virulent IBDV,vvIBDV)的同源性也达到了97．8％以上,并在关键氨基酸位点符合vvIBDV特征,采用Phylip3．5软件分析作出进化树,其结果从分子水平说明六个毒株均为vvIBDV,与欧洲和日本的超强毒株有较近的亲缘关系,而与美洲株的较远,从而为IBDV分子流行病学研究和疫苗的研制提供了科学依据。     

IBDVvp2基因高变区序列测定与进化分析

本实验采用来源于江苏地区的六株不同鸡传染性法氏囊病病毒(Infectious bursal disease virus,IBDV)毒株,应用RT-PCR法对vp2基因高变区进行了扩增,构建重组质粒pMD18T-vp2,测序.与有代表性的IBDV毒株VP2基因高变区序列进行比较分析,以ClustalX软件进行序列比对,得到基因序列及氨基酸序列同源性,IBDVY3、P2G、P8G、SZ、Y5和W04(6株)IBDV与D6984(荷兰)的同源性达到99.0%以上,与其它一些超强毒株(very virulentIBDV,vvIBDV)的同源性也达到了97.8%以上,并在关键氨基酸位点符合vvIBDV特征,采用Phylip3.5软件分析作出进化树,其结果从分子水平说明六个毒株均为vvIBDV,与欧洲和日本的超强毒株有较近的亲缘关系,而与美洲株的较远,从而为IBDV分子流行病学研究和疫苗的研制提供了科学依据.