Molecular characterization of lapinized classical Swine Fever vaccine strain by full-length genome sequencing and analysis

The complete genome of a lapinized classical swine fever virus (CSFV) vaccine strain was amplified into nine overlapping fragments by RT-PCR, and nucleotide sequences were determined. Complete genome sequence alignment and phylogenetic analysis indicated 92.6-98.6% identities at the nucleotide level with other reported CSFV strains and could be grouped into subgroup 1.1 along with other attenuated strains of CSFV. The 5'-UTR demonstrated >97.0% nucleotide similarity with most of vaccine CSFV strains from China. Further, its 3'-UTR sequence indicated a length similar to all the CSFV strains from China with >98.0% nucleotide similarity, although high length heterogeneity of 3'-UTR was reported among different CSFV strains. There was 12 nt (TTTTCTTTTTTT) insertion in 3'-UTR similar to other reported attenuated vaccine strains. However, secondary structure of 3'-UTR indicated that Indian CSFV strain requires further passage to obtain a 3'-UTR structure similar to most of the attenuated strains.     

Time-calibrated phylogenomics of the porcine epidemic diarrhea virus: genome-wide insights into the spatio-temporal dynamics

Porcine epidemic diarrhea virus (PEDV), the causative agent of porcine epidemic diarrhea (PED), has led to tremendous economic losses in the global swine industry. Although the phylogeny of PEDV has been investigated extensively at the molecular level, there was no time-calibrated phylogenomic study on the virus. To improve insight into this topic, we analyzed 138 published genome sequences using the Bayesian coalescent analyses as well as Bayesian inferences and maximum likelihood methods. All of the global PEDV isolates were divided into six groups, except for one unclassified isolate. Of the six groups, Groups 1–5 comprised pandemic viruses while the remaining Group 6 contained classical isolates. Interestingly, the two clades, both pandemic and classical, consisted of clade-specific amino acid sequences in five genes: ORF1a, ORF1b, S, ORF3, and N. Within the pandemic clade, Group 1 and Group 2 originated from North America, whereas Group 3–Group 5 were derived from Asia. In Group 2, there was a common origin of S INDEL isolates. Within each group, there was no apparent association between temporal or geographic origin and heterogeneity of PEDVs. Our findings also showed that the PEDV virus evolved at a rate of 3.38?×?10^?4 substitutions/site/year, and the most recent common ancestor of the virus emerged 75.9 years ago. Our Bayesian skyline plot analysis indicated that the PEDV had maintained constant effective population size excluding only a short period, around 2012, when a valley shaped decline in the effective number of infections occurred.     

Genetic variation in the 5' end and NS5B regions of classical swine fever virus genome among Japanese isolates.

Sixteen clinical strains of classical swine fever virus (CSFV) isolated in Japan were subjected to analyses of nucleotide sequence variations in the 5' end and NS5B regions of the genome. These isolates were divided into three genovars, CSFV-1, CSFV-2 and CSFV-3, based on palindromic nucleotide substitutions at the three variable loci in the 5' untranslated region (UTR). Phylogenetic trees constructed from nucleotide sequences in the 5'-UTR and NS5B gene indicated that the CSFV strains were divided into three clusters, I, II and III. CSFV strains included in clusters I, II and III were identical to those in the CSFV-1, CSFV-2 and CSFV-3 genovars, respectively.     

Complete genome sequences of porcine reproductive and respiratory syndrome viruses: perspectives on their temporal and spatial dynamics

Porcine reproductive and respiratory syndrome virus (PRRSV) has been investigated extensively at the molecular level. Nevertheless, genome wide study on the temporal and spatial dynamics of the virus is non-existed. To explore this topic, we determined complete coding genome sequences for four PRRSV isolates and analyzed them together with 122 global published ones using the Bayesian coalescent approach as well as Bayesian inferences and maximum likelihood methods. All EU-type viruses belonged to one of two groups or were unclassified (5 isolates), and all NA-type isolates were divided into one of three major groups or were unclassified (1 isolate). Here, there was no apparent association between temporal or geographic origin and heterogeneity of global PRRSVs. Of the eight ORFs, ORF1a showed the most powerful evolutionary signal. Our findings also indicated that the PRRS virus evolved at a rate of 1.98 × 10^?3 substitutions/site/year, and the most recent common ancestor of the virus existed 786.4 years ago. Here, EU-type viruses segregated 115.7 years ago, while NA-type isolates diverged 179.8 years before the present. In addition, our reconstruction of the effective population size depicted five phases of epidemic growth: an initial constant, followed sequentially by slow decrease, slight increase, sharp decline, and then a rapid expansion approaching the present.     

Prediction of recognition sites for genomic replication of classical swine fever virus with information analysis

In order to explore the mechanism for the genomic replication of classical swine fever virus (CSFV), so as to make a basis for investigating its pathogenicity, an introduction of the information theory is presented in connection with the statistical mechanics, whence small-sample statistics appears naturally as a consequence of the Bayesian approach. Furthermore, a selection rule for identifying the pattern of a recognition site for an RNA-binding protein is proposed by means of the maximum entropy principle. Based on those, the information contents of 3'-untranslated regions (3'UTRs) of genomes of 20 CSFV strains and 5'-untranslated regions (5'UTRs) of genomes of 58 CSFV strains are analyzed with a computational algorithm in a reduction mode, and the 3'UTR sites of 20 strains and 5'UTR sites of 58 strains containing important motifs are extracted from the unaligned RNA sequences of unequal lengths. These sites, which have the patterns of sequence and structure similar to the putative cis elements related to the regulation of genomic replication, would be identified as the potential recognition sites in 3'UTRs and 5'UTRs for CSFV replicase responsible for classical swine fever virus genomic replication, and to some extent, this identification is supported by experimental evidence. Finally, information analysis allows a presumption to be made about the CSFV RNA replication initiation mechanism.     

Prediction of Recognition Sites for Genomic Replication of Classical Swine Fever Virus with Information Analysis

In order to explore the mechanism for the genomic replication of classical swine fever virus (CSFV), so as to make a basis for investigating its pathogenicity, an introduction of the information theory is presented in connection with the statistical mechanics, whence small-sample statistics appears naturally as a consequence of the Bayesian approach. Furthermore, a selection rule for identifying the pattern of a recognition site for an RNA-binding protein is proposed by means of the maximum entropy principle. Based on those, the information contents of 3"-untranslated regions (3"UTRs) of genomes of 20 CSFV strains and 5"-untranslated regions (5"UTRs) of genomes of 58 CSFV strains are analyzed with a computational algorithm in a reduction mode, and the 3"UTR sites of 20 strains and 5"UTR sites of 58 strains containing important motifs are extracted from the unaligned RNA sequences of unequal lengths. These sites, which have the patterns of sequence and structure similar to the putative cis elements related to the regulation of genomic replication, would be identified as the potential recognition sites in 3"UTRs and 5"UTRs for CSFV replicase responsible for classical swine fever virus genomic replication, and to some extent, this identification is supported by experimental evidence. Finally, information analysis allows a presumption to be made about the CSFV RNA replication initiation mechanism.     

Expression and characterization of a recombinant porcinized antibody against the E2 protein of classical swine fever virus

Applied Microbiology and Biotechnology - Classical swine fever virus (CSFV) is the causative agent of classical swine fever (CSF), a highly contagious and economically important disease of pigs....     

The expression of classical swine fever virus structural protein E2 gene in tobacco chloroplasts for applying chloroplasts as bioreactors

It has been reported that genes encoding antigens of bacterial and viral pathogens can be expressed in plants and are shown to induce protection antibodies. The structural protein E2 of classical swine fever virus (CSFV), which has been shown to carry critical epitopes, has been expressed in different systems. Here, we report the expression of CFSV E2 gene in tobacco chloroplasts. Mice immunized with leaf extracts elicited specific antibodies. This indicated that the expressed E2 proteins had a certain degree of immunogenicity. To our knowledge, this is the first report showing induction of protective antibody in response to classical swine fever virus (CSFV) by immunization with antigen protein E2 expressed in tobacco chloroplasts, which will open a new way to protection from CSFV by plant chloroplasts as bioreactors.     

猪瘟病毒与宿主天然免疫系统的相互作用

猪瘟(Classical swine fever,CSF)是由猪瘟病毒(Classical swine fever virus,CSFV)感染引起的一种高度接触性传染病,临床上以出血综合征与免疫抑制为主要特征。它在多个国家流行,给中国乃至世界养猪业造成巨大的经济损失。研究表明,猪瘟病毒感染能够诱导宿主的天然免疫应答,也能通过影响天然免疫效应分子的表达来抑制宿主的天然免疫功能。本文将对猪瘟病毒感染与天然免疫应答及其免疫抑制的现象与机理进行综述。     

Production and characterization of monoclonal antibodies against a local isolate of classical swine fever virus

Monoclonal antibodies (mAbs) against a classical swine fever virus (CSFV; subgenogroup 1:1) isolate from Assam, India were produced and characterized. Four fusions of myeloma cells (SP2/0Ag) were made with spleenocytes of 8-10 weeks old BALB/C mice immunized with the viral antigen. Several hybridoma clones secreting antibodies to the virus were obtained after four fusions, but five hybridoma clones secreting antibody specific to the virus could be stabilized. All the mAbs belong to the IgG2a isotype. Except one, none of the four mAbs showed cross reaction with bovine viral diarrhoea virus and border disease virus (BDV). One mAb showed cross reaction with BDV. All the four mAbs specific to CSFV showed reactivity with the parental virus in immunoperoxidase test (IPT) and with a single protein band (molecular weight 55 kD approximately) of the virus in western blotting. In neutralization peroxidase linked assay (NPLA) all the mAbs reacted with 13 CSFV local isolates as well as with the cell culture adapted lapinized vaccine virus strain belonging to the subgenogroup 1:1. This is the first report on production and characterization of mAbs against CSFV in India.     

猪瘟病毒在PK细胞和MPK细胞中繁殖过程的研究

以猪瘟病毒疫苗Ｔｈｉｖｅｒｖａｌ株（Ｔ株）为实验材料,研究该病毒株在ＰＫ１５细胞中增殖的基本特性与规律。在ＰＫ１５细胞中,猪瘟病毒Ｔ株在感染后１２ｈ即可检测到子代病毒粒子。接毒后４８ｈ,几乎所有的细胞都被病毒感染;到６０ｈ,释放到培养液中有活性的病毒粒子达到最高峰,为１０７ＴＣＩＤ５０／ｍＬ。培养液中的病毒粒子在３７℃半寿期只有３个小时。同时,建立了ＭＰＫ细胞ＣＳＦＶＴ株的感染模式,其ＣＳＦＶ的滴度可达１０８ＴＣＩＤ５０／ｍＬ。在此基础上,用抗ＣＳＦＶ包膜蛋白Ｅ２和非结构蛋白ｐ１２０的单克隆抗体显示了病毒在细胞中增殖的部位,进而应用电镜技术观察到成熟的病毒粒子及可能处在不同发育阶段的子代病毒粒子     

Selection of classical swine fever virus with enhanced pathogenicity reveals synergistic virulence determinants in E2 and NS4B

Classical swine fever virus (CSFV) is the causative agent of classical swine fever (CSF), a highly contagious disease of pigs. There are numerous CSFV strains that differ in virulence, resulting in clinical disease with different degrees of severity. Low-virulent and moderately virulent isolates cause a mild and often chronic disease, while highly virulent isolates cause an acute and mostly lethal hemorrhagic fever. The live attenuated vaccine strain GPE(-) was produced by multiple passages of the virulent ALD strain in cells of swine, bovine, and guinea pig origin. With the aim of identifying the determinants responsible for the attenuation, the GPE(-) vaccine virus was readapted to pigs by serial passages of infected tonsil homogenates until prolonged viremia and typical signs of CSF were observed. The GPE(-)/P-11 virus isolated from the tonsils after the 11th passage in vivo had acquired 3 amino acid substitutions in E2 (T830A) and NS4B (V2475A and A2563V) compared with the virus before passages. Experimental infection of pigs with the mutants reconstructed by reverse genetics confirmed that these amino acid substitutions were responsible for the acquisition of pathogenicity. Studies in vitro indicated that the substitution in E2 influenced virus spreading and that the changes in NS4B enhanced the viral RNA replication. In conclusion, the present study identified residues in E2 and NS4B of CSFV that can act synergistically to influence virus replication efficiency in vitro and pathogenicity in pigs.     

Genetic variance of Trichomonas vaginalis isolates by Southern hybridization

In the present study, genomic DNAs were purified from Korean isolates (KT8, KT6, KT-Kim and KT-Lee) and foreign strains (CDC85, IR78 and NYH 286) of Trichomonas vaginalis, and hybridized with a probe based on the repetitive sequence cloned from T. vaginalis to observe the genetic differences. By Southern hybridization, all isolates of T. vaginalis except the NYH286 strain had 11 bands. Therefore all isolates examined were distinguishable into 3 groups according to their banding patterns; i) KT8, KT6 and KT-Kim isolates had 11 identical bands such as 1 kb, 1.2 kb, 1.6 kb, 1.9 kb, 2.3 kb, 2.7 kb, 3.2 kb, 3.4 kb, 3.8 kb, 4.9 kb and 6.0 kb. ii) The metronidazole-resistant IR78 strain had the same bands as KT-Lee isolate at bands of 1 kb, 1.2 kb, 1.6 kb, 1.8 kb, 2.1 kb, 2.5 kb, 2.7 kb, 2.9 kb, 3.4 kb, 5.0 kb and 6.0 kb. Bands of CDC85, metronidazole-resistant strain, were similar to those of IR78 and KT-Lee, except that 3.2 kb replaced 2.9 kb. iii) NYH286 particularly had 12 bands and band patterns were similar to IR78 with a few exceptions as follows: i) 6.2 kb in place of 6.0 kb, ii) 2.0 kb and 2.2 kb instead of 2.1 kb. Through the results obtained, genetic variance of T. vaginalis isolates was demonstrated by Southern hybridization.     

猪瘟病毒E2基因在Pichia pastoris中的表达及其免疫活性的初步研究

将猪瘟病毒的E2基因克隆入酵母分泌型表达载体pPIC9K中,酶切线性化后电穿孔导入Pichia pastoris进行整合,经G418筛选得到高拷贝转化子,甲醇诱导表达。SDS－PAGE和Western blit结果证实了酵母培养上清液中含有E2蛋白。免疫活性研究证明P.pastoris表达的E2蛋白能刺激动物产生抗猪瘟病毒的抗体。     

Cytopathogenic and noncytopathogenic RNA replicons of classical swine fever virus.

To determine the minimal requirements for autonomous RNA replication of classical swine fever virus (CSFV), genomes having in-frame deletions within the genes for structural and flanking nonstructural proteins were constructed, based on an infectious cDNA clone of CSFV Alfort/187. RNA was transcribed in vitro from the respective plasmids and transfected into SK-6 swine kidney cells. The replication competence of the RNA was determined by immunostaining transfected cells for CSFV NS3 protein and by analysis of cell extracts for viral RNA, as well as protein synthesis at different times after transfection. The genes encoding N(pro), C, E(rns), E1, E2, p7, and NS2 proved to be dispensable for RNA replication, but the efficiency of replication varied strongly between individual constructs. RNA replicons containing the complete NS2-NS3 gene persisted in transfected cells and continued to replicate without causing any obvious morphological or functional damage to the cells, whereas genomes lacking the NS2 gene replicated more efficiently and induced a cytopathic effect. These findings suggest that NS2, although it is not essential for pestivirus RNA replication, has a regulatory function therein. Both cytopathogenic and noncytopathogenic replicons were packaged into virus particles provided in trans by a cotransfected full-length helper virus genome.     

The Complete Genome Phylogeny of Geographically Distinct Dengue Virus Serotype 2 Isolates (1944-2013) Supports Further Groupings within the Cosmopolitan Genotype

Dengue virus serotype 2 (DENV-2) isolates have been implicated in deadly outbreaks of dengue fever (DF) and dengue hemorrhagic fever (DHF) in several regions of the world. Phylogenetic analysis of DENV-2 isolates collected from particular countries has been performed using partial or individual genes but only a few studies have examined complete whole-genome sequences collected worldwide. Herein, 50 complete genome sequences of DENV-2 isolates, reported over the past 70 years from 19 different countries, were downloaded from GenBank. Phylogenetic analysis was conducted and evolutionary distances of the 50 DENV-2 isolates were determined using maximum likelihood (ML) trees or Bayesian phylogenetic analysis created from complete genome nucleotide (nt) and amino acid (aa) sequences or individual gene sequences. The results showed that all DENV-2 isolates fell into seven main groups containing five previously defined genotypes. A Cosmopolitan genotype showed further division into three groups (C-I, C-II, and C-III) with the C-I group containing two subgroups (C-IA and C-IB). Comparison of the aa sequences showed specific mutations among the various groups of DENV-2 isolates. A maximum number of aa mutations was observed in the NS5 gene, followed by the NS2A, NS3 and NS1 genes, while the smallest number of aa substitutions was recorded in the capsid gene, followed by the PrM/M, NS4A, and NS4B genes. Maximum evolutionary distances were found in the NS2A gene, followed by the NS4A and NS4B genes. Based on these results, we propose that genotyping of DENV-2 isolates in future studies should be performed on entire genome sequences in order to gain a complete understanding of the evolution of various isolates reported from different geographical locations around the world.     

Proteomic analysis of primary porcine endothelial cells after infection by classical swine fever virus

Endothelial cells are the main target of classical swine fever virus during infection, and extensive hemorrhage is the most typical clinical sign of classical swine fever. To investigate the molecular mechanism of hemorrhagic pathogenesis, two-dimensional difference gel electrophoresis with fluorescent dyes (2D-DIGE) was used to analyze the proteomic profile of primary porcine umbilical vein endothelial cells (PUVECs) following CSFV infection. Of 15 protein spots with differential expression, 8 were characterized by MALDI-TOF-MS/MS in infected PUVECs at 48 h p.i.: moesin, peroxiredoxin 6, stathmin-1, a protein similar to nascent polypeptide-associated complex alpha subunit isoform 2, phosphoglycerate kinase 1, glucosidase II, transketolase and α-tubulin. These could be sorted into 5 functional groups: glycometabolism, cell proliferation, anti-oxidative stress, inflammatory response and cytoskeleton. Western blot and real-time RT-PCR analysis confirmed the down-regulation of phosphoglycerate kinase 1 (PGK1) and up-regulation of moesin identified by 2D-DIGE. Pathway analysis of these 15 differentially expressed proteins showed that CSFV infection altered the metabolism, cytoskeleton and cell proliferation of PUVECs, and that consequently an inflammatory response was induced.     

Phylogenomic Analysis Reveals Deep Divergence and Recombination in an Economically Important Grapevine Virus

The evolutionary history of the exclusively grapevine (Vitis spp.) infecting, grapevine leafroll-associated virus 3 (GLRaV-3) has not been studied extensively, partly due to limited available sequence data. In this study we trace the evolutionary history of GLRaV-3, focussing on isolate GH24, a newly discovered variant. GH24 was discovered through the use of next-generation sequencing (NGS) and the whole genome sequence determined and validated with Sanger sequencing. We assembled an alignment of all 13 available whole genomes of GLRaV-3 isolates and all other publicly available GLRaV-3 sequence data. Using multiple recombination detection methods we identified a clear signal for recombination in one whole genome sequence and further evidence for recombination in two more, including GH24. We inferred phylogenetic trees and networks and estimated the ages of common ancestors of GLRaV-3 clades by means of relaxed clock models calibrated with asynchronous sampling dates. Our results generally confirm previously identified variant groups as well as two new groups (VII and VIII). Higher order groups were defined as supergroups designated A to D. Supergroup A includes variant groups I-V and supergroup B group VI and its related unclassified isolates. Supergroups C and D are less well known, including the newly identified groups VII (including isolate GH24) and VIII respectively. The inferred node ages suggest that the origins of the major groups of GLRaV-3, including isolate GH24, may have occurred prior to worldwide cultivation of grapevines, whilst the current diversity represents closely related isolates that diverged from common ancestors within the last century.     

猪瘟病毒C株共感染口蹄疫病毒影响口蹄疫病毒复制

【背景】猪瘟(Classical Swine Fever)是由猪瘟病毒(Classical Swine Fever Virus,CSFV)引起的猪高度接触性传染病,致死率极高。在临床中存在着CSFV与猪其他病原菌共感染的情况,例如CSFV与口蹄疫病毒(Foot-and-Mouth Disease Virus,FMDV)的共感染。【目的】利用CSFV与FMDV共感染猪源宿主细胞,研究CSFV与FMDV共感染对FMDV病毒复制的影响。【方法】构建体外共感染细胞模型,在正常PK-15细胞上进行CSFV共感染FMDV实验,通过观察细胞病变效应(Cytopathic Effect,CPE)、实时荧光定量PCR(RT-qPCR)、Western Blot、间接免疫荧光检测CSFV和FMDV共感染及FMDV单独感染情况下FMDV复制水平的差异。利用RT-qPCR筛选鉴定能够影响FMDV复制的CSFV蛋白。【结果】CSFVC株共感染FMDV能够抑制FMDV的复制,而且灭活的CSFV同样抑制FMDV的复制。通过筛选鉴定出CSFV的C蛋白能够抑制FMDV复制。【结论】研究发现CSFV C株共感染FMDV能够抑制FMDV复制,而其C蛋白具有抑制FMDV复制的能力。     

表达猪瘟病毒E2蛋白的重组腺病毒的构建及其在兔体内的免疫原性分析

为了构建猪瘟重组腺病毒载体疫苗,通过细菌内同源重组法构建了含有猪瘟病毒E2基因的重组腺病毒rAdV-E2.测定其一步生长曲线,同时用间接免疫荧光试验和Western blotting检测外源基因表达,然后用rAdV-E2免疫家兔,免疫后6周用猪瘟兔化弱毒疫苗株(c株)进行攻击,攻毒后3 d取其脾脏,用实时荧光定量RT-PCR检测C株病毒RNA.结果表明,该重组腺病毒传至第10代时,毒价可达1.0×1010TCID<,50/mL;外源基因可在其中得到稳定表达;rAdV-E2接种兔免疫后2周产生猪瘟特异性抗体,免疫后5 W抗体达到峰值,攻毒后rAdV-E2接种兔和C株接种兔均未出现定型热反应,从其脾脏也未检测到C株病毒RNA,而野生型腺病毒接种兔均出现了定型热反应,并且从其脾脏检测大量C株病毒RNA,其含量达到了103拷贝/μL以上.由此表明,rAdV-E2可望开发为猪瘟候选疫苗.