Real‐time RT‐PCR for the detection and quantitative analysis of equine rhinitis viruses

Reasons for performing study: Equine rhinitis viruses (ERV) cause respiratory disease and loss of performance in horses. It has been suggested that the economic significance of these viruses may have been underestimated due to insensitive methods of detection. Objectives: To develop a sensitive, rapid, real‐time RT‐PCR (rRT‐PCR) assay suitable for the routine diagnosis and epidemiological surveillance of the A and B variants of ERV. Methods: TaqMan primer probe sets for ERAV and ERBV were designed from conserved regions of the 5′ UTR of the ERV genome. Over 400 samples from both clinically affected and asymptomatic horses were employed for validation of the assays. ERAV samples positive by rRT‐PCR were verified by virus isolation and ERBV positive samples were verified by rRT‐PCR using a different set of primers. Results: The detection limit of the rRT‐PCR for both viruses was 10–100 genome copies. Of 250 archival nasal swabs submitted for diagnostic testing over a 7 year period, 29 were ERAV positive and 3 were ERBV positive with an average incidence rate per year of 10 and 1.5%, respectively. There was evidence of co‐circulation of ERAV and ERBV with equine influenza virus (EIV). Of 100 post race urine samples tested, 29 were ERAV positive by rRT‐PCR. Partial sequencing of 2 ERBV positive samples demonstrated that one was 100% identical to ERBV1 from a 270 bp sequence and the other was more closely related to ERBV2 than ERBV1 (95% compared to 90% nucleotide identity in 178 bp). Conclusions: The rRT‐PCR assays described here are specific and more sensitive than virus isolation. They have good reproducibility and are suitable for the routine diagnosis of ERAV and ERBV. Potential relevance: These assays should be useful for investigating the temporal association between clinical signs and rhinitis virus shedding.     

猪腹泻相关肠道病毒分离研究进展

猪腹泻是全球养猪生产中最常见的疾病之一,病毒性腹泻具有传播快、致死率高和防控难的特点。常见的引起仔猪腹泻的病毒包括猪流行性腹泻病毒(PEDV)、猪传染性胃肠炎病毒(TGEV)和猪轮状病毒(PoRV),近几年新发现的猪δ冠状病毒(PDCoV)、猪嵴病毒(PKV)和猪急性腹泻综合征冠状病毒(SADS-CoV)也与仔猪腹泻相关。病毒分离是病毒感染诊断的金标准,也是进行病毒研究的前提。对上述6种常见猪肠道病毒的分离进展进行综述,可为掌握这些病毒的分离情况、疾病发展动向监测、疫苗研发以及猪腹泻病的防控提供参考。     

传染病诊断方法的验证

诊断敏感性和特异性是诊断方法验证过程中的两个重要参数。本文通过分析和比较,详细阐述了诊断敏感性和特异性在动物检疫工作中的重要性,厘清了其与分析敏感性和特异性的区别。通过计算分析比较了不同流行率对检测结果可信度的影响,以及在同一流行率下,诊断敏感性和特异性变化对检测结果可信度的影响。结果显示,当流行率低时,诊断特异性对结果可信度的影响更大,诊断特异性的降低会导致阳性检测结果可信度显著下降。因此在进出境动物检疫工作中,不要一味强调分析特性,而要重视诊断特性;既要关注诊断敏感性,做到不漏检;也要关注诊断特异性,做到不误检。     

猪圆环病毒基因组结构及其分子特征研究进展

目前,国际上已分离获得2个不同血清型的猪圆环病毒（PCV）,并命名为猪圆环病毒1型（PCV-1）和猪圆环病毒2型（PCV-2）。PCV-1对猪无致病性,而PCV-2被认为是引起断奶仔猪多系统衰竭综合征（PMWS）的主要病原。PCV基因组为单股环状双向DNA,由2个头一头相对排列的开放性阅读框和基因间隔区组成,包含rep基因、cap基因及病毒DNA复制起始区茎环序列。rep基因编码2种不同的复制酶相关蛋白,cap基因编码病毒结构蛋白或衣壳蛋白,茎环序列在病毒蛋白合成、DNA自身复制及子代病毒产生中发挥重要作用。PCV-2衣壳蛋白110位（P→A）和191位（R→S）氨基酸突变,提高PCV-2在体外组织培养中的增殖效率,而减弱其对动物的致病性和毒力。     

兔黏液瘤病快速检测方法的建立

兔黏液瘤病是由兔黏液瘤病毒引起的兔的一种高度接触性、致死性传染病。为了加强口岸对进境野生及实验用兔中兔黏液瘤病的筛查和流行病学调查,本研究建立了PCR和Real-time PCR快速高通量检测兔黏液瘤病的方法,证实两种检测方法具有良好的特异性和灵敏性,适用于兔黏液瘤病的快速检测。     

Molecular Characterization by LSSP‐PCR and DNA Sequencing of a Pathogenic Isolate of Leptospira interrogans from Brazil

We report the initial characterization of a leptospiral isolate, Leptospira interrogans, serogroup Sejroe, serovar Hardjo, genotype Hardjoprajitno, strain Norma, and its relatedness with L. interrogans, serogroup Sejroe, serovar Hardjo, genotype Hardjoprajitno, strain Hardjo and Leptospira borgpetersenii, serogroup Sejroe, serovar Hardjo, genotype Hardjobovis, strain Sponselee. The Norma strain singled out during a leptospirosis outbreak in cattle immunized with antigens from the reference strain Hardjoprajitno (OMS). By applying a microscopic agglutination serological test (MAT) to cattle (n = 2966) with symptoms of leptospirosis between 2003 and 2007, more than 50% of sera were found positive for one of the following serotypes: Hardjoprajitno (31–21%), Hardjo Norma (46–40%), Hardjo hardjobovis (18–10%), Mini (8–4%) and Wolffi (7–4%). In immunization trials using six isolates plus Norma isolate, the remission of MAT in these isolates was observed following 6 months of the initial vaccination. To provide molecular ground for the high MAT Norma frequency found in these isolates, a DNA polymorphic analysis was conducted by comparing the Norma isolate with reference strains Hardjoprajitno and Sponselee. The polymorphic analysis in secY showed five base changes in Norma relative to Hardjoprajitno strain, corresponding to 98% identity, while Sponselee displayed 49 polymorphic sites relative to the Hardjoprajitno strain, representing 80% identity. The alignment of secY translated sequences shows no differences between Hardjoprajitno and Norma, and eight polymorphisms between genotype hardjoprajttno and strain Sponselee. Three‐dimensional modelling located these variations within the loop region connecting helices 7 and 8 from secY which is less conserved. DNA sequencing of 23S ribosomal conserved fragment revealed a single polymorphism between Hardjoprajitno and Norma, and 13 polymorphisms between strains Sponselee, Hardjoprajitno and Norma. The differences between Hardjo and Norma were confirmed by low stringency single‐specific primer polymerase chain reaction (LSSP‐PCR) signature experiments with the primer G2, using as template the 285 bp fragment initially amplified with G1/G2 primers.     

检测猪伪狂犬病病毒和猪细小病毒的二重PCR方法的建立

作者建立了一种同时检测猪细小病毒(PPV)和猪伪狂犬病病毒(PRV)的二重PCR方法。根据GenBank上发表的PPV和PRV基因序列,针对各自保守区各设1对特异性引物,用这2对引物对同一样品中的PPV和PRV进行检测,结果同时扩增出942 bp(PPV)和485 bp(PRV)2条特异性片段。特异性试验表明,对其他几种病原的PCR扩增结果均为阴性。敏感性试验结果表明,该二重PCR能检出PPV 和PRV最低浓度分别为22、11.7 pg/L。该方法的建立对临床上进行这2种疾病的鉴别诊断和混合感染的检测都具有重要意义。     

猪链球菌PCR检测技术研究进展

猪链球菌是猪的一种重要病原菌,并且也会引起人的链球菌病。有35个荚膜血清型(1/21、~34),通常自发病或死亡猪体分离获得1,2,7,9型和14型菌株,其中2型是毒力最强的血清型。根据已知猪链球菌16 SrRNA及溶血素(sly)、谷氨酸脱氢酶(gdh)、荚膜多糖(cps)、胞壁蛋白或溶菌酶释放相关蛋白(mrp)、胞外因子(epf)编码基因序列设计特异性引物,建立猪链球菌群和1(14),2(1/2),7型和9型特异性PCR或多重PCR,建立2型致病性菌株和1型高致病性菌株毒力鉴定PCR或多重PCR,用于检测和鉴别临床病料和细菌分离物中的猪链球菌,具有高敏感性和高特异性,与其他致病菌及其他血清的猪链球菌型无交叉反应,为疫病诊断及流行病学的研究提供了快速、简便和有用的工具。     

猪传染性胸膜肺炎PCR诊断方法的建立与应用

为调查猪传染性胸膜肺炎的流行状况,本试验建立了检测胸膜肺炎放线杆菌（Actinobacillus pleuropneaumoniae, App）的PCR方法。对186份病死猪病变组织及545份无临床症状健康猪鼻拭子进行了App的PCR检测。结果186份病料中App阳性率占43.0%（80/186）,545份猪鼻拭子中App阳性占9.4%（51/545）。该PCR方法可作为App临床诊断的重要手段之一。通过调查表明,聊城地区存在猪传染性胸膜肺炎放线杆菌的隐性感染及流行。     

Cloning and Molecular Characterization Analysis of M Gene of Porcine Epidemic Diarrhea Virus

In order to study the porcine epidemic diarrhea (PED) epidemic situation recently,small intestine tissue from piglets suspected porcine epidemic diarrhea virus (PEDV) were collected in this study. The PEDV M gene was amplified using RT-PCR method and the molecular characterization were analysed. The results showed that the ORF of M gene was 681 bp which encoded 226 amino acids. The percent identity of M gene amino acid between PEDV in this study and reference strains in GenBank were higher than 96.0%,and that with CH/SD-M/2012 strain was highest (96.9%).The phylogenetic tree based on the Neighbor-Joining (NJ) and Minimum-Evolution (ME) showed that the PEDV in this study was closely related to CH/SD-M/2012 strain which were belonged to the same evolutionary branch. The phylogenetic tree analysis illustrated that M gene of PEDV was relatively conservative. The results of homology modeling analysis found that crystal model of M protein was similar to coronavirus nsp14-nsp10 complex 5c8s.1 and NAD kinase Ⅰ 2i1w.1.B which shared 27.69% and 15.07% sequence similarity,respectively. The protein structure prediction analysis found seven α-helix structures located in 110 to 113,118 to 125,132 to 136,140 to 145,147 to 152,154 to 157 and 160 to 173 amino acid regions,and five ligand structures of zinc finger located in 98 to 100,102 to 107,135 to 137, 139 to 145 and 149 to 154, amino acid regions. The protein structure prediction analysis indicated that the M protein might be a polyprotein of viral genome replication enzyme.     

猴痘病毒PCR检测方法的建立

从GenBank上调取猴痘病毒的基因序列,经过分析,找出了猴痘病毒的特异性靶基因序列F3L片段,人工合成猴痘病毒MPV(AF380138)F3L基因片段(48048-48509bp)并插入质粒,作为病毒检测的模拟阳性模板。根据该序列设计并合成PCR引物,对模拟的阳性模板进行扩增,结果能扩增出与目的片段大小一致的条带。建立了PCR检测方法,经条件优化后,对鸡痘、禽痘、羊痘等14种相似病毒核酸进行PCR扩增,发现具有良好的特异性。PCR方法能扩增出0.3pg的阳性模板,显示建立的PCR方法具有高效、快速、特异、灵敏的特点,可用于口岸猴痘病毒的检疫。     

猪流行性腹泻病毒M基因克隆与分子特征分析

为更好地了解近年来中国暴发的猪流行性腹泻（porcine epidemic diarrhea,PED）疫情,本研究采集荣昌及其周边地区疑似患有PED的猪小肠上皮组织进行RNA的提取,扩增猪流行性腹泻病毒（porcine epidemic diarrhea virus,PEDV）M基因序列,进行序列分析及M蛋白分子特性研究。结果显示,M基因开放阅读框（ORF）长为681 bp,编码226个氨基酸。通过DNAMAN软件及系统进化树分析发现,本试验中PEDV与GenBank中参考毒株的M基因氨基酸同源性在96.0%以上,其中与广东毒株CH/SD-M/2012株亲缘关系最为相近,同源性高达96.9%,表明M基因相对比较保守。通过M蛋白同源建模及功能预测发现,M蛋白晶体模型同SARS冠状病毒nsp14-nsp10复合体5c8s.1.A及NAD激酶Ⅰ2i1w.1.B模型序列相似性为27.69%、15.07%;其高级结构中在第110-113、118-125、132-136、140-145、147-152、154-157、160-173位氨基酸处存在7个α螺旋,在第98-100、102-107、135-137、139-145、149-154氨基酸存在5个锌指结构配体,M蛋白为PEDV病毒基因组复制酶的多聚蛋白。