云南锦鲤养殖场鲤浮肿病毒的鉴定及基因型分析

锦鲤睡眠病(Koi sleepy disease,KSD)是一种由鲤浮肿病毒(Carp edema virus,CEV)引起鲤科鱼类死亡的病毒性传染病,已经对世界鲤科鱼类养殖业造成危害。2016年,中国云南某锦鲤养殖场养殖的锦鲤出现以体表出血、眼睛凹陷、沉于池底昏睡为主要临床症状的疾病,发病水温为11℃~20℃,累计死亡率30%~50%。从该养殖场不同池塘采集两个样品,使用nested PCR和real-time PCR方法进行实验室诊断。结果表明,两个样品CEV检测结果均为阳性,发病锦鲤鳃和肾脏CEV病毒载量为250.02~1 332.94拷贝/250ng,鳃中CEV病毒载量约为肾脏的6~7倍。在排除寄生虫、细菌、SVCV和KHV感染后,推测CEV可能是引起此次云南锦鲤场发生疫情的病原,但还需回归感染实验做进一步验证。基于CEV P4a基因的遗传进化分析结果表明,此次从云南发病锦鲤检出的两个CEV毒株均属于IIa基因型,且与英国(R083株)和日本CEV毒株(CyPP-3)的遗传进化关系最近。     

鲤浮肿病毒Ⅱb基因亚型的鉴定

2018年6月,河南某鲤养殖场部分池塘暴发"鲤急性烂鳃病"疫情,发病水温25℃,死亡率为50％.从该养殖场分别采集发病鲤和无症状鲤共4个样品进行鱼体解剖、细菌和寄生虫检测、病理组织观察、PCR检测和系统进化分析.结果显示,发病鲤鱼体出血、头萎缩变形、吻端与鼻之间凹陷、头部骨骼不平整、体色发黑、鳃边发白坏死,肾脏肿大至鳔间隔;组织病理学检查可见鳃小片间隙及鳃小片顶端大量细胞增生,鳃丝呈棒状;病鱼体表和鳃中并未见任何寄生虫,细菌学检测也未分离到任何与鲤烂鳃病相关的病原菌;Real-time PCR和nested PCR方法从发病鲤和无症状鲤中检出鲤浮肿病毒(Carp edema virus,CEV)核酸阳性;基于CEV P4a的357 bp基因片段的遗传进化分析结果表明,本次试验检测到两种基因亚型CEV,从发病鲤中检出Ⅱa基因亚型CEV,从无症状鲤中检出Ⅱb基因亚型CEV,这是中国首次报道检出Ⅱb基因亚型CEV.     

岩原鲤微卫星富集文库的构建及微卫星分子标记的筛选

用磁珠富集法构建了岩原鲤Procypris rabaudi AC重复和GATA重复的微卫星富集文库.采用PCR方法分别以人工合成的oligoA和探针(AC)12或(GATA)6为引物筛选含有微卫星的阳性克隆.(AC)n 富集库和(GATA)n富集库的阳性克隆率分别为30%和7%左右.对40个AC重复的阳性克隆和30个GATA重复的阳性克隆测序,共获得61个微卫星序列,其中包含了一个三碱基重复(TGA)的微卫星序列.选择设计了19对AC重复和16对GATA重复的微卫星引物以及1对TGA重复的微卫星引物,通过PCR优化,共有20对引物能够产生稳定、清晰的目的产物带.为了检测获得的岩原鲤微卫星座位是否能用于近缘物种的研究,我们将20对岩原鲤微卫星引物用于中华倒刺鲃Spinibarbus sinensis基因组DNA PCR扩增,有60%的引物对能产生特异性的目的条带.本研究获得的20个岩原鲤微卫星座位可以用于岩原鲤及近缘物种的遗传多样性、种群遗传结构等的进一步研究.     

兴国红鲤 MHC Ⅱ类 α 基因多态性、表达及其与鱼体抗病力关系的分析简

对41尾感病和22尾抗病兴国红鲤的308个有效克隆进行测序,获得171条不同的MHCⅡ类α基因编码序列,分属26个不同的等位基因,其中Cyca-DXA24—Cyca-DXA36为新发现的13个等位基因。MHCⅡ类α基因片段的长度为624 bp,包括第1—4个外显子,分别编码信号肽、α1和α2结构域及连接肽/跨膜区。α1结构域的变异明显大于α2结构域,表现在α1结构域中核苷酸和氨基酸变异位点比例(55.16%和79.76%)明显高于α2结构域的变异位点比例(45.96%和68.42%)。α1结构域的PBR区的非同义碱基替换率(dN)与同义碱基替换率(dS)的比值ω(ω=dN/dS)为5.742,远远高于非抗原结合位点(non-PBR)及α2结构域的0.755、0.592,揭示兴国红鲤MHCⅡ类α基因的α1结构域在进化过程中受到正向选择作用。等位基因Cyca-DXA24(P0.01)与兴国红鲤对嗜水气单胞菌的抗性相关,等位基因Cyca-DXA3(P0.05)、Cyca-DXA4(P0.01)、Cyca-DXA6(P0.05)、Cyca-DXA33(P0.05)与兴国红鲤对嗜水气单胞菌的易感性相关。荧光定量PCR结果表明,MHCⅡ类α基因在健康兴国红鲤的肾、肝、鳃等10个组织均能普遍表达。人工感染嗜水气单胞菌后,肾、肝、脾3个组织中的MHCⅡ类α基因的表达量均发生了不同程度的变化,表明MHCⅡ类α分子在兴国红鲤的免疫反应中起到重要作用。     

与“全红”瓯江彩鲤体色相关的SRAP及SCAR分子标记

利用相关序列扩增多态性(Sequence Related Amplified Polymorphism,SRAP)技术分析"全红"和"粉玉"瓯江彩鲤,筛选与瓯江彩鲤体色相关的分子遗传标记。从88个SRAP引物组合筛选出的12个引物组合共获得扩增条带104个,并筛选出1个SRAP特异扩增带,即"全红"瓯江彩鲤家系SR2,7173 bp带。该条SRAP特异扩增条带经回收、克隆和测序,并将测序结果进行BLAST分析,发现该片段在GenBank中与斑马鱼的POl多蛋白基因和尿红素基因有较高的同源性。根据序列信息分别设计了4对正、反向引物(22—26 bp)。用4对引物分别在"全红"瓯江彩鲤F2和"粉玉"瓯江彩鲤F2群体中进行PCR扩增,仅发现SC-3(154 bp)能够在"全红"瓯江彩鲤群体中特异扩增,而且在"粉玉"瓯江彩鲤F2群体中未出现此扩增带。采用大样本对该SC-3标记进行验证,结果发现,在"全红"瓯江彩鲤群体中呈现阳性,而在"粉玉"瓯江彩鲤群体中为阴性,可以区分这两种群体。因此SC-3标记可以作为"全红"瓯江彩鲤群体一个重要的分子遗传特征指标,为进一步进行分子标记辅助育种奠定了基础。     

鲤和鲫线粒体(mtDNA)全基因组分析

为研究鲤(Cyprinus carpio)和鲫(Carassius auratus) mtDNA上的基因分布特征,丰富鱼类mtDNA数据库。本研究通过PCR扩增和测序,获得了鲤和鲫mtDNA基因组序列,经比对分析表明,鲤和鲫的mtDNA序列全长均为16 596 bp,共有13个蛋白质编码基因、22个tRNA基因、2个rRNA基因和1个D-Loop区。鲤和鲫的mtDNA序列中(A+T)百分含量分别为57.2%和57.1%,其碱基组成均具有一定的A/T碱基偏向性。N-J系统发育树分析表明,鲤和鲫与琵琶湖鮈亲缘关系最近,与达氏深水尾魟亲缘关系最远。本研究揭示了鲤和鲫mtDNA遗传变异特征及基因分布规律,为鱼类遗传资源保护及开发利用提供了参考依据。     

转基因鲤鱼与对照鲤肠道微生物群落差异研究

以转“全鱼”生长激素基因鲤(Cyprinus carpio L.)和野生对照鲤为对象, 采用454高通量测序技术对其肠道微生物16S rRNA基因进行测序并分析了3个不同发育阶段微生物群落结构的变化, 进而探讨了转基因鲤与对照鲤肠道微生物群落的差异。基于转基因鲤和对照鲤不同发育时期(6日龄、2月龄、5月龄)肠道微生物群落组成的DCA排序分析显示, 2月龄转基因鲤与对照鲤肠道微生物组成不同。Alpha多样性及均匀度都显示转基因鲤肠道微生物多样性高于对照鲤。从门水平的比较分析发现, 转基因鲤肠道中存在较多的厚壁菌门(Firmicutes)细菌, 而对照鲤中拟杆菌门(Bacteroidetes)细菌较多, 其中2月龄转基因鲤肠道内Bacteroidetes/Firmicutes比值低于对照鲤。研究结果表明, 在所分析的3个发育时期, 转基因鲤的肠道微生物组成与对照鲤相比发生了改变, 且在2月龄时存在差异。该研究为进一步揭示转基因鱼肠道微生物与宿主的相互影响和作用机制提供了很好的参考。     

基于不同PCR方法的Ⅱ型鲤疱疹病毒检测技术研究

异育银鲫"鳃出血病"是一种因感染了鲤疱疹病毒Ⅱ型(Cy HV-2)而引起的疾病,近年来给江苏异育银鲫养殖业造成了巨大的经济损失。为了能够建立及时、有效检出Ⅱ型鲤疱疹病毒的技术,本研究在克隆了Cy HV-2解旋酶基因和三联体蛋白基因的基础上,建立了检测CyHV-2的普通PCR、双重PCR、巢式PCR、环介导等温扩增、实时荧光定量PCR等方法,并对这5种PCR技术检测Cy HV-2的灵敏性进行了系统研究。结果表明,针对CyHV-2病毒的解旋酶基因和三联体蛋白基因,普通PCR能够检测出的极限值是2.4×10~4 copies/μL,双重PCR是1.4×10~4 copies/μL,巢式PCR是2.4×10~(-2)copies/μL,荧光定量PCR是2.4×10~(-2)copies/μL,环介导等温扩增是3.5×10~2 copies/μL。通过采用以上方法对从不同地区采集的54尾异育银鲫提取的DNA为模板进行临床检验,测定不同检测方法的阳性检出率。结果表明,实时荧光定量PCR和巢式PCR的检出率很高,分别为89%和90.7%;普通PCR的检出率最低,为68.5%。综合检测灵敏度和阳性检出率,环介导等温扩增(LAMP)是一种适用于生产实践的能有效检测CyHV-2的良好技术。     

兴国红鲤MHCⅡ类基因多态性、表达及其与鱼体抗病力关系的分析

对41尾感病和22尾抗病兴国红鲤的308个有效克隆进行测序,获得171条不同的MHC Ⅱ类基因编码序列,分属26个不同的等位基因,其中Cyca-DXA24Cyca-DXA36为新发现的13个等位基因。MHCⅡ类基因片段的长度为624 bp,包括第14个外显子,分别编码信号肽、1和2结构域及连接肽/跨膜区。1结构域的变异明显大于2结构域,表现在1结构域中核苷酸和氨基酸变异位点比例（55.16%和79.76%）明显高于2结构域的变异位点比例（45.96%和68.42%）。1结构域的PBR区的非同义碱基替换率（dN）与同义碱基替换率（dS）的比值 （=dN/dS）为5.742,远远高于非抗原结合位点（non-PBR）及2结构域的0.755、0.592,揭示兴国红鲤MHC Ⅱ类基因的1结构域在进化过程中受到正向选择作用。等位基因Cyca-DXA24 （P0.01）与兴国红鲤对嗜水气单胞菌的抗性相关,等位基因Cyca-DXA3 （P0.05）、Cyca-DXA4 （P0.01）、Cyca-DXA6 （P0.05）、Cyca-DXA33 （P0.05）与兴国红鲤对嗜水气单胞菌的易感性相关。荧光定量PCR结果表明,MHCⅡ类基因在健康兴国红鲤的肾、肝、鳃等10个组织均能普遍表达。人工感染嗜水气单胞菌后,肾、肝、脾3个组织中的MHCⅡ类基因的表达量均发生了不同程度的变化,表明MHCⅡ类分子在兴国红鲤的免疫反应中起到重要作用。       

用PCR-DGGE对岩原鲤×锦鲤杂交F1代进行分子鉴定

运用变性梯度凝胶电泳(DGGE)技术,选用核基因光间受体视黄类物质结合蛋白(IRBP)作为分子标记,成功鉴定了岩原鲤Procypris rabaudi×锦鲤Cyprinus carpio的杂交F1代.DGGE胶图显示,杂交个体IRBP基因的等位基因条带分别与岩原鲤和锦鲤的IRBP基因条带相对应.对各条带切胶回收后的测序表明,岩原鲤等位基因的相似性为99.8％,锦鲤等位基因的相似性为98.8％,而杂交个体等位基因的相似性为95.8％ ～96.7％,与岩原鲤和锦鲤间基因的相似性(95.5％～96.9％)接近.这一方法将有助于鱼类的杂种鉴定和种质研究.     

Initial characteristics of koi herpesvirus and development of a polymerase chain reaction assay to detect the virus in koi,Cyprinus carpio koi

Since 1998, episodes of mass mortality have occurred in populations of common carp Cyprinus carpio carpio in Israel and in populations of koi Cyprinus carpio koi in Israel and the USA. A herpesvirus isolated from infected fish has been shown in experimental studies to induce disease and mortality similar to those observed in outbreaks at infected farms. Initial characteristics of the virus show that it is clearly different from Herpesvirus cyprini (CHV), the most commonly known herpesvirus from cyprinid fish. The koi herpesvirus (KHV) has 31 virion polypeptides. Twelve of the virion polypeptides of KHV have similar molecular weights to those of CHV and 10 are similar to those of channel catfish virus (CCV). Both virion polypeptide and restriction fragment length polymorphism analyses of genomic DNA showed that the first KHV isolates from Israel and the USA were identical. In contrast, the genomic DNA restriction fragments clearly distinguish KHV from CHV and CCV. A polymerase chain reaction (PCR) assay to detect the virus in koi tissues was developed with sequences obtained from 1 restriction fragment of KHV DNA. The PCR assay effectively detected a 484 base pair sequence from KHV but did not amplify genomic DNA from either CHV or CCV. The PCR assay detected as little as 1 pg of KHV DNA mixed with 100 ng of host DNA. Viral sequences were amplified from koi obtained from field collections and from koi that were experimentally exposed to 10(2) TCID50 ml(-1) of KHV via the waterborne route. All KHV exposed fish dying of infection between 8 and 10 d post exposure or surviving to 14 d post exposure were found to be positive by PCR, while unexposed control koi were all negative. The assay also showed the presence of KHV DNA in tissues of koi obtained from farms in Israel. The PCR assay should assist virus isolation procedures and histologic and electron microscopic analyses now commonly used to detect KHV infection. Current studies are examining the possibility of using the PCR to detect KHV DNA in live fish and the relative sensitivity and specificity of the KHV PCR assay compared with other diagnostic tests.     

Pathogenesis of acute viral disease induced in fish by carp interstitial nephritis and gill necrosis virus

A lethal disease of koi and common carp (species Cyprinus carpio) has afflicted many fish farms worldwide since 1998, causing severe financial losses. Morbidity and mortality are restricted to common carp and koi and appear in spring and autumn, when water temperatures are 18 to 28 degrees C. We have isolated the virus causing the disease from sick fish, propagated it in koi fin cell culture, and shown that virus from a single clone causes lethal disease in carp and koi upon infection. Intraperitoneal virus injection or bathing the fish in virus-containing water kills 85 to 100% of the fish within 7 to 21 days. This virus is similar to the previously reported koi herpesvirus; however, it has characteristics inconsistent with the herpesvirus family, and thus we have called it carp interstitial nephritis and gill necrosis virus. We examined the pathobiology of this disease in carp by using immunohistochemistry and PCR. We found large amounts of the virus in the kidneys of sick fish and smaller amounts in liver and brain. A rapid increase in the viral load in the kidneys was detected by using both immunofluorescence and semiquantitative PCR. Histological analyses of fish at various times after infection revealed signs of interstitial nephritis as early as 2 days postinfection, which increased in severity up to 10 days postinfection. There was severe gill disease evidenced by loss of villi with accompanying inflammation in the gill rakers. Minimal focal inflammation was noted in livers and brains. This report describes the etiology and pathology of a recently described viral agent in fish.     

Description of an as yet unclassified DNA virus from diseased Cyprinus carpio species

Numerous deaths of koi and common carp (Cyprinus carpio) were observed on many farms throughout Israel, resulting in severe financial losses. The lethal viral disease observed is highly contagious and extremely virulent, but morbidity and mortality are restricted to koi and common carp populations. Diseased fish exhibit fatigue and gasping movements in shallow water. Infected fish had interstitial nephritis and gill necrosis as well as petechial hemorrhages in the liver and other symptoms that were not consistent with viral disease, suggesting a secondary infection. Here we report the isolation of carp nephritis and gill necrosis virus (CNGV), which is the etiologic agent of this disease. The virus propagates and induces severe cytopathic effects by 5 days postinfection in fresh koi or carp fin cell cultures (KFC and CFC, respectively), but not in epithelioma papillosum cyprini cells. The virus harvested from KFC cultures induced the same clinical signs, with a mortality of 75 to 95%, upon inoculation into naive koi and common carp. Using PCR, we provide final proof that the isolated virus is indeed the etiologic agent of food and ornamental carp mortalities in fish husbandry. Electron microscopy revealed viral cores with icosahedral morphology of 100 to 110 nm that resembled herpesviruses. Electron micrographs of purified pelleted CNGV sections, together with viral sensitivities to ether and Triton X-100, suggested that it is an enveloped virus. However, the genome of the isolated virus is a double-stranded DNA (dsDNA) molecule of 270 to 290 kbp, which is larger than known herpesviruses. The viral DNA seems highly divergent and bears only small fragments (16 to 45 bp) that are similar to the genomes of several DNA viruses. Nevertheless, amino acid sequences encoded by CNGV DNA fragments bear similarities primarily to members of the Poxviridae and Herpesviridae and to other large dsDNA viruses. We suggest, therefore, that the etiologic agent of this disease may represent an as yet unclassified virus species that is endemic in C. carpio (carp).     

Detection of carp interstitial nephritis and gill necrosis virus in fish droppings

Carp interstitial nephritis and gill necrosis virus (CNGV) is an unclassified large DNA virus that morphologically resembles members of the Herpesviridae but contains a large (ca. approximately 280-kbp) linear double-stranded DNA. This virus has also been named koi herpesvirus, koi herpes-like virus, and cyprinid herpesvirus 3. CNGV is the cause of a lethal disease that afflicts common carp and koi. By using immunohistochemistry, molecular analysis, and electron microscopy we previously demonstrated that this virus is present mainly in the intestine and kidney of infected fish. Based on these observations, we postulated that viruses and/or viral components may appear in droppings of infected carp. Here we report that (i) by using PCR we demonstrated that fish droppings contain viral DNA, (ii) fish droppings contain viral antigens which are useful for CNGV diagnosis, and (iii) fish droppings contain active virus which can infect cultured common carp brain cells and induce the disease in na?ve fish following inoculation. Thus, our findings show that CNGV can be identified by using droppings without taking biopsies or killing fish and that infectious CNGV is present in the stools of sick fish. The possibility that fish droppings preserve viable CNGV during the nonpermissive seasons is discussed.     

Koi herpesvirus infection in experimentally infected common carp Cyprinus carpio (Linnaeus, 1758) and three potential carrier fish species Carassius carassius (Linnaeus, 1758); Rutilus rutilus (Linnaeus, 1758); and Tinca tinca (Linnaeus, 1758) by quantitative real‐time PCR and in‐situ hybridization

Only single cells in the carrier fish species Carassius carassius (Linnaeus, 1758) for koi herpesvirus (KHV) are infected in contrast to large numbers in the susceptible species common carp Cyprinus carpio (Linnaeus 1758). Several species of the family Cyprinidae have been described as virus carrier species, showing no clinical signs of a KHV disease but able to transmit the virus to other susceptible fish. In this study, 72 common carp Cyprinus carpio (Linnaeus, 1758), 36 tench Tinca tinca (Linnaeus, 1758), 36 crucian carp Carassius carassius (Linnaeus, 1758) and 36 common roach Rutilus rutilus (Linnaeus, 1758) were experimentally infected with KHV (isolate “Israel”) by immersion and kept at 20°C. The fish were euthanized at 12 timepoints over a period of 90 days and virus DNA was quantified in tissues by a real‐time TaqMan PCR. Whereas KHV‐DNA was found in Cyprinus carpio for up to 90 days, the virus DNA was detectable only in single individuals of Rutilus rutilus, Tinca tinca and Carassius carassius for up to 25 days after experimental virus exposure. Tissue samples of Cyprinus carpio and Carassius carassius were screened by in‐situ hybridization. Positive signals were found in various organs of the common carp tested crucian carp. In the latter species a much smaller number of virus‐positive stained cells was detected compared to the infected carp.     

草鱼出血病混合感染的嗜水气单胞菌的分离、鉴定与理化特性

从患出血病草鱼的肝脏病灶中分离筛选出2株致病菌。取病鱼样品组织过滤液接种CIK细胞、培养, 电镜下观察到细胞质中含有草鱼呼肠孤病毒样颗粒和包涵体, 病毒颗粒大小65 nm~ 70 nm, 包涵体0.46 μm~1.81 μm。人工回归感染实验显示分离的菌株及细胞毒悬液均能使草鱼致病死亡。对分离菌株进行细胞形态学、理化特性分析及药敏试验, 初步判定所分离的2株菌均为嗜水气单胞菌。进一步对菌株进行DNA分子鉴定, 结果显示2株菌的16S rRNA基因、促旋酶亚单位蛋白(gryB)基因均与GenBank上的嗜水     

Cloning of the koi herpesvirus (KHV) gene encoding thymidine kinase and its use for a highly sensitive PCR based diagnosis

Background  

Outbreaks with mass mortality among common carp Cyprinus carpio carpio and koi Cyprinus carpio koi have occurred worldwide since 1998. The herpes-like virus isolated from diseased fish is different from Herpesvirus cyprini and channel catfish virus and was accordingly designated koi herpesvirus (KHV). Diagnosis of KHV infection based on viral isolation and current PCR assays has a limited sensitivity and therefore new tools for the diagnosis of KHV infections are necessary.     

Concentrations of a Koi herpesvirus (KHV) in tissues of experimentally infected Cyprinus carpio koi as assessed by real-time TaqMan PCR

The Koi herpesvirus (KHV) is a herpes-like virus now recognized as a worldwide cause of mortality among populations of koi Cyprinus carpio koi and common carp Cyprinus carpio carpio. Temperature is a key factor influencing virus replication both in cell culture and in the tissues of experimentally infected fish. Genomic DNA sequences were used to optimize a rapid real-time TaqMan PCR assay to detect and quantify KHV DNA as found in the tissues of virus-exposed fish. The assay allowed analytical enumeration of target KHV genome copies ranging from 10(1) to 10(7) molecules as present in infected cell lines or fish tissues. The new assay was specific for KHV and did not detect DNA from 3 related herpes-like viruses found in fish, the Cyprinid herpesvirus 1 (CyHV-1), Cyprinid herpesvirus 2 (CyHV-2), Ictalurid herpesvirus 1 (IcHV-1) or the KF-1 cell line used for virus growth. Concentrations of KHV DNA were evaluated in 7 different tissues of replicate groups of virus-exposed koi held at water temperatures of 13, 18, 23 and 28 degrees C. Viral DNA was detected among virus-exposed koi at all 4 water temperatures but mortality was only observed among fish at 18, 23, and 28 degrees C. Time and temperature and the interactions between them affected concentrations of viral DNA detected in tissues of koi exposed to KHV. Although there were no recognized patterns to viral DNA concentrations as found in different tissues over time, KHV genome copies for all tissues increased with time post virus exposure and with water temperature. The remarkably rapid and systemic spread of the virus was demonstrated by the presence of viral DNA in multiple tissues 1 d post virus exposure. The greatest DNA concentrations found were in the gill, kidney and spleen, with virus genome equivalents consistently from 10(8) to 10(9) per 10(6) host cells. High levels of KHV DNA were also found in the mucus, liver, gut, and brain. Koi surviving infection at 62 to 64 d post virus exposure contained lower KHV genome copies (up to 1.99 x 10(2) per 10(6) host cells) as present in gill, kidney or brain tissues.