猪戊型肝炎病毒分子流行病学分析及基因3型猪戊型肝炎病毒感染性克隆的构建
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摘要
戊型肝炎(Hepatitis E, HE)以前称非甲-非乙型肝炎,是由戊型肝炎病毒(Hepatitis E virus, HEV)感染引起的一种经粪口途径传播的疾病,呈全球分布。该病属于人畜共患病,对人类健康具有很大的危害,已引起亚洲、非洲等许多发展中国家暴发急性肝炎。研究证实HEV可感染猪、野猪、牛、山羊、绵羊、鹿、灵长类、鸡、犬、贝类、啮齿类等多种动物,在这些动物宿主中以猪的感染率最高,病毒载量最大,而且从中分离到的病毒和人源毒株也有较高的同源性。因此,调查清楚猪群中HEV的存在状况,对防控人戊型肝炎具有重要的公共卫生学意义。
     1上海地区戊型肝炎病毒分子流行病学研究
     为了能够准确的了解上海地区戊型肝炎在猪群中的流行情况,从上海郊区的39个猪场中采集1487份粪便样品,通过RT-nPCR(反转录套式PCR)的方法,扩增HEV ORF2的部分片断,通过测序和遗传进化分析来研究病毒的存在状况。试验结果表明,1487份样品中的297份样品为HEV RNA阳性,阳性率20%。297份阳性样品中158份为基因3型阳性,139份为基因4型阳性,分别占总阳性率的10.6%和9.30%,基因3型HEV在感染中占主导优势。各个猪场HEV阳性率在12.1%-36%之间,分型结果显示上海郊区猪场HEV基因型为基因3型和4型,从中选取的12株代表性毒株中8株3型HEV属于3b亚型。4株4型HEV分属于4b、4d和一个新的基因亚型。
     对不同猪场基因3型和4型HEV的流行情况进行相关性分析后发现,上海郊区猪场基因3型和4型HEV的感染率呈负相关,提示两个基因型在生存和进化过程中可能存在相互竞争的关系。本次调查所关注的3个群体中,2-6月龄的猪群中HEV的感染率最高,为29.7%,其次为1-8周龄的猪群,感染率为6.9%,母猪的感染率仅为3.1%,在调查的群体中为最低。
     遗传进化分析表明,发现两株新的HEV基因4型亚型病毒株。此外,基因3型HEV在进化树中和一株日本分离株的同源性最高。这说明基因3型HEV在上海分布已经较为广泛,但以前的研究表明,中国境内猪群中只存在基因4型HEV,因此其来源还有待进一步研究。
     2猪基因3型戊型肝炎病毒上海分离株全基因组序列的测定及遗传进化分析
     为了进一步分析上海地区猪群中基因3型HEV与人源HEV的关系,本研究采用RT-nPCR方法对前面分子流行病学研究中从猪粪便样品中分离到的一株基因3型HEV(命名为SAAS-JDY5)的全基因组序列进行分片段扩增,并对其5’端和3’端两个末端的序列采用cDNA末端快速扩增技术(Rapid Amplification of cDNA Ends, RACE)进行扩增、克隆和测序。
     测序结果表明SAAS-JDY5去除3’端poly(A)尾全长为7225bp,5’-非编码区(NCR)为26bp,3'-NCR为73bp。5’和3’非编码区之间有3个开放阅读框(ORF),ORF1从27到5135位核苷酸,全长5109bp,编码1702个氨基酸。ORF2从5170-7152位核苷酸,全长1983bp,编码660个氨基酸。ORF3从5159到5500位核苷酸,全长342bp,编码113个氨基酸,此序列已经登陆GenBank,序列号为FJ527832。通过生物学软件,将SAAS-JDY5与其它已报道的88个HEV病毒株核苷酸和氨基酸序列比较后发现,SAAS-JDY5HEV全序列与HEV Ⅰ、Ⅱ、Ⅳ型的同源性在74-87%之间,而与3型HEV的同源性最高为90.8%,其中ORF1与3型HEV核苷酸的同源性为86.1-88.7%,氨基酸同源性为96.3-96.9%;ORF2与3型HEV核苷酸的同源性为88.7-90.8%,氨基酸同源性为97.6-98.9%。ORF3与3型HEV核苷酸的同源性为93.8-98.1%,氨基酸同源性为92.6-98.4%。
     遗传进化分析表明,核苷酸的进化与基因3型HEV在一个分枝上,表明SAAS-JDY5病毒株为基因3型HEV。本研究首次报道了在中国上海地区分离到的基因3型HEV的全基因组序列。3重组HEV衣壳蛋白的原核表达、鉴定及多克隆抗体的制备
     由于HEV缺乏成熟的细胞培养模型,目前一般采用ORF2编码的蛋白作为表达抗原,以此来检测HEV特异性抗体。本研究选取猪基因3型HEVSAAS-JDY5ORF21141-1842区域(a.a381-614)基因,在构建重组表达载体pET-32a-p234的基础上,成功地表达了SAAS-JDY5株的p234蛋白,通过进一步的研究证实该重组蛋白具有较好的免疫原性,能够与猪源HEV阳性血清发生免疫学反应。用该蛋白免疫新西兰大白兔,获得了较高的抗体效价,为进行下一步的研究奠定了基础。
     4猪基因3型HEV上海分离株感染性克隆的构建及体外转录活性的研究
     由于缺乏合适的体外细胞培养系统,影响了HEV的进一步研究。通过反向遗传学手段获得HEV的感染性克隆后,就可在DNA水平上通过突变、缺失、插入等手段来研究HEV的复制、表达、病毒的重组、病毒与宿主的相互作用等,也可进行抗病毒策略研究,还可以构建新的病毒载体。本研究在已知猪HEVSAAS-JDY5株全基因组序列的基础上,根据基因组和克隆载体的酶切位点,将已经克隆到的9段3型猪HEV克隆片段经过一系列的克隆和亚克隆后,构建了含有基因组全长cDNA克隆的pGEM4z-HEV重组质粒。在pGEM4z-HEV质粒中,cDNA克隆的5’端上游引入了T7启动子序列,并且在T7启动子的上游引入了单一酶切位点Xba I,3'端引入单一酶切位点Hind Ⅲ.基因组进行全长测序后发现了14个核苷酸的突变。不改变其中的沉默突变序列以作为遗传标志,对于其中的错义突变运用大引物PCR技术(Megaprimer PCR)进行定点突变修补突变的碱基,最终获得了含有遗传标志的基因3型HEV SAAS-JDY5林基因组全长cDNA的重组质粒pGEM4z-HEV.
     为了验证所构建感染性克隆的感染性,首先在Huh7细胞中进行了细胞试验。将含有猪基因3型戊型肝炎病毒SAAS-JDY5株全基因组的以T7启动子启动转录的重组质粒pGEM4z-HEV进行体外转录,成功获得纯化的HEV基因组RNA。将其转染Huh7细胞后连续培养6天,对转染的细胞通过RT-nPCR和间接免疫荧光等方法检测,证明病毒蛋白在转染的细胞中成功进行了表达。结果表明所构建的感染性克隆pGEM4z-HEV具有感染性,为下一步的体内试验提供了可行性参考。
     5基因3型HEV人工感染SD大鼠的初步研究
     体外转录后的HEV RNA转染Huh7细胞,通过间接免疫荧光试验和RT-nPCR初步检测为阳性后,进行了动物试验。pGEM4z-HEV感染性克隆线性化后作为模板用体外转录试剂盒进行体外转录,转录后的RNA肝内注射SD大鼠(SPF级),同时设立阴性和阳性对照。所有动物接种后连续观察55天,分别于注射后的0、3、7、14、21、28、35、45、50、55天分别采集大鼠的粪便和血清样品,粪便样品用RT-nPCR检测HEV RNA,血清样品用北京万泰生产的HEV总抗体检测试剂盒检测血清中的抗体,用RT-nPCR检测HEV RNA.检测结果表明大鼠在感染后7天左右在粪便中检测到HEV RNA;感染后14天左右开始出现病毒血症,一直持续到第28天还能在血清中检测到HEV RNA;感染后14天左右血清anti-HEV抗体阳性,而阴性对照中均没检测到HEV RNA和特异性抗体。为了检测是否自然感染的可能,采用两套引物对遗传标志部位进行测序验证,结果证实能够检测到遗传标志。通过本研究证实猪基因3型HEV可以跨种传播给SD大鼠,提示该动物可以作为研究HEV复制及致病机理方面一种理想的动物模型。
     以上体外体内试验结果证明,含有HEV SAAS-JDY5病毒株基因组全长cDNA的pGEM4z-HEV重组质粒具有感染性。本研究首次在我国构建出了猪HEV基因3型的感染性克隆。
     综上所述,本研究在充分普查上海市猪群中HEV的流行分布及分析猪群中流行的HEV两个基因型之间相互关系的基础上,对来源于猪粪便中的SAAS-JDY5HEV进行了全基因组序列分析,确定了该地区猪群中流行的HEV的基因型,有利于更深入分析猪源HEV与人源HEV的关系。而且在获得全基因组序列的基础上构建了含有T7启动子的感染性克隆,并通过体外及体内试验证实所获得的转录本具有感染性,成功拯救出了基因3型猪HEV,为HEV的分子生物学研究及基因工程疫苗研究打下基础,填补了国内空白。此外,通过本研究证实了猪基因3型HEV可以经人工感染的方式跨种传播给SD大鼠,提示该动物可以作为研究HEV复制及致病机理方面一种可选的动物模型。
Hepatitis E (HE), formerly known as non A, non B hepatitis, is a fecal-oral transmission disease caused by hepatitis E virus (HEV) and showing the global distribution. It is a zoonotic disease that has significant harm to human health, and has caused the outbreak of acute hepatitis in many developing countries. Studies have confirmed that HEV can infect pigs, cattle, goats, sheep, deer, primates, chickens, dogs, shellfish, rodents and other animals. Pigs have the highest infection rate and maximum viral load in these animal hosts, and the viruses isolated from pigs have high homology with human strains. Therefore, the existence status of the disease in pig herds has important public health significance on preventing and controlling the incidence of human hepatitis E.
     1Molecular epidemiological study of Hepatitis E Virus in Shanghai
     In order to accurately understand the prevalence of hepatitis E in shanghai,1487stool samples were collected from39pig farms in the suburbs of Shanghai. The partial sequence of HEV ORF2region was amplified by RT-nPCR method, and then sequenced and phylogenetic analyzed for studying the existing state of the virus. The results showed that297of1487samples were positive for HEV RNA (positive rate was20%). In the297samples,158samples were positive for the genotype3HEV,139were positive for the genotype4HEV, the total positive rate of each was10.6%and9.3%, respectively. Genotype3HEV accounted for the dominance in the infection. The HEV positive rate of all tested farms was from12.1%to36%, and the classification results showed that the genotypes of the HEV infection in the suburbs of Shanghai was genotype3and genotype4, among the12selected representative strains,8strains belonged to3b sub-genotype,4strains belonged to4b,4d and a new sub-genotype.
     We found that there was a middle scale negative relevance between positivity rates of genotype3and4HEVs in the different farms, which suggested a competition for niches between the two genotypes. In addition, the2-6months pigs had the highest infection rate in the three concerned groups (29.7%), the infection rate of1-8weeks pigs took second place in the survey, i.e.6.9%, the sows were only3.1%, which was the lowest among the three groups.
     Phylogenetic analysis showed that two new strains of subtype4HEV were identified. In addition, the genotype3HEV had the highest homology with a Japanese strain in the phylogenetic tree. The results showed that genotype3HEV was more widely distributed in Shanghai. However, previous studies had shown that there was only genotype4HEV in mainland China, thus its origin required further study.
     2The complete genome sequence determination and phylogenetic analysis of the SAAS-JDY5genotype3HEV
     To further analyze the genotype3HEV infection in Shanghai suburb, the complete sequence of the genotype3HEV strain (SAAS-JDY5) was amplified by RT-nPCR and Overlap PCR method, and the both ends of5'and3'end sequences were amplified by the RACE (rapid amplification of cDNA ends) method.
     The sequencing results showed that the full-length genome of SAAS-JDY5strain was7225bp (excluding the3'poly (A) tail) with26bp of5'-NCR and73bp of3'-NCR. There were3ORFs between the5'-NCR and3'-NCR, ORF1, from nt27to5135, has5109bp by encoding1702amino acids; ORF2, from nt5170to7152, has1983bp by encoding660amino acids; and ORF3, from nt5159to5500, has342bp by encoding113amino acids. The obtained sequence was submitted to the GenBank database and the accession number was FJ527832. The obtained sequence of SAAS-JDY5was compared with other88reported HEV sequences at nucleotide and amino acid level, and we found that the SAAS-JDY5complete sequences had74-87%nucleotide homology with the genotype Ⅰ, Ⅱ, Ⅳ HEV; However, it had the highest homology (90.8%) with genotype3HEV. In the ORF1region, the SAAS-JDY5strain shared86.1%to88.7%and96.3%to96.9%sequence identities with other genotype3HEV at the nucleotide and amino acid levels, respectively. The sequence and amino acid similarities in the ORF2region were88.7%to90.8%and97.6%to98.9%, respectively. In the ORF3region, they were93.8%to98.1%and92.6%to98.4%, respectively.
     Phylogenetic analysis showed that the nucleotide of SAAS-JDY5was in the same branch with genotype3HEV. Our study firstly report the complete genome sequence of genotype3HEV isolated from swine in Shanghai, China.
     3The expression, identification of the recombinant HEV capsid protein and preparation of polyclonal antibodies
     Since there is a lack of an efficient in vitro cell culture system and a practical animal model for HEV study, HEV-specific antibodies are detected by the ORF2antigen at present.
     In this study, the ORF2region (a.a381-614) of SAAS-JDY5was expressed by constructing a expression vector pET-32a-p234, which was designated p234protein. It was confirmed that the recombinant protein (p234) had a good immunogenicity and the ability to response to swine anti-HEV positive serum. High titer antiserum was obtained by immunization of rabbits by the purified protein, which laid a solid foundation for our further research.
     4Construction the swine genotype3HEV infectious cDNA clone of a Shanghai strain and the research on the in vitro transcription activity of the clone
     Due to the lack of a suitable in vitro cell culture system, it was diffcult to proceed the futher study of HEV, thus greatly hampered the progress of HEV research. Reverse genetic system can be a valuable tool for studying the molecular biology of HEV. In this study, based on the obtained complete sequence of SAAS-JDY5strain, we cloned9overlapping DNA fragments through a series of DNA cloning and subcloning, and then constructed the recombinant plasmid designated pGEM4z-HEV which containing the full-length genome. In the pGEM4z-HEV plasmid, we introduced a unique XbaI restriction site and a T7RNA polymerase core promoter at the extreme5'terminus, and short stretch of15adenosines (A) and HindⅢ site at the3'end of the HEV cDNA clone. The plasmid pGEM4z-HEV was subjected to complete sequencing and14nucleotides mutations were identified. Silent mutations were kept as genetic markers and non-silent mutations were corrected by megaprimer PCR mutagenesis.
     In order to verify the infectivity of the constructed infectious cDNA clone, we firstly carried out cell transfection test with huh7cells. Swine genotype3HEV complete genomic RNA was synthesized by in vitro transcription with pGEM4z-HEV as template. Transfected huh7cells were cultured for6days and tested by RT-nPCR and fluorescence assay (IFA). Results proved that the viral protein synthesis was successfully expressed in the infected cells, which indicated that the infectious HEV cDNA clone was successfully constructed.
     5The preliminary study of artifical infect SD rats by genotype3HEV
     Following the successful test on Huh7cells, we conducted animal experiments to check infection nature of the HEV cDNA clone. The recombinant plasmid pGEM4z-HEV were linearized and used as a template for in vitro RNA transcription, and SD rats (SPF) was injected with the in vitro synthesized RNA intrahepaticly. Feces and serum samples were collected from the animals at0,3,7,14,21,28,35,45,50,55days post the injection, then the fecal samples were conducted RT-nPCR detection of HEV RNA. The serum samples were conducted double antigen sandwich ELISA and RT-nPCR for the detection of anti-HEV specific antibody and HEV RNA. Our results showed that HEV RNA was detected in the stool samples at7days post infection; The viremia began at about14days post infection and existed till28days post infection; Rats had their sero conversion at about14days post inoculation, however, the animals in the negative group remained sero negative throughout the study. In order to detect the possibility of natural infection, two sets of primers were used for the detection of the genetic markers. The results identified the genetic markers in the extracted HEV RNA. Our research confirmed that the genotype3swine HEV can infect SD rats, which suggested that the SD rat can be used as an animal model for the research of HEV replication and pathogenesis.
     In summary, a detailed epidemiological investigation of hepatitis E prevalence in Shanghai revealed a middle scale negative relationship between genotype3and4HEV. The complete sequence of the SAAS-JDY5strain which was isolated from our previous investigation was obtained and a complete sequence analysis was carried out. In addition, an infectious HEV cDNA clone was constructed and confirmed to be able to infect cultured cells and SD rats. The research laid the foundation for more advanced research on HEV molecular biology. The research also suggested the possibility that SD rats be used as an animal model of HEV replication and pathogenesis study.
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