新的成人腹泻轮状病毒J19株NSP4和NSP5基因克隆和序列分析

目的克隆新的成人腹泻轮状病毒J19株NSP4和NSP5基因,并分析其基因序列.方法利用一种改进的非依赖核酸序列的单引物扩增方法扩增J19株NSP4和NSP5基因,克隆到pMD18-T载体中并进行测序.在此基础上,将J19株NSP4和NSP5的蛋白序列与其他轮状病毒蛋白序列进行比较分析和种系进化分析.结果J19株NSP4和NSP5基因为基因10和11,全长为739 bp和649 bp,它们分别编码213个和176个氨基酸.与J19株NSP4和NSP5蛋白序列一致性较高的分别是B组成人腹泻轮状病毒Bang373株（20.3%）和B组猪轮状病毒db101株（29.5%）.对J19株的NSP4和NSP5的遗传进化分析表明,J19株在进化树上的位置都靠近A、B和C组轮状病毒分支的根部,而且它比较偏向B组轮状病毒的分支.结论J19株的NSP4和NSP5与其他轮状病毒的相应蛋白序列存在显著差异.J19株NSP4和NSP5的蛋白序列比较和遗传进化分析表明新的成人腹泻轮状病毒与成人腹泻轮状病毒可能有共同起源;但是新的成人腹泻轮状病毒与成人腹泻轮状病毒存在显著差异.     

成人腹泻轮状病毒J19株依赖RNA的RNA聚合酶基因序列分析

目的 进一步了解新的成人腹泻轮状病毒J19株依赖RNA的RNA聚合酶基因特征。方法 利用一种改良的非依赖核酸序列的单引物扩增方法扩增新的成人腹泻轮状病毒J19株的VP1基因，克隆至pMD18-T中并进行测序。利用DNAStar和PHYLIP软件包进行序列之间的比较分析并绘制系统发生树。结果 J19株的VP1基因为基因1，全长3538个核苷酸，编码1167个氨基酸。氨基酸序列同源性分析表明J19株的VP1蛋白序列对B组轮状病毒IDIR株的一致性为55．7％，对A组轮状病毒SA11株和C组轮状病毒Bristol株的一致性分别为20．4％、19．2％。对J19株的VP1蛋白序列的遗传进化分析表明，J19株在系统发生树上的位置是靠近外群蛋白并靠近A、B和C组轮状病毒分支的根部，而且它比较偏向于B组轮状病毒的分支。结论 J19株的VP1蛋白序列与其他轮状病毒的VP1蛋白序列存在显著差异。J19株可能是一个与B组轮状病毒的起源和进化密切相关的毒株之一。     

B组轮状病毒WH-1株 NSP2基因序列和蛋白质结构分析

目的 克隆成人腹泻标本WH-1中B组轮状病毒组(group Brotavirus，GBRV)非结构蛋白NSP2基因，分析其核苷酸序列，比较与其它GBRV基因同源性，预测其mRNA二级结构、蛋白质二级结构。方法利用逆转录-聚合酶链反应(RT-PCR)技术，从成人腹泻标本WH-1中扩增GBRV NSP2基因，克隆载体pUCmT，对NSP2基因进行核苷酸序列分析。利用GeneBee软件比较与其它GBRV毒株NSP2基因同源性，Rnaviz2．0软件绘制NSP2基因的二级结构，PredictProtein软件分析NSP2蛋白结构。结果成人腹泻标本WH-1中GBRV非结构蛋白NSP2基因全长1007bD，与ADRV核苷酸序列的同源性达98％，与印度加尔各达分离株CAI-1达82％，与IDIR(鼠)同源性仅为79％。氨基酸序列与ADRV的同源性达98．4％，与CAL-1达97．7％，而与IDIR仅为89．0％。其mRNA折叠形成多达26个发卡环状结构。NSP2蛋白是由301个氨基酸残基组成的多肽，含有2个潜在的N-糖基化位点和多个磷酰化位点。结论成人腹泻标本WH-1中GBRV非结构蛋白NSP2基因和氨基酸序列与人GBRV有较高的同源性，而与动物中GBRV同源性相对较低，其中与ADRV的同源性最高，推测GBRV WH-1株与ADRV具有相同起源。     

一种改良方法克隆新的成人腹泻轮状病毒J19株的大片段基因

目的扩增、克隆新的成人腹泻轮状病毒J19株的大片段基因。方法以新成人腹泻轮状病毒J19株的病毒核酸为材料，利用非依赖核酸序列的单引物扩增方法，扩增新的成人腹泻轮状病毒J19株的第5～11基因；根据第5～11基因序列设计7对抑制性引物，通过在PCR扩增体系中添加小片段基因的抑制性引物来提高大片段基因的PCR产量。结果当在PCR反应体系中添加2对抑制性引物时，大于2kb的大片段基因的PCR产量得到显著提高。将扩增的基因片段克隆至pMD18-T后进行测序，最后得到J19株第2、3、4基因的全长cDNA克隆。结论这种改良的非依赖核酸序列的单引物扩增方法可以用于对轮状病毒大片段基因的扩增和克隆。     

中国轮状病毒非结构蛋白NSP4基因变异特征的分析

目的　研究我国轮状病毒流行株NSP4基因的变异特点。方法　对近年来从我国不同地区获得的 2 7份人轮状病毒流行株的NSP4基因用RT PCR进行扩增 ,克隆后进行全长cDNA序列分析 ,并利用Clustal× 1.8,TreeView3 2及DNAStar软件与参比株Wa、KUN、AU 1、EW及来自GenBank的OSU、SA11、Hochi、US2 44、Bristol株的NSP4序列进行分析比较。采用PCR分型方法对VP7血清型进行鉴定 ,确定轮状病毒G型与NSP4基因型的关系。结果　氨基酸同源性比较表明 ,我国轮状病毒不同流行株NSP4之间同源性为 81.7%～ 99.4% ,据此可将 2 7株RVNSP4分为 2组 ,分别以Wa株和KUN株为代表 ,其中以Wa组为主。组内同源性分别为 92 .0 %～ 99.4%和 92 .0 %～ 98.9% ,组内变异率分别为 0～ 8 5 %及 1 2 %～ 8 5 %。两组间变异率达 16 6%～ 2 1 0 %。氨基酸进化树提示在Wa组内包括 3个亚组。轮状病毒G血清型与NSP4基因型之间的联系不确定。结论　我国流行株NSP4基因主要可分为Wa组和KUN组 ,在Wa组内可形成三个亚组 ,并且在高变区有特征性的氨基酸位点。NSP4的变异与年份有关而与地域关系不密切     

人轮状病毒NSP4蛋白131和133位氨基酸变异对毒力影响的研究

目的研究两株A组人轮状病毒NSP4蛋白131位和133位氨基酸位点的变异对毒力的影响。方法从昆明地区2002年和2005年秋冬季婴幼儿腹泻流行期不同程度腹泻患儿中分离得到两株轮状病毒流行株02k38和05k44,RT-PCR扩增NSP4全长基因,进行cDNA序列测序。通过pGEX-5X-1载体,转化E.coliBL21以谷胱苷肽S-转移酶融合蛋白的形式表达两株病毒的NSP4蛋白C-端86～170位氨基酸（GST-NSP486-170）;并酶切融合头纯化得到两种NSP486-170蛋白,在ICR乳鼠中比较这两种蛋白致小鼠腹泻的差异。结果两种NSP486-170蛋白毒性无差异。结论两株轮状病毒131位和133位氨基酸位点的变异不影响毒力的改变,其致腹泻活性没有明显差异（P〉0.05）。     

人A组轮状病毒VP6和NSP4编码基因的独立进化

轮状病毒是引起儿童重症腹泻的主要病原.目前,绝大多数研究认为A组轮状病毒的VP6和NSP4基因在进化上紧密联系[1].我们曾报道过一株在世界上极为罕见的人A组轮状病毒GSP[6]毒株[2](LL3354),通过对该毒株的VP6和NSP4全基因的分析,发现LL3354的VP6和NSP4编码基因是通过独立进化而来.     

两株Wa株人源轮状病毒NSP4蛋白的表达及其致ICR小鼠腹泻的毒力比较

目的研究两株Wa株人源轮状病毒NSP4蛋白139位氨基酸位点的变异对毒力的影响。方法从2002～2004年昆明地区婴幼儿轮状病毒感染者大便样品中,通过RT-PCR,PCR扩增了22株轮状病毒株的NSP4全长基因、cDNA序列,并对cDNA序列测序,发现这些病毒株的NSP4氨基酸序列高度保守,仅在79位、139位氨基酸位点存在差异。选取139位氨基酸不同(V/I)的两株病毒株,在E.coli BL21中,用pGEX5X-1载体融合表达了两株病毒的86～175位氨基酸(GST-NSP4_(86-175);并酶切融合头得到两种NSP4_(86-175)蛋白,在ICR乳鼠中比较这4种不同蛋白致小鼠腹泻的差异。结果发现GST-NSP4_(86-175)蛋白毒性比NSP4_(86-175)蛋白强,而139位氨基酸不同(V/I)的两株病毒株的NSP4_(86-175)蛋白毒性没有明显的差异。结论139位氨基酸位点的变异并不影响NSP4蛋白的毒力改变。     

河北省卢龙地区猪与人G9型A组轮状病毒进化关系研究

目的 了解河北省卢龙地区猪与人G9型A组轮状病毒（GARV）主要基因的分子特征及进化关系.方法 选取1株2008年河北卢龙地区G9型GARV阳性的腹泻仔猪粪便标本LLP48及4株2009年至2011年卢龙地区G9型GARV阳性的5岁以下住院腹泻患儿粪便标本进行主要基因片段的扩增,测序后对获得的基因序列通过MEGA、DNAStar等生物软件进行序列比对、同源性分析和系统进化分析.结果 卢龙猪GARV LLP48与4株卢龙人GARV编码的VP7、VP6、NSP2和NSP4基因具有高度同源性,核苷酸和氨基酸同源性分别是89.4％～94％和94.8％ ～98.2％;VP4片段的核苷酸（氨基酸）同源性较低,为71.4％～71.6％（68.2％～69.0％）.系统进化分析表明,LLP48编码的VP7、VP6、NSP2和NSP4基因与人来源的毒株关系密切,而VP4基因与猪来源的毒株关系密切.结论 卢龙猪GARV LLP48可能是猪的VP4与人的VP7、VP6、NSP2和NSP4自然重组.     

柯萨奇B组3型病毒中国分离株VP4、3D基因序列及系统发生树分析

目的研究柯萨奇B组3型病毒（CVB3）中国分离株结构蛋白VP4、非结构蛋白3D基因序列及变异性。方法在HeLa细胞中增殖病毒，用RT-PCR扩增目的基因片段，与pMDl8-T载体连接，PCR初步鉴定后测序，进行序列同源性及系统发生分析。结果CVB3中国分离株VP4基因含207个碱基，编码69个氨基酸，与Nancy株氨基酸同源性为97．10％；3D基因含1386个碱基，编码462个氨基酸，与Nancy株氨基酸同源性为97．62％。在系统发生中，CVB3中国株VP4基因、3D基因均与Nancy株聚簇。结论CVB3中国分离株VP4和3D基因长度与Nancy株一致，进化上属同一分支。     

Whole genomic characterization of a human rotavirus strain B219 belonging to a novel group of the genus Rotavirus

Novel rotavirus strains B219 and ADRV-N derived from adult diarrheal cases in Bangladesh and China, respectively, are considered to belong to a novel rotavirus group (species) distinct from groups A, B, and C, by genetic analysis of five viral genes encoding VP6, VP7, NSP1, NSP2, and NSP3. In this study, the nucleotide sequences of the remaining six B219 gene segments encoding VP1, VP2, VP3, VP4, NSP4, and NSP5 were determined. The nucleotide sequences of the group B human rotavirus VP1 and VP3 genes were also determined in order to compare the whole genome of B219 with those of group A, B, and C rotavirus genomes. The nucleotide and deduced amino acid sequences of all B219 gene segments showed considerable identity to the ADRV-N (strain J19) sequences (87.7-94.3% and 88.7-98.7%, respectively). In contrast, sequence identity to groups A-C rotavirus genes was less than 61%. However, functionally important domains and structural characteristics in VP1-VP4, NSP4, and NSP5, which are conserved in group A, B, or C rotaviruses, were also found in the deduced amino acid sequences of the B219 proteins. Hence, the basic structures of all B219 viral proteins are considered to be similar to those of the known rotavirus groups.     

Sequence analysis of genes encoding structural and nonstructural proteins of a human group B rotavirus detected in Calcutta, India

Nucleotide sequences of RNA segments encoding structural proteins(VP4, VP6, and VP7) and nonstructural proteins(NSP1 and NSP3) of a human group B rotavirus CAL-1, which was detected in Calcutta, India, were determined and their relatedness with cognate genes of other group B rotaviruses was analyzed. The CAL-1 genes showed generally high sequence identities (more than 90%) to those of human group B rotavirus, adult diarrheal rotavirus (ADRV) in China, while identities with bovine, murine, and ovine viruses were considerably lower (58-73%). Among RNA segments analyzed, sequence identity of the VP6 gene was relatively high compared with other gene segments. In the CAL-1 VP7 sequence, many characteristics were shared by ADRV, but not by other animal group B rotaviruses. In contrast, VP4 and NSP3 of CAL-1 were single amino acid and 23 amino acids longer than those of ADRV strain, respectively, due to differences of a few nucleotides. These findings suggested that human group B rotaviruses CAL-1 and ADRV might have originated from a common ancestral virus distinct from animal group B rotaviruses reported so far, while some notable sequence differences indicated the distinct nature of these viruses.     

Species-specific but not genotype-specific primary and secondary isotype-specific NSP4 antibody responses in gnotobiotic calves and piglets infected with homologous host bovine (NSP4[A]) or porcine (NSP4[B]) rotavirus

Using recombinant baculoviruses expressing rotavirus NSP4 [A], [B], [C], and [D] genotypes of bovine, porcine, human, simian, or murine origin, we analyzed serum antibody responses to NSP4s in gnotobiotic calves and piglets infected by the oral/alimentary or intraamniotic route with bovine (NSP4[A]) (Wyatt, R.G., Mebus, C.A., Yolken, R.H., Kalica, A.R., James, H.D., Jr., Kapikian, A.Z., Chanock, R.M., 1979. Rotaviral immunity in gnotobiotic calves: heterologous resistance to human virus induced by bovine virus. Science 203(4380), 548-550) or porcine (NSP4[B]) (Hoshino, Y., Saif, L.J., Sereno, M.M., Chanock, R.M., Kapikian, A.Z., 1988. Infection immunity of piglets to either VP3 or VP7 outer capsid protein confers resistance to challenge with a virulent rotavirus bearing the corresponding antigen. J. Virol. 62(3), 744-748) rotaviruses. Following primary infection and challenge with virulent rotaviruses, the animals developed higher or significantly higher antibody titers to homologous host homotypic NSP4s than to heterologous host homotypic or heterologous host heterotypic NSP4s, indicating that antibody responses were species specific rather than genotype specific. Antibody responses to NSP4s corresponded closely with the phylogenetic relationships of NSP4s within a species-specific region of amino acids (aa) 131-141. In contrast, NSP4 genotypes determined by amino acid full-length sequence identity predicted poorly their "serotypes". In piglets, antibodies to NSP4 induced by previous oral infection failed to confer protection against challenge from a porcine rotavirus bearing serotypically different VP4 and VP7 but essentially identical NSP4 to the porcine rotavirus in primary infection. Thus, in an approach to immunization with a live oral rotavirus vaccine, the NSP4 protein does not appear to play an important role in protection against rotavirus disease and infection.     

Molecular characterization of VP4, VP6, VP7, NSP4, and NSP5/6 genes identifies an unusual G3P[10] human rotavirus strain

An unusual strain of human rotavirus G3P[10] (CMH079/05) was detected in a stool sample of a 2‐year‐old child admitted to the hospital with severe diarrhea in Chiang Mai, Thailand. Analysis of the VP7 gene sequence revealed highest identities with unusual human rotavirus G3 strain CMH222 at 98.7% on the nucleotide and 99.6% on the amino acid levels. Phylogenetic analysis of the VP7 sequence confirmed that the CMH079/05 strain formed a cluster with G3 rotavirus reference strains and showed the closest lineage with the CMH222 strain. Analysis of partial VP4 gene of CMH079/05 revealed highest degree of sequence identities with P[10] rotavirus prototype strain 69M at nucleotide and amino acid levels of 92.9% and 94.6%, respectively. Phylogenetic analysis of the VP4 sequence revealed that CMH079/05 and 69M clustered closely together in a monophyletic branch separated from other rotavirus genotypes. To our knowledge, this is a novel G–P combination of G3 and P[10] genotypes. In addition, analyses of VP6, NSP4, and NSP5/6 genes revealed these uncommon genetic characteristics: (i) the VP6 gene differed from the four other known subgroups; (ii) the NSP4 gene was identified as NSP4 genetic group C, an uncommon group in humans; and (iii) the NSP5/6 gene was most closely related with T152, a G12P[9] rotavirus previously isolated in Thailand. The finding of uncommon G3P[10] rotavirus in this pediatric patient provided additional evidence of the genetic diversity of human group A rotaviruses in Chiang Mai, Thailand. J. Med. Virol. 81:176–182, 2009. © 2008 Wiley‐Liss, Inc.     

The evolution of human group B rotaviruses: correction and an update.

The Chinese adult diarrhea rotavirus (ADRV) and the Indian CAL strains of human group B rotaviruses were reported to be conserved in genes encoding structural proteins but divergent in NSP2 and NSP3 genes, raising the questions about the origin and the evolution of these strains. We repeated sequencing of the ADRV NSP2 and NSP3 genes and demonstrated high amino acid sequence identities with the CAL NSP2 and NSP3. Here we report the consequences of publishing and interpreting incorrect nucleotide sequences and provide evidence that the ADRV and CAL strains have evolved from a common ancestor.     

Complete nucleotide sequence of a group A avian rotavirus genome and a comparison with its counterparts of mammalian rotaviruses

The nucleotide sequences encoding four structural proteins (VP1-4) and six nonstructural proteins (NSP1-6) of avian rotavirus PO-13 were determined. Based on the results of earlier sequencing studies [Ito et al., 1995, Sequence analysis of cDNA for the VP6 protein of group A avian rota viruses. Arch. Vriol. 140, 605-612; Rohwedder et al., 1997, Chicken rotavirus Ch-1 shows a second type of avian VP6 gene, Virus Genes 15, 65-71; Rohwedder et al., 1997, Bovine rotavirus 993/83 shows a third subtype of avian VP7 protein, Virus Genes 14, 147-151], determination of PO-13 genome sequence has been completed. The PO-13 genome is 18845 nucleotides in length. It is 290 nucleotides longer than the genome of SA11. The amino acid sequence homology between PO-13 and mammalian rotaviruses ranged from 76-77% (VP1) to 16-18% (NSP1). The features of gene and amino acid sequence were compared with those of the corresponding protein of mammalian rotaviruses. Based on results of the phylogenetic analyses of NSP1, we speculate that an ancestral rotavirus could have separated into groups A, B and C rotaviruses at an early evolutionary stage and that group A rotavirus separated into mammalian and avian rotaviruses with host evolution.     

A Human Vaccine Strain of Lamb Rotavirus (Chinese) NSP4 Gene: Complete Nucleotide Sequence and Phylogenetic Analyses

A lamb strain of rotavirus has recently been licensed for use in China as a live vaccine to prevent rotavirus diarrhea in children. As rotavirus NSP4, especially the cytotoxic domain alone is considered to be associated with diarrhea, we sequenced gene segment 10, which encodes NSP4, of lamb rotavirus. Comparative analyses was performed to identify differences from human rotavirus strains, that might be associated with attenuation, and to ascertain whether the lamb rotavirus gene fits among the NSP4 of other sequenced rotavirus strains. Our comparative nucleotide sequence analysis suggests its close identity (91.17% homology) with that of group-A equine rotavirus (strain HI23). Multiple alignment of the deduced amino acid sequence of lamb NSP4 with that of other group A rotaviruses demonstrated homology ranging from 63.42% with that of porcine YM strain to 93.71% with equine HI23 strain of rotavirus. A group A-specific NSP4 monoclonal antibody recognized the glycosylated and unglycosylated forms of the protein from virus-infected lysates, suggesting a well-conserved group-specificity of the lamb NSP4. Phylogenetic analysis of the lamb rotavirus gene, with 60 other NSP4 gene sequences of human and animal rotavirus strains, demonstrated that the lamb rotavirus strain belongs to genotype A. Comparative analysis also revealed that although it is a vaccine strain, the NSP4 cytotoxic domain of lamb strain demonstrated an overall amino acid conservation similar to that of other strains, whose NSP4 alone causes diarrhea in animal models. These results taken together with our previous observations clearly reaffirm the idea that the attenuation phenotype of rotaviruses does not involve NSP4 cytotoxic domain, perhaps due to the suppression of NSP4 cytotoxic activity by other rotaviral proteins.