Nucleotide and deduced amino acid sequences of genes encoding the structural and nonstructural NS1 proteins of a dengue-2 virus isolated in China

We have determined the nucleotide and encoded amino acid sequences of the capsid, membrane precursor, membrane, envelope, and nonstructural NS1 protein genes of a dengue-2 virus (D2-04) isolated from a patient in Hainan, China. The sequenced region contains a gene organization similar to that of other flaviviruses. The overall amino acid sequence similarity between D2-04 and other dengue-2 viruses is greater than 92%, whereas that between D2-04 and members of the other dengue serotypes is about 65%.The nucleotide sequence data reported in this paper have been deposited in the EMBL database under the following accession numbers: X 65239 for the capsid (C), X 65240 for the envelope (E), X 65241 for the nonstructural (NS1), and X 65242 for the premembrane/membrane (prM/M) protein genes.     

登革2型病毒广东流行株结构蛋白基因序列测定及分析

目的 对广东省90年代以来流行的3株登革2型病毒(DEN2)的结构蛋白基因序列测定及分析，了解流行株之间的相互关系、变异及基因型：方法 应用RT-PCR技术扩增广东省不同年份流行的3株DEN2型病毒的结构蛋白基因(C、PrM、E基因)。分别克隆到pMD18T载体，转化JM109宿主菌，挑取阳性克隆进行鉴定及序列测定。结果 3株DEN2病毒结构蛋白基因序列长度均为2325bv，编码775个氨基酸。三者核苷酸(氨基酸)的同源性分别是：GD06／93与GD19／2001为96％(97％)、GD06／93与GD08／98为94％(97％)、GD08／98与GD19／2001为92％(94％)。其在相关毒力位点E383～385处均为GLU—PRO-GLY、E126处均为GLU。3株DEN2与国际参考株比较表明：GD06／93与GD19／2001和澳大利亚TSV01株共享序列非常接近，核苷酸(氨基酸)的同源性为98％(98％)；GD08／98与泰国株ThNH-P28／93核苷酸(氨基酸)同源性为98％(98％)。此3株DEN2二级结构与对乳鼠不致病的04株比较，主要差别位于其393～400氨基酸处，本室分离的3株对乳鼠致病毒株为EEEEHHHH，而04株为EEEE----；337～343处本室分离的3株对乳鼠致病毒株为HH-------HHHHH，而04株为--------HHHHE-，恰好位于Dengue病毒E基因的Ⅲ区：结论 GD06／93、GD19／2001与TSV01亲缘关系较近，属同一基因型。GD08／98与ThNH—P28／93共享序列非常接近，属同一基因型。3株DEN2病毒在E蛋白Ⅲ区结构有一定变异，可能与毒力有关。     

登革2型病毒04株基因组全序列的测定

目的 对我国登革２型病毒０４株（Ｄ２－０４）基因组进行全序测定及分析，为了解其基因组织结构与生物功能的关系及研究开发登革病毒新型疫苗奠定基础。方法 根据登革２型国际标准株ＮＧＣ的序列，设计１３对重叠引物，通过ＲＴ－ＰＸＣＲ扩增同Ｄ２－０４株不同的ｃＤＮＡ片段，分别克隆到ｐＧＥＭ－Ｔ载体，转化受体菌ＤＨ５α，挑取阳性克隆进行ＰＣＲ、酶切鉴定及序列测定。结果 Ｄ２－０４株的基因组全长１０７２３个碱基，     

登革2型病毒海南分离株全长E基因的测定与分析

目的 测定我国登革2型病毒海南分离株E基因的全序列，并分析其病毒学特性和分子进化特征。方法 运用RT-PCR法扩增我国登革2型病毒海南分离株D2V—HN89)E基因，测序并用计算机分析序列，作毒株感染细胞及乳小白鼠试验。结果 D2V-HN89株E基因核苷酸全长1464bp，核苷酸和氨基酸序列与D2V—NGC株的同源性分别为95％和980A，系统树分析显示其与登革2型牙买加株及登革2型巴西90株的亲缘关系最近。D2V—HN89株的细胞病变效应与D2V—NGC株相同，但对乳小白鼠神经毒力较弱。结论 D2V-HN89株的E基因区有缺失，该流行毒株可能来源于牙买加或巴西登革热流行区。     

Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines

We have identified 72 completely conserved amino acid residues in the E protein of major groups of the Flavivirus genus by computational analyses. In the dengue species we have identified 12 highly conserved sequence regions, 186 negatively selected sites, and many dengue serotype-specific negatively selected sites. The flavivirus-conserved sites included residues involved in forming six disulfide bonds crucial for the structural integrity of the protein, the fusion motif involved in viral infectivity, and the interface residues of the oligomers. The structural analysis of the E protein showed 19 surface-exposed non-conserved residues, 128 dimer or trimer interface residues, and regions, which undergo major conformational change during trimerization. Eleven consensus T_h-cell epitopes common to all four dengue serotypes were predicted. Most of these corresponded to dengue-conserved regions or negatively selected sites. Of special interest are six singular sites (N₃₇, Q₂₁₁, D₂₁₅, P₂₁₇, H₂₄₄, K₂₄₆) in dengue E protein that are conserved, are part of the predicted consensus T_h-cell epitopes and are exposed in the dimer or trimer. We propose these sites and corresponding epitopic regions as potential candidates for prioritization by experimental biologists for development of diagnostics and vaccines that may be difficult to circumvent by natural or man-made alteration of dengue virus. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

我国登革2型病毒43株基因组全长cDNA的构建

目的 构建我国登革2型病毒43株基因组全长cDNA,为进一步研究其体外RNA转录产物的感染性,阐明致病机理及探索新型疫苗奠定基础。方法 根据登革2型病毒参考株NGC株的核苷酸序列,利用DNASTAR软件设计覆盖登革2型病毒43株基因组的6对重叠引物。从感染登革2型病毒43株的乳鼠脑中提限病毒基因组RNA,采用RT－PCR分别扩增6条基因片段,并将其分别与pGEM－T载体进行连接。重组质粒用PCR进行快速鉴定,并在377A型自动测序仪进行序列分析。然后利用单一酶切位点,分别自阳性重组子上切下各基因片段,在体外分别进行5′半分子和3′半分子的连接,最后将5′和3′半分子连接成基因全长的cDNA。扩增各接头两侧长约457－691bp的基因片段,连接至T载体后测序,从而对全长cDNA进行鉴定。结果 共扩增出6条约1．5－2．5kb的基因自然,并在体外进行连接,获得了全长cDNA。结论 通过测序证实成功地构建了我国登革2型病毒43株基因组全长cDNA分子。本研究结果将为阐明我国登革病毒株的毒力及致病机理奠定基础。     

临床分离2型登革病毒突变株E蛋白N端158氨基酸基序免疫原性初探

目的:Ⅱ型登革病毒临床分离突变株(B株)E基因区部分序列的原核表达载体构建,蛋白表达、复性和纯化,及其免疫原性的初探。方法:将B株E基因1～476bp序列克隆入原核表达载体pET28a(+),经酶切、测序鉴定正确后转入表达菌,IPTG诱导后将包涵体变性,复性,纯化后的蛋白免疫C57BL/6和BALB/c小鼠制备多克隆抗体,并通过Western blot和ELISA进行抗体鉴定。结果:成功构建了pET28a(+)-B-E原核表达载体,在表达菌中以包涵体形式稳定高表达,分子量为20kD。利用蛋白的His标签进行Western blot鉴定确定该蛋白为重组B-E蛋白,得到的可溶蛋白纯度大于90%。B-E蛋白免疫BALB/c和C57BL/6小鼠均可以得到有效的多克隆抗体。结论:B-E蛋白对BALB/c和C57BL/6小鼠具有免疫原性,其中ELISA鉴定免疫C57BL/6小鼠抗体的滴度为1∶12800,Western blot鉴定免疫BALB/c小鼠抗体滴度为1∶500。     

Phylogeography and molecular evolution of dengue 2 in the Caribbean basin, 1981-2000

We sequenced the envelope (E) genes of 59 DEN-2 isolates collected from ten Caribbean islands, six South American countries, and two Central American countries between 1981 and 2000, a period characterized by hyperendemicity and increased incidence of severe dengue. Fifty-two isolates belonged to "American/Asian" subtype IIIb, possessing a characteristic polar residue at envelope aa position 390 (N [n = 48] or S [n = 4]) common to that group. Six isolates from Trinidad (1981), Honduras (1991 [4]), and El Salvador (1987) fell into the "Native American" subtype V (D at aa 390), and one from Honduras (1986) belonged to "Asian" subtype I. The data suggest that after its first isolation in the Caribbean in 1981, genotype IIIb spread throughout the Americas and effectively replaced subtype V throughout the Caribbean basin. The strain also evolved into several distinct lineages, based on substitutions in the E glycoprotein (amino acids 91 and 131), two of which were still in circulation in 2000. Interestingly, a molecular clock did not fit the data well, suggesting that other sources of rate variation, such as differential selection or differences in effective population sizes, may exist among lineages. Our results indicate the importance of large temporal- and geographical-scale phylogenetic studies in understanding disease dynamics, particularly where replacements between regions can occur.     

Detection of the dengue non-structural 1 antigen in cerebral spinal fluid samples using a commercially available enzyme-linked immunosorbent assay

The involvement of the central nervous system in dengue infections has been reported in countries where the disease in endemic. The purpose of this study was to determine whether an enzyme-linked immunosorbent assay kit designed to detect the dengue NS1 antigen in serum was able to detect this antigen in cerebral spinal fluid (CSF) samples from patients with fatal outcomes. To evaluate the sensitivity of the kit, 26 dengue-positive CSF samples were used. The Pan-E Dengue Early kit was able to detect the NS1 antigen in 13 of 26 dengue-positive CSF samples, resulting in a sensitivity of 50% (95% confidence interval, 29.9-70.1%) and specificity of 100% (95% confidence interval, 75.3-100%). The kit was able to detect the NS1 antigen in CSF of individuals who had died of dengue. When used in combination with IgM, the detection rate rose to 92.3%. This study reports a method for rapidly detecting the dengue virus in CSF, thereby increasing the diagnosis of dengue fever cases with unusual neurological manifestations.     

细胞因子在登革病毒感染人皮肤成纤维细胞中的作用

目的探讨登革病毒（dengue virus，DV）对人皮肤成纤维细胞（HSF）的感染性和细胞因子在DV感染HSF中的作用。方法采用微量病毒空斑法检测登革Ⅱ型病毒（dengue type-2 virus，DV2）感染HSF后病毒繁殖动态变化，间接免疫荧光法检测HSF内DV抗原。透射电镜观察病毒感染细胞的超微结构改变。用不同浓度的IL-6、TNF-α、GM—CSF分别作用于DV2感染HSF的不同环节（病毒吸附时和病毒吸附后），于感染后48h收集感染上清，测病毒滴度；用DV2感染HSF后，于不同时间收集感染上清，用ELISA法定量测定IL-6、TNF-α的含量。结果病毒感染后24h即可在培养上清中测出病毒，病毒滴度在48h达到高峰，以后逐渐下降。用间接免疫荧光法证明感染的HSF胞浆及胞膜上携带DV抗原。在光镜和电镜下，感染细胞均朱见明显的形态和结构改变。在病毒吸附时10．g／ml浓度的IL-6能显著提高病毒产量；在病毒吸附时和吸附后100ng／ml浓度的TNF-α能抑制病毒的产量。GM-CSF对DV感染HSF无明显影响。DV感染能促进HSF分泌IL-6；对TNF-α的分泌无明显影响。结论HSF是DV的允许性细胞。HSF可能是蚊叮咬后在原位组织中首先支持DV感染的细胞之一；细胞因子在DV感染HSF的致病和免疫过程中起重要作用。     

Glycosylation of the dengue 2 virus E protein at N67 is critical for virus growth in vitro but not for growth in intrathoracically inoculated Aedes aegypti mosquitoes

To determine the importance of dengue 2 virus (DEN2V) envelope (E) protein glycosylation, virus mutants in one or both of the N-linked glycosylation motifs were prepared. We found that while the E2 mutant virus (N153Q) replicated in mammalian and mosquito cells, the E1 (N67Q) and E1/2 (N67Q and N153Q) mutant viruses were unable to grow in mammalian cells. Infection of C6/36 mosquito cells with either the E1 or E1/2 mutants resulted in the introduction of a compensatory mutation, K64N, restoring glycosylation in the area. All mutants replicated similarly in inoculated Aedes aegypti mosquitoes, with no change in their mutations. These results suggest that N-linked glycosylation of the E protein is not necessary for DEN2V replication in mosquitoes, however N-linked glycosylation at amino acid N67 (or nearby N64) is critical for the survival of the virus in either mammalian or insect cell culture.     

Phylogenetic analysis of North American West Nile virus isolates, 2001-2004: evidence for the emergence of a dominant genotype

The distribution of West Nile virus has expanded in the past 6 years to include the 48 contiguous United States and seven Canadian provinces, as well as Mexico, the Caribbean islands, and Colombia. The suggestion of the emergence of a dominant genetic variant has led to an intensive analysis of isolates made across North America. We have sequenced the pre-membrane and envelope genes of 74 isolates and the complete genomes of 25 isolates in order to determine if a dominant genotype has arisen and to better understand how the virus has evolved as its distribution has expanded. Phylogenetic analyses revealed the continued presence of genetic variants that group in a temporally and geographically dependent manner and provide evidence that a dominant variant has emerged across much of North America. The implications of these findings are discussed as they relate to transmission and spread of the virus in the Western Hemisphere.     

Construction of an infectious cDNA clone for a Brazilian prototype strain of dengue virus type 1: characterization of a temperature-sensitive mutation in NS1

To help understand the mechanism of pathogenesis of dengue virus (DV), we set out to create an infectious cDNA of the Brazilian prototype strain of DV serotype 1 (DV1-BR/90). PCR-amplified fragments of DV1-BR/90 cDNA were readily assembled into a subgenomic cDNA that could be used to produce replicating RNAs (replicons), lacking the structural protein-encoding regions of the genome. However, assembly of a cDNA capable of producing infectious virus was only possible using a bacterial artificial chromosome plasmid, indicating that DV1 sequences were especially difficult to propagate in E. coli. While characterizing our cDNA we discovered a fortuitous temperature-sensitive mutation in the NS1 encoding region. Using our infectious cDNA and a renilla luciferase-expressing replicon we were able to demonstrate that this mutation produced a defect in RNA replication at 37 degrees C, demonstrating that the DV1 NS1 protein plays an essential role in RNA replication.     

Sustained transmission of dengue virus type 1 in the Pacific due to repeated introductions of different Asian strains

Outbreaks of dengue due to dengue virus type 1 (DENV-1) occurred almost simultaneously in 2001 in Myanmar and at multiple sites almost 10,000 km away in the Pacific. Phylogenetic analyses of the E protein genes of DENV-1 strains recovered from Asia and the Pacific revealed three major viral genotypes (I, II, and III) with distinct clades within each. The majority of strains from the Pacific and Myanmar, and a number of other Asian strains fell into genotype I. Genotype II comprised a smaller set of Asian and Pacific strains, while genotype III contained viruses from diverse geographical localities. These analyses suggested that the continuing outbreak of dengue in the Pacific has been due to multiple, direct, introductions of dengue viruses from a variety of locations in Asia followed by local transmission. There was no evidence that the introduction of these viruses into the Pacific was associated with any adaptive changes in the E protein of the viruses.     

深圳市首例本地登革热3型病例的病原学检测与分析

目的对2016年深圳市报告的首例本地疑似登革热病例查明病因.分离鉴定病原体,从分子水平分析分离株的生物学特征.方法对疑似患者血清标本采用ELISA、胶体金免疫层析法和荧光RT-PCR方法分别检测登革病毒抗体、NS1抗原和病毒核酸,并用C6/36细胞分离登革病毒.采用RT-PCR方法扩增病毒PrM/M-E基因后进行序列测定,并与不同国家和地区的登革毒株进行同源性比较和进化树分析.结果从患者血清标本中检测到登革病毒IgM抗体、NS1抗原和登革3型病毒核酸,并成功分离到登革3型病毒,将其命名为DENV3-SZ1648.深圳市登革3型病毒分离株SZ1648与登革3型国际标准株H87株、国内外流行株80-2、GWL-25株在PrM/M-E基因上核苷酸同源性分别为92.0％、91.8％和90.3％,而与登革1、2、4型国际标准株HAWAII、NGC、H241同源性分别为68.7％、64.2％和63.2％.进化树显示SZ1648株与2007年印度尼西亚分离株MKS-0098亲缘关系最近,在进化树的同一分支上,和85-159株(Indonedia 1985)、2167株(Tahiti 1989)、29472株(Fiji1992)等同属基因Ⅰ亚型.患者发病前1个月在深圳居住,无输血史、无外出史.结论从病原学、血清学和分子生物学特征上均证实该本地病例是由登革3型病毒引起,这也是深圳市首次报道存在本地登革3型病毒的疫情,该毒株最有可能来源于印度尼西亚.     

Genome type analysis of chilean adenovirus strains isolated in a children's hospital between 1988 and 1990

In a study designed to evaluate the genetic variability of adenovirus strains associated with infantile cases of respiratory disease requiring hospitalization, a collection of 136 adenovirus isolates obtained in the Roberto del Rio Children's Hospital of Santiago, Chile between June 1988 and November 1990 was studied by restriction enzyme analysis. Nasopharyngeal aspirates were obtained on admission from children under 2 years. During the study period a total of 227 adenovirus respiratory infections (ARI) were diagnosed at the ward for ARI by immunofluorescence, representing 23% of all admissions. Fifty percent of the 136 typed strains were found to belong to subgenus B, and the other 50% corresponded to subgenus C. Digestion with a set of seven enzymes allowed the identification of nine different genome types of subgenus C, three of which had not been previously described, exhibiting novel restriction patterns with either Bgl II or BstEII. Ad7h, identified in 66 isolates, was the predominant genome type and was associated with the nine cases requiring mechanical respiratory assistance and with the two fatalities recorded during the 29 months. No differences were found between the age and sex distribution of subgenus B and C genomic variants, but the mean length of hospital stay (X ± 2 SE) recorded among patients infected with subgenus B types was significantly higher (17.72 + 4.52 days (n = 55) vs. 7.54 + 1.70 days (n = 53); F = 17.22; P < 0.0001) © 1994 Wiiey-Liss, Inc.     

DNA vaccines against dengue virus based on the ns1 gene: the influence of different signal sequences on the protein expression and its correlation to the immune response elicited in mice

We analyzed four DNA vaccines based on DENV-2 NS1: pcENS1, encoding the C-terminal from E protein plus the NS1 region; pcENS1ANC, similar to pcENS1 plus the N-terminal sequence from NS2a (ANC); pcTPANS1, coding the t-PA signal sequence fused to NS1; and pcTPANS1ANC, similar to pcTPANS1 plus the ANC sequence. The NS1 was detected in lysates and culture supernatants from pcTPANS1-, pcENS1- and pcENS1ANC-transfected cells and not in cells with pcTPANS1ANC. Only the pcENS1ANC leads the expression of NS1 in plasma membrane, confirming the importance of ANC sequence for targeting NS1 to cell surface. High levels of antibodies recognizing conformational epitopes of NS1 were induced in mice immunized with pcTPANS1 and pcENS1, while only few pcENS1ANC-inoculated animals presented detectable anti-NS1 IgG. Protection against DENV-2 was verified in pcTPANS1- and pcENS1-immunized mice, although the plasmid pcTPANS1 induced slight higher protective immunity. These plasmids seem to activate distinct patterns of the immune system.     

Genetic and phylogenetic analysis of the non-structural proteins NS1, NS2 and NS3 of epizootic haemorrhagic disease virus (EHDV)

Three unique non-structural (NS) proteins are produced by Epizootic haemorrhagic disease virus (EHDV) during infection of a host cell; NS1, NS2 and NS3. This study presents a complete genetic and phylogenetic analysis of these proteins (and the genes that code for them) to allow comparison of the selective pressures acting on each. Accession numbers, gene and protein sizes, ORF positions, G + C contents, terminal hexanucleotides, start and stop codons and phylogenetic relationships are all presented. Unlike the core, or outer-coat proteins, there are no characteristic genetic or phylogenetic traits common to all of the EHDV NS proteins; indicating that each is evolving under different selection pressures. These differences are discussed. Evidence of genetic recombination in genome segment 8 (coding for NS2) is also presented, together with evidence of gene duplication and mutation, suggesting the EHDV genome may have evolved using mechanisms such as these.     

Effect of gene location on the evolutionary rate of amino acid substitutions in herpes simplex virus proteins

In an effort to understand the organization of genes in the herpes simplex virus (HSV-1) genome, I tested the idea that the location of a gene may be related to the evolutionary rate of amino acid sequence variation in the encoded protein. A measure of protein sequence divergence was calculated for homologous proteins in the UL region of six alphaherpesviruses including HSV-1, and this parameter was plotted against position in the HSV-1 genome. The results revealed a cluster of highly conserved proteins (UL27-UL33) encoded near the middle of UL. A similar analysis was restricted to HSV-1 and HSV-2 permitting an examination of U(S) proteins and proteins encoded in repeated regions at the segment ends. This analysis showed that U(S) proteins as a group are more highly divergent than those encoded in UL. A high degree of divergence was also observed in proteins coded at the segment ends including RL1 (gamma(1)34.5), RL2 (alpha0), UL1 (glycoprotein L), UL56, U(S)1, and U(S)12. It is suggested that conserved proteins UL27-UL33 are encoded near the middle of UL to take advantage of a low local mutation rate. Highly divergent proteins are suggested to be encoded selectively in U(S) because of a comparatively rapid evolutionary rate with which genes can be introduced and removed from S in response to environmental variation.