DEVELOPMENT OF HEPATITIS E 3 GENOTYPE RECOMBINANT PROTEIN CAPSID OF: CLONING, EXPRESSION, PURIFICATION, EVALUATION OF THE ANTIGENIC PROPERTIES

Aim. The development of the hepatitis E virus (HEV) genotype 3 recombinant capsid protein.Materials and methods. E.coli strains, plasmid vectors, serological and clinical samples, ELISA reagent kits, molecular biological, bioinformatic, biotechnological, biochemical and serological methods.Results. Using viruscontaining material from pigs of Belgorod region (Russian Federation) we made E.coli strains producing recombinant capsid protein, containing C-terminal of viral ORF2 protein fragment fused to E.coli β-galactosidase. Recombinant protein ORF2 had been isolated from the bacterial inclusion bodies and purified by size exclusion chromatography. Antigenic specificity of the recombinant polypeptide was confirmed by ELISA and Western blotting with sera of hepatitis E patients and reference groups (healthy donors, patients with hepatitis A, B, C, infectious mononucleosis, cytomegalovirus infection and HIV-infected patients). Conclusion. HEV genotype 3 ORF2 recombinant antigen had been developed, and the possibility to use it in diagnostic tests had been experimentally shown.

DESIGN OF HEPATITIS E VIRUS GENOTYPE 1 RECOMBINANT ORF3 PROTEIN BY CODON OPTIMIZATION METHOD

Aim. The development of the hepatitis E virus (HEV) genotype 1 full-size ORF3 recombinant polypeptide. Materials and methods. Escherichia coli strains, plasmid vectors, serological and clinical samples, ELISA reagent kits, molecular biological, bioinformatic, biotechnological, biochemical and serological methods. Results. HEV genotype 1 RNA had been isolated from clinical samples collected in Kyrgyzstan. DNA copy of subgenomic virus RNA had been cloned and used for further development of E.coli strains producing full-size recombinant protein ORF3 fused to E.coli beta-galactosidase. Codons optimization method was used in aim to increase expression level of recombinant protein. Recombinant protein ORF3 had been isolated from the inclusion bodies of the E.coli biomass and purified by size exclusion chromatography. Antigenic specificity of recombinant polypeptide had been confirmed by enzyme-linked immunosorbent assay and Western blotting with the specific sera. Conclusion. HEVgenotype 1 ORF3 recombinant antigen had been designed, and it’s applicability in diagnostic tests had been experimentally confirmed.

DESIGN OF HEPATITIS E VIRUS GENOTYPE 1 RECOMBINANT CAPSID PROTEIN: CLONING, EXPRESSION, PURIFICATION, EVALUATION OF THE ANTIGENIC PROPERTIES

Aim. The development of the hepatitis E virus (HEV) genotype 1 recombinant capsid protein. Materials and methods. Escherichia coli strains, plasmid vectors, serological and clinical samples, ELISA reagent kits, molecular biological, bioinformatic, biotechnological, biochemical and serological methods. Results. Using HEV genotype 1 DNA copy of subgenomic virus RNA we made E.coli strains producing recombinabt capsid protein, containing C-terminal fragment of ORF2 protein fused to E.coli beta-galactosidase. Recombinant protein ORF2 had been isolated from the inclusion bodies of the E.coli biomass and purified by size exclusion chromatography. By Western blotting it had been shown specific interaction of the recombinant polypeptide with anti-HEV IgG from pool of positive sera. Antigenic specificity of the recombinant polypeptide had been confirmed by enzyme-linked immunosorbent assay with sera of hepatitis E patients and reference groups: healthy donors, patients with hepatitis А, В, C, infectious mononucleosis and cytomegalovirus infection, HIV-infected patients. Conclusion. HEV genotype 1 ORF2 recombinant antigen had been developed, and its possible use in diagnostic tests had been experimentally shown.

[Viral component of the human genome]

Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent. One of the most common ways of reinforcing anti-viral barriers is the horizontal transfer of viral genes into the host genome. Within the host genome, these genes may be modified and extensively expressed to compete with viral copies and inhibit the synthesis of their products or modulate their functions in other ways. This review summarizes the available data on the horizontal gene transfer between viral and human genomes and discusses related problems.

Viral component of the human genome

Relationships between viruses and their human host are traditionally described from the point of view taking into consideration hosts as victims of viral aggression, which results in infectious diseases. However, these relations are in fact two-sided and involve modifications of both the virus and host genomes. Mutations that accumulate in the populations of viruses and hosts may provide them advantages such as the ability to overcome defense barriers of host cells or to create more efficient barriers to deal with the attack of the viral agent. One of the most common ways of reinforcing anti-viral barriers is the horizontal transfer of viral genes into the host genome. Within the host genome, these genes may be modified and extensively expressed to compete with viral copies and inhibit the synthesis of their products or modulate their functions in other ways. This review summarizes the available data on the horizontal gene transfer between viral and human genomes and discusses related problems.

[Cell analogs of viral proteins]

Horizontal transfer of genes between viruses and their hosts played an important role in the evolution of various eukaryotes including contemporary mammals as well as the pathogens themselves. Elements of viruses of various types can be found in the genome of animals. Endogenous retroviral elements composing up to 8% of human genome length not only determine its high flexibility and rapid adaptation potential. Many of virus genes such as Fv1, Lv1, Lv2 being analogues of capsid and other proteins determine effective suppression of viral replication after cell penetration by the causative agent. Introduction of these elements into genome of a wide variety of animals from fish to primates could have taken place against the background of global natural cataclysms of viral origin. Integration of retrovirus genes coding surface glycoproteins with immunosuppressing domains into genetic apparatus of animals served as an impetus to the development of viviparity and spread ofplacental mammals. Their cell analogs syncytins perform a dual function: take direct part in the formation of syncytiotrophoblast layer of placenta and ensure tolerance of immune system of mother to embryo. The acquisition of cell genes by viruses also played an important role in their evolution: various interleukins and other modulators of immune response introduced into viral genome from cell genetic apparatus became one of the most important factors of pathogenicity of a wide variety of causative agents including poxviruses, cytomegalovirus, Epstein-Barr virus and many others. Evolutionary pathways of the virus and host are thus inseparable from each other, and character of one of these directions is largely dictated by the vector of another.

[Mechanisms of retroviral immunosuppressive domain-induced immune modulation]

Immunosuppressive domains (ISD) of viral envelope glycoproteins provide highly pathogenic phenotypes of various retroviruses. ISD interaction with immune cells leads to an inhibition of a response. In the 1980s it was shown that the fragment of ISD comprising of 17 amino acids (named CKS-17) is carrying out such immune modulation. However the underlying mechanisms were not known. The years of thorough research allowed to identify the regulation of Ras-Raf-MEK-MAPK and PI3K-AKT-mTOR cellular pathways as a result of ISD interaction with immune cells. By the way, this leads to decrease of secretion of stimulatory cytokines (e.g., IL-12) and increase of inhibitory, anti-inflammatory ones (e.g., IL-10). One of the receptor tyrosine kinases inducing signal in these pathways acts as the primary target of ISD while other key regulators--cAMP and diacylglycerol (DAG), act as secondary messengers of signal transduction. Immunosuppressive-like domains can be found not only in retroviruses; the presence of ISD within Ebola viral envelope glycoproteins caused extremely hard clinical course of virus-induced hemorrhagic fever. A number of retroviral-origin fragments encoding ISD can be found in the human genome. These regions are expressed in the placenta within genes of syncytins providing a tolerance of mother's immune system to an embryo. The present review is devoted to molecular aspects of retroviral ISD-induced modulation of host immune system.

[Somatic mutations of the P53 gene in stomach cancer]

The paper deals with a study of p53 gene somatic mutations in tumor cell genomes from patients with stomach cancers of different histological patterns. It used sequential and molecular cloning methods. The former involved amplicones characterized by abnormal volatility following SSCP analysis of plasmids from 9 tumors. Replacement nucleotides were identified in 4 tumors (intestinal--2, diffuse--2). Among 8 mutations were 1 single-nucleotide deletion in codon-249 with shifting sensing frame and one targeted mutation. Five of the former were missens-mutations which caused amino acid replacement while the other two silent mutations did not. Exon-assisted analysis of p53 ("wild") gene identified cells with stable structure in each tumor (1 mutation--2; 3 mutations--2 including genuinely-paired mutations in 1 exon). All mutations occurred in structurally and functionally important codons. Our evidence corroborated earlier data of SSCP analysis on tumor cell presence in populations with variable p53 genomes.

[Molecular characteristic of influenza virus A H5N1 Strains isolated from poultry in Kurgan Region in 2005]

During the latter half of 2005 a widespread outbreak caused by influenza highly pathogenic H5N1 virus among wild and domestic birds occurred in Russia. As pathogenicity level is a polygenic feature and majority of individual genes of influenza A viruses contribute to pathogenicity of influenza viruses to birds, animals and humans. Nucleotide sequencing of the entire genome of influenza H5N1 virus isolates obtained in Kurgan region (Western Siberia) was performed. Structure of viral proteins was analyzed according to the predicted amino acid sequences. HA receptor-binding site of A/chicken/Kurgan/05/2005 and A/duck/Kurgan/08/2005 strains was typical for avian influenza viruses and contained Glu and Gly at positions 226 and 228, respectively. Structure of the cluster of positively charged amino acid residues at the cleavage site was identical for all isolates: QGERRRKKR. According to the data of neuraminidase structure analysis NA of the H5N1 isolates tested was suggested to belong to Z genotype. Amino acid residues typical for birds were revealed in 30 out of 32 positions of M1, M2, NP, PA and PB2 proteins determining host range specificity. One strain isolated in Kurgan contained lysine in position 627 of PB2 protein. Kurgan isolates was shown to have remantadine-sensitive genotype. Glutamic acid was found at position 92 of NS1 protein in both strains indicating virus resistance to interferon. Phylogenetic analyses allowed relating Kurgan isolates to subclade II of clade II of highly pathogenic H5N1 influenza viruses.

Novel conjugate of moxifloxacin and carboxymethylated glucan with enhanced activity against Mycobacterium tuberculosis

Mycobacterium tuberculosis is an intracellular pathogen that persists within macrophages of the human host. One approach to improving the treatment of tuberculosis (TB) is the targeted delivery of antibiotics to macrophages using ligands to macrophage receptors. The moxifloxacin-conjugated dansylated carboxymethylglucan (M-DCMG) conjugate was prepared by chemically linking dansylcadaverine (D) and moxifloxacin (M) to carboxymethylglucan (CMG), a known ligand of macrophage scavenger receptors. The targeted delivery to macrophages and the antituberculosis activity of the conjugate M-DCMG were studied in vitro and in vivo. Using fluorescence microscopy, fluorimetry, and the J774 macrophage cell line, M-DCMG was shown to accumulate in macrophages through scavenger receptors in a dose-dependent (1 to 50 microg/ml) manner. After intravenous administration of M-DCMG into C57BL/6 mice, the fluorescent conjugate was concentrated in the macrophages of the lungs and spleen. Analyses of the pharmacokinetics of the conjugate demonstrated that M-DCMG was more rapidly accumulated and more persistent in tissues than free moxifloxacin. Importantly, therapeutic studies of mycobacterial growth in C57BL/6 mice showed that the M-DCMG conjugate was significantly more potent than free moxifloxacin.

[Identification of changes in gene loci potentially associated with cervical cancer using NotI microarrays]

The investigation of the cancer-associated structural and epigenetic changes in cell genome is a major approach for understanding mechanisms of cancerogenesis. To investigate these genome changes, novel technique of microarrays comprising NotI-linking genome clones was developed. Twenty eight samples from patients with cervical cancer were analyzed using NotI microarrays of human chromosome 3. Deletions, amplifications and methylation were detected for 109 out of 182 NotI clones with different frequency. Notably, 17 NotI-linking clones showed genomic changes in more than 35% of tumor samples investigated, which suggests involvement of genes associated with these clones in development of cervical cancer.

[Study of antituberculous activity of moxifloxacin conjugate with macrophage scavenger-receptor ligand]

Mycobacterium tuberculosis is an intracellular pathogen that persists in macrophages of the human host. An approach to improving the treatment of tuberculosis is target delivery of antibiotics to macrophages using ligands to macrophage receptors. The antituberculous activity of the conjugate of the antituberculous antibiotic moxifloxacin with carboxymethylglucan was studied in vitro using the J774 macrophage cell line and peritoneal macrophages. The antituberculous activity of the conjugate was higher than of the free moxifloxacin. The target antibiotic delivery to macrophage cells in tuberculosis infection was shown perspective.

[Designing of the pp65 recombinant antigen of human cytomegalovirus and investigation of its immunochemical properties]

The primary and secondary structures of the pp65 phosphoprotein of human cytomegalovirus coded by the UL83 gene were studied by the methods of computer-aided analysis. An immunodominant protein fragment with 3 antigenic determinant was detected. The UL83 fragment coding the selected region was amplified and cloned in bacterial expressing vector. The recombinant protein was obtained and purified. On the basis of ELISA findings it was acknowledged as possible to use the pp65 recombinant protein jointly with pp150 and p52 in the diagnosis of antibodies specific to human cytomegalovirus.

Differences between HA receptor-binding sites of avian influenza viruses isolated from Laridae and Anatidae

A comparative study of the hemagglutinin (HA) receptor binding site (RBS) of a number of H13 influenza viruses isolated from Laridae family of birds (gulls) and other influenza viruses obtained from the Anatidae family (ducks) was conducted. The affinity of all viruses to alpha N-acetylneuraminic acid (Neu5Ac alpha), 3'sialyllactose (3'SL), and sialylglycopolymers bearing 3'-sialyl(N-acetyllactosamine) (3'SLN-PAA), [Neu5Ac alpha(2-3)Gal beta(1-4)][-Fuc alpha(1-3)]GlcNAc beta (SLe(x)-PAA), and [Neu5Ac alpha(2-3)Gal beta(1-3)][-Fuc alpha(1-4)]GlcNAc beta (SLe(a)-PAA), was determined. The last three polymer glycoconjugates were synthesized for determining the contribution of carbohydrate chains after the galactose link to the binding with the receptor. The difference in affinity between 3'SL and Neu5Ac alpha in all studied H13 viruses is small, which indicates a less significant role of the galactose moiety in the binding to the receptor. The results of virus binding with polymer sialylglycoconjugates indicates that the method of linking, the third monosaccharide moiety, and the presence of an extra fucose substitute in this moiety may influence the binding considerably. For viruses isolated from ducks, the suitable polymer is SLe(a)-PAA (i.e., a 1-3 linkage between galactose and glucosamine is optimal). This finding is in accord with the data that H13 viruses isolated from the gulls differ based on their ability to interact with polymer sialylglycoconjugates. The affinity to all three polymers is uniform, and the presence of GlcNAc-linked fucose does not prevent the binding. A comparative analysis of six sequenced HA H13 viruses and other subtype viruses showed presence of substantial differences in the composition of amino acids of this region in H13 viruses.

[Identification of orthopoxvirus species using oligonucleotide micro-chips]

A method for describing the Orthopoxviruses that are pathogenic both to man and animals is described in the article. The method is based on hybridization of a fluorescently labelled amplified DNA sample with oligonucleotides, which were immobilized in a microchip. Species-specific regions within the crmB gene encoding a viral analogue of the tumor necrosis factor receptor, i.e. an important gene determining the pathogenicity of the mentioned Orthopoxviruses type, were used as a target for identification. The identification procedure takes around 6 hours and does not demand any costly equipment (a portable fluorescent microscope can be used).

[Molecular-genetic comparison of morbilliviruses which caused epizooty in Baikal (Phoca siberica) and Caspian (Phoca caspica) seals]

The nucleotide sequences were determined for a phosphoprotein gene fragment of canine distemper virus (CDV) by using the RT-PCR method with the subsequent sequencing of amplicons from total RNA isolated from 2 samples of Caspian seals, 15 samples of Baikal seals and from samples of dog's and sea-lion's brains. The above materials were phylogenetically analyzed. The heterogeneity of the virus circulating in the Baikal-seal population was demonstrated. Morbillivirus, that caused epizooty in Caspian seals, was shown to be a CDV variant, whose phosphoprotein gene structure was not different, within the analyzed stretch, from the corresponding gene of the most widespread variant of the Baikal seal virus. The data obtained suggest that morbillivirus could be transmitted by birds during their seasonal migrations.

[Structural organization of the human genome: distribution of nucleotides, Alu-repeats and exons in chromosomes 21 and 22]

Analysis of DNA sequences of the human chromosomes 21 and 22 performed using a specially designed MegaGene software allowed us to obtain the following results. Purine and pyrimidine nucleotide residues are unevenly distributed along both chromosomes, displaying maxima and minima (Y waves phi) with a period of about 3 Mbp. Distribution of G + C along both chromosomes has no distinct maxima and minima, however, chromosome 21 contains considerably less G + C than chromosome 22. Both exons and Alu repeats are unevenly distributed along chromosome 21: they are scarce in its left part and abundant in the right part, while MIR elements are quite monotonously spread along this chromosome. The Alu repeats show a wave-like distribution pattern similar for both repeat orientations. The number of the Alu repeats of opposite orientations was equal for both studied chromosomes, and this may be considered a new property of the human genome. The positive correlation between the exon and Alu distribution patterns along the chromosome, the concurrent distribution of Alu repeats in both orientations along the chromosome, and the equal copy numbers for Alu in direct and inverted orientations within an individual chromosome point to their important role in the human genome, and do not fit the notion that Alu repeats belong to parasitic (junk) DNA.

[Production of stable Bacillus thuringiensis suspensions in an electromagnetic apparatus]

The experiment demonstrated the podibility of obtaining stable suspensions of B. subtilis, a microorganism used as an experimental model, in an electromagnetic apparatus with a bilateral inductor. The optimum conditions of obtaining such suspensions were chosen, these conditions excluding the inactivation of the bacteria used as a model in the course of the process. Suspensions containing 75% of culture fluid were shown to have the highest stability during prolonged storage. Suspensions on the basis of the crystal-forming bacteria B. thuringiensis sp. kurstaki, strain Z-52, used in the production of entomopathogenic preparations and characterized by high stability and good viability in the process of storage were prepared under the selected conditions. The apparatus used in these experiments was recommended for use in the technology of the production of biopreparations of the basis of the above-mentioned bacteria.

[Preparation of P52 recombinant antigenic protein from human cytomegalovirus (HCMV)]

Analysis of published reports helped us single out the most potent antigens among HCMV proteins: phosphoproteins pp150(UL32) and p52(UL44). Theoretical computer analysis of p52 epitopes showed the main antigenic determinants not cross-reacting with antigens of other viruses. Virus-containing (strain AD169) material was obtained and genome DNA was isolated. Amplification of a site of gene UL44 coding for unique determinants detected a PCR fragment of required electrophoretic mobility. The fragment was cloned in vector pLBE. The specificity of cloning was confirmed by restriction analysis of theoretical sites. Nucleotide sequence of cloned fragment of UL44 gene was studied by Maxam-Gilbert's method. Cloning in expressing bacterial vectors helped obtain HCMV recombinant protein p52 in the pure form and fused with beta-galactosidase. Enzyme immunoassay with HCMV-positive and negative donor sera and ABBOTT HCMV sera showed that recombinant p52 increased the sensitivity and specificity of a previously obtained recombinant pp150 as an antigen to HCMV-IgG and HCMV-IgM. The sensitivity and specificity is 100% with 98-99% reliability.

Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger peptidyl-tRNA hydrolysis

Although the primary structures of class 1 polypeptide release factors (RF1 and RF2 in prokaryotes, eRF1 in eukaryotes) are known, the molecular basis by which they function in translational termination remains obscure. Because all class 1 RFs promote a stop-codon-dependent and ribosome-dependent hydrolysis of peptidyl-tRNAs, one may anticipate that this common function relies on a common structural motif(s). We have compared amino acid sequences of the available class 1 RFs and found a novel, common, unique, and strictly conserved GGQ motif that should be in a loop (coil) conformation as deduced by programs predicting protein secondary structure. Site-directed mutagenesis of the human eRF1 as a representative of class 1 RFs shows that substitution of both glycyl residues in this motif, G183 and G184, causes complete inactivation of the protein as a release factor toward all three stop codons, whereas two adjacent amino acid residues, G181 and R182, are functionally nonessential. Inactive human eRF1 mutants compete in release assays with wild-type eRF1 and strongly inhibit their release activity. Mutations of the glycyl residues in this motif do not affect another function, the ability of eRF1 together with the ribosome to induce GTPase activity of human eRF3, a class 2 RF. We assume that the novel highly conserved GGQ motif is implicated directly or indirectly in the activity of class 1 RFs in translation termination.

Characterization of the L gene and 5' trailer region of Ebola virus

The nucleotide sequences of the L gene and 5' trailer region of Ebola virus strain Mayinga (subtype Zaire) have been determined, thus completing the sequence of the Ebola virus genome. The putative transcription start signal of the L gene was identical to the determined 5' terminus of the L mRNA (5' GAGGAAGAUUAA) and showed a high degree of similarity to the corresponding regions of other Ebola virus genes. The 3' end of the L mRNA terminated with 5' AUUAUAAAAAA, a sequence which is distinct from the proposed transcription termination signals of other genes. The 5' trailer sequence of the Ebola virus genomic RNA consisted of 676 nt and revealed a self-complementary sequence at the extreme end which may play an important role in virus replication. The L gene contained a single ORF encoding a polypeptide of 2212 aa. The deduced amino acid sequence showed identities of about 73 and 44% to the L proteins of Ebola virus strain Maleo (subtype Sudan) and Marburg virus, respectively. Sequence comparison studies of the Ebola virus L proteins with several corresponding proteins of other non-segmented, negative-strand RNA viruses, including Marburg viruses, confirmed a close relationship between filoviruses and members of the Paramyxovirinae. The presence of several conserved linear domains commonly found within L proteins of other members of the order Mononegavirales identified this protein as the RNA-dependent RNA polymerase of Ebola virus.

[The structural and functional organization of the promoter region of the human CD4-receptor gene]

Receptor CD4, expressed on the surface of immunocompetent cells, plays the key role in the pathogenesis of HIV infection, facilitating the penetration of the virus into the susceptible tissues of the host body. In this work the nucleotide sequence of the site on the gene of receptor CD4, responsible for the regulation of its transcription, has been determined.

[Characteristics of the LTR of endogenous retrovirus in the human T-lymphocyte CD4 receptor gene]

The nucleotide sequence of the long terminal repeat (LTR) of human endogenous retrovirus element (HERV), localized in the first introne of the CD4 gene in the antisense direction, is determined. This new retrotransposon is highly homologous with different LTR HERV and belongs to HERV-K family. A peculiar feature of this element is an insertion of the Alu repeated sequence inside LTR. This Alu repeat has the same orientation as LTR HERV and contains two short open frames with a high level of homology with DAF (decay accelerating factor) proteins and the fifth complement component. In addition, this Alu repeat of LTR HERV contains regulatory elements: enhancer, TATAA box, poly A site, etc. Preservation of putative regulatory elements in the LTR suggests that they can render distinct regulatory properties to CD4 receptor gene.

[Characteristics of parotitis virus, isolated in Siberia]

Two strains of parotitis virus were isolated from patients with clinical symptoms of the disease in epidemiological screening which was carried out during an outbreak of epidemic parotitis in the village of Koltsovo in 1994. The strains were isolated from the saliva of children aged 7 and 8 years vaccinated with live parotitis vaccine at the age of 1.5 years. Primers for the genome site coding for the gene F terminal and the SH gene (a total of 509 n. p.) were estimated and synthesized and the site was amplified. Electron-microscopic examination of purified virus and Vero cells infected with it and serological tests showed a similarity of the newly isolated virus with the Anders strain of parotitis virus. The Dragun-1 and Dragun-2 strains of parotitis virus have been deposited in the collection of viruses at the Vektor State Research Center of Virology and Biotechnology in the village of Koltsovo, Novosibirsk district.

[The study of protective properties of attenuated strain of Argentinian hemorrhagic fever]

Immunization of BALB/c, C57BL/6, CBA/calac mice with strain XJ44 of Argentine hemorrhagic fever resulted in changes of nonspecific immunity parameters, such as interferon, interleukin-1, tumor necrosis factor, and natural killers. The formation of a specific humoral and cellular immune response in BALB/c mice immunized with this strain has been demonstrated. Immunization of BALB/c mice with strain XJ44 protected the animals from infection with a heterogeneous strain Carvallo of Bolivian hemorrhagic fever.

The complete nucleotide sequence of the Popp (1967) strain of Marburg virus: a comparison with the Musoke (1980) strain

The nucleotide sequence of genomic RNA of Marburg virus strain Popp was determined. Strain Popp was isolated in 1967 during the first filoviral outbreak. The virus was purified from blood of infected guinea pigs in which it had been maintained. The length of the determined sequence was 19112 nucleotides. Amino acid sequences of seven known virion proteins were deduced. Nucleotide and amino acid sequences were compared with those of strain Musoke of Marburg virus isolated in 1980 in Kenya and purified from Vero cells. Homology between nucleotide sequences of two strains was 93.9%. Comparisons revealed conserved and variable regions of the nucleotide and amino acid sequences. The GP, the envelope protein of the virion, was found to be the most variable protein. The greatest differences in the protein were located in the supposedly external part of the molecule. Amino acid substitutions in the L protein, the main component of viral RNA-dependent RNA polymerase, were also distributed extremely non-randomly. It was shown that the non-coding regions of the genome were more variable than the coding ones; 37.6% of nucleotide differences corresponded to the former. 72.6% of nucleotide substitutions located in the coding regions were found to be at the third codon position.

[Study of the structure-function organization of the variola virus genome. IV. Sequencing and analysis of the nucleotide sequence of the right terminus of the India-1967 strain genome]

Sequencing and computer analysis of the variola major virus strain India-1967 (VAR-IND) genome segment (53,018 bp) from the right terminal region have been carried out. Fifty nine potential open reading frames (ORFs) of over 60 amino acid residues have been identified. Structure-function organization of VAR-IND DNA segment under study was compared with the previously reported sequences from the analogous genomic regions of vaccinia virus strains Copenhagen (VAC-COP) and Western Reserve (VAC-WR) and variola virus strain Harvey (VAR-HAR). Multiple distinctions in the genetic map of VAR-IND from VAC-COP and VAC-WR have been revealed along with the high similarity to the corresponding VAR-HAR segment. Possible functions of the predicted viral proteins and the effect of their differences on the features of orthopoxviruses are discussed.

[Nucleotide sequence of two exons of the human T-lymphocyte CD4 receptor gene]

Genome DNA encoding the N-part of human CD4 gene located in the 15 kilobase (kb) Sau3a restriction fragment was cloned and nucleotide sequence of a part (3430 b.p.) of this fragment determined. Exons 2 and 3, intron 2, and partially introns 2 and 3 of this gene were located in the sequenced fragment. Six Alu repeats and open reading frames (ORFs) coding for proteins very close to C5 and C3 components of the complement were detected in this fragment.

Complete nucleotide sequences of Marburg virus genes 5 and 6 encoding VP30 and VP24 proteins

Nucleotide sequences of the genes 5 and 6 of the Marburg virus, Popp strain, were determined. ORFs encoding polypeptides VP30 (281 a.a., MW 32,640) and VP24 (253 a.a., MW 28,621) were found. The putative transcription start and stop signals for viral RNA-dependent RNA polymerase were revealed for both genes. Overlapping of genes 5 and 6 was shown. The deduced amino acid sequences of VP30 and VP24 proteins displayed significant homology with the analogous proteins of another filovirus, the Ebola virus (33% and 37%, respectively). The VP24 appeared to have a hydrophobic amino acid composition; content of hydrophobic amino acids was 40.7%. Model of VP24 location in the virion was suggested.

ALIGNMENT SERVICE: creation and processing of alignments of sequences of unlimited length

A package for the creation and processing of multiple sequence alignment is described. There is no limit on the lengths of the processed nucleotide or amino acid sequences, and the number of sequences in the alignment is also unlimited. The main groups of functions are: a semiautomatic alignment editor; a wide set of functions for technical processing of alignments; nucleotide alignment mapping and translation; and similarity search functions. A user-friendly interface and a set of generally used file actions provide a special operational subsystem for everyday tasks.

Analysis of the nucleotide sequence of 53 kbp from the right terminus of the genome of variola major virus strain India-1967

Sequencing and computer analysis of a variola major virus strain India-1967 (VAR-IND) genome segment (53,018 bp) from the right terminal region has been carried out. Fifty-nine potential open reading frames (ORFs) of over 60 amino acid residues were identified. Structure-function organization of the VAR-IND DNA segment was compared with the previously reported sequences from the analogous genomic regions of vaccinia virus strains Copenhagen (VAC-COP) and Western Reserve (VAC-WR) and variola virus strain Harvey (VAR-HAR). Multiple differences between VAR-IND and the strains of VAC but the high identity of VAR-IND with VAR-HAR in the genetic maps are revealed. Possible functions of the predicted viral proteins and the effect of their differences on the features of orthopoxviruses are discussed.

Analysis of the nucleotide sequence of 48 kbp of the variola major virus strain India-1967 located on the right terminus of the conservative genome region

Computer analysis of a variola major virus (VAR) genomic fragment bounded by the open reading frames (ORFs) D1R and A33L, which is 47,961 bp long, revealed 46 potential ORFs. The VAR proteins were compared to the analogous proteins of vaccinia virus strain Copenhagen. The subunits of DNA-dependent RNA polymerase, as well as the transcription factors, mRNA-capping enzymes, and proteins necessary for the virion morphogenesis proved to be highly conservative within orthopoxviruses. The most pronounced differences between the VAR genome fragment under study and the corresponding vaccinia virus fragment were revealed in the vicinity of the gene encoding the A-type inclusion bodies protein. Possible functions of the analysed viral proteins are discussed.

[The detection of antibodies to the hepatitis C virus and to HBsAg in donors with viral hepatitis and cancerous diseases in the Republic of Moldova]

Large-scale and uneven distribution of hepatitis C and B (HC and HB) among free blood donors of different regions of the Moldova Republic was established. The rate of detection of anti-HCV (South 6.2%, North 3.6%) correlated with that of HBsAg detection (south 12.5%, north 4.5%). A great role of HCV in the etiology of acute (among them posttransfusion) hepatitis and chronic hepatitis was demonstrated. A significant frequency of detection of anti-HCV (15%) in children treated in oncohematology wards and receiving multiple hemotransfusions as well as the detected cases of acute posttransfusion HC attest to active realization of this virus transmission in the transfusions of blood and/or its components. The necessity of urgent introduction into the Blood Transfusion Service of the republic of the examination of blood donors for HBsAg, alongside with their examination for the presence of anti-HCV and vaccination prophylaxis of HB in high risk groups is substantiated.

[Structure-activity organization of the variola virus genome. III. Sequencing and analysis of the nucleotide sequence of the conserved region of HindIII-F, -N-, and -A-fragments of the India 1967 strain genome]

Computer analysis of variola major virus (VAR) genomic fragment bounded by open reading frames (ORFs) D1R and A33L which is 47,961 bp long revealed 46 potential ORFs. The VAR proteins were compared with the analogous proteins of vaccinia virus strain Copenhagen. The subunits of DNA-dependent RNA polymerase, as well as the transcription factors, mRNA capping enzymes, and proteins necessary for the virion morphogenesis proved to be highly conservative within orthopoxviruses. The most pronounced differences between the VAR genome fragment under study and the corresponding vaccinia virus fragment were revealed in the vicinity of the gene encoding the A-type inclusion body protein. The possible functions of the analyzed viral proteins are discussed.

Computer-assisted predictions of the secondary structure in the plant virus single-stranded DNA genome

Coconut foliar decay virus (CFDV) contains the single-stranded circular DNA molecules of 1291 nucleotides which were found to replicate autonomously in the cells of the diseased palms. The special features of the CFDV DNA sequence, including putative secondary structure and the distribution of the inverted repeat motifs, are investigated with computer-assisted prediction methods. It is evident that the structural principle of the branched series of long and short double helixes interspersed by short non-helical regions is existed for CFDV virion DNA. The total degree of base pairing is near 62%. We have also predicted the presence of several sequence elements formed by inverted repeat motifs which are potentially capable of binding the eukaryotic transcriptional regulatory factors.

[An analysis of the amino acid sequence of the heavy subunit of the hemagglutinin in influenza virus A/Alma-Ata/1417/84]

An analysis of the amino acid sequence of influenza A/Alma-Ata/1417/84 (H1N1-Hsw1N1 serovariant) virus hemagglutinin heavy chain deduced from the nucleotide sequence of cloned full-size DNA complementary to the 4th segment of genome RNA was carried out. Unlike A/New Jersey/8/76 virus, the hemagglutinin of the virus under study was found to be more similar in the rate of HA1 homology, amino acid sequence of the signal peptide, antigenic sites Sa, Ca, and the receptor-binding site to human influenza viruses isolated in the 1930-1980-ies, in particular to influenza A/Taiwan/1/86 virus. It is assumed that an influenza virus more adapted to the human population like the strain A/Alma-Ata/1417/84 may be an etiological factor of a new influenza pandemic.

Analysis of the nucleotide sequence of a 43 kbp segment of the genome of variola virus India-1967 strain

Sequencing and computer analysis of the nucleotide sequence of the variola virus strain India-1967 (VAR) genome segment (43069 bp) from the region of HindIII C, E, R, Q, K, H DNA fragments has been carried out. Forty-three potential open reading frames (ORFs) have been identified, and the polypeptides encoded by them have been compared with the analogous proteins of vaccinia virus strain Copenhagen (COP). ORF E7R of VAR is much shorter than the COP analog. The other polypeptides coded by the potential ORFs of VAR are highly conserved in comparison with COP. Possible functions of the predicted viral polypeptides are discussed.

[An analysis of the potential areas of recombination in the hemagglutinin genes of animal influenza viruses in relation to their adaptation to a new host--man]

The authors tried to decode the mechanism of influenza viruses species adaptation in the process of host changing. The functionally important replacement in the surface pocket domains were revealed, particularly in the conservative region 221-241, involving fibronectin-like part. Close replacements were revealed in the region 141-161. The method of construction of heteroduplexes between hemagglutinin RNA of duck, pig, and human viruses was used. The method showed that all heteroduplexes formed recombinogene structures. An unexpected effect of directional recombination was elicited for hemagglutinin RNA heteroduplexes in cases of duck-pig and human-pig viruses. During the directional recombination the following processes took place: the receptor-binding site of animal type was transmitted to the duck virus, while the human receptor-binding site was transmitted to the pig virus. According to the experimental data, a new hypothesis is formulated: the cascade mechanism of directional recombination for duck, animal and human viruses makes it possible for the recombinant viruses to overcome interspecies barriers.

[Study of the structure-activity organization of the variola virus genome. II. Analysis of the nucleotide sequence of the HindIII region (C,E,R,Q,K and H)-DNA fragments of the India-1967 strain]

Sequencing of variola virus (VAR) genome region of 43069 bp was carried out. This area contains 42 potential genes. Computer analysis of proteins coding for these viral genes was done. We compared VAR proteins with the those of vaccinia virus. The region studied is conservative for orthopoxviruses.

[Inhibition of reproduction of the human immunodeficiency virus by sense and antisense oligodeoxynucleotides]

Inhibitory effects on human immunodeficiency virus (HIV) reproduction on lymphoid cell line MT-4 were characterized for antisense and sense oligodeoxynucleotides. It was established that antisense oligonucleotide pCGTAGTTCGTCGAGGTCCGT (MP-20) (ID50 = 0.1 microM) is a more effective HIV inhibitor than the previously described pTGGCGTACTCACCAGTCGCCGC (DSS-22) (ID50 = 4.7 microM) and pTTTTTTTTTTTTTTTT (PA-16) (ID50 = 8.0 microM). A sense oligonucleotide pGCATCAAGCAGCTCCAGGCA (PM-20) (ID50 = 0.5 microM) complementary to the region of the start of translation of the open reading frame on the (+)-chain virus DNA was also investigated. Specificity of the anti-HIV-I action of oligonucleotides was confirmed by experiments with HIV-II.

Comparison of the genetic maps of variola and vaccinia viruses

The complete genetic map of the variola major virus strain India-1967 is built basing on the sequence data. The suggested map is compared with the maps of the sequenced genomic regions of Copenhagen and Western Reserve strains of vaccinia virus and Harvey strain of variola major virus. The principle differences revealed in the genomic organization of these viruses are discussed.

The GP-protein of Marburg virus contains the region similar to the 'immunosuppressive domain' of oncogenic retrovirus P15E proteins

cDNA was synthesized and cloned on the template of the genomic RNA of Marburg virus (strain Popp). Recombinant plasmids with specific cDNA inserts were selected and sequenced. The length of the open reading frame encoding the GP-protein is 681 amino acids. GP-protein is proposed to be an integral membrane protein. Computer-assisted comparison of the deduced amino acid sequence with those of different viruses revealed significant homology with the GP-protein of Ebola virus and with the 'immunosuppressive domain' of the P15E envelope proteins of some oncogenic retroviruses.