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PubMed2000

PCR detection of host and HIV-1 sequences from archival brain tissue.

Mutations in CCR5 and CCR2b have been recently shown to affect disease progression towards AIDS. A role for these host genotypes in AIDS dementia complex (ADC) has also been postulated but remains unclear. Additionally, brain-derived envelope sequences from HIV-1 have been associated with ADC but their specific contribution to pathogenesis remains uncertain. This study demonstrates the successful use of PCR techniques to isolate host CCR5 and CCR2b, and HIV-1 V3 sequences from paraffin embedded tissues from patients with and without ADC. PCR amplification from archival tissue offers a novel approach for studying the interactions between potential neuroprotective elements in the host and virulence determinants in HIV that may contribute to differences in susceptibility to ADC.

AIDS Dementia Complex↗
PubMed2005

Classifying genotype F of hepatitis B virus into F1 and F2 subtypes.

AIM: To explore the propriety of providing hepatitis B virus (HBV) genotypes F and H with two distinct genotypes. METHODS: Eleven HBV isolates of genotype F (HBV/F) were recovered from patients living in San Francisco, Japan, Panama, and Venezuela, and their full-length sequences were determined. Phylogenetic analysis was carried out among them along with HBV isolates previously reported. RESULTS: Seven of them clustered with reported HBV/F isolates in the phylogenetic tree constructed on the entire genomic sequence. The remaining four flocked on another branch along with three HBV isolates formerly reported as genotype H. These seven HBV isolates, including the four in this study and the three reported, had a sequence divergence of 7.3-9.5% from the other HBV/F isolates, and differed by > 13.7% from HBV isolates of the other six genotypes (A-E and G). Based on a marked genomic divergence, falling just short of > 8% separating the seven genotypes, these seven HBV/F isolates were classified into F2 subtype and the former seven into F1 subtype provisionally. In a pairwise comparison of the S-gene sequences among the 7 HBV/F2 isolates and against 47 HBV/F1 isolates as well as 136 representing the other six genotypes (A-E and G), two clusters separated by distinct genetic distances emerged. CONCLUSION: Based on these analyses, classifying HBV/F isolates into two subtypes (F1 and F2) would be more appropriate than providing them with two distinct genotypes (F and H).

Amino Acid Sequence↗
PubMed2004

Cloning and sequencing analysis of the repressor gene of temperate mycobacteriophage L1.

The wild-type and temperature-sensitive (ts) repressor genes were cloned from the temperate mycobacteriophage L1 and its mutant L1cIts391, respectively. A sequencing analysis revealed that the 131st proline residue of the wild-type repressor was changed to leucine in the ts mutant repressor. The 100% identity that was discovered between the two DNA regions of phages L1 and L5, carrying the same sets of genes including their repressor genes, strengthened the speculation that L1 is a minor variant of phage L5 or vice versa. A comparative analysis of the repressor proteins of different mycobacteriophages suggests that the mycobacteriophage-specific repressor proteins constitute a new family of repressors, which were possibly evolved from a common ancestor. Alignment of the mycobacteriophage-specific repressor proteins showed at least 7 blocks (designated I-VII) that carried 3-8 identical amino acid residues. The amino acid residues of blocks V, VI, and some residues downstream to block VI are crucial for the function of the L1 (or L5) repressor. Blocks I and II possibly form the turn and helix 2 regions of the HTH motif of the repressor. Block IV in the L1 repressor is part of the most charged region encompassing amino acid residues 72-92, which flanks the putative N-terminal basic (residues 1-71) and C-terminal acidic (residues 93-183) domains of L1 repressor.

Amino Acid Sequence↗
PubMed1998

[The biological characterization of HIV-1 isolated in patients with a rapid clinical evolution].

The biological characteristics of 11 HIV-1 strains isolated from patients with a fast clinical evolution to AIDS were studied. The viral isolates were classified according to their replication kinetics and cell tropism. Taking into account these criteria, it was observed that 8 of the isolated strains (72.7%) were of rapid high growth (RH) or slow low 3 (SL3) with preferential tropism to the lymphocytic stock, as it corresponds to AIDS patients. 3 (27.3%) had characteristics of slow low 1 (SL1). The cytopathogenicity of the strains was studied in the MT4 cellular line, and it was observed that most of them (72.7%) were syncytium-inducing strains (SI), which allowed to prove the in vivo and in vitro relation of the biological properties. It was not so in 3 of the cultures (27.3%) that behaved as non-syncytium inducers.

Acquired Immunodeficiency Syndrome↗
PubMed1998

Analysis of nucleotide sequence variations in herpes simplex virus types 1 and 2, and varicella-zoster virus.

To analyze the difference in the degree of divergence between genes from identical herpesvirus species, we examined the nucleotide sequence of genes from the herpes simplex virus type 1 (HSV-1) strains VR-3 and 17 encoding thymidine kinase (TK), deoxyribonuclease (DNase), protein kinase (PK; UL13) and virion-associated host shutoff (vhs) protein (UL41). The frequency of nucleotide substitutions per 1 kb in TK gene was 2.5 to 4.3 times higher than those in the other three genes. To prove that the polymorphism of HSV-1 TK gene is common characteristic of herpesvirus TK genes, we compared the diversity of TK genes among eight HSV-1, six herpes simplex virus type 2 (HSV-2) and seven varicella-zoster virus (VZV) strains. The average frequency of nucleotide substitutions per 1 kb in the TK gene of HSV-1 strains was 4-fold higher than that in the TK gene of HSV-2 strains. The VZV TK gene was highly conserved and only two nucleotide changes were evident in VZV strains. However, the rate of nonsynonymous substitutions in total nucleotide substitutions was similar among the TK genes of the three viruses. This result indicated that the mutational rates differed, but there were no significant differences in selective pressure. We conclude that HSV-1 TK gene is highly diverged and analysis of variations in the gene is a useful approach for understanding the molecular evolution of HSV-1 in a short period.

Amino Acid Sequence↗
PubMed2000

Primary angiitis of CNS : neuropathological study of three autopsied cases with brief review of literature.

Primary angiitis of CNS(PACNS) or granulomatous angiitis of CNS is a rare inflammatory disease of small blood vessels mostly confined to the CNS. The clinical and pathological features of 3 autopsied cases are described. Clinically all the three PACNS patients were young males, age ranging from 19 to 31 years. All presented with varied neurological manifestations. There was no evidence of systemic disease in any of the cases. The ESR was normal and CSF analysis showed chronic meningitic pattern. The cerebral angiogram in one case was normal and the CT scan done in another case showed multiple intracerebral haematoma due to vasculitis. Brain biopsy was not done. Diagnosis was made at post-mortem examination. Histology showed characteristic but variable degree of granulomatous and non-granulomatous angiitis of small vessels. Venulitis with parenchymal haemorrhages was the predominant feature and in one case phlebitis with thrombosis was noted. Since the disease responds to steroids and immunosuppressive therapy, establishing antemortem diagnosis is important. In view of the association of angiitis of CNS with bacteria and viral infections, their role in the evolution of the disease needs to be investigated.

Adolescent↗
PubMed2000

Molecular evolution of oral poliovirus vaccine strains during multiplication in humans and possible implications for global eradication of poliovirus.

The oral poliovirus vaccine (OPV) has been effectively used in the control of poliomyelitis and in the eradication of wild polioviruses. Although there are many advantages in using attenuated OPV strains in the campaign to eradicate poliomyelitis, several studies have demonstrated that there are some disadvantages such as (a) excretion by vaccines of OPV-derived polioviruses with genomic modifications known to increase the neurovirulence, (b) appearance of vaccine-associated paralytic poliomyelitis (VAPP) and other adverse effects in vaccinees, (c) occurrence of persistent infections caused by OPV-derived strains in immunodeficient patients with VAPP, (d) transmission of OPV-derived polioviruses to susceptible individuals which develop VAPP, and (e) detection of OPV-derived polioviruses in the environment, which could be a source of infection for humans in the future. Different studies indicate that it is important to consider the possibility of persistent infections and excretion of OPV-derived polioviruses for long periods by humans, and also the survival in the environment of OPV-derived polioviruses excreted by humans, which could be transmitted and circulate in a non-immune population after stopping poliovirus vaccination. The findings reported here may have important implications for global poliomyelitis eradication initiative and indicate that surveillance of OPV-derived strains will also be important in the final step of eradication of poliomyelitis from the planet.

Animals↗
PubMed2000

Herpesvirus homologues of cellular genes.

For millions of years viruses have adapted strategies to interfere with the immune defense of the host, which in turn has to deal with this challenge. In general the antiviral defense remains one step behind the pathogen. To achieve this strategic advantage large DNA-containing Viruses encode cellular homologues that mimic or counteract key molecules of the host immune system. Understanding how these cellular homologues enable the viruses to evade the antiviral defense and persist in the host for the lifetime will ultimatively lead also to a better understanding of the principle functions of the immune system. In this review we focused on cellular homologues encoded by human herpesviruses and discuss the functional consequences of their expression.

Amino Acid Sequence↗
PubMed2000

Molecular evolution, distribution and genetic relationship among the dengue 2 viruses isolated from different clinical severity.

Twenty-two strains of dengue 2 virus, isolated in China, Latin America, New Guinea and Thailand were subjected to phylogenetic analysis. The UPGMA analysis was carried out on each gene region of dengue virus and demonstrated that outcome from most of the gene regions showed similar results except those from NS4B and YUTR with very short nucleotide length. Among ten regions examined, the results from E gene documented the geographical differences of the virus strains most clearly and all the American strains (Mara 4, IQT1797 and S1) were distantly related to the Asian isolates. As for the 16 Thai strains isolated in 1993, they were clustered into three groups and a strain from a DSS patient formed a distinct branch compared to the other two groups. This finding from phylogenetic analysis is consistent with earlier conclusion and support the severity related subtyping of dengue 2 virus based on amino acid changes.

3' Untranslated Regions↗
PubMed1992

Treatment of polyarteritis nodosa and Churg-Strauss syndrome. A meta-analysis of 3 prospective controlled trials including 182 patients over 12 years.

To define the most effective treatment for polyarteritis nodosa (PAN) and Churg-Strauss syndrome (CSS), we undertook 3 consecutive prospective therapeutic trials including 182 patients and tried to answer several important questions: should cyclophosphamide (CYC) be given as the first-line treatment? what is the place of plasma exchanges (PE) in the treatment of systemic vasculitis? does hepatitis B virus (HBV)-related PAN require specific treatment? Our first randomized trial in 71 patients compared the association of CYC with corticosteroids (CS) and PE to CS and PE, in order to evaluate the efficacy of CYC given as the first-line treatment to control disease activity and subsequent survival of PAN and CSS patients. Between December, 1983, and December, 1988, we conducted two trials simultaneously: one aimed at patients without HBV markers and the second at patients with HBV markers. In 78 patients without HBV markers, we compared prednisone and PE to prednisone alone as the initial therapeutic regimen. In 33 patients with PAN related to HBV, a new therapeutic strategy was applied as an alternative to long-term steroid and immunosuppressive therapy: short-term steroid therapy and PE were used to control the evolution of PAN and anti-viral therapy was administered to suppress the etiological agent of the vasculitis. Twelve years after the beginning of the trials on PAN and CSS patients, we think that the therapeutic strategy should be as follow: in PAN without HBV and CSS: Prednisone in association with CYC improves the control of the disease despite infectious side effects which may be reduced by better CYC dose adaptation. It is also possible that CYC could be more effective in some subgroups of PAN, for instance those with clinical symptoms of poor prognosis. We are presently attempting to optimize the CYC prescription (pulses of CYC) in PAN and CSS in the hope of improving prognosis; in PAN related to HBV: The first-line treatment should be the association of anti-viral agents and PE. This treatment was effective and cured a majority of patients within 2 to 3 months; half of them seroconverted. The length of HBV infection before its diagnosis, delay before initiation of treatment and previous immunosuppressive therapy led to a poor seroconversion rate; the role of PE in the treatment of systemic necrotizing angiitis: PE are obviously useful in PAN related to HBV where immune complex deposition has been demonstrated.(ABSTRACT TRUNCATED AT 400 WORDS)

Adolescent↗
PubMed2003

[Osteopathies that weaken HIV-infected patients].

OSTEOPOROSIS AND OSTEOPENIA: The use of multiple antiretroviral therapies has transformed the prognosis of HIV infection. However, the potential disadvantages of these treatments have rapidly appeared: lipodystrophy, cardiovascular complications and, more recently bone affections with osteonecrosis, followed by other weakening osteopathies (osteoporosis and osteopenia). Osteoporosis is a reduction in bone mineral density (BMD) leading to a high risk of fracture. It is measured by dual energy x-ray absorptiometry and is defined by a T-score<-2.5 standard deviations from the mean value of a young adult. Osteopenia corresponds to low bone density with, avec -1>T-score>-2.5. REGARDING THE AVAILABILITY OF RETROVIRAL AGENTS: During HIV infections, an osteopathy (most often osteopenia) is observed in a quarter to more than half of patients who have never received antiretroviral agents, and in up to three quarters in those in whom treatment in ongoing. The transversal nature of the majority of the studies, the heterogeneity of the treatments, the inclusion of both male and female patients in some studies, and the differences in the results observed do not permit one to draw any conclusions as to the possible responsibility of antiretroviral agents. An association between an osteopathy and a lipodystrophy is inconstant. Lastly, the substitution of a class of a antiretroviral agents by another does not lead to any significant modification in BMD. THE MECHANISM OF OCCURRENCE OF AN OSTEOPATHY: Has not been clearly established. The modifications in serum concentrations of biochemical markers of bone formation and resorption observed in HIV-infected patients and their evolution under antiretroviral treatment, suggest a viral origin, mediated by pro-inflammatory cytokines. The rare in vitro studies, or on animal models, are contradictory, with the results of clinical trials regarding the inherent role of antiretroviral drugs. However, it is probable that the classical risk factors for osteoporosis are often implied.

Anti-Retroviral Agents↗
PubMed2004

Molecular biological analysis of genotyping and phylogeny of severe acute respiratory syndrome associated coronavirus.

BACKGROUND: SARS-CoV is the causative agent of severe acute respiratory syndrome (SARS) which has been associated with outbreaks of SARS in Guangdong, Hong Kong and Beijing of China, and other regions worldwide. SARS-CoV from human has shown some variations but its origin is still unknown. The genotyping and phylogeny of SARS-CoV were analyzed and reported in this paper. METHODS: Full or partial genomes of 44 SARS-CoV strains were collected from GenBank. The genotype, single nucleotide polymorphism and phylogeny of these SARS-CoV strains were analyzed by molecular biological, bioinformatic and epidemiological methods. RESULTS: There were 188 point mutations in the 33 virus full genomes with the counts of mutation mounting to 297. Further analysis was carried out among 36 of 188 loci with more than two times of mutation. All the 36 mutation loci occurred in coding sequences and 22 loci were non-synonymous. The gene mutation rates of replicase 1AB, S2 domain of spike glycoprotein and nucleocapsid protein were lower (0.079% - 0.103%). There were 4 mutation loci in S1 domain of spike glycoprotein. The gene mutation rate of ORF10 was the highest (3.333%) with 4 mutation loci in this small domain (120 bp) and 3 of 4 loci related to deletion mutation. By bioinformatics processing and analysis, the nucleotides at 7 loci of genome (T:T:A:G:T:C:T/C:G:G:A:C:T:C) can classify SARS-CoV into two types. Therefore a novel definition is put forward that according to these 7 loci of mutation, 40 strains of SARS-CoV in GenBank can be grouped into two genotypes, T:T:A:G:T:C:T and C:G:G:A:C:T:C, and named as SARS-CoV Yexin genotype and Xiaohong genotype. The two genotypes can be further divided into some sub-genotypes. These genotypes can also be approved by phylogenetic tree of three levels of 44 loci of mutation, spike glycoprotein gene and complete genome sequence. Compared to various strains among SARS-CoV Yexin genotype and Xiaohong genotype, GD01 strain of Yexin genotype is more closely related to SARS-CoV like-virus from animals. CONCLUSION: The results mentioned above suggest that SARS-CoV is responding to host immunological pressures and experiencing variation which provide clues, information and evidence of molecular biology for the clinical pathology, vaccine developing and epidemic investigation.

Evolution, Molecular↗
PubMedDate not supplied

[Hantaviruses and hantavirus infections].

Hemorrhagic fever with renal syndrome (HVRS) has been for decades a topical problem for healthcare systems of many countries in the Eurasian continent. Viruses triggering HVRS alongside with other related viruses (but not pathogenic to man) were discovered in 70-80-ies and formed a new genus Hantavirus of the Bunyaviridae family. The study results of a severe outbreak of the respiratory disease with the mortality rate of 60% (South-West of the USA, 1933) showed that hantaviruses were also among the causative agents. Later, the disease was designated as hantavirus cardio-pulmonary syndrome. By now, it has been established that hantaviruses are wide spread with different rodents being their carriers. The discussed viruses cause, in rodents, a chronic asymptomatic infection and are transferred, later, to man by the aerogenic path through excretions of infected animals. Studies of hantaviruses have been restricted for a long time due to their high pathogenicity (protection equipment not below than the P-3 level is needed), because of a lack of a laboratory model of infected animals and because of a low growth in cell cultures. With the rapid development and application of molecular biological techniques of the recent years, substantial progress has been made in studies of hantaviruses. Different aspects of hantavirus ecology, molecular biology, morphology, pathogenesis and diagnostics are discussed in the offered survey.

Animals↗
PubMed2004

A survey of the relationships among the viruses not considered arboviruses, vertebrates, and arthropods.

No single group of organisms demonstrates more extensive and diverse associations with animal viruses than the phylum Arthropoda. Compared with the well-recognized relationship found in arboviruses, however, most of the atypical arthropod-vertebrate relationships of the viruses normally not considered arboviruses have received much less attention, as they remain in the marginal areas of interest for most researchers in animal virology, veterinary medicine, medical entomology, and invertebrate pathology. However, this comprehensive review of the information gathered from several branches of virology by profession reveals highly valuable information potentially useful in the fields of research ranging from investigations of the mode of transmission of poorly understood or emerging viral diseases to studies of the evolution of biological transmission of animal viruses by arthropod vectors. The observations and data obtained for the animal virus relationships with arthropods and vertebrates outside the boundaries of arboviruses, in turn, can be used to reexamine more closely the definition of arboviruses. With increasing number of reports challenging one of the basic tenets of the definition of arbovirus (requirement of viremia in vertebrate host) and others describing virus-host relationships that complicate the definition of arbovirus, the accumulated information clearly demonstrates the difficulty of defining the boundaries of arboviruses.

Animals↗
PubMed2005

[Comparison of the genome for phylogenetically related bacteriophages phiKZ and EL of Pseudomonas aeruginosa: evolutionary aspects and minimal genome size].

Bacteriophages of the family Myoviridae represent one of the most widespread domains of the biosphere substantially affecting the ecological balance of microorganisms. Interestingly, sequence analysis of genomic DNAs of large bacteriophages revealed many genes coding for proteins with unknown functions. A new approach is proposed to improve the functional identification of genes. This approach is based on comparing the genome sequence for phylogenetically and morphologically related phages showing no considerable homology at the level of genomic DNA. It is assumed that gene functions essential for the development of phages of a given family are conserved and that the corresponding genes code for similar orthologous proteins even when lacking sequence homology. The genome was sequenced and compared for two Pseudomonas aeruginosa giant bacteriophages, phiKZ and EL, which belong to a group of (phiKZ-related phages. A substantial difference in genome organization was observed, suggesting specific features of phage evolution. In addition, the problem of the minimal genome of the superfamily is discussed on the basis of the difference in size and structure between the phiKZ and EL genomes.

Base Sequence↗