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PubMed1986

Molecular evolution of bacteriophages: evidence of selection against the recognition sites of host restriction enzymes.

Restriction enzymes produced by bacteria serve as a defense against invading bacteriophages, and so phages without other protection would be expected to undergo selection to eliminate recognition sites for these enzymes from their genomes. The observed frequencies of all restriction sites in the genomes of all completely sequenced DNA phages (T7, lambda, phi X174, G4, M13, f1, fd, and IKe) have been compared to expected frequencies derived from trinucleotide frequencies. Attention was focused on 6-base palindromes since they comprise the typical recognition sites for type II restriction enzymes. All of these coliphages, with the exception of lambda and G4, exhibit significant avoidance of the particular sequences that are enterobacterial restriction sites. As expected, the sequenced fraction of the genome of phi 29, a Bacillus subtilis phage, lacks Bacillus restriction sites. By contrast, the RNA phage MS2, several viruses that infect eukaryotes (EBV, adenovirus, papilloma, and SV40), and three mitochondrial genomes (human, mouse, and cow) were found not to lack restriction sites. Because the particular palindromes avoided correspond closely with the recognition sites for host enzymes and because other viruses and small genomes do not show this avoidance, it is concluded that the effect indeed results from natural selection.

Bacillus subtilis↗

PubMed1994

Epidemiology of hepatitis C virus in Europe.

Epidemiology of Hepatitis C virus (HCV) infection in Europe is changing very rapidly since the main source of contamination was blood transfusion and the use of surrogate markers allowed to diminish dramatically the number of patients contaminated through HCV post transfusion hepatitis. The recent description of several genotypes with different distributions over Europe and different pathogenicity will allow to explain various evolutive aspects of the disease. At present, groups at risk are drug addicts (70%), hemophiliacs (contaminated with blood products before 1985), hemodialysis patients (20%) and patients with cirrhosis with or without hepatocellular carcinoma. The detection of HCV markers prior to blood transfusion allowed to detect asymptomatic carriers of HCV, some of them with latent chronic hepatitis which can be predicted by the detection of HCV RNA in the serum. Vertical and sexual transmission are rare but possible events observed with certainty in patients co-infected with HIV and controversial in other situations.

Carrier State↗

PubMed2005

Dynamics of enfuvirtide resistance in HIV-infected patients during and after long-term enfuvirtide salvage therapy.

Enfuvirtide (ENF) is the first of a novel class of drugs that blocks HIV fusion to host cells. We analyzed the dynamics of genotypic and phenotypic resistance to ENF during and after long-term ENF therapy and its clinical implications in eight heavily treatment-experienced HIV-infected patients who underwent salvage therapy with enfuvirtide along with other antiretroviral agents. All patients showed a rapid decline in plasma HIV-RNA followed by viral rebound. Changes at codons 36, 42, 43 and/or 44 within the HR1 region of gp41 were selected in all cases, resulting in high-level phenotypic resistance to ENF, ranging from 15- to 445-fold. Both genotypic and phenotypic resistance to ENF rapidly disappeared after discontinuation of the drug, suggesting that ENF-resistant viruses may have an impaired replicative capacity.

Amino Acid Sequence↗

PubMed2002

Plant-specific promoter sequences carry elements that are recognised by the eubacterial transcription machinery.

During evolution the promoter elements from prokaryotes and eukaryotes have developed differently with regard to their sequence and structure, implying that in general a transfer of eukaryotic promoter sequences into prokaryotes will not cause an efficient gene expression. However, there have been reports on the functionality of the 35S promoter from cauliflower mosaic virus (CaMV) in bacteria. We therefore decided to experimentally investigate the capability of plant promoter sequences to direct gene expression in various bacteria. Accordingly, we tested ten different plant-specific promoters from Solanum tuberosum, Nicotiana tabacum, CaMV, Agrobacterium tumefaciens, and A. rhizogenes for their ability to initiate transcription in five different eubacterial species (Escherichia coli, Yersinia enterocolitica, A. tumefaciens, Pseudomonas putida, and Acinetobacter sp. BD413). To monitor the strength of the plant-specific promoters in bacteria we created fusions between these promoters and the coding region of the luciferase genes from Vibrio harveyi and measured the luminescence in the bacteria. Heterologous gene expression was observed in 50% of the combinations analysed. We then mapped the transcription start site caused by one of the plant-specific promoters, the ST-LS1 promoter from S. tuberosum, in these bacterial species. The location of the mapped transcription start site indicated that the sequences of the plant promoter themselves were recognised by the bacterial transcription apparatus. The recognition of plant-specific promoter sequences by the bacterial RNA polymerase was further confirmed by site-directed mutagenesis of the ST-LS1 promoter and the analysis of the effects of the mutations on the strength of gene expression in E. coli. Using these mutants in our reporter assays we could localise the sequences of the ST-LS1 promoter serving as -10 region in E. coli. The results of our study show that promoter sequences are much less specific than is generally assumed. This is of great importance for our knowledge about the evolution of gene expression systems and for the construction of optimised expression vectors.

Bacteria↗

PubMed2000

Antiretroviral resistance mutations in human immunodeficiency virus type 1 reverse transcriptase and protease from paired cerebrospinal fluid and plasma samples.

Twenty-four adults infected with human immunodeficiency virus type 1 (HIV-1) with central nervous system symptoms were studied for antiretroviral resistance mutations in HIV-1 RNA obtained from paired cerebrospinal fluid (CSF) and plasma samples. Paired sequences were obtained from 21 and 13 patients for reverse transcriptase (RT) and for protease, respectively. Mutations conferring resistance to the RT inhibitors zidovudine, lamivudine, or nevirapine were detected in 14 patients, including 11 pretreated and 3 drug-naive subjects. The mutation patterns in the 2 compartments were different in most patients. Genotypic resistance to protease inhibitors was detected in both plasma and CSF from 1 patient treated with multiple protease inhibitors. However, accessory protease inhibitor resistance mutations at polymorphic sites were different in plasma and CSF in several patients. Partially independent evolution of viral quasispecies occurs in plasma and CSF, raising the possibility that compartmentalization of drug resistance may affect response to antiretroviral treatment.

Adult↗

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↗

PubMed1999

The matrix protein gene sequence analysis reveals close relationship between peste des petits ruminants virus (PPRV) and dolphin morbillivirus.

The gene encoding the matrix protein of peste des petits ruminants virus (PPRV) has been cloned and its nucleotide sequence determined. This gene is 1466 nucleotides long and contains an open reading frame (ORF) capable of encoding a basic protein of 335 amino acid residues with a predicted molecular weight of 38,057 Da. This ORF starts at position 33-35 and ends with the codon TAA at position 1038-1040 thus leaving a long untranslated region (426 nucleotides) at the 3' end of the messenger RNA. This fragment is very G/C rich (68.5%) and in contrast to the ORF region appears to be least conserved in the M gene sequence of the morbilliviruses. A comparison of the PPRV M protein with those of other viruses in the group confirms the previously noted high degree of conservation for this protein sequence. The percent of identity within the group ranges from 76.7 to 86.9%, the highest being with the dolphin morbillivirus matrix protein.

Amino Acid Sequence↗

PubMedDate not supplied

Polymerase-chain-reaction-based semi-quantification of hepatitis D viraemia in patients treated with high doses of alpha 2b interferon.

To study the antiviral efficacy of high doses of alpha 2b interferon (alpha 2b-IFN) for chronic hepatitis D treatment, we used polymerase-chain-reaction(PCR)-based semi-quantitative detection of HDV RNA. The semi-quantification method used was based on the appearance of a positive amplification signal as a function of the number of PCR cycles. By amplifying dilutions (10(-1)-10(-8)) of an HDV-positive woodchuck liver RNA, we confirmed that exponential amplification efficacy occurred at between 20 and 30 cycles. Positive signals were observed from dilution 10(-2) (gel electrophoresis after 20 cycles of PCR) to dilution 10(-7) (hybridization after 30 cycles of PCR). To characterize the HDV RNA level in sera of 8 patients treated with alpha 2b-IFN (10 MU/3 times a week) for 1 year, we extracted RNA from serum samples taken every 6 months. All samples were amplified in parallel for 20 and 30 PCR cycles. Analysis of HDV cDNA after ethidium bromide/agarose gel electrophoresis and after molecular hybridization (100 times more sensitive than gel analysis), enabled us to grade the signals observed from negative to positive as 1+, 2+, 3+ and 4+, with all results being positive. Three types of evolution of HDV viraemia were evidenced among the 8 treated patients. HDV replication continued to occur at a high level at the 6th and 12th month in 2 patient sera. For 2 other patients, an HDV RNA decrease or disappearance was evidenced in the serum at the 6th month; however, viral replication recurred at a higher level at the 12th month.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2003

Clinical implications of HIV-1 drug resistance in the neurological compartment.

The tropism of human immunodeficiency virus type 1 (HIV-1) for the central nervous system (CNS) develops early during the course of the infection. Potent antiretroviral therapy has been demonstrated to be effective in controlling the replication of HIV-1 in cerebrospinal fluid (CSF), even though a variable response in this compartment compared with that in plasma has been observed. Different concentrations of antiretroviral drugs are found in CSF and the use of antiretroviral drugs penetrating across the blood-brain barrier is considered to be required for controlling CNS infection in advanced patients, particularly in those with neurological disorders. The compartmentalization of HIV-1 infection in the CNS may affect the treatment response, which may cause a different evolution of viral drug resistance in the 2 compartments. Although HIV-1 resistance testing in CSF is not recommended for the routine management of patients with virological failure, treatment decisions in patients with neurological disorders may require knowledge of the resistance profile of the virus in the CSF.

AIDS Dementia Complex↗

PubMed1993

Coevolution of persistently infecting small DNA viruses and their hosts linked to host-interactive regulatory domains.

Although most RNA viral genomes (and related cellular retroposons) can evolve at rates a millionfold greater than that of their host genomes, some of the small DNA viruses (polyomaviruses and papillomaviruses) appear to evolve at much slower rates. These DNA viruses generally cause host species-specific inapparent primary infections followed by life-long, benign persistent infections. Using global progressive sequence alignments for kidney-specific Polyomaviridae (mouse, hamster, primate, human), we have constructed parsimonious evolutionary trees for the viral capsid proteins (VP1, VP2/VP3) and the large tumor (T) antigen. We show that these three coding sequences can yield phylogenetic trees similar to each other and to that of their host species. Such virus-host "co-speciation" appears incongruent with some prevailing views of viral evolution, and we suggest that inapparent persistent infections may link virus and most host evolution. Similarity analysis identified three specific regions of polyoma regulatory gene products (T antigens) as highly conserved, and two of these regions correspond to binding sites for host regulatory proteins (p53, the retinoblastoma gene product p105, and the related protein p107). The p53 site overlaps with a conserved ATPase domain and the retinoblastoma site corresponds to conserved region 1 of E1A protein of adenovirus type 5. We examined the local conservation of these binding sequences and show that the conserved retinoblastoma binding domain is characteristic and inclusive of the entire polyomavirus family, but the conserved p53-like binding domain is characteristic and inclusive of three entire families of small DNA viruses: polyomaviruses, papillomaviruses, and parvoviruses. The evolution of small-DNA-virus families may thus be tightly linked to host evolution and speciation by interaction with a subset of host regulatory proteins.

Amino Acid Sequence↗

PubMed1995

Identification and simulation of shifted periodicities common to protein coding genes of eukaryotes, prokaryotes and viruses.

The distribution of nucleotides in protein coding genes is studied with autocorrelation functions. The autocorrelation function YRY(N)iYRY, analysing the occurrence probability of the i-motif YRY(N)iYRY (two motifs YRY separated by any i bases N, R = purine = Adenine or Guanine, Y = pyrimidine = Cytosine or Thymine, N = R or Y) in the protein coding genes of eukaryotes, prokaryotes and viruses, reveals the classical periodicity 0 modulo 3 associated with the normal frame 0 (maximal values of the function at i = 0, 3, 6, etc). The specification of YRY(N)iYRY on the alphabet [A, C, G, T] leads to 64 i-motifs: CAC(N)iCAC, CAC(N)iCAT, ..., TGF(N)iTGT. The 64 autocorrelation functions associated with these 64 i-motifs in protein coding genes have all the periodicity modulo 3, but, surprisingly, not always the expected periodicity 0 modulo 3. Two new types of periodicities are identified: a periodicity 1 modulo 3 associated with the shifted frame +1 (maximal values of the function at i = 1, 4, 7, etc) and a periodicity 2 modulo 3 associated with the shifted frame -1 (maximal values of the function at i = 2, 5, 8 etc). Furthermore, the classification of i-motifs according to the type of periodicity demonstrates a strong coherence relation between the 64 i-motifs, which is, in addition, common to the three gene populations, as the same i-motifs in the three gene populations have the same periodicities. The three periodicities 0, 1 and 2 modulo 3 can be simulated by an evolutionary model at two successive processes. The simulated genes are generated by a process of gene construction, with a stochastic automaton followed by a process of gene evolution with random insertions and deletions of trinucleotides simulating RNA editing. For almost all i-motifs, the autocorrelation functions in these simulated genes are strongly correlated with those in protein coding genes, for both the type and the probability level of periodicities. This paper describes the process of ribosomal frameshifting leading to the shifted periodicities, which may reveal overlapping genes or concatenated genes from different frames. It also presents the evolutionary aspects of the shifted periodicities. The shifted periodicities cannot be associated with the RNY model (Eigen & Schuster, 1978, Naturwissenschaften 65, 341-369) or the RRY model (Crick et al., 1976, Origins of Life 7, 389-397), but are compatible with the oligonucleotide mixing model (Arquès & Michel, 1990, Bull. math. Biol. 52, 741-772). Finally, a variant of the primitive translation model of Crick et al. (1976) is proposed to explain the shifted periodicities.

Animals↗

PubMed2002

Molecular classification of coxsackie A viruses on the basis of the 5'-UTR: structural and evolutionary aspects.

The sequences from a large part of the 5'-UTR of 21 coxsackie A virus (CAV) reference strains for which such data did not exist in the past were obtained. Those sequences, along with the respective available sequences from the rest of the CAV reference strains and many other enteroviruses, were compared. According to the results of this comparison, enteroviruses are classified into two genetic clusters on the basis of 5'-UTR, and CAVs are divided into these two clusters. Specifically, it was found that CAV1, -11, -13, -15, -17 to -22, and -24 are classified together with polioviruses and enterovirus 70, whereas the rest of the CAVs are classified along with coxsackie B viruses, echoviruses, and the rest of the other enteroviruses. No correlation between overall 5'-UTR identity and the currently recognized human enterovirus species was found. The phenomenon of "covariance" in the 5'-UTR was followed for the prediction of the possible secondary structure of the 5'-UTR of the CAVs sequenced in the present study.

5' Untranslated Regions↗

PubMed1991

Characterization of the terminal regions of hepatitis C viral RNA: identification of conserved sequences in the 5' untranslated region and poly(A) tails at the 3' end.

We have determined the nucleotide sequence at the extreme 5' and 3' termini of the hepatitis C virus (HCV) genome. Our analyses of these sequences show (i) the nucleotide sequence in the 5' untranslated region is highly conserved among HCV isolates of widely varying geographical origin, (ii) within this region, there are blocks of nucleotide sequence homology with pestiviruses but not with other viruses, (iii) the relative position of short open reading frames present in the same region of the HCV genome is similar to that of the pestiviral genome, (iv) RNAs truncated at the 5' and 3' ends are found, but the origin and functions of these RNAs are unknown, and (v) poly(A) tails appear to be present on 3' subgenomic RNAs. These data differentiate HCV from the flaviviruses and indicate a closer evolutionary relationship of HCV with the pestiviruses. However, HCV also appears to be substantially different from other known pestiviruses. These data are consistent with the assignment of HCV to a separate viral genus.

Amino Acid Sequence↗

PubMed2003

Evolution of hepatitis C virus in blood donors and their respective recipients.

This paper describes the study of hepatitis C virus (HCV) evolution in the largest cohort of HCV-infected blood donors (BDs)/blood recipients (BRs) reported to date (25 pairs). A molecular analysis of partial sequences in the E1 (envelope) and NS5-B (polymerase) genes was performed. Phylogenetic reconstruction showed that the evolution of dominant strains was qualitatively and quantitatively different in BDs and BRs. The evolutionary rate was significantly higher in BRs, in which, in addition, most substitutions observed were antonymous. These findings corroborate the hypothesis that a large part of virus evolution - which was evaluated to be equivalent to approximately 20 years of chronic evolution - is acquired during the early phase of infection. These findings should be taken into account for the modelling of the long-term evolution of HCV and their possible contribution to improve our understanding of HCV natural history is discussed.

Blood Donors↗

PubMed2002

Evaluation of hepatitis C virus serotypes and IgM anti-HCV antibodies in two groups of anti-HCV positive subjects in south-east Italy.

We investigated the relation between the presence of IgM antibodies to hepatitis C virus (HCV) and serotypes of HCV, in particular when a high level of IgM antibodies are present in patients infected with HCV serotype I and may be associated with the source, duration and evolution of infection. The study involved two anti-HCV positive groups with chronic liver disease from the same area, one of which was a group of haemodialysis patients attending the same haemodialysis centre.

Adult↗

PubMedDate not supplied

Primary structure of influenza virus genome regions coding for polypeptides from the major antigenic sites of H3 hemagglutinin.

Nucleotide sequences for some regions of the hemagglutinin (HA) gene of influenza virus A/Leningrad/385/80 (H3N2) were analyzed. A double-stranded complementary DNA was synthesized on the influenza genome RNA in the presence of synthetic oligodeoxyribonucleotides A GCAAAAGCAGG and A GTAGAAACAAG and inserted into the Pst I-site of the pBR322 plasmid through G-C-tailing. Nucleotide sequences were determined by a solid phase modification of the Maxam and Gilbert procedure. A comparison of our data with those for influenza virus A/Bangkok/1/79, which is the nearest sequenced prototype of the strain investigated, revealed only two base changes in the variable region of the HA gene. One of them was accompanied by a change in the coded amino acid (Asp53----Tyr) located in the antigenic site E of the HA glycoprotein. There also were some point mutations in the constant region of the gene. The results obtained are discussed in terms of the evolution of "Hong Kong" influenza viruses during their circulation.

Antigens, Viral↗

PubMed2002

Evolution, synthesis and SAR of tripeptide alpha-ketoacid inhibitors of the hepatitis C virus NS3/NS4A serine protease.

N-terminal truncation of the hexapeptide ketoacid 1 gave rise to potent tripeptide inhibitors of the hepatitis C virus NS3 protease/NS4A cofactor complex. Optimization of these tripeptides led to ketoacid 30 with an IC50 of 0.38 microM. The SAR of these tripeptides is discussed in the light of the recently published crystal structures of a ternary tripetide/NS3/NS4A complexes.

Carboxylic Acids↗

PubMed2004

Genetic characterization of equine arteritis virus during persistent infection of stallions.

Equine arteritis virus (EAV) causes a persistent infection of the reproductive tract of carrier stallions. The authors determined the complete genome sequences of viruses (CW96 and CW01) that were present 5 years apart in the semen of a carrier stallion (CW). The CW96 and CW01 viruses respectively had only 85.6 % and 85.7 % nucleotide identity to the published sequence of EAV (EAV030). The CW96 and CW01 viruses had two 1 nt insertions and a single 1 nt deletion in the leader sequence, and a 3 nt coding insertion in ORF1a; thus their genomes included 12 708 nt as compared to the 12 704 nt in EAV030. Variation between viruses present in the semen of stallion CW and EAV030 was especially marked in the replicase gene (ORF1a and 1b), and the greatest variation occurred in the portion of ORF1a encoding the nsp2 protein. The ORFs 3 and 5, which respectively encode the GP3 and GP5 envelope proteins, showed greatest variation amongst ORFs encoding structural EAV proteins. Comparative sequence analyses of CW96 and CW01 indicated that ORFs 1a, 1b and 7 were highly conserved during persistent infection, whereas there was substantial variation in ORFs 3 and 5. Although the variation that occurs in ORF5 results in the emergence of novel phenotypic viral variants as determined by neutralization assay, all variants were neutralized by high-titre polyclonal equine antisera, suggesting that immune evasion is unlikely to be responsible for the establishment of persistent EAV infection of carrier stallions. Northern blot analyses of RNA extracted from cell culture propagated viruses isolated from 10 different persistently infected stallions failed to demonstrate any large genomic deletions, suggesting that defective interfering particles are also unlikely to be important in either the maintenance or clearance of persistent EAV infection of the reproductive tract of carrier stallions.

Amino Acid Sequence↗