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[Factors associated with severe evolutive forms of chronic infection with hepatitis C virus].

To assess the factors associated with the development of moderate and severe fibrosis, the medical records of 426 patients with chronic hepatitis C virus infection attended at the Infectious and Parasitic Diseases Clinic of the University of São Paulo Faculty of Medicine from January 1 to December 31, 2000 were reviewed. Of the patients included in the study, 56.3% were male and 43.7%, female. Patient age ranged from 18 to 69 years. Blood transfusion was the most frequent form of hepatitis C virus transmission, detected in 128 (30%) cases, and no risk factor was detected in 187 (43.9%) patients. Patient distribution regarding architectural changes observed in a liver biopsy was: grade 0 (14.1%); grade 1 (51.2%); grade 2 (20.6%); grade 3 (8%); grade 4 (6.1%). Multivariate analysis revealed a positive correlation between fibrosis severity and age greater than 40 years at the time of the liver biopsy, serum albumin levels below normal lower limits, gamma-glutamyltransferase levels equal to or higher than twice upper normal limits, platelet numbers less than 150,000/mm(3) and high necroinflammatory activity. The data obtained were inconclusive regarding a possible correlation between severity of fibrosis and alcoholism.

Adolescent↗
PubMed2001

[Evolution of isolation and identification techniques of waterborne viruses].

The paralytic potential of the poliovirus was recognized as early as the 14th century B.C. as illustrated in Egyptian art. But it is only after the four last decades that methods for their concentration from water and their identification were performed. Among several of them the adsorption-elution method was retained. Nevertheless two important barriers had to be ran-over. The first one was the concentration-elution steps on different materials which had to be improved. The second one was the typing method which had to move from particle by particle identification to entire viral population. Despite of these advances only a few cytopathogenic serotypes were found. The reverse transcriptase-polymerase chain reaction with its far more wide spectrum allows the fast and direct identification of viral nucleic acids (or their fragments) of almost all viruses, cytopathogenic or not. With this method elevated amounts of drinking water samples were found positive for several non cytopathogenic viruses. The sanitary significance of these results has still to be proved.

Adsorption↗
PubMed1975

Evolution and modes of transmission of RNA tumor viruses. Parke-Davis Award lecture.

Most vertebrates contain sets of gene sequences (virogenes) which are an integral part of the chromosomal DNA and which can code, in some instances, for the production of Type C RNA tumor viruses. These genes are transmitted from parent to progeny along with other cellular genes, and their activation from a normally reressed state may be part of the mechanism by which RNA tumor viruses produce cancer. Isolates of endogenous genetically transmitted baboon Type C viruses are morphologically and biochemically related to other mammalian Type C viruses but can clearly be distinguished from the other groups (mouse, rat, cat, etc.) by immunologic and nucleic acid hybridization criteria. Within the primates, Type C viral gene sequences have evolved as the species have evolved, with virogenes from the most closely related genera and families showing the most sequence homology; all higher primate, including man, however, do have detectable virogene sequences in their normal tissues. Type C viruses have also been transferred under natural conditions between species only remotely related phylogenetically. The results show three clear examples where viral genes from one group of animals have become incorporated into the germ line of genetically distant groups of animals (inheritance of acquired genes). Infectious Type C viruses of primates, distinct from the endogenous primate virus group, have also been isolated (woolly monkey and gibbon isolates) and can be shown to produce tumors in other primates. Related viral information (nucleic acid sequences, enzymes, and antigens) have been reported in human tumors. The significance of infectious and/or genetically transmitted viruses in naturally occurring cancer is a major focus of current research. The presence of genetically transmitted viral genes in so many vertebrate species and the evidence that they have been conserved in several distinct vertebrate lineages suggests that they may provide some normal function(s) advantageous to the species carrying them and that their potential to cause cancers is a pathologic manifestation of normal, as yet undefined, physiologic processes.

Animals↗
PubMed1998

Genetic variation in the PRRS virus.

Porcine reproductive and respiratory syndrome (PRRS) is characterized by late-term abortions and stillbirths in sows and respiratory difficulties in nursery pigs. The disease appeared in Europe and North America at approximately the same time between 1985 and 1990. The PRRS virus was isolated shortly thereafter and demonstrated unexpectedly profound differences between European (Lelystad) and North American (VR2332) isolates as measured by serological crossreactivity and nucleotide sequence similarity. In order to determine the amount of genetic variation in the PRRS virus and to understand the molecular mechanisms of viral evolution, nucleotide sequences of PRRS virus strains were determined. Comparisons among ten U.S. strains showed that variation in primary nucleotide sequence between isolates ranged from 2.5% to 7.9% for ORFs 2-7. In contrast, Lelystad virus was, on average, 35% different from US clones. These results provided direct molecular evidence that US and European PRRSV isolates represented genetically distinct groups of the same viral family. A further analysis of more than 150 isolates in the United States and Canada demonstrated that the PRRS virus in North America represents a single large and diverse genetic group that is distinct from European forms of the virus.

Animals↗
PubMed2003

[Post-transcriptional gene silencing--a plant defense strategy to viruses invasion].

Gene silencing is a kind of epigenetic phenomenon discovered in transgenic plants in recent years. Gene silencing can be divided into two types: position effect and homology dependent gene silencing (HdGS). Homology-dependent gene silencing (HdGS), which is the generic term for transcriptional gene silencing (TGS), post-transcriptional gene silencing (PTGS) and RNA-mediated virus-resistance (RmVR) have been shown to frequently occur in transgenic plants. Post-transcriptional gene silencing (PTGS) is an antiviral defense system of plants, which has led to a new understanding of the relationship between viruses and plants. And it's a co-evolution result between plants and viruses. A few hypothesis models have been proposed to elucidate the mechanism of gene silencing, but they could not explain all the phenomena in gene silencing. In this paper, we reviewed the relationship between PTGS and the plants defense mechanism to virus, and proposed a model of gene silencing based on our experiments results.

Gene Silencing↗
PubMed1997

Long-term evolution of the 5'UTR and a region of NS4 containing a CTL epitope of hepatitis C virus in two haemophilic patients.

Haemophilic patients exposed to unsterilized clotting factor concentrates prior to 1985 have become infected with hepatitis C virus (HCV). We have studied the sequence evolution of the 5'UTR and a region of NS4 over 12 years in one human immunodeficiency virus (HIV) positive haemophilic patient and 14 years for one HIV negative haemophilic patient. One sample each year from the date of HCV infection to 1994 was analysed for genotype, virus load and nucleotide sequence of the two genetic loci. Both patients were infected with HCV genotype 1 throughout the study period. The virus load profiles were similar except that the profile for the HIV infected patient was displaced 4 years earlier relative to the other patient. Mean divergence of the quasispecies at both the 5'UTR and NS4 loci was higher in the HIV coinfected patient. Phylogenetic analysis indicated that evolution of the 5'UTR was host independent, whereas the NS4 region containing a CD8 restricted CTL epitope evolved in a host specific fashion.

Amino Acid Sequence↗
PubMed2004

Phylogenetic analysis of avian infectious bronchitis virus strains isolated in Japan.

To define the origin and evolution of recent avian infectious bronchitis virus (IBV) in Japan, a genetic analysis was performed. By phylogenetic analysis based on the S1 gene including the sequence of the hypervariable regions, IBV isolates in Japan were classified into five genetic groups, which included two already-known groups (Mass and Gray). Among them, three major genetic groups were associated with the recent outbreaks of IB in Japan. One group is indigenous to Japan and could not be placed within the known existing groups in other countries. The remaining two groups, which have emerged recently, are related to isolates in China and Taiwan.

Amino Acid Sequence↗
PubMed1999

Biochemical and structural studies with neutralizing antibodies raised against foot-and-mouth disease virus.

The function of a loop exposed on the aphthovirus capsid (the G-H loop of protein VP1) has been explored by combining genetic and structural studies with viral mutants. The loop displays a dual function of receptor recognition and interaction with neutralizing antibodies. Remarkably, some amino acid residues play a critical role in both such disparate functions. Therefore residues subjected to antibody pressure for variation may nevertheless maintain a role in receptor recognition for which invariance is a requirement. Evolution of FMDV in cell culture may relax the requirements at this site and allow further increase of antigenic diversification. Essential residues at one stage of virus evolution may become dispensable at another not very distant point in the evolutionary landscape. Implications for FMDV evolution and vaccine design are discussed.

Animals↗
PubMed1997

Avian tumor viruses: persistent and evolving pathogens.

Most neoplasias of lymphoid and other hematopoietic cells in commercial poultry are caused by viruses which belong to one of four distinct groups. Marek's disease virus (MDV) is an oncogenic herpesvirus. Avian leukosis virus (ALV), reticuloendotheliosis virus (REV) and lymphoproliferative disease virus (LPDV) are oncogenic retroviruses. Each group is distinguished by nucleic acid type, molecular structure, antigenicity, epidemiology, host range and other characteristics. However, most of these viruses have in common a unique ability to persist, both in the host and in the ecosystem. In addition, both the viruses and the virus-host relationships for several members of the group have demonstrated a propensity to evolve with time, creating new dilemmas for diagnosis and control. A focus on the persistence and evolution of avian tumor viruses will be used to address a number of current issues with individual viruses of economic importance. Issues of primary concern include (1) the evolution of MDV towards greater virulence with concomitant reduction of vaccine efficacy and expansion of host range, (2) the emergence of subgroup J ALV as a major pathogen in meat-type breeder stocks, and (3) the increasing prevalence of REV and its evolving role as a pathogen in chickens and turkeys.

Animals↗
PubMed2002

Comparative rates of nucleotide sequence variation in the hypervariable region of E1/E2 and the NS5b region of hepatitis C virus in patients with a spectrum of liver disease resulting from a common source of infection.

The association of the severity of liver disease and the molecular evolution of hepatitis C virus (HCV) during chronic infection remains unclear and controversial. To address this we have studied the interpatient variability in the nucleotide sequence of two regions of the HCV genome, E1/E2, which contain the hypervariable region 1 and the nonstructural NS5b region, in a cohort of Irish female patients who were all recipients of a single source of HCV genotype 1b-contaminated anti-D immunoglobulin in 1977 and 1978 and who over the subsequent 20 years developed a spectrum of liver disease. In addition, quasispecies analysis was used to evaluate intrapatient variability in the E1/E2 region in four patients with mild and four with severe disease. Phylogenetic and evolutionary rate analyses of the nucleotide sequences demonstrated that there was no significant difference between those who developed mild disease and those who had progressed to severe disease or cirrhosis. These findings suggest that other factors, either additional viral or host, may be important in the pathogenesis and clinical outcome of chronic hepatitis C virus infection.

Amino Acid Sequence↗
PubMed2002

Experimental genomic evolution: extensive compensation for loss of DNA ligase activity in a virus.

Deletion of the viral ligase gene drastically reduced the fitness of bacteriophage T7 on a ligase-deficient host. Viral evolution recovered much of this fitness during long-term passage, but the final fitness remained below that of the intact virus. Compensatory changes occurred chiefly in genes involved in DNA metabolism: the viral endonuclease, helicase, and DNA polymerase. Two other compensatory changes of unknown function also occurred. Using a method to distinguish compensatory mutations from other beneficial mutations, five additional substitutions from the recovery were shown to enhance adaptation to culture conditions and were not compensatory for the deletion. In contrast to the few previous studies of viral recovery from deletions, the compensatory changes in T7 did not restore the deletion or duplicate major regions of the genome. The ability of this deleted genome to recover much of the lost fitness via mutations in its remaining genes reveals a considerable evolutionary potential to modify the interactions of its elements in maintaining an essential set of functions.

Adaptation, Physiological↗
PubMed2006

Quasispecies in time-dependent environments.

In recent years, quasispecies theory in time-dependent (that is, dynamically changing) environments has made dramatic progress. Several groups have addressed questions such as how the time scale of the changes affect viral adaptation and quasispecies formation, how environmental changes affect the optimal mutation rate, or how virus and host co-evolve. Here, we review these recent developments, and give a nonmathematical introduction to the most important concepts and results of quasispecies theory in time-dependent environments. We also compare the theoretical results with results from evolution experiments that expose viruses to successive regimes of replication in two or more different hosts.

Adaptation, Physiological↗
PubMed2006

The genetic stability of a conditional live HIV-1 variant can be improved by mutations in the Tet-On regulatory system that restrain evolution.

Live attenuated human immunodeficiency virus type 1 (HIV-1) vaccines are considered unsafe because more quickly replicating pathogenic virus variants may evolve after vaccination. As an alternative vaccine approach, we have previously presented a doxycycline (dox)-dependent HIV-1 variant that was constructed by incorporating the tetracycline-inducible gene expression system (Tet-On system) into the viral genome. Replication of this HIV-rtTA variant is driven by the dox-inducible transcriptional activator rtTA and can be switched on and off at will. A large scale evolution study was performed to test the genetic stability of this conditional live vaccine candidate. In several long term cultures, we selected for HIV-rtTA variants that no longer required dox for replication. These evolved variants acquired a typical amino acid substitution either at position 19 or 37 in the rtTA protein. Both mutations caused rtTA activity and viral replication in the absence of dox. We designed a novel rtTA variant with a higher genetic barrier toward these undesired evolutionary routes. The corresponding HIV-rtTA variant did not lose dox control in long term cultures, demonstrating its improved genetic stability.

AIDS Vaccines↗
PubMed1990

Evolution of natural populations in the Drosophila melanogaster sigma virus system I. Languedoc (southern France).

In natural populations of Drosophila melanogaster, sigma virus is usually present in a minority of individuals. The virus is transmitted transovarially but is not contagious from fly to fly. Two viral Types (I and II) are found in populations. One of them (Type II) is better adapted to an allele for resistance to the virus, present as a polymorphism in fly populations. Previous observations have led to the hypothesis that a viral Type II originating in central France might be invading populations. The study of Languedoc populations was undertaken to examine this hypothesis. Two striking phenomena were observed. The strong increase in Type II clones frequency (from 0.53 to 0.91) confirmed that there was invasion in this region. The frequency of infected flies also increased dramatically, at levels never observed elsewhere yet, which indicates that Languedoc should present some unusual characteristics. The epidemiological consequences of such a burst, in the case of a pathogenic virus would have to be taken into consideration. Significant changes in other viral characteristics, from 1983 to 1987, in Languedoc populations have also been documented.

Adaptation, Physiological↗