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At least 1,009 records · Page 56Linked to original sources
PubMed1993

Complete nucleotide sequences of six hepatitis B viral genomes encoding the surface antigen subtypes ayw4, adw4q-, and adrq- and their phylogenetic classification.

The complete nucleotide sequences of six hepatitis B viral (HBV) genomes were determined by dideoxy chain termination sequencing of ten overlapping nucleotide fragments obtained by the polymerase chain reaction. Four of the genomes belonged to the two genomic groups E and F of HBV which have been previously identified by us on the basis of sequence divergences within the S gene. Genomic group E encodes the HBsAg subtype ayw4, group F adw4q-. The other two genomes were of Pacific origin within group C and encoded adrq-. The relationship of these complete human HBV genomes to 21 that have been previously published, together with one chimpanzee virus and four rodent hepadnaviral genomes, was investigated by constructing a phylogenetic tree utilizing a combination of distance matrix and approximate parsimonious methods. Thereby, the previously demonstrated segregation of human HBV strains into six genomic groups was confirmed. Both of the representatives of the groups E and F were found to differ by 8.1-13.6% and by 12.8-15.5% from the genomes of the other genomic groups and by 1.5 and 3.7% from each other. Since they differed by more than 8% from the genomes in the other groups, the limit originally used to define HBV, genomic groups their status as new genomic groups was confirmed. The two Pacific group C strains were found to differ by 2.7% from each other and by 4.1 to 5.4% from other group C genomes, suggesting that they diverged early from the other group C genomes. According to both the overall similarity and the phylogenetic dendrogram the F strains formed the most divergent cluster of HBV genomes favoring the concept that they represented the original HBV strains of the New World. The next split in the dendrogram segregated the A, D, E and the chimpanzee strains from the Asian B and C strains. Information on the nucleotide sequences and their encoded products of HBV strains of different genomic groups will provide a basis to understand biological variations of the HBV infection in different parts of the world.

Animals↗
PubMed2003

Emerging viral infections of the nervous system.

New viral infections of the nervous system have been appearing with great regularity. Some result from the evolution of new agents and others from the entry of viruses into new hosts or environments. The emergence of neurovirulent enteroviruses causing a paralytic poliomyelitis syndrome and rhomboencephalitis represent the evolution of new human viruses. Most emerging viral infections represent movement of an agent into new geographic areas or across species barriers. The transport of neurovirulent strains of West Nile virus into the Western Hemisphere and the penetration of Nipah virus, a newly recognized paramyxovirus, across species barriers from bat to pig to man are examples that are highlighted in this review. The burgeoning human population and the speed and frequency of travel favor the evolution, preservation, and spread of new viral agents.

Animals↗
PubMed1986

Structural features of ribonucleotide reductase.

Herpes simplex virus type 1 (HSV-1) encodes a ribonucleotide reductase which comprises two polypeptides with sizes of 136,000 (RR1) and 38,000 mol. wt. (RR2). We have determined the entire DNA sequence specifying HSV-1 RR1 and have identified two adjacent open reading frames in varicella-zoster virus (VZV) which have homology to HSV RR1 and RR2; the predicted sizes for the VZV RR1 and RR2 polypeptides are 87,000 and 35,000 mol. wt. respectively. Amino acid comparisons with RR1 and RR2 polypeptides from other organisms indicate that HSV-1 RR1 contains a unique N-terminal domain which is absent from other RR1 polypeptides apart from HSV-2 RR1. These N-terminal amino acid sequences are poorly conserved between HSV-1 and HSV-2 in contrast to the remainder of the protein which shows greater than 90% homology. Polypeptide structural predictions suggest that the HSV-1 N-terminal domain may be separated into two regions, namely, a beta-sheet structure followed by a nonstructured area. Across the remainder of RR1 and RR2, comparisons also reveal blocks of amino acids conserved between the different ribonucleotide reductases, and these may be important for enzyme activity. From predictions on the structure of these conserved blocks, we have proposed that the location of a substrate binding site within RR1 is centered on three conserved glycine residues in a region which is predicted to adopt a beta-sheet/turn/alpha-helical structure; this approximates to the structure for ADP nucleotide binding folds. Finally, we propose that the promoters for the HSV and Epstein-Barr virus (EBV) RR2 transcripts have evolved by separate evolutionary routes.

Amino Acid Sequence↗
PubMed1997

HIV genetic variation is directed and restricted by DNA precursor availability.

The effects of deoxynucleoside triphosphate (dNTP) imbalances on the fidelity of human immunodeficiency virus type 1 (HIV-1) replication were investigated. Using detergent permeabilized virions and biased dNTP concentrations different types of hypermutants were readily produced. However, the mutant spectrum was different from naturally occurring hypermutants demonstrating that the host cell may restrict variation. Using a genetic screen based on the blue/white beta-galactosidase complementation assay, G --> A hypermutants were recovered from HIV-infected thymidine treated U937 cells. Furthermore, hypermutants were recovered from 1 to 2% of resting or activated peripheral blood mononuclear cells indicating that small proportions of primary cells had distorted intracellular [dTTP] and [dCTP]. Such imbalances may underlie a proportion of somatic and germline point mutations and shape to some extent the evolution of mammalian and viral genomes.

Base Sequence↗
PubMed1999

KSHV strains: the origins and global spread of the virus.

Nucleotide sequence analysis at five distinct loci across the 140, 000 bp genomes of more than 60 KSHV samples from KS and PEL tumors from North America, Africa, the Middle East, Asia and the Pacific revealed that they cluster into four major subtypes (A, B, C and D) that have close associations with the geographic and ethnic background of the patients. In particular, the ORF-K1 protein subtypes encoded at the extreme LHS of the genome display up to 30% amino acid variability resulting from 85% non-synonymous nucleotide substitution rates. In addition, two alternative highly diverged forms of the complex spliced ORF-K15 gene (P or M) map at the extreme RHS of the genome and are essentially unlinked to the ORF-K1 genotypes. We conclude that: (1) KSHV is an ancient human virus with several major subtypes that reflect the migrationary divergence of modern human populations over the past 35,000-60,000 years; (2) the novel immunoglobulin receptor-like signal transducing protein ORF-K1 is subject to unusually strong biological selective pressures; and (3) a minority of KSHV genomes have undergone recombination events with a related virus producing two different alleles of the ORF-K15 latency membrane protein.

Alleles↗
PubMed1993

Identification of a new subgroup of SIVagm in tantalus monkeys.

Simian immunodeficiency viruses from African green monkeys (SIVagm) can be classified into three subgroups based upon the species from which they were isolated. The most extensively studied subgroup are composed of SIVagm isolated from vervet monkeys (Cercopithicus pygerythrus). Fewer isolates have been characterized from either grivets (Cercopithicus aethiops) or green monkeys (Cercopithicus sabeus). An additional distinct species of African green monkeys, tantalus monkeys (Cercopithicus tantalus), has not been characterized in terms of SIV infection. A high seroprevalence of SIV-specific antibodies was identified in sera collected from Ugandan tantalus monkeys. SIV was isolated from PBMC (SIVagm/tan), the gag region amplified by polymerase chain reaction, cloned, and sequenced. Based upon gag, SIVagm/tan isolates cluster genetically with other previously recognized SIVagm strains. However, SIVagm from tantalus monkeys forms a distinct genetic subgroup. These data confirm earlier observations of species-specific subtypes of SIVagm viruses and support the hypothesis that these viruses may have coevolved with their host during geographic dispersion throughout Africa.

Amino Acid Sequence↗
PubMed1994

Genetic analysis and molecular phylogeny of simian T-cell lymphotropic virus type I: evidence for independent virus evolution in Asia and Africa.

Type C retroviruses, designated simian T-cell lymphotropic virus type I (STLV-I), have been isolated from several genera of Old World monkeys and apes, but not from New World monkeys and prosimians. To determine the genomic diversity and molecular evolution of STLV-I and to clarify their genetic relationship to human T-cell lymphotropic virus type I (HTLV-I), we enzymatically amplified, then directly sequenced selected regions of the gag, pol, env, and pX genes of STLV-I strains from Asia and Africa. STLV-I strains Si-2, Matsu, and JM86 from Japanese macaques, which exhibited sequence similarities ranging from 98.5 to 99.8% among themselves, diverged by 12.9 to 13.3% from STLV-I strain MM39-83 from a naturally infected rhesus macaque, by 9.7 to 11.2% from STLV-I strains from Africa, and by 8.8 to 11.2% from HTLV-I strains originating in Japan, India, Africa, the Caribbean, the Americas, Polynesia, and Melanesia. By contrast, the interspecies nucleotide sequence similarity among African STLV-I strains from green monkey, yellow baboon, sooty mangabey, and common chimpanzee was remarkably high, ranging from 96.9 to 97.4%, and these STLV-I strains diverged by only 2.2 to 2.8% from HTLV-I strain EL from equatorial Zaire. Phylogenetic trees constructed by using the neighbor-joining and maximum parsimony methods indicated that the Asian STLV-I strains diverged from the common ancestral virus prior to African STLV-I and cosmopolitan and Melanesian HTLV-I strains. Thus, our data are consistent with an archaic presence of STLV-I in Asia, probably predating macaque speciation, with subsequent independent virus evolution in Asia and Africa.

Africa↗
PubMed1995

European swine virus as a possible source for the next influenza pandemic?

According to phylogenetic data, about 100 years ago an avian influenza virus passed the species barrier (possibly first) to pigs and (possibly from there) to humans. In 1979 an avian influenza A virus (as a whole, without reassortment) again entered the pig population in northern Europe, forming a stable lineage. Here it is shown that the early North European swine viruses exhibit higher than normal evolutionary rates and are highly variable with respect to plaque morphology and neutralizability by monoclonal antibodies. Our results are consistent with the idea that, in order to pass the species barrier, an influenza A virus needs a mutator mutation to provide an additional number of variants, from which the new host might select the best fitting ones. A mutator mutation could be of advantage under such stress conditions and might enable a virus to pass the species barrier as a whole even twice, as it seems to have happened about 100 years ago. This stressful situation should be over for the recent swine lineage, since the viruses seem to be adapted already to the new host in that the most recent isolates--at least in northern Germany--are genetically stable and seem to have lost the putative mutator mutation again.

Animals↗
PubMed1998

Differences in the evolutionary pattern of feline panleukopenia virus and canine parvovirus.

Canine parvovirus (CPV) suddenly appeared in the late 1970s after which it showed continuous antigenic changes. Virological and molecular genetic analyses mainly focused on feline panleukopenia virus (FPLV) were conducted in this study because FPLV is the suspected ancestor of CPV; the way in which FPLV evolves may help to explain the emergence of CPV. Analysis of escape mutants against FPLV-specific monoclonal antibody showed that viruses possessing CPV-like properties were not easily detected in FPLV virus stocks. Phylogenetic analysis revealed that the nonstructural protein 1 (NS1) and capsid protein 2 (VP2) genes of FPLV changed with time. A similar tendency, however, was not observed in the FPLV VP2 proteins. In contrast, the topology of the phylogenetic tree of VP2 proteins of CPV basically concurred with that of the VP2 genes. Analysis of the ratio of nonsynonymous and synonymous substitutions revealed that synonymous substitutions exceeded nonsynonymous substitutions in both the NS1 and VP2 genes of FPLV, even when the analysis focused on specific regions in the VP2 gene that are known to be located on the capsid surface. Comparison of the CPV VP2 genes revealed that nonsynonymous substitution was found to dominate over synonymous substitution in one specific region in the VP2 gene. These results suggested that FPLV has changed mainly by random genetic drift. In contrast, after the appearance of CPV, changes in the CPV VP2 gene appear to be partly selected by certain positive selection forces. CPV and FPLV are known to be closely related viruses genetically and biologically, but the evolutionary mechanisms of the two viruses appeared to be different.

Amino Acid Substitution↗
PubMed2000

Coevolution of host and virus: the pathogenesis of virulent and attenuated strains of myxoma virus in resistant and susceptible European rabbits.

Myxoma virus was introduced into the European rabbit population of Australia in 1950. Although the virus was initially highly lethal in rabbits, there was rapid selection for less virulent strains of virus and innately resistant rabbits. To investigate the basis of resistance to myxoma virus, we have compared the pathogensis of the virulent strain of myxoma virus originally released into Australia and an attenuated, naturally derived field strain of myxoma virus. This was done in laboratory rabbits, which have not been selected for resistance, and in wild rabbits that have developed significant resistance. Wild rabbits were able to recover from infection with virus that was always lethal in laboratory rabbits. Laboratory rabbits were able to control and recover from infection with attenuated virus. This virus caused a trivial disease in wild rabbits. There was little difference between laboratory and wild rabbits in titers of either virulent or attenuated virus in the skin at the inoculation site. However, resistant wild rabbits had a 10- to 100-fold lower titer of virulent virus within the lymph node draining the inoculation site and controlled virus replication in tissues distal to the draining lymph node. Replication of virus in lymphocytes or fibroblasts cultured from wild and laboratory rabbits demonstrated that resistance was not due to altered cellular permissivity for replication. Neutralizing antibodies were present in both susceptible and resistant rabbits, suggesting that these have no significant role in resistance. We hypothesise that resistance is due to an enhanced innate immune response that allows the rabbit to mount an effective cellular immune response.

Animals↗
PubMed1998

Antiviral cell-mediated immune responses during hepatitis B and hepatitis C virus infections.

Cell-mediated immune responses to hepatitis B (HBV) and hepatitis C virus (HCV) antigens are vigorous and multispecific in acute, self-limited infections. Moreover, the prevalent cytokine pattern of circulating virus-specific T cells from patients who recover spontaneously from acute hepatitis is Th1-like. Longitudinal analysis of the T cell response to HCV antigens from the early stages of HCV infection in patients who recover from hepatitis and those who do not indicates that weaker responses and a prevalent Th2 pattern of cytokine production is associated with viral persistence and chronic evolution of disease. Although similar sequential studies are missing in hepatitis B, the observation that HBV-specific T cell responses are very weak or totally undetectable in the peripheral blood of patients with long-lasting chronic hepatitis B suggests that strength and quality of virus-specific T cell responses at the early stages of infection may influence the final outcome of both hepatitis B and C. While T cell hyporesponsiveness seems to be an important determinant for HBV persistence once chronic hepatitis has developed, this mechanism appears to be less critical in chronic HCV infection, because the vigor and quality of HCV-specific T cell responses seem to improve as a function of the duration of infection. This is shown by the finding that HCV-specific CD4- and CD8-mediated responses are easily detectable in the peripheral blood of patients with long-lasting chronic hepatitis C and that production of Th1 cytokines predominates within their livers. HCV therefore seems to be able to persist even in the face of an active T cell response and to acquire the capacity to survive within a host environment apparently unfavorable to its persistence. The high variability of HCV may explain its efficiency in escaping immune surveillance.

Hepatitis B↗
PubMed1996

HIV-1 subtype O: epidemiology, pathogenesis, diagnosis, and perspectives of the evolution of HIV.

HIV-1 subtype O is a new HIV variant originating in the West-Central African region, with highest prevalences in countries such as Cameroon, Equatorial Guinea and Gabon. Detection of antibodies to HIV-1 subtype O can pose problems in unmodified ELISA tests, and confirmation of anti-HIV-1 subtype O in immunoblot may give false negative results in some specimens. Nucleic acid-based assays designed for HIV-1 detection do not amplify or detect sequences from HIV-1 subtype O. In their env sequences, HIV-1 subtype O strains show a higher heterogeneity than the classical HIV-1 subtypes, leading to the conclusion that HIV-1 subtype O has been introduced into the human population only recently. Further, unidentified subtypes are also likely to exist.

Acquired Immunodeficiency Syndrome↗
PubMed1993

Network models for sequence evolution.

We introduce a general class of models for sequence evolution that includes network phylogenies. Networks, a generalization of strictly tree-like phylogenies, are proposed to model situations where multiple lineages contribute to the observed sequences. An algorithm to compute the probability distribution of binary character-state configurations is presented and statistical inference for this model is developed in a likelihood framework. A stepwise procedure based on likelihood ratios is used to explore the space of models. Starting with a star phylogeny, new splits (nontrivial bipartitions of the sequence set) are successively added to the model until no significant change in the likelihood is observed. A novel feature of our approach is that the new splits are not necessarily constrained to be consistent with a treelike mode of evolution. The fraction of invariable sites is estimated by maximum likelihood simultaneously with other model parameters and is essential to obtain a good fit to the data. The effect of finite sequence length on the inference methods is discussed. Finally, we provide an illustrative example using aligned VP1 genes from the foot and mouth disease viruses (FMDV). The different serotypes of the FMDV exhibit a range of treelike and network evolutionary relationships.

Aphthovirus↗
PubMed1990

Distribution of mouse mammary tumor virus-related sequences does not correlate with the taxonomic position of their hosts.

Sequences (MRS) distantly related to mouse mammary tumor virus (MMTV) were found in genomes of a wide range of mammalian species using blot hybridization. The number of MRS copies and the degree of their homology with the hybridization probe varied and did not correlate with the taxonomic position of the species. Nevertheless, within a genus the set of MRS was species specific and reflected the taxonomic relation between the species. MRS were also found in avian genomes and the degree of their homology did not correlate with the taxonomic position of the species either. The origin and distribution of MRS is discussed on the basis of the authors' and published data.

Animals↗