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At least 919 records · Page 51Linked to original sources

PubMed1993

Genetic variability and evolution of the satellite RNA of cucumber mosaic virus during natural epidemics.

The genetic structure of populations of cucumber mosaic virus (CMV) satellite RNA (satRNA) and its evolution were analyzed during the course of a CMV epidemic in tomatoes in eastern Spain. A total of 62 variants of CMV-satRNA from epidemic episodes in 1989, 1990, and 1991 were characterized by RNase protection assay (RPA); RPA patterns defined 60 haplotypes in the CMV-satRNA population. RPA of nine CMV-satRNAs of known sequences showed that numbers of nucleotide substitutions per site (dij) between different satRNAs can be estimated from RPA data. Thus, dij were estimated for any possible pair of field CMV-satRNA types, and nucleotide diversities within and between yearly subpopulations were calculated. Also, phylogenetic relationships among CMV-satRNAs were derived from RPA data (by parsimony) or from dij (by neighbor joining). From these analyses, a model for the evolution of CMV-satRNAs in field epidemics can be built. High genetic variability of CMV-satRNA results in very heterogeneous populations, even compared with those of other RNA genomes. The high diversity of the population is maintained through time by the continuous generation of variants by mutation, counterbalanced by negative selection; this results in a certain replacement of haplotypes from year to year. The sequential accumulation of mutations in CMV-satRNA leads to fast genetic divergence to reach what appears to be an upper permitted threshold.

Biological Evolution↗

PubMed1995

RNA determinants of junction site selection in RNA virus recombinants and defective interfering RNAs.

RNA recombination plays an important role in the diversification and evolution of RNA viruses. Most of these events are believed to be mediated by an actively copying viral replicase switching from a donor template to an acceptor template, where it resumes synthesis. In addition, intramolecular replicase-mediated events (i.e., rearrangements) can lead to the generation of replicable deleted forms of a viral genome, termed defective interfering (DI) RNAs. To gain further insight into the recombination process, the effect of various primary and secondary structures on recombination site selection in vivo was examined using plant RNA tombusviruses. The effect of sequence identity and complementarity on deletion events that generate DI RNAs was also investigated. Our results suggest that (1) 5' termini and strong hairpin structures in donor templates represent preferred sites for recombinations, (2) junction sites in acceptor templates do not occur in double-stranded regions, (3) nucleotide homology can shift donor and acceptor recombination sites closer to regions of identity and, (4) both sequence identity and complementarity can direct deletion sites in DI RNAs. These results further define RNA determinants of tombusvirus RNA recombination and rearrangement.

Base Sequence↗

PubMed2006

An increase in viral replicative capacity drives the evolution of protease inhibitor-resistant human immunodeficiency virus type 1 in the absence of drugs.

Little is known about the factors which drive the evolution of protease inhibitor-resistant human immunodeficiency virus type-1 in the absence of drugs. To examine if viral replicative capacity (RC) is an important determinant, we performed in vitro evolution experiments in the absence of drugs with a unique panel of 6 drug-resistant human immunodeficiency virus type-1 recombinant protease variants with a range of different RC. The experiments revealed that an increase in viral RC was indeed an important determinant of evolution. Initial protease inhibitor-resistant viruses with only a few protease mutations and a lowered RC evolved into viruses with an increased RC, either by reversion of primary resistance mutations or by the acquisition of compensatory mutations. For these viruses with a lowered RC, higher fitness peaks are most likely available in the sequence space. Evolution of these viruses in the absence of drugs will therefore drive them to new fitness peaks. In contrast, viruses with an RC comparable to wild type or even higher than wild type did not show any evolution. In the case of these viruses, it is not so likely that higher fitness peaks are present within the sequence space, and therefore, these variants will persist in the absence of drug pressure.

Amino Acid Substitution↗

PubMed2000

Mutualism, parasitism and competition in the evolution of coviruses.

Coviruses are viruses with the property that their genetic information is divided up among two or more different viral particles. I model the evolution of coviruses using information on both viral virulence and the interactions between viruses and molecules that parasitize them: satellite viruses, satellite RNAs and defective interfering viruses. The model ultimately, and inevitably contains within it single-species dynamics as well as mutualistic, parasitic, cooperative and competitive relationships. The model shows that coexistence between coviruses and the self-sufficient viruses that spawned them is unlikely, in the sense that the quantitative conditions for coexistence are not easy to satisfy I also describe an abrupt transition from mutualistic two-species to single-species dynamics, showing a new sense in which questions such as 'Is a lichen one species or two?' can be given a definite answer.

Animals↗

PubMed2000

Experimental evolution recapitulates natural evolution.

Genomes of the closely related bacteriophages phiX174 and S13 are 5386 bases long and differ at 114 nucleotides, affecting 28 amino acids. Both parental phages were adapted to laboratory culture conditions in replicate lineages and analysed for nucleotide changes that accumulated experimentally Of the 126 experimental substitutions, 90% encoded amino-acid changes, and 62% of the substitutions occurred in parallel in more than one experimental line. Furthermore, missense changes at 12 of the experimental sites were at residues differing between the parental phages; in ten cases the phiX174 experimental lineages were convergent with the S13 parent, or vice versa, at both the nucleotide and amino-acid levels. Convergence at a site was even obtained in both directions in three cases. These results point to a limited number of pathways taken during evolution in these viruses, and also raise the possibility that much of the amino-acid variation in the natural evolution of these viruses has been selected.

Bacteriophage phi X 174↗

PubMed2002

Rapid evolution of two discrete regions of the caprine arthritis-encephalitis virus envelope surface glycoprotein during persistent infection.

Five major regions of sequence diversity between strains (V1-V5) have been described in the caprine arthritis-encephalitis lentivirus (CAEV) envelope surface unit glycoprotein (SU). To determine which of these variable regions is important in persistent infection in vivo, we evaluated SU sequence diversity in five neutralization variants from two goats and proviral DNA from five additional goats infected with CAEV-63 for up to 7 years. Overall amino acid sequence divergence in the SU encoded by provirus and neutralization variants compared to parental CAEV-63 ranged from 1.1 to 4%. However, most of the amino acid substitutions and all of the deletions and insertions were present in two discrete regions designated HV1 and HV2. The HV2 region was variable in all neutralization variants and provirus sequences from most animals. This region overlapped the V4 domain of CAEV SU and the neutralization domain of the closely related ovine maedi-visna lentivirus. HV1 was located in a region of SU strictly conserved in all small ruminant lentivirus strains except CAEV-63. This region only varied in a subset of neutralization variants and proviruses, all derived from goats with arthritis. In contrast, sequences in the V1,V2,V3, and V5 regions were stable in neutralization variants and proviruses from infected goats, indicating that sequence diversity between strains in these regions is not due to selection of variants in persistently infected animals. Our results define two discrete regions of CAEV SU that undergo rapid sequence variation in persistently infected goats which may have important roles in virus-host interactions.

Amino Acid Sequence↗

PubMed1998

Long-term evolution of the hypervariable region of hepatitis C virus in a common-source-infected cohort.

The long-term evolution of the hepatitis C virus hypervariable region (HVR) and flanking regions of the E1 and E2 envelope proteins have been studied in a cohort of women infected from a common source of anti-D immunoglobulin. Whereas virus sequences in the infectious source were relatively homogeneous, distinct HVR variants were observed in each anti-D recipient, indicating that this region can evolve in multiple directions from the same point. Where HVR variants with dissimilar sequences were present in a single individual, the frequency of synonymous substitution in the flanking regions suggested that the lineages diverged more than a decade previously. Even where a single major HVR variant was present in an infected individual, this lineage was usually several years old. Multiple lineages can therefore coexist during long periods of chronic infection without replacement. The characteristics of amino acid substitution in the HVR were not consistent with the random accumulation of mutations and imply that amino acid replacement in the HVR was strongly constrained. Another variable region of E2 centered on codon 60 shows similar constraints, while HVR2 was relatively unconstrained. Several of these features are difficult to explain if a neutralizing immune response against the HVR is the only selective force operating on E2. The impact of PCR artifacts such as nucleotide misincorporation and the shuffling of dissimilar templates is discussed.

Amino Acid Sequence↗

PubMed1996

HIV viral dynamics.

BACKGROUND: Elucidation of the underlying rapid turnover of virus and HIV infected cells in vivo was perhaps the most informative and exciting discovery in HIV and AIDS research in the last few years. This observation, based on the rapid drop in virus load following antiviral drug therapy promises to change significantly the way we view important aspects of interaction of the virus and its host. As a result, the paradigm for HIV infection has shifted from considering the long period of clinical latency as one of viral inactivity, to viewing it as an active steady state of constant virus replication and cell death. This period should also be viewed as an integral part of the disease process, not simply a prolog to frank AIDS. METHODS: Here, I discuss the theoretical basis of the steady state model of HIV infection as well as its important consequences for understanding and controlling HIV pathogenesis. These include the significance of genetic variation and the establishment and evolution of the virus quasispecies, the evolution of resistance of the virus to antiviral therapy, and the theoretical and practical significance of virus load measurements. Emphasis is on discussion of recent developments as well as areas where our understanding still has significant gaps.

Antiviral Agents↗

PubMed1991

Arthropod vectors in the evolution of bunyaviruses.

Viruses from each genus of Bunyaviridae have preferential relationships to the arthropods of only one or two families, i.e. Bunyavirus to mosquitoes (Culicidae), Phlebovirus to sand flies (Psychodidae) and mosquitoes, Uukuvirus and Nairovirus to ticks (Ixodidae and Argasidae). An exception is genus Hantavirus not proven to be transmitted by vectors. Within the Bunyavirus genus 16 serogroups have been recognized on the basis of their antigenic relationship. Based on isolations from the nature each serogroup is preferentially linked with arthropod species (mostly mosquitoes) of one, or two genera. For 8 out of 16 serogroups Culex mosquitoes are the main insect vectors. Two serogroups are linked with Aedes mosquitoes, three with Anopheles mosquitoes. Aedeomyia mosquitoes, Culicoides bitting miges and Hyalomma ticks are vectors of one serogroup each. Evolutionary trends within the genus Bunyavirus and within the family Bunyaviridae can be recognized based on relationships of bunyaviruses to their arthropod vectors.

Animals↗

PubMed2003

Searching for the advantages of virus sex.

Sex (genetic exchange) is a nearly universal phenomenon in biological populations. But this is surprising given the costs associated with sex. For example, sex tends to break apart co-adapted genes, and sex causes a female to inefficiently contribute only half the genes to her offspring. Why then did sex evolve? One famous model poses that sex evolved to combat Muller's ratchet, the mutational load that accrues when harmful mutations drift to high frequencies in populations of small size. In contrast, the Fisher-Muller Hypothesis predicts that sex evolved to promote genetic variation that speeds adaptation in novel environments. Sexual mechanisms occur in viruses, which feature high rates of deleterious mutation and frequent exposure to novel or changing environments. Thus, confirmation of one or both hypotheses would shed light on the selective advantages of virus sex. Experimental evolution has been used to test these classic models in the RNA bacteriophage phi6, a virus that experiences sex via reassortment of its chromosomal segments. Empirical data suggest that sex might have originated in phi6 to assist in purging deleterious mutations from the genome. However, results do not support the idea that sex evolved because it provides beneficial variation in novel environments. Rather, experiments show that too much sex can be bad for phi6; promiscuity allows selfish viruses to evolve and spread their inferior genes to subsequent generations. Here I discuss various explanations for the evolution of segmentation in RNA viruses, and the added cost of sex when large numbers of viruses co-infect the same cell.

Biological Evolution↗

PubMed2005

Plasmacytoid dendritic cells in acute and chronic hepatitis C virus infection.

Chronic evolution of acute hepatitis C (aHC) occurs in more than 80% of patients but can frequently be prevented by early treatment with interferon (IFN)-alpha. Plasmacytoid dendritic cells (pDCs) are the major endogenous IFN-alpha producers, but their role in aHC is unknown. In this study, frequency, phenotype, and pDC function were analyzed in 13 patients with aHC and 32 patients with chronic hepatitis C (cHC) compared with 20 healthy controls, 33 sustained responders to antiviral treatment, 14 patients with acute hepatitis B (aHB), and 21 patients with nonviral inflammatory disease. In aHC, pDCs in the peripheral blood were significantly reduced compared with healthy controls (median, 0.1% vs. 0.36%, P < .0005) and were inversely correlated to alanine aminotransferase levels (r = -0.823; P < .005). Circulating pDCs in aHC were immature, as determined via reduced expression of HLA-DR and CCR7, and produced little amounts of IFN-alpha (median, 3.5 pg/50,000 peripheral blood mononuclear cells [PBMCs] vs. 498.4 pg/50,000 PBMCs in healthy controls; P < .0005). Less pronounced changes were present in cHC (median, 0.17%, 28.0 pg/50,000 PBMCs IFN-alpha, respectively). However, a significantly reduced frequency and IFN-alpha production was also found in self-limited aHB (median 0.1%, 8.6 pg/50,000 PBMCs) and in patients with nonviral inflammatory disease (median 0.19%, 7.5 pg/50,000 PBMCs). In conclusion, in aHC frequency and IFN-alpha-producing capacity of peripheral blood pDCs are dramatically reduced and inversely correlated with the degree of liver inflammation. In cHC there is incomplete recovery of pDC function, which, however, could be solely due to the chronic inflammatory state.

Acute Disease↗

PubMed2000

Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages.

We report the complete genome DNA sequences of HK97 (39,732 bp) and HK022 (40,751 bp), double-stranded DNA bacteriophages of Escherichia coli and members of the lambdoid or lambda-like group of phages. We provide a comparative analysis of these sequences with each other and with two previously determined lambdoid family genome sequences, those of E. coli phage lambda and Salmonella typhimurium phage P22. The comparisons confirm that these phages are genetic mosaics, with mosaic segments separated by sharp transitions in the sequence. The mosaicism provides clear evidence that horizontal exchange of genetic material is a major component of evolution for these viruses. The data suggest a model for evolution in which diversity is generated by a combination of illegitimate and homologous recombination and mutational drift, and selection for function produces a population in which most of the surviving mosaic boundaries are located at gene boundaries or, in some cases, at protein domain boundaries within genes. Comparisons of these genomes highlight a number of differences that allow plausible inferences of specific evolutionary scenarios for some parts of the genome. The comparative analysis also allows some inferences about function of genes or other genetic elements. We give examples for the generalized recombination genes of HK97, HK022 and P22, and for a putative headtail adaptor protein of HK97 and HK022. We also use the comparative approach to identify a new class of genetic elements, the morons, which consist of a protein-coding region flanked by a putative delta 70 promoter and a putative factor-independent transcription terminator, all located between two genes that may be adjacent in a different phage. We argue that morons are autonomous genetic modules that are expressed from the repressed prophage. Sequence composition of the morons implies that they have entered the phages' genomes by horizontal transfer in relatively recent evolutionary time.

Amino Acid Sequence↗

PubMedDate not supplied

Evolution: the long evolutionary reach of viruses.

The structure of a phage capsid protein provides good evidence this phage shares ancestry with an animal virus. In this and similar cases, either the viral lineages predate the emergence of the three contemporary domains of life, or viruses have been leaping the phylogenetic chasms that separate the domains.

Animals↗

PubMed1998

Common themes of antibody maturation to simian immunodeficiency virus, simian-human immunodeficiency virus, and human immunodeficiency virus type 1 infections.

Characterization of virus-specific immune responses to human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency virus (SIV) is important to understanding the early virus-host interactions that may determine the course of virus infection and disease. Using a comprehensive panel of serological assays, we have previously demonstrated a complex and lengthy maturation of virus-specific antibody responses elicited by attenuated strains of SIV that was closely associated with the development of protective immunity. In the present study, we expand these analyses to address several questions regarding the nature of the virus-specific antibody responses to pathogenic SIV, SIV/HIV-1 (SHIV), and HIV-1 infections. The results demonstrate for the first time a common theme of antibody maturation to SIV, SHIV, and HIV-1 infections that is characterized by ongoing changes in antibody titer, conformational dependence, and antibody avidity during the first 6 to 10 months following virus infection. We demonstrate that this gradual evolution of virus-specific antibody responses is independent of the levels of virus replication and the pathogenicity of the infection viral strain. While the serological assays used in these studies were useful in discriminating between protective and nonprotective antibody responses during evaluation of vaccine efficacy with attenuated SIV, these same assays do not distinguish the clinical outcome of infection in pathogenic SIV, SHIV, or HIV-1 infections. These results likely reflect differences in the immune mechanisms involved in mediating protection from virus challenge compared to those that control an established viral infection, and they suggest that additional characteristics of both humoral and cellular responses evolve during this early immune maturation.

Animals↗

PubMed1988

[Killer systems of Saccharomyces cerevisiae yeasts].

The killer systems of Saccharomyces cerevisiae are a peculiar group of cytoplasmic symbionts of primitive eukaryotes. The genetic material of these symbionts is double-stranded RNA. Their basic properties are linearity of genome, its fragmentation, resulting in two separately replicating major and minor segments, and the ability to control the synthesis of secretory proteins--mycocins which can kill the taxonomically related strains. Secretion of mycocins also confers immunity to their action. The strains containing killer symbionts are toxigenic and resistant to their own toxins, while those with no killer double-stranded RNA are sensitive to mycocins. The killer systems of Saccharomyces cerevisiae possess some properties relevant to viruses and evidently are evolved during the evolution of infectious viruses. Occurrence of such systems in monocellular eucaryotic organisms is an example of genome complication in the course of putting together the virus-like components. The peculiarities of replication and expression of killer systems and their utilization for the construction of vector molecules are discussed.

Cytoplasm↗

PubMed2004

Evolutional analysis of human influenza A virus N2 neuraminidase genes based on the transition of the low-pH stability of sialidase activity.

The 1957 and 1968 human pandemic influenza A virus strains as well as duck viruses possess sialidase activity under low-pH conditions, but human H3N2 strains isolated after 1968 do not possess such activity. We investigated the transition of avian (duck)-like low-pH stability of sialidase activities with the evolution of N2 neuraminidase (NA) genes in human influenza A virus strains. We found that the NA genes of H3N2 viruses isolated from 1971 to 1982 had evolved from the side branches of NA genes of H2N2 epidemic strains isolated in 1968 that were characterized by the low-pH-unstable sialidase activities, though the NA genes of the 1968 pandemic strains preserved the low-pH-stable sialidase. These findings suggest that the prototype of the H3N2 epidemic influenza strains isolated after 1968 probably acquired the NA gene from the H2N2 low-pH-unstable sialidase strain by second genetic reassortment in humans.

Amino Acid Sequence↗

PubMed2004

Structure and function of the C-terminal domain of the polymerase cofactor of rabies virus.

The phosphoprotein (P) of rabies virus binds the viral polymerase to the nucleoprotein (N)-RNA template for transcription and replication. By limited protease digestion we defined a monomeric C-terminal domain of P that can bind to N-RNA. The atomic structure of this domain was determined and previously described mutations that interfere with binding of P to N-RNA could now be interpreted. There appears to be two features involved in this activity situated at opposite surfaces of the molecule: a positively charged patch and a hydrophobic pocket with an exposed tryptophan side-chain. Other previously published work suggests a conformational change in P when it binds to N-RNA, which may imply the repositioning of two helices that would expose a hydrophobic groove for interaction with N. This domain of rabies virus P is structurally unrelated to the N-RNA binding domains of the phosphoproteins of Sendai and measles virus that are members of the same order of viruses, the non-segmented negative strand RNA viruses. The implications of this finding for the evolution of this virus group are discussed.

Amino Acid Sequence↗

PubMed1985

Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution.

The sequence of the entire RNA genome of the type flavivirus, yellow fever virus, has been obtained. Inspection of this sequence reveals a single long open reading frame of 10,233 nucleotides, which could encode a polypeptide of 3411 amino acids. The structural proteins are found within the amino-terminal 780 residues of this polyprotein; the remainder of the open reading frame consists of nonstructural viral polypeptides. This genome organization implies that mature viral proteins are produced by posttranslational cleavage of a polyprotein precursor and has implications for flavivirus RNA replication and for the evolutionary relation of this virus family to other RNA viruses.

Base Sequence↗