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At least 415 records · Page 23Linked to original sources
PubMed2003

Microarray analysis of evolution of RNA viruses: evidence of circulation of virulent highly divergent vaccine-derived polioviruses.

Two approaches based on hybridization of viral probes with oligonucleotide microarrays were developed for rapid analysis of genetic variations during microevolution of RNA viruses. Microarray analysis of viral recombination and microarray for resequencing and heterogeneity analysis were able to generate instant genetic maps of vaccine-derived polioviruses (VDPVs) and reveal the degree of their evolutionary divergence. Unlike conventional methods based on cDNA sequencing and restriction fragment length polymorphism, the microarray approaches are better suited for analysis of heterogeneous populations and mixtures of different strains. The microarray hybridization profile is very sensitive to the cumulative presence of small quantities of different mutations, including those that cannot be revealed by sequencing, making this approach useful for characterization of profiles of nucleotide sequence diversity in viral populations. By using these methods, we identified a type-3 VDPV isolated from a healthy person and missed by conventional methods of screening. The mutational profile of the polio strain was consistent with >1 yr of circulation in human population and was highly virulent in transgenic mice, confirming the ability of VDPV to persist in communities despite high levels of immunity. The proposed methods for fine genotyping of heterogeneous viral populations can also have utility for a variety of other applications in studies of genetic changes in viruses, bacteria, and genes of higher organisms.

Animals↗
PubMed2025

Making sense of the virome in light of evolution and ecology.

Understanding the patterns and drivers of viral prevalence and abundance is of key importance for understanding pathogen emergence. Over the last decade, metagenomic sequencing has exponentially expanded our knowledge of the diversity and evolution of viruses associated with all domains of life. However, as most of these 'virome' studies are primarily descriptive, our understanding of the predictors of virus prevalence, abundance and diversity, and their variation in space and time, remains limited. For example, we do not yet understand the relative importance of ecological predictors (e.g. seasonality and habitat) versus evolutionary predictors (e.g. host and virus phylogenies) in driving virus prevalence and diversity. Few studies are set up to reveal the factors that predict the virome composition of individual hosts, populations or species. In addition, most studies of virus ecology represent a snapshot of single species viromes at a single point in time and space. Fortunately, recent studies have begun to use metagenomic data to directly test hypotheses about the evolutionary and ecological factors which drive virus prevalence, sharing and diversity. By synthesizing evidence across studies, we present some over-arching ecological and evolutionary patterns in virome composition, and illustrate the need for additional work to quantify the drivers of virus prevalence and diversity.

Virome↗
PubMed2002

A natural intergenotypic recombinant of hepatitis C virus identified in St. Petersburg.

Hepatitis C virus (HCV) evolution is thought to proceed by mutations within the six genotypes. Here, we report on a viable spontaneous HCV recombinant and we show that recombination may play a role in the evolution of this virus. Previously, 149 HCV strains from St. Petersburg had been subtyped by limited sequencing within the NS5B region. In the present study, the core regions of 41 of these strains were sequenced to investigate the concordance of HCV genotyping for these two genomic regions. Two phylogenetically related HCV strains were found to belong to different subtypes, 2k and 1b, according to sequence analysis of the 5' untranslated region (5'UTR)-core and the NS5B regions, respectively. By sequencing of the E2-p7-NS2 region, the crossover point was mapped within the NS2 region, probably between positions 3175 and 3176 (according to the numbering system for strain pj6CF). Sequencing of the 5'UTR-core regions of four other HCV strains, phylogenetically related to the above-mentioned two strains (based on analysis within the NS5B region), revealed that these four strains were also recombinants. Since a nonrecombinant 2k strain was found in St. Petersburg, the recombination may have taken place there around a decade ago. Since the frequency of this recombinant is now high enough to allow the detection of the recombinant in a fraction of the city's population, it seems to be actively spreading there. The reported recombinant is tentatively designated RF1-2k/1b, in agreement with the nomenclature used for HIV recombinants. Recombination between HCV genotypes must now be considered in the classification, laboratory diagnosis, and treatment of HCV infection.

5' Untranslated Regions↗
PubMed1983

The evolution of bluetongue virus serotype 17.

Four serotypes of bluetongue virus (BTV-10, 11, 13 and 17) have been identified in the United States. Analyses of the genome RNA segments and viral induced polypeptides of U.S. prototype BTV-17 virus by comparison with the corresponding macromolecules of earlier isolates of BTV-11 serotype support the hypothesis that BTV-17 originated by genotypic and antigenic drift from a BTV-11 serotype virus.

Bluetongue virus↗
PubMedDate not supplied

[Supplementary data on the theory concerning the cyclic evolution of influenza viruses].

The distribution per age groups of antibodies to influenza viruses A/Hong Kong/1/68, A/England/837/69 and A/England/42/72 in the sera collected in 1970 demonstrates that antigenically similar strains also dominated the epidemiologic picture of influenza in the past century. The results suggest that the pandemic of 1893 and infection in persons born before 1885 were caused by a strain similar to A/Hong Kong/1/68 and in those born in 1895-1897 by the antigenic variant A/England/42/72. The anamnestic response to the A/England/69 variant, following upon vaccination with the Hong Kong strain shows that the primary infection in persons born before 1900 was caused by a strain antigenically similar to the first variant. The data obtained lend support to the hypothesis of antigenic recycling of influenza virus and of the finite character of the antigenic variation of influenza viruses.

Age Factors↗
PubMedDate not supplied

[The importance of the Epstein-Barr virus and other viruses in the evolution of human host homeostatic systems].

There is a great number (150) DNA sequence homology with genes and mRNA of man. They are involved in expression of biological active matters, which are participate in homeostasis of host. This is an evidence of a long-time co-evolution EBV and host-man populations. It play a great role in a vertical and horizontal dissemination some important for homeostasis genes of man.

Biological Evolution↗
PubMed2004

A 30 kb region of the Epstein-Barr virus genome is colinear with the rearranged human immunoglobulin gene loci: implications for a "ping-pong evolution" model for persisting viruses and their hosts. A review.

The left part of the Epstein-Barr virus (EBV) genome exhibits a strong colinearity of structural and functional elements with the immunoglobulin (Ig) gene loci which is only partially reflected in nucleotide sequence homologies. We propose that this colinearity may be the result of an inter-dependent co-evolution of the immunoglobulin loci together with EBV. Our observation could help elucidating the mechanisms of somatic hypermutation, explaining the ability of EBV to accidentally cause tumors, and shedding more light on the general mechanisms of viral and organismal evolution. We suggest that persisting viruses served as a complement for the organismal germline like in a ping-pong game and outline The Ping-Pong Evolution Hypothesis.

Chromosome Mapping↗
PubMed1995

Geographic distribution and evolution of Ross River virus in Australia and the Pacific Islands.

We examined the molecular epidemiology and evolution of Ross River (RR) virus in Australia and the Pacific Islands. Nucleotide sequences of the E2 and E3 genes of five RR virus strains revealed remarkable conservation between 1959 and 1989 with a maximum divergence of only 3.3%. Sequence data from a 505-base pair fragment of the E2 gene from 51 additional strains showed that RR virus has diverged genetically into three separate groups although at least 95% sequence homology was still maintained between all 56 strains. Each genetic type predominates in a particular geographic region of Australia and can be broadly defined as occurring in the western, northeastern, and southeastern regions of Australia. However, some RR virus strains did not follow this pattern of geographic distribution indicating movement of virus by the travel of viremic humans or livestock across the continent. The Pacific Islands isolates all belong to the southeastern genotype. These findings suggest genetic divergence and independent evolution of RR virus within geographically isolated enzootic foci; however, selective pressures maintain high nucleotide conservation in nature.

Australia↗
PubMed1987

The genome of herpes simplex virus: structure, replication and evolution.

The objectives of this paper are to discuss the structure and genetic content of the genome of herpes simplex virus type 1 (HSV-1), the nature of virus DNA replicative processes, and aspects of the evolution of the virus DNA, in particular those bearing on DNA replication. We are in the late stages of determining the complete sequence of the DNA of HSV-1, which contains about 155,000 base pairs, and thus the treatment is primarily from a viewpoint of DNA sequence and organization. The genome possesses around 75 genes, generally densely arranged and without long range ordering. Introns are present in only a few genes. Protein coding sequences have been predicted, and the functions of the proteins are being pursued by various means, including use of existing genetic and biochemical data, computer based analyses, expression of isolated genes and use of oligopeptide antisera. Many proteins are known to be virion structural components, or to have regulatory roles, or to function in synthesis of virus DNA. Many, however, still lack an assigned function. Two classes of genetic entities necessary for virus DNA replication have been characterized: cis-acting sequences, which include origins of replication and packaging signals, and genes encoding proteins involved in replication. Aside from enzymes of nucleotide metabolism, the latter include DNA polymerase, DNA binding proteins, and five species detected by genetic assays, but of presently unknown functions. Complete genome sequences are now known for the related alphaherpesvirus varicella-zoster virus and for the very distinct gammaherpesvirus Epstein-Barr virus. Comparisons between the three sequences show various homologies, and also several types of divergence and rearrangement, and so allow models to be proposed for possible events in the evolution of present day herpesvirus genomes. Another aspect of genome evolution is seen in the wide range of overall base compositions found in present day herpesvirus DNAs. Finally, certain herpesvirus genes are homologous to non-herpesvirus genes, giving a glimpse of more remote relationships.

Base Sequence↗