Abstract: Evolution of receptor specificity by viruses has several implications for viral pathogenesis, host range, virus-mediated gene targeting, and viral adaptation after organ transplantation and xenotransplantation, as well as for the emergence of viral diseases. Recent evidence suggests that minimal changes in viral genomes may trigger a shift in receptor usage for virus entry, even into the same cell type. A capacity to exploit alternative entry pathways may reflect the ancient evolutionary origins of viruses and a possible role as agents of horizontal gene transfers among cells.

Abstract: Epidemic outbreaks of dengue fever (DF) were first recorded in Venezuela in 1978 and were followed by the emergence of dengue haemorrhagic fever (DHF) outbreaks in 1989. To gain a better understanding of the nature of these epidemics, the complete envelope (E) gene sequence of 34 Venezuelan dengue type 2 (DEN-2) viruses, isolated between 1997 and 2000 was determined. Of these isolates, 16 were from patients with DF and 17 were from patients diagnosed with DHF. There were no diagnostic sequence differences between them, suggesting that the E gene alone does not determine disease severity. These sequence data were also used in phylogenetic comparisons with a global sample of DEN-2 viruses, including strains collected previously from Venezuela. This analysis revealed that the ancestors of the Venezuelan viruses were Asian in origin, implying that a DEN-2 virus strain from this region was introduced into Venezuela and the wider Caribbean region during the late 1970s or the early 1980s. The phylogenetic trees further indicate that evolution of DEN-2 virus in Venezuela has occurred in situ, with differentiation into a number of distinct but co-circulating lineages, rather than the repeated introduction of new strains from other localities. By incorporating additional sequence data from the virus capsid, premembrane and membrane genes, evidence is provided that a single Venezuelan strain sequenced previously, designated Mara4, is a recombinant virus, incorporating genome sequence from Venezuelan and Asian parental viruses.

Abstract: The mutant spectrum of a virus quasispecies in the process of fitness gain of a debilitated foot-and-mouth disease virus (FMDV) clone has been analysed. The mutant spectrum was characterized by nucleotide sequencing of three virus genomic regions (internal ribosome entry site; region between the two AUG initiation codons; VP1-coding region) from 70 biological clones (virus from individual plaques formed on BHK-21 cell monolayers) and 70 molecular clones (RT–PCR products cloned in E. coli). The biological and molecular clones provided statistically indistinguishable definitions of the mutant spectrum with regard to the distribution of mutations among the three genomic regions analysed and with regard to the types of mutations, mutational hot-spots and mutation frequencies. Therefore, the molecular cloning procedure employed provides a simple protocol for the characterization of mutant spectra of viruses that do not grow in cell culture. The number of mutations found repeated among the clones analysed was higher than expected from the mean mutation frequencies. Some components of the mutant spectrum reflected genomes that were dominant in the prior evolutionary history of the virus (previous passages), confirming the presence of memory genomes in virus quasispecies. Other components of the mutant spectrum were genomes that became dominant at a later stage of evolution, suggesting a predictive value of mutant spectrum analysis with regard to the outcome of virus evolution. The results underline the observation that greater insight into evolutionary processes of viruses may be gained from detailed clonal analyses of the mutant swarms at the sequence level.

Abstract: Human immunodeficiency virus type 1 (HIV-1) variants resistant to protease (PR) and reverse transcriptase (RT) inhibitors may display impaired infectivity and replication capacity. The individual contributions of mutated HIV-1 PR and RT to infectivity, replication, RT activity, and protein maturation (herein referred to as "fitness") in recombinant viruses were investigated by separately cloning PR, RT, and PR-RT cassettes from drug-resistant mutant viral isolates into the wild-type NL4-3 background. Both mutant PR and RT contributed to measurable deficits in fitness of viral constructs. In peripheral blood mononuclear cells, replication rates (means +/- standard deviations) of RT recombinants were 72.5% +/- 27.3% and replication rates of PR recombinants were 60.5% +/- 33.6% of the rates of NL4-3. PR mutant deficits were enhanced in CEM T cells, with relative replication rates of PR recombinants decreasing to 15.8% +/- 23.5% of NL4-3 replication rates. Cloning of the cognate RT improved fitness of some PR mutant clones. For a multidrug-resistant virus transmitted through sexual contact, RT constructs displayed a marked infectivity and replication deficit and diminished packaging of Pol proteins (RT content in virions diminished by 56.3% +/- 10.7%, and integrase content diminished by 23.3% +/- 18.4%), a novel mechanism for a decreased-fitness phenotype. Despite the identified impairment of recombinant clones, fitness of two of the three drug-resistant isolates was comparable to that of wild-type, susceptible viruses, suggestive of extensive compensation by genomic regions away from PR and RT. Only limited reversion of mutated positions to wild-type amino acids was observed for the native isolates over 100 viral replication cycles in the absence of drug selective pressure. These data underscore the complex relationship between PR and RT adaptive changes and viral evolution in antiretroviral drug-resistant HIV-1.

Abstract: The quasispecies model of RNA virus evolution differs from those formulated in conventional population genetics in that neutral mutations do not lead to genetic drift of the population, and natural selection acts on the mutant distribution as a whole rather than on individual variants. By computer simulation, we show that this model could be inappropriate for many RNA viruses because the neutral sequence space may be too large to allow the formation of a quasispecies distribution. This view is supported by our analysis of gene sequences from vesicular stomatitis virus, which is considered a prototype RNA virus quasispecies. Our results are relevant to the evolution of RNA systems in general.

Abstract: Contents * Preface * Chapter 1. The Principles and Current Practice of Plant Virus Taxonomy * Introduction * The Underlying Principles * The Role of ICTV * The Current System of Plant Virus Classification * Future Prospects * Chapter 2. How to Write The Names of Virus Species * Chapter 3. Genes Involved in Insect-Mediated Transmission of Plant Viruses * Introduction * Insect Vectors of Plant Viruses * Classification of Transmission Modes * Nonpersistent and Semipersistent Transmission * Circulative Nonpropagative Transmission * Circulative Propagative Transmission * Concluding Remarks * Chapter 4. Characteristic Features of Virus Transmission by Nematodes * Introduction * Vector Nematodes * Viruses Transmitted by Nematodes * Mechanism of Virus Transmission * Control of Nematode-Transmitted Viruses * Chapter 5. Virus Transmission by Fungal Vectors * Introduction * Fungal Vectors * Fungus-Transmitted Viruses * Modes of Transmission * Mechanism of Virus-Vector Association * Epidemiology and Control of fungus-Borne Viruses * Conclusions * Chapter 6. Seed Transmission of Viruses: Biological and Molecular Insights * Introduction * Biological Characteristics * Genetic Determinants * Conclusions * Chapter 7. Molecular Biology of Plant Virus Movement * Introduction * Movement of Plant Viruses * Current Status * Chapter 8. Mechanism of RNA Synthesis by a Viral RNA-Dependent RNA Polymerase * Introduction * Initiation of RNA Synthesis * Abortive Synthesis * Transition from Initiation to Elongation * Termination of RNA Synthesis * Comparison of RNA-Dependent and DNA-Dependent RNA Synthesis * Final Comments * Chapter 9. Gene Expression Strategies of RNA Viruses * Introduction * Subgenomic RNAs and Genome Segmentation * Initiation of Translation * Elongation of Translation * Termination of Translation * Polyprotein Processing and Host Factors * Outlook * Chapter 10. Recombination in Plant RNA Viruses * Introduction * Overview of Research History on The Recombination of Plant RNA Viruses * Recombination in Cucumoviruses * Newly Evolved Recombinant Viruses Between CMV and TAV * Summary and Conclusion * Chapter 11. Variability and Evolution of Potato virus Y (PVY), The Type-Member of the Potyvirus Genus * Introduction * The Family Potyviridae * Relationship Between Potyvirus Species * Biological Diversity of PVY * Genetic Variability of PVY * Mechanisms Leading to RNA Genome Polymorphisms * Conclusions * Chapter 12. Geminvirus Replication and Gene Expression * Introduction * Geminivirus Classification * Genome Structure * Geminivirus Infection Cycle: A Brief Overview * Geminivirus Replication * Control of Viral Gene Expression * Concluding Remarks * Chapter 13. The Molecular Epidemiology of Begomoviruses * Introduction * Begomoviruses: Distribution and Characteristics * Detection, Identification, and Classification of Begomoviruses * Begomoviruses Suscepts and Hosts in Relation to Epidemiology * Whitefly Vector Biology that Influences Epidemiology * Vector Biotypes, Races, and Variants on Virus Spread * New Diseases, Epidemics, and Pandemics * Conclusions * Chapter 14. Translational Strategies in Members of the Family Caulimoviridae * Introduction * Architecture of Viral RNA * General Enhancement of Expression * Shunting, The Concept * Shunting, The Details and Mechanism * Leaky Scanning (Bacilliform Caulimoviruses) * Activated Polycistronic Translation * Transactivation and Shunting * Biological Significance of Ribosome Shunt * Gag-Pol Translation * Making Use of Translational Control * Concluding Remarks * Chapter 15. Recombination in Plant DNA Viruses * Introduction * Recombination in Plant ssDNA Viruses * Recombination in Plant dsDNA Viruses * Conclusions * Chapter 16. Natural Resistance to Viruses * Introduction * Distinguishing a Non-Host from a Host * The Terms Describing Virus-Host Interactions and Resistance * Host Responses Conferring Resistance to Viruses * Identification of the Genes Involved in Resistance * Recognition of the Virus: The Gene-for-Gene Theory * Viral Suppressor of Resistance * Future Uses of the Natural Virus Resistance Genes * Chapter 17. Engineering Virus Resistance in Plants * Introduction * Structure and Genetic Organization of Plant Viral Genomes * Engineered Virus Resistance to Viruses * Advantages of RNA-Mediated Resistance * Concluding Remarks * Chapter 18. Antibody Expression in Plants * Introduction * Antibody-Mediated Viral Resistance in Transgenic Plants * Expression of Recombinant Antibodies Using Plant Virus Gene Vectors * Conclusions * Chapter 19. Nucleic Acid Molecular Hybridization for Plant Virus and Viroid Detection * Introduction * The Principle of the Nucleic Acid Hybridization Method * Types of Labels * Sample Preparation * Pre-Hybridization * Hybridization * Washing Procedures * Detection Procedures * Sensitivity of the Detection * Application to Viruses and Viroids * Conclusions * Chapter 20. Application of PCR in Plant Virology * Introduction * Aspects of PCR Template Preparation * Plant Virus Detection and Differentiation * Real Time, Quantitative PCR * Virus Strain Discrimination * Viral Genome Characterization * Molecular Plant Virology Applications * Conclusions * Chapter 21. Plant Virus Detection in Animal Vectors * Introduction * Detection by Earlier Methods * Detection by a New Method * Detection in Animal Vectors * The Presence of Virus in a Vector and Biological Transmission to Plants * Conclusions * Tables * Index * Reference Notes Included

Abstract: ESSENTIALS OF PATHOGENESIS Historical roots The sequential steps in viral infection Cellular receptors and viral tropism Virus-cell interactions HOST RESPONSE TO VIRAL INFECTION Innate immunity Immune responses to viral infection Virus-induced immunopathology Virus-induced immunosuppression VIRUS-HOST INTERACTIONS Viral virulence Viral persistence Viral oncogenesis: retroviruses Viral oncogenesis: DNA viruses Host susceptibility to viral diseases HIV, SIV, and the pathogenesis of AIDS ECOLOGY AND CONTROL OF VIRAL INFECTIONS Emerging viral diseases Antiviral therapy Viral vaccines

Abstract: Viral quasispecies dynamics and variations of viral fitness are reviewed in connection with viral disease control. Emphasis is put on resistance of human immunodeficiency virus and some human DNA viruses to antiviral inhibitors.

Abstract: One of the most unusual features of RNA viruses is their enormous genetic variability. Among the different processes contributing to the continuous generation of new viral variants RNA recombination is of special importance. This process has been observed for human, animal, plant and bacterial viruses. The collected data reveal a great susceptibility of RNA viruses to recombination. They also indicate that genetic RNA recombination (especially the nonhomologous one) is a major factor responsible for the emergence of new viral strains or species. Although the formation and accumulation of viral recombinants was observed in numerous RNA viruses, the molecular basis of this phenomenon was studied in only a few viral species. Among them, brome mosaic virus (BMV), a model (+)RNA virus offers the best opportunities to investigate various aspects of genetic RNA recombination in vivo. Unlike any other, the BMV-based system enables homologous and nonhomologous recombination studies at both the protein and RNA levels. As a consequence, BMV is the virus for which the structural requirements for genetic RNA recombination have been most precisely established. Nevertheless, the previously proposed model of genetic recombination in BMV still had one weakness: it could not really explain the role of RNA structure in nonhomologous recombination. Recent discoveries concerning the latter problem give us a chance to fill this gap. That is why in this review we present and thoroughly discuss all results concerning nonhomologous recombination in BMV that have been obtained until now.

Abstract: Major receptor group common cold virus HRV89 was adapted to grow in HEp-2 cells, which are permissive for minor group human rhinoviruses (HRVs) but which only marginally support growth of major-group viruses. After 32 blind passages in these cells, each alternating with boosts of the recovered virus in HeLa cells, HRV89 acquired the capacity to effectively replicate in HEp-2 cells, attaining virus titers comparable to those in HeLa cells although no cytopathic effect was observed. Several clones were isolated and shown to replicate in HeLa cells whose ICAM-1 was blocked with monoclonal antibody R6.5 and in COS-7 cells, which are devoid of ICAM-1. Blocking experiments with recombinant very-low-density lipoprotein receptor fragments and enzyme-linked immunosorbent assays indicated that the mutants bound a receptor different from that used by minor-group viruses. Determination of the genomic RNA sequence encoding the capsid protein region revealed no changes in amino acid residues at positions equivalent to those involved in the interaction of HRV14 or HRV16 with ICAM-1. One mutation was within the footprint of a very-low-density lipoprotein receptor fragment bound to minor-group virus HRV2. Since ICAM-1 not only functions as a vehicle for cell entry but has also a “catalytic” function in uncoating, the use of other receptors must have important consequences for the entry pathway and demonstrates the plasticity of these viruses.

Abstract: Several factors play a role during the replication and transmission of RNA viruses. First, as a consequence of their enormous mutation rate, complex mixtures of genomes are generated immediately after infection of a new host. Secondly, differences in growth and competition rates drive the selection of certain genetic variants within an infected host. Thirdly, but not less important, a random sampling occurs at the moment of viral infectious passage from an infected to a healthy host. In addition, the availability of hosts also influences the fate of a given viral genotype. When new hosts are scarce, different viral genotypes might infect the same host, adding an extra complexity to the competition among genetic variants. We have employed a two-fold approach to analyse the role played by each of these factors in the evolution of RNA viruses. First, we have derived a model that takes into account all the preceding factors. This model employs the classic Lotka-Volterra competition equations but it also incorporates the effect of mutation during RNA replication, the effect of the stochastic sampling at the moment of infectious passage among hosts and, the effect of the type of infection (single, coinfection or superinfection). Secondly, the predictions of the model have been tested in an in vitro evolution experiment. Both theoretical and experimental results show that in infection passages with coinfection viral fitness increased more than in single infections. In contrast, infection passages with superinfection did not differ from the single infection. The coinfection frequency also affected the outcome: the larger the proportion of viruses coinfecting a host, the larger increase in fitness observed.

Abstract: Genetic ‘budget’ of viruses and the cost to the infected host: A theory on the relationship between the genetic capacity of viruses, immune evasion, persistence and disease

Abstract: A latent pool of HIV-1 is established early in memory CD4+ T lymphocytes and persists during antiretroviral therapy. Also, viral replication may continue in subjects despite undetectable viremia. H...

Abstract: In order to study the evolution in vivo of human immunodeficiency virus type 1 (HIV-1) in patients with normal clinical evolution, six individuals were selected from a group of 46 patients followed for 1 to 4 years. Patients were selected not by clinical progression characteristics but on the basis of virus genetic variability, as analysed by heteroduplex mobility assay and RNase A mismatch cleavage method. Two patients displayed a homogeneous virus population, two showed very heterogeneous quasispecies and two presented two distinct variants within the virus population. Virus quasispecies were studied by nucleotide sequencing of the C2-fusion domain of the env gene. Virus evolution was approached by analysing the distribution of genetic distances, calculation of divergence and heterogeneity as well as the K a/K s ratio and by the construction of the phylogenetic trees. Three patients displayed the same tree topology, characterized by the presence of independent clades supported by high bootstrap values, whereas this pattern was not present in the other three patients. In the three patients displaying independent clades, a recombination analysis was carried out between distinct subpopulations and recombinant variants were identified. In one patient of this group, different selective pressures were detected in distinct virus clades, measured by their corresponding K a/K s ratios, revealing that different evolutionary forces are occurring at the same time within the same patient. These results show that multiple evolutionary patterns can be found in typical HIV-1-infected patients.

Abstract: We have analysed complete or partial VPI sequences of 31 foot-and-mouth disease (FMD) viruses belonging to serotypes A, O and C to determine the genetic relatedness of field strains of FMD virus (FMDV) that have circulated in Argentina between 1961 and 1994. Phylogenetic analysis, which also included 15 previously published Argentinean sequences and six reference strains, revealed that (i) FMD type A strains showed the highest genetic heterogeneity and could be divided into five lineages with a sequence divergence of 0.9-18.5% between strains (ii) most of the FMD type O viruses grouped in two clusters (within cluster sequence divergence ranging from 0.2% to 6.0%) circulating in Argentina since the early 1960s, and (iii) FMD type C viruses were grouped in two clusters with a 13.4% nucleotide sequence divergence between each cluster. The availability of sequence data for many more field isolates from the region will enable us to understand the genetic relationships between FMDV strains and to rapidly trace the source of an FMD outbreak for epidemiological surveillance.

Abstract: Antibody interactions with rhinovirus lessons for mechanisms of neutralization and the role of immunity in viral evolution.- Structural studies on antibody with viruses.- Shape and electrostatic complementarity at viral antigen-antibody complexes.- Structural studies on viral escape from antibody neutralization.- Affinity, complementarity, cooperativity, and specificity in antibody recognition.- Mechanisms of virus neutralization by antibody.- Neutralization of viruses is achieved by antibody coating of the virion surface.- Anti-mediated enhancement of viral disease.- The role of antibody response in influenza virus infection.- Role of antibodies in controlling alphavirus infection of neurons.- Role of mucosal antibodies in viral infections.- The role of the complement system in virus infection.- Intrabodies as anti-viral agents.- T-bodies as anti-viral agents.- Subject index.

Abstract: A high heterogeneity is found in the HIV-1 genome in vivo, not only between individuals, but also within a single individual. Different types of genetic heterogeneity of HIV-1 can be analyzed: the extension and the evolution of the viral quasispecies in blood, the variation between the virus obtained from different body compartment, the differences between isolates from diverse individuals and between HIV-1 subtypes. The virus population during primary HIV-1 infection is generally homogeneous and the intrahost viral evolution is thought to be forced (in absence of antiviral therapy) by the immune system pressure and is generally related to the length of the immunocompetent period. A group of 12 Italian and Swedish well characterized HIV-1 infected long-term nonprogressors (LNTP) have been analyzed for the viral heterogeneity, calculated in the nef gene and in the long terminal repeat (LTR). The intra-sample variations in LTNP were found comparable with those from 8 progressor patients, while a lower inter-individual diversity was observed in the former. In one LTNP the viral evolution during a four-years period was extremely low suggesting that other factors than the host immune pressure may be involved in modulating the intra- and inter-sample HIV-1 diversity.

Abstract: Viruses exhibit vast diversity in their form and function and are by far the most numerous (estimates 1030–1032) organisms on earth. The largest group among viruses is bacteriophages, the viruses that infect bacteria, with over 5000 identified members. Majority of the phages are composed of protein and nucleic acid with a head–tail morphology. Polyhedral, filamentous or pleomorphic phages comprise only less than 4% of the described bacteriophages, and a minority of these have lipid constituents in addition to nucleic acid and protein. These lipid-containing bacteriophages form a diverse group of viruses and they are classified in four virus families Corticoviridae, Cystoviridae, Plasmaviridae and Tectiviridae. The lipids can be either as the outermost layer of the virion or they can locate internally enclosed within the virus capsid. In both cases, the viral membranes are involved in cell entry processes. Key Concepts: The lipid-containing bacteriophages are a diverse group of bacterial viruses. The lipid-containing bacteriophages are sensitive to organic solvents and detergents. Lipids in the viral membrane have a bilayer structure. The virion proteins are all virus specific, but lipids are derived from host cytoplasmic membrane. During virus morphogenesis, the virus-specific proteins exclude host proteins during formation of the viral membrane. The viral protein-rich membranes have an essential role during entry mediating the translocation of the genome across the host cell envelopes. Keywords: bacterial viruses; lipid-containing bacteriophages; virus evolution; life cycles

Abstract: In this study we develop a new phylogenetic method to describe within-host (patient) viral evolution. Our method accommodates ordinary phylogenetic tree with viral evolution. Viral genomic data often arise from longitudinal sampling and at each observation time we have many types of viral variants. Our method establishes the phylogenetic relation between these viral variants observed at consecutive time points. Our method also can incorporate both neutral evolution and Darwinian selective evolution. In several viral genomic sites, the Darwinian evolutions are seen, so that the phylogenetic method for the viral evolution should deal with both neutral and selective modes of evolution. We apply Yang's codon-based method to specify when and how neutral and adaptive modes of evolution take place in the course of viral evolution. In our previous study, we proposed the preliminary formulation of our longitudinal phylogenetic tree method, based on the maximum likelihood method. But calculation of likelihood takes much time and number of possible tree topologies increase exponentially according to the increase of number of variants. In this study, we propose another new algorithm, distance-based sequential-linking algorithm using neighbor-joining (NJ) method. We applied this new algorithm to a data of the V3 region of the HIV-1 envelope genes sequenced at different years after the infection of a single patient. The results suggest that this algorithm successfully reconstruct a longitudinal phylogenetic tree that describes the within-host viral evolution.

Abstract: Amantadine and rimantadine are anti-influenza A drugs that target the M2 protein, located within the viral envelope. Over the last century, the circulating human Influenza A viruses in the UK have included H1N1, H2N2 and H3N2 antigenic subtypes. The main aim of this study was to analyse the national archive of influenza A viruses for amantadine susceptibility as there is limited data on natural resistance over the entire period of circulation of influenza A viruses. Over 2300 influenza A viruses were screened from a period representing all influenza seasons and antigenic variants over the last 40 years in the UK. Phenotypic and genotypic analyses determined the frequency of amantadine-resistance. Enzyme- linked immunoassay and plaque reduction assay determined resistance to be 2.4% and 2.1% for H3N2 and MINI viruses, respectively. No evidence of amantadine-resistance was found in the limited number of H2N2 viruses screened. Amino acid mutations within the M2 protein transmembrane domain were found in 22/48 of resistant viruses. Serine to asparagine substitutions at amino acid position 31 were most frequent, conferring resistance in 9/22 viruses. A large group of phenotypically resistant viruses did not contain any M2 transmembrane mutations; no other mutations within the matrix genes could be attributed to the resistance. The occurrence of resistance over time was sporadic and often occurred in clusters. Some of the clusters were traced to outbreaks of influenza where amantadine had been used to limit the spread of disease. The emergence of natural resistance within the population was low and did not persist through influenza seasons. Analysis of the M gene sequence indicated that the two matrix gene products. M1 and M2, evolved independently of each other. M2 evolved at a faster rate of nucleotide and amino acid change than M1. Twelve influenza A H3N2 viruses were isolated from a persistent infection of an immunocompromised host. An amantadine-resistant virus population emerged following a short course of amantadine treatment and was maintained for eighteen months in the absence of drug pressure. Virus isolates were mixtures of amantadine-sensitive and -resistant variants, which varied over time. Mutations within the haemagglutinin (HA) molecule suggested that the viral population had undergone antigenic drift over the study period. There was no detectable immune response within the host, therefore the drift, or evolution of these viruses had occurred without the selection pressure of a competent immune system. Fixed mutations within antigenically important regions of the HA molecule were found to affect receptor-binding properties of the viruses. The HA molecule had an increased rate of evolution compared to field virus strains that circulated over the same period as the persistent infection. The emergence and progression of amantadine-resistance and viral evolution within the normal and immunocompromised host will be discussed.