Abstract: The negative-strand RNA viruses are a broad group of animal viruses that comprise several important human pathogens, including influenza, measles, mumps, rabies, respiratory syncytial, Ebola, and hantaviruses. The development of new strategies to genetically manipulate the genomes of negative-strand RNA viruses has provided us with new tools to study the structure-function relationships of the viral components and their contributions to the pathogenicity of these viruses. It is also now possible to envision rational approaches--based on genetic engineering techniques--to design live attenuated vaccines against some of these viral agents. In addition, the use of different negative-strand RNA viruses as vectors to efficiently express foreign polypeptides has also become feasible, and these novel vectors have potential applications in disease prevention as well as in gene therapy.

Abstract: We review and update the work on genetic elements, e.g., viruses and plasmids (excluding IS elements and transposons) in the kingdom Crenarchaeota (Thermoproteales and Sulfolobales ) and the orders Thermococcales and Thermoplasmales in the kingdom Euryachaeota of the archael domain, including unpublished data from our laboratory. The viruses of Crenarchaeota represent four novel virus families. The Fuselloviridae represented by SSV1 of S. shibatae and relatives in other Sulfolobus strains have the form of a failed spindle. The envelope is highly hydrophobic. The DNA is double-stranded and circular. Members of this group have also been found in Methanococcus and Haloarcula . The Lipothrixviridae (e.g., T TV1 to 3) have the form of flexible filaments. They have a core containing linear double-stranded DNA and DNA-binding proteins which is wrapped into a lipid membrane. The ‘Bacilloviridae’ (e.g., TTV4 and SIRV) are stiff rods lacking this membrane, but also featuring linear double-stranded DNA and DNA-binding proteins. Both virus type carry on both ends structures involved in the attachment to receptors. Both types are represented in Thermoproteus and Sulfolobus . The droplet-formed novel Sulfolobus virus SNDV represents the ‘Guttaviridae’ containing circular double-stranded DNA. Though head and tail viruses distantly resembling T phages or lambdoid phages were seen electronmicroscopically in solfataric water samples, no such virus has so far been isolated. SSV1 is temperate, TTV1 causes lysis after induction, the other viruses found so far exist in carrier states. The hosts of all but TTV1 survive virus production. We discuss the implications of the nature of these viruses for understanding virus evolution. The plasmids found so far range in size from 4.5 kb to about 40 kb. Most of them occur in high copy number, probably due to the way of their detection. Most are cryptic, pNOB8 is conjugative, the widespread pDL10 alleviates in an unknown way autotrophic growth of its host Desulfurolobus by sulfur reduction. The plasmid pTIK4 appears to encode a killer function. pNOB8 has been used as a vector for the transfer of the lac S (β-galactosidase) gene into a mutant of S. solfataricus .

Abstract: Poxviruses encode a broad range of proteins that counteract the formidable attack of the immune response initiated in the host after infection, among which are proteins that mimic the extracellular binding domain of host cytokine receptors and are secreted from virus-infected cells. A soluble interferon-gamma receptor (IFN-gamma R) is produced early after infection and efficiently blocks the binding of IFN-gamma to cellular receptors, thus inhibiting both the anti-viral and immune functions of IFN-gamma. An IFN-gamma R is highly conserved among members of the poxvirus family, suggesting a major role in viral pathogenesis. The highly species-specific nature of the IFN system enables questions concerning the evolutionary relationship between poxviruses and their hosts to be addressed. The IFN-gamma R encoded by myxoma virus, a natural pathogen of rabbits, is specific for rabbit IFN-gamma. However, the IFN-gamma R encoded by orthopoxviruses (vaccinia, cowpox, camelpox, ectromelia) shows a novel, broad species specificity suggesting that these viruses have evolved in several species. The implications for the unknown origin and natural host(s) of vaccinia virus are discussed.

Abstract: The gene encoding the p60 capsid protein from a Spanish isolate of the rabbit hemorrhagic disease virus (RHDV) has been cloned and sequenced. Both cDNA and the derived protein sequences have been compared with those from several contemporary European RHDV isolates. Genetic heterogeneity among co-circulating viruses is nearly constant along the p60-encoding gene, around 0.034 substitutions per nucleotide, and it does not allow prediction of the preferential regions for long-term fixation of mutations. However, sequence comparisons with the more distant, but phylogenetically closely related calicivirus, the European brown hare syndrome virus (EBHSV), reveal a great extent of genetic variability within both a segment of p60 gene (nucleotides 900-1300) and the encoded polypeptide, suggesting the existence of strong selective pressures acting over this region of the capsid protein.

Abstract: Virus Genes.- A Short Introduction to the Origin and Molecular Evolution of Viruses.- A: Role of Retrons, Retroelements, and Reverse Transcription in the Evolution of Retroviruses and in Eukaryotic Genome Plasticity.- Structure, Function, and Evolution of Bacterial Reverse Transcriptase.- Bacterial Reverse Transcriptase and msDNA.- Retroelements: Propagation and Adaptation.- Origin and Evolution of Viroids and Viroid-like Satellite RNAs.- Evolution and Biological Significance of Human Retroelements.- Endogenous env Elements: Partners in Generation of Pathogenic Feline Leukemia Viruses.- Reverse Transcriptase: Mediator of Genomic Plasticity.- B: Molecular Processes Involved in the Evolution of RNA and DNA Viruses.- Analysis of the Phylogenetic Placement of Different Spumaretroviral Genes Reveals Complex Pattern of Foamy Virus Evolution.- Retrovirus and Filovirus "Immunosuppressive Motif" and the Evolution of Virus Pathogenecity in HIV-1, HIV-2, and Ebola Viruses.- Molecular Evolution of Aphthoviruses.- Molecular Evolution of Influenza Viruses.- Analysis of Matrix Protein Gene Nucleotide Sequence Diversity Among Newcastle Disease Virus Isolates Demonstrates that Recent Disease Outbreaks Are Caused by Viruses of Psittacine Origin.- Molecular Epidemiology and Evolution of Mosquito-Borne Flaviviruses and Alphaviruses Enzootic in Australia.- Evolution of Small DNA Viruses of Eukaryotes: Past and Present Considerations.- Retrotransposition and Herpesvirus Evolution.- Evolution of Viral DNA-Dependent RNA Polymerases.- Evolution of T4-Related Phages.- Molecular Evolution of Viruses: An Interim Summary.

Abstract: The evolution of HIV-1 viral populations was studied in a set of MT-2-co-cultured viruses isolated from five patients at the beginning of treatment with zidovudine and after 11-36 months of drug therapy. We first characterized the HIV-1 pol gene to detect the zidovudine-resistance mutations at codons 215 and 219. To analyse the effect that the selective pressure of zidovudine on pol exerted on other genomic regions, we also studied the env gene. The env gene sequence of virus isolated from one individual was unchanged, whereas three other sample pairs had minor alterations in env. In one individual, we detected a significant change in the env gene sequence, and so performed a clonal analysis on viruses isolated before and after treatment. In this individual, the zidovudine-resistant variant that became predominant in the resistant virus population was an undetected minority variant of the viral population before treatment was initiated. These results indicate that the evolution of quasispecies produced by selective pressure on the pol gene from zidovudine treatment could select, in a random process, important changes in other genomic regions; in particular, we describe alterations in the env gene.

Abstract: INTRODUCTION A SUMMARY OF VIRUS CLASSIFICATION THE REPLICATION CYCLE COMPARATIVE DIAGRAMS DNA VIRUSES ssDNA Viruses dsDNA Viruses with Cubic or Helical Symmetry dsDNA Viruses with Binary Symmetry VIRUSES USING REVERSE TRANSCRIPTION Retrovirdae Others RNA VIRUSES ssRNA Viruses with (+) Strands ssRNA Viruses with (-) Strands dsRNA Viruses MISCELLANY Virus-Like Particles Agents with Circular ssRNA Prions ABBREVIATIONS AND UNITS GLOSSARY REFERENCES INDEX

Abstract: In recent years computer viruses have grown to be of great concern. They have also been proposed as prototypical artificial life, but the possibility of their evolution has been dismissed due to modern computer programs being computationally brittle (i.e. a random change to a functional program will almost certainly render it non-functional) and the series of steps required for the evolution of a new virus being improbable. These allegations are examined by studying homology between functional program sequences. It is concluded that programs are far less brittle than expected. While the evolution of viruses de novo is still unlikely, evolution of pre-existing viruses and programs is feasible. This has significant implications for computer security and evolutionary computation.

Abstract: based on \"ecological functionalism\" or \"selectionist\" approaches, and, while crediting each with explanatory value, they fault them for failing to recognize the capacity of aggressive, charismatic leaders to shape the course of history. Along with cultural and natural forces, the actions of such individuals are seen as producing rapid change followed by periods of relative stability in, as anthropologists refer to them, generalized \"stages\" or \"levels\" of egalitarian band, ranked chiefdom, and stratified state integration. Because individual action during the periods of rapid transition is singular, the authors acknowledge that action theory has limited value for a comparative study of evolutionary process. The value of action theory, as Marcus and Flannery put it, is that it \"responds to complaints that most evolutionary theory makes humans little more than cogs in a machine.\" In the end this book leaves us with the perplexing problem of accounting for the fact that, despite the unique actions of its leaders, every civilization of antiquity, from Mexico to Mesopotamia, appears to have advanced through a similar sequence of stages and to have evolved quite comparable political and economic institutions. What, we ask, were the cultural and environmental limits to self-serving individual action in effecting this evolutionary change? This is a question addressed at length by Leslie White almost a half a century ago. Unfashionable as they may be in certain intellectual circles at the moment, such questions are of much broader interest to the general public than that of Zapotec prehistory, for they touch on issues of universal social and cultural behavior. We can, however, begin to answer them fruitfully and move toward a comparative study of evolutionary process only when we have at hand studies of other civilizations as thorough and thoughtful as that which Marcus and Flannery have presented us for the ancient Zapotec. Robert N. Zeitlin Department of Anthropology, Brandeis University, Waltham, MA 02254, USA

Abstract: Within the field of medical virology, pathogenesis (seeCh 45) concerns the processes by which viruses infect individuals and cause disease, whereas epidemiology examines the transfer and persistence of viruses in human populations Epidemiology and evolution are linked because epidemiologic mechanisms of transfer largely determine the natural selection component of viral evolution Since viruses multiply only within cells, the epidemiology of viral diseases does not involve multiplication in food, water, or soil However, some viruses that infect man may multiply and persist in other animals, such as arthropods, rodents and bats

Abstract: Cytotoxic T lymphocytes (CTLs) which recognize viral antigens in association with human leukocyte antigens (HLAs) play an important role in controlling persistent virus infections. These viruses use several mechanisms to evade the immune response, including mutations that affect either T-cell receptor recognition or binding of viral epitopes to the HLA. It has recently been proposed that the distribution of HLA frequencies and the specific CTL response may influence the long-term evolution of Epstein-Barr virus (EBV) by selecting variants which lack immunodominant CTL epitopes. To test this hypothesis, we have studied EBV isolates from two genetically distinct Papua New Guinea (PNG) populations, residing in coastal and highland regions, for polymorphism within seven viral CTL epitope sequences restricted through several class I HLAs. Surprisingly, all EBV isolates analyzed displayed identical amino acid substitutions within HLA A11-, B35- and B8-restricted CTL epitope sequences which completely abrogated CTL recognition and binding of synthetic peptides to HLA molecules. Furthermore, these substitutions revealed no correlation with the contemporary distribution of HLAs in the different PNG populations, which argues for a minimal influence of immune pressure. The sequence homology between EBV isolates from coastal and highland PNG suggests that the virus may have had a single origin and, more importantly, that these isolates are genetically distinct from those present in a Caucasian population.