Abstract: In this report we examine the hypothesis that aquatic birds are the primordial source of all influenza viruses in other species. Two partly overlapping reservoirs of influenza A viruses exist in migrating water-fowl and shorebirds throughout the world. These species harbor influenza viruses of all the known hemagglutinin and neuraminidase subtypes. In contrast to the rapid, progressive changes in both the nucleotide and amino acid sequences of mammalian virus gene lineages, avian virus genes show far less variation and, in most cases, appear to be in evolutionary stasis. There are periodic exchanges of influenza virus genes or whole viruses between species, giving rise to pandemics of disease in humans, lower animals, and birds. The periodic exchange of influenza viruses between species has been illustrated by the appearance of new pandemic influenza viruses in humans, including the Spanish influenza of 1918, the Asian influenza of 1957, and the Hong Kong influenza of 1968. Transmission of avian influenza viruses to swine in Europe in 1979 has resulted in the appearance of human-avian reassortant influenza viruses in pigs in Italy and in children in the Netherlands. These studies provide evidence supporting the possibility that pigs serve as a mixing vessel for reassortment between influenza viruses in mammalian and avian hosts and raise the question of whether the avian influenza viruses now circulating in European swine are the precursors of the next human pandemic virus.

Abstract: Phylogenetic analysis was used to study in vivo genetic variation of the V3 region of human immunodeficiency virus type 1 in relation to disease progression in six infants with vertically acquired human immunodeficiency virus type 1 infection. Nucleotide sequences from each infant formed a monophyletic group with similar average branch lengths separating the sets of sequences. In contrast to the star-shaped phylogeny characteristic of interinfant viral evolution, the shape of the phylogeny formed by sequences from the infants who developed AIDS tended to be linear. A computer program, DISTRATE, was written to analyze changes in DNA distance values over time. For the six infants, the rate of divergence from the initial variant was inversely correlated with CD4 cell counts averaged over the first 11 to 15 months of life (r 52 0.87, P 5 0.024). To uncover evolutionary relationships that might be dictated by protein structure and function, tree-building methods were applied to inferred amino acid sequences. Trees constructed from the full-length protein fragment (92 amino acids) showed that viruses from each infant formed a monophyletic group. Unexpectedly, V3 loop protein sequences (35 amino acids) that were found at later time points from the two infants who developed AIDS clustered together. Furthermore, these sequences uniquely shared amino acids that have been shown to confer a T-cell line tropic phenotype. The evolutionary pattern suggests that viruses from these infants with AIDS acquired similar and possibly more virulent phenotypes. Since the discovery of human immunodeficiency virus type 1 (HIV-1), it has been recognized that the virus is characterized by extensive genetic variation and biological heterogeneity (3, 27, 39, 47). Furthermore, it has been suspected that these properties of HIV-1 are related to viral pathogenesis. Numerous studies have shown that HIV-1 strains that are isolated fromindividualswithAIDSdifferinbiologicalpropertiesfrom those isolated from asymptomatic persons (6, 11, 34, 46). In addition, strains recovered from an individual early during the course of infection differ from those isolated from the same individual at a later time, when disease has developed. Among the properties of HIV-1 that have been shown to change over time in infected individuals are efficiency of viral replication in vitro, differential tropism for macrophages and T-cell lines, and ability to induce syncytium formation in T-cell lines (13, 20, 26, 30, 37, 40, 48). The genetic determinants of these biologicalpropertiesofHIV-1havebeenlocalizedprimarilyto the V3 region of theenvgene. Although HIV-1 strains appear to change over time and to acquire properties associated with virulence, how this process occurs is unknown.

Abstract: Aphthoviruses are an important group of animal pathogens. A combination of genetic and structural studies has revealed one of the main principles governing their evolution: severe limitations to variation imposed by functional and structural constraints, in conjunction with high mutation and recombination rates operating during genome replication. Evolution occurs by positive selection and random drift acting on complex quasispecies distributions. The mutant composition of a quasi-species (or mutant spectrum) is largely dictated by tolerance to nucleotide and amino acid substitutions in viral RNAs and proteins, which must remain functionally competent. We review recent evidence to support this proposal, and we suggest that similar concepts may apply to other RNA viruses as well.

Abstract: Historically, viral evolution has often been considered from the perspective of the ability of the virus to maintain viral pathogenic fitness by causing disease. A predator-prey model has been successfully applied to explain genetically variable quasi-species of viruses, such as influenza virus and human immunodeficiency virus (HIV), which evolve much faster rates than the host. In contrast, small DNA viruses (polyomaviruses, papillomaviruses, and parvoviruses) are species specific but are stable genetically, and appear to have co-evolved with their host species. Genetic stability is attributable primarily to the ability to establish and maintain a benign persistent state in vivo and not to the host DNA proofreading mechanisms. The persistent state often involves a cell cycle-regulated episomal state and a tight linkage of DNA amplification mechanisms to cellular differentiation. This linkage requires conserved features among viral regulatory proteins, with characteristic host-interactive domains needed to recruit and utilize host machinery, thus imposing mechanistic constrains on possible evolutionary options. Sequence similarities within these domains are seen amongst all small mammalian DNA viruses and most of the parvo-like viruses, including those that span the entire spectrum of evolution of organisms from E. coli to humans that replicate via a rolling circle-like mechanism among the entire spectrum of organisms throughout evolution from E. coli to humans. To achieve benign inapparent viral persistence, small DNA viruses are proposed to circumvent the host acute phase reaction (characterized by minimal inflammation) by mechanisms that are evolutionarily adapted to the immune system and the related cytokine communication networks. A striking example of this is the relationship of hymenoptera to polydnaviruses, in which the virus is crucial to the recognition of self, development, and maintenance of genetic identity of both the host and virus. These observations in aggregate suggest that viral replicons are not recent “escapies” of host replication, but rather provide relentless pressure in driving the evolution of the host through cospeciation.

Abstract: Recently published evidence for sequence repetition in potyvirus genomes prompted us to analyse the published complete genome sequences and coat protein gene sequences of viruses of this family for evidence of replication slippage. Five of nine complete genomic sequences and 17 of 32 coat protein genes had significant sequence repetitions. Most of these were in coat protein genes, although the 5′ region of the turnip mosaic virus genome also showed evidence of slippage. The results suggest that replication slippage may be involved in the evolution of viruses, as well as prokaryotes and eukaryotes, and that slippage can occur in both RNA and DNA when it is being replicated.

Abstract: Introduction In the introduction to his classical textbook Molecular Evolutionary Genetics Nei (1987) says: ‘in the study of evolution there are two major problems. One is to clarify the evolutionary histories of various organisms, and the other is to understand the mechanisms of evolution’. These two problems have been traditionally addressed by paleontologists (and taxonomists) and by population geneticists, respectively. The introduction of molecular techniques, first protein electrophoresis and sequencing, later restriction analysis and sequencing of nucleic acids, has removed the boundary between these two aspects of evolutionary studies. Molecular techniques have allowed the analysis of a large and representative sample of viral genomes, and make viruses especially suitable for molecular evolutionary studies. In fact, a large amount of information on viral evolution has been collected during the last 20 years. As a perusal of the contents of this book will clearly show, virologists have been concerned mainly with the evolutionary histories of viral species or groups as analysed by different procedures of phylogenetic reconstruction. This may be related perhaps to the traditional interest of virologists (particularly animal virologists) in following the track of epidemic developments. Phylogenetic analyses, in addition to clarifying evolutionary histories, can also serve other purposes, from the simplest graphic representation of genetic distance (Dopazo et al ., 1988; Air et al ., 1990) to the testing of different evolutionary models (Gojobori, Moriyama & Kimura, 1990; Fitch et al ., 1991). This approach can, and we dare say should, be complemented with a population genetics’ view of viral evolution, ranging from the quantitative description of genetic variation within and between populations to ascertain what mechanisms are responsible for the observed genetic structure of these populations.

Abstract: This is a practical laboratory guide to current techniques of molecular biology and genetics. It is concerned with the methods for the analysis of viral genes and chromosomes. DNA viruses and RNA viruses, including HIV, are also discussed. Detailed experimental protocols are included for: viral vectors - construction and use of DNA virus vectors (adenovirus, adeno-associated virus, vaccinia virus, Epstein-Barr virus); DNA viruses - virus/host interactions, viral chromosomes, transcription regulation (viruses discussed include herpes simplex, hepatitis B, SV40, JC, Epstein-Barr, adenovirus); human immunodeficiency virus/retroviruses - quantitation of HIV-1 virus stocks and RNA, retrovirus reverse transcription/integration, retro-virus-mediated cell fusion, use as cell lineage markers; RNA viruses - RNA virus assembly, analysis of RNA genomes, assays for RNA-binding proteins (viruses discussed include poliovirus, influenza virus, hepatitus delta virus).

Abstract: The present review deals with conceptual and experimental approaches to two aspects of the origin and molecular evolution of viruses. In the section “Role of Retrons, Retroelements, and Reverse Transcriptase in the Evolution of Retroviruses and in Eukaryotic Genome Plasticity”, Temin’s concept that retrons are an ancient genetic element that during evolution of the species gave rise to retroviruses is presented. An opposing view of Xiong and Eickbush that the most probable ancestor of current retroelements is a retrotransposable element with gag- and pol-like genes is presented. Minus-strand RNA viruses are also discussed. The second aspect of this review is the molecular evolution of viruses at the level of the virus genome. Spiegelman’s experiment on the evolution of self-replicating nucleic acid molecules outside living cells and Eigen’s experimental and conceptual approaches to this subject are presented, along with studies on the evolutionary rates of base substitutions in viral RNA and defective molecules generated during replication.

Abstract: The present invention relates, in general, to a methodology for the generation of nonsegmented negative-strand RNA viruses (Pringle, 1991) from cloned deoxyribonucleic acid (cDNA). Such rescued viruses are suitable for use as vaccines, or alternatively, as plasmids in somatic gene therapy applications. The invention also relates to cDNA molecules suitable as tools in this methodology and to helper cell lines allowing the direct rescue of such viruses. Measles virus (MV) is used as a model for other representatives of the Mononegavirales, in particular the family Paramyxoviridae.

Abstract: ‘Classical’ has connotations of ‘ancient’, but for this book the word relates to studies on virus evolution dating from the time before the sequencing of viral genomes became a way of life for evolutionary virologists. Classical ideas on the origins of viruses were pure speculation and are not worth pursuing further; it was suggested that viruses had arisen either from host cell components in some unknown way, or that some of the more complex viruses may have evolved by progressive degeneration along the sequence bacterium, mycoplasma, rickettsia, chlamydia, poxvirus. Since the focus of this book is the role of molecular biology in understanding viral evolution, I have selected as examples the only two viruses that were discussed in an evolutionary context in books on animal virology published before the emergence of recombinant DNA technology in the early 1970s, namely influenza A virus and myxoma virus (Burnet, 1955, 1960; Andrewes, 1967; Fenner et al ., 1974). Early studies on the evolution of influenza A virus Here I describe our knowledge of the evolution of influenza viruses as it appeared in 1975, when the only methods of study were serology and peptide mapping of selected proteins. Chapter 34 takes over from that time and tells how molecular biological methods have expanded our understanding of the evolution of these very interesting viruses. Structure of the virion First, a little background is needed. There are three species of influenza virus, A, B, and C, each of which can produce respiratory disease in humans.

Abstract: The origin and molecular evolution of viruses in this issue is dealt with at two levels: (1) tracing the past evolutionary pathways of viruses belonging to RNA virus families, retroviruses, and small and large DNA viruses; (2) tracing current changes in the RNA and DNA viral genomes that lead to the evolution of new virus mutants. In this interim summary, a time scale for the evolutionary processes is given, based on the accumulated published knowledge concerning the postulated origins of life on planet Earth, and the hypothesis that living cells with RNA genomes may have emerged (the “RNA world hypothesis”) that then developed into cells with DNA genomes in eukaryotic and pro-karyotic cells (1–3). The ideas about the evolution of RNA and DNA viruses from ancient cellular RNA and DNA molecules over a period of 3.5 billion years are discussed. It may be possible that by studying virus genes and molecular processes in virus-infected cells, and their involvement in the shaping of the genomes of bacteria, yeast, plants, insects, mammals, and humans, it will be possible to understand the importance of viruses in past evolution and to predict their possible impact on current and future evolutionary trends in biology.

Abstract: Foamy or spumaviruses are complex retroviruses. Phylogenetic trees have been constructed previously for either the polymerase or integrase domains showed a clustering of the foamy viruses relatively distant from other retroviruses. The most related retrovirus was found to be murine leukemia virus, irrespective of the method used or foamy viral gene analyzed. We analyze bel genes of different foamy viruses and compared the corresponding phylogenetic trees with those obtained from the pol genes that were constructed with refined computer programs. In addition, the nucleocapsid protein sequence of foamy viruses was used for a comparative phylogenetic analysis. Known biological properties of the individual FV protein domains are discussed to ascertain the apparent phylogenetic relatedness.

Abstract: Human parainfluenza virus type 1 (hPIV1) is a major cause of upper and lower respiratory tract infections among children. Immunity is mediated at least in part by antibody to the fusion (F) surface glycoprotein. Thus, genetic variation in the F gene could influence host range, virulence, and immunity. To examine the genetic diversity among hPIV1 isolates, the F genes of hPIV1 isolates from a single geographic location were sequenced and compared with the F gene of a strain isolated in 1957. Genetic variation was 2.2%-3.4%, averaging 0.8 amino acid changes per year. Changes were progressive over time, and virus evolution was dominated by a single lineage. Three of 7 isolates tested did not induce syncytium formation in tissue culture. This phenotype could not be ascribed to a single unique mutation in the F gene, but these 3 isolates had mutations in the transmembrane region of the HN gene. It is unlikely that the limited genetic evolution of the F gene will be an obstacle to vaccine development.

Abstract: Abstract There are many reasons why a clear understanding of the genetic relationship between different strains of a virus and of their evolution is desirable. It can provide information on the origins and geographical distribution of particular strains, on routes of transmission, and for the development of vaccines. With the increasingly widespread use of rapid nucleotide sequencing methods, and particularly since the advent of the polymerase chain reaction, extensive genetic data have been obtained on many viruses. Whereas previously mainly serological methods may have been used to distinguish strains, detecting limited numbers of variable epitopes, a much more complete description of the relatedness between strains using genetic analysis is now possible. This has been particularly prominent in the analysis of the evolution and origins of influenza viruses (1-7) and of human immunodeficiency virus type 1 (HIV-1), where the determination of relatedness by sequence analysis has preceded a successful serological classification (8-14). Recently there have been significant developments in the phylogenetic analysis of other viruses as well, notably papillomaviruses, feline immunodeficiency virus, and hepatitis Cvirus (15-17). The principles involved in the analysis of genetic relationships between viral strains, or phylogenies,

Abstract: Introduction The influenza viruses of the Orthomyxoviridae family totally depend on higher vertebrates as hosts, and are transmitted by a respiratory or a faecal-oral route. In contrast, two new members of the family, Thogoto (THO) and Dhori (DHO) viruses, here called the orthoacarivirus group, replicate in both vertebrate and tick cells, and are transmitted by tick bite. This chapter compares orthoacariviruses with orthomyxoviruses (influenza viruses), and speculates on their evolutionary origins. Natural history of Thogoto and Dhori viruses The first reported isolation of THO virus was from a pool of ticks removed from cattle in Thogoto forest near Nairobi, Kenya, in 1960 (Haig, Woodall & Danskin, 1965). To date, the virus has been isolated from ixodid tick species collected in several countries extending across central Africa, and in Egypt, Iran, Sicily, and Portugal (Davies, Jones & Nuttall, 1986). Dhori virus was first isolated in 1971 from ticks removed from camels in north-west India (Anderson & Casals, 1973). Subsequent isolations have been made from ticks in the former USSR, Portugal, and Egypt (Jones et al ., 1989). Experimental studies confirmed that both THO and DHO viruses are true arboviruses (Davies et ai , 1986; Jones et al ., 1989) in that uninfected ticks become infected as they feed on THO or DHO virus-infected vertebrate hosts; the viruses replicate in the ticks, and are then transmitted by tick bite when the infected ticks take their next bloodmeal. Both THO and DHO viruses have a wide vertebrate host range (Table 28.1).