Introduction

Satellite viruses and satellite RNAs are sub-viral microbes which depend on another virus, referred to as the ‘helper virus’, for their replication within a host cell. The basis of satellite dependence is not completely understood, but it is presumed that satellite genomes are replicated by the RNA-dependent RNA polymerase encoded by the helper virus. Along with viroids, satellites are the smallest and simplest biological entities known, with single-stranded RNA genomes ranging from 194 to 1376 nt. Satellites are uniquely prevalent in plant hosts, and have been found associated with 28 different plant viruses from diverse virus groups (Roossinck, Sleat & Palukaitis, 1992). To date, no examples of satellites of animal viruses are known. The only satellite-like entity associated with an animal virus, hepatitis delta virus, is not a true satellite because it is capable of autonomous replication, and appears to need its helper virus only for encapsidation and transmission (Taylor, 1990).

The classical definition of a satellite involves three main features (Murant & Mayo, 1982). These are that satellites are not capable of replicating in the absence of the helper virus, they are not required for the life cycle of the helper virus, and that they share little or no sequence similarity with the helper virus genome. Thus, satellites differ from other sub viral entities such as viroids, which are capable of independent replication in a host cell, and defective interfering (DI) RNAs, which are comprised of helper virus genetic sequences. Satellites often interfere with the replication of their helper viruses, and the symptoms caused by helper virus/satellite co-infections can differ dramatically from those of the helper virus alone.

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.

Introduction

A virus receptor is defined as a component of the cell surface that contains a domain which is structurally and conformationally complementary with a domain on the viral attachment protein (VAP) and forms a stable complex with the VAP. Association of the VAP with the receptor is followed by a biological response which may include internalization and replication of the virus, cytopathic changes in the cell, activation of second messenger systems, inhibition of host protein synthesis, or down regulation of receptors. The interaction with the host cell receptor is the initial stage in the viral infectious cycle. Besides being necessary for entrance of the virus into the cell, the receptor plays a major role in determining cell and species tropisms. Binding of virions to host cell receptors places them in intimate physical contact with the cell surface, and sets the stage for crossing the membrane barrier. Viruses then enter the cell either by direct fusion with the plasma membrane or by adsorptive- or receptor-mediated endocytosis. Many viruses have been shown to enter by both mechanisms, although some may preferentially utilize one of the two pathways. With either process, the viral genome gains entrance to the cytoplasm without lysing the cell membrane, which would be fatal to the cell. Paulson (1985) and Marsh and Helenius (1989) reviewed data on the entry of enveloped and non-enveloped viruses into cells.

Virus receptors

Any normal constituent comprising or associated with the cell membrane of the host cell is potentially a virus receptor.

Introduction

Papillomaviruses (PVs) are members of the genus Papillomavirus which, along with viruses of the genus Polyomavirus, comprise the family Papovaviridae (papillomavirus, polyomavirus and vacuolating agent). PVs are small, non-enveloped structures with icosahedral symmetry and a circular double-stranded DNA genome. They infect humans in addition to multiple other animal vertebrate species, resulting in a variety of proliferative epithelial lesions and tumours. Most papillomaviruses are species specific and have a cellular tropism for squamous epithelial cells. In benign papillomatous lesions, the viral genomes replicate as extrachromosomal episomes in the nuclei of basal and suprabasal epithelial cells. Complete vegetative replication with production of intact virions is found in the superficial and differentiated epithelial cells. In contrast, malignant lesions do not support vegetative viral replication, but instead often contain an integrated disrupted viral genome.

Sixty years ago, Richard Shope (1933) linked the presence of the cottontail rabbit papillomavirus (CRPV) to cutaneous papillomatosis in rabbits, and Francis Peyton Rous described the conversion of papilloma to squamous cell carcinoma in rabbits, initiating the field of tumour virology (Rous & Beard, 1935). Much of the current interest in papillomavirus research can be attributed to the recent association of human papillomaviruses (HPVs) with cervical cancer, one of the leading causes of cancer-attributed death in women.

Most of our knowledge of PVs has been obtained during the last decade through the use of recombinant DNA techniques. The small double-stranded DNA genomes of PVs have been readily amenable to cloning and sequencing. In the absence of a serological classification, HPVs have been categorized according to their genotype.

Introduction

The family Bunyaviridae is one of the largest groupings of viruses. More than 300 viruses, arranged in numerous serogroups, are contained in the family, and this number is taken as evidence of their evolutionary success and potential. Some of these viruses are associated with serious diseases of humans, such as haemorrhagic fever with renal syndrome, Crimean-Congo haemorrhagic fever, and Rift Valley fever. Hence the family warrants continual epidemiological surveillance. Characteristics that unite the Bunyaviridae include the following: tripartite, singlestranded RNA genome of negative- or ambi-sense polarity; enveloped virus particle comprising four structural proteins - two glycoproteins termed Gl and G2, a nucleocapsid protein, N and an RNA polymerase, the L protein; cytoplasmic site of viral replication with intracellular maturation at the Golgi; viral mRNA transcription primed by capped oligonucleotides cleaved from the 5’ ends of host-cell mRNAs. Considering the large number of viruses that fulfil these criteria, it is perhaps not unexpected that considerable diversity exists at the molecular level in terms of genome coding and replication strategies, and at the biological level in terms of vector and host interactions. These factors will be briefly reviewed in this Chapter.

Biology of Bunyaviridae

The family Bunyaviridae is currently (Calisher, 1991) divided into five genera: Bunyavirus, Hantavirus, Nairovirus, Phlebovirus and Tospovirus. Such subdivision was originally made by serological comparisons but the availability of nucleotide sequence data has enabled more precise classification. (In this chapter ‘Bunyaviridae’ is used to refer to familial traits and the terms bunyavirus, hantavirus, etc, to generic traits.

Alphavirus structure, replication and transmission cycles

Structure and replication

Alphavirus is a genus of arthropod-borne viruses (arboviruses) in the family Togaviridae (Calisher et al., 1980; Calisher & Karabatsos, 1988). These viruses have unsegmented, single-stranded RNA genomes of 11–12 kb which are of positive or messenger sense. Alphavirus genomic RNA encodes four non-structural proteins, designated nsP1–4, as well as three structural proteins: the capsid, and two envelope glycoproteins, El and E2 (Fig. 33.1). A sub-genomic 26S RNA species, which encodes only the structural proteins, is also produced in infected cells.

Alphaviruses replicate in the cytoplasm of infected cells. Entry into vertebrate cells occurs via receptor-mediated endocytosis (Kielian & Helenius, 1986). The high-affinity laminin receptor serves as a mammalian and mosquito cell (in vitro) receptor for the alphavirus, Sindbis (SIN) (Wang et al., 1992), whereas other protein receptors for SIN have been identified in mouse neural (Ubol & Griffin, 1991) and chicken cells (Wang et al., 1991). Wang et al. (1992) believe that the wide host range of Sindbis virus is the result of its utilization of a highly conserved receptor, found in a variety of vertebrates and in mosquito cells (laminin receptor), as well as its use of multiple receptors. The mechanism of alphavirus entry into mosquito cells has not been identified, although the very specific infectivity patterns of some alphaviruses for their mosquito vectors suggest use of a less conserved protein receptor during initial infection of the midgut.

Genomic alphavirus RNA is translated by cellular components to produce the non-structural proteins, and also serves as a template for minus-strand RNA synthesis involving the non-structural proteins.

Introduction

Genealogical relationships among prokaryotes have traditionally been defined by very diverse morphological, physiological and biochemical properties as well as by immunological comparisons of a few proteins. The main problems in interpreting the results of this deductive approach come from uncertainty about whether or not these characters are actually homologous. These genealogies can only be verified by inductive methods such as the analysis of palaeochemical data, the identification of fossils and the determination of the order of their appearance in time, and also by the biochemical investigation of the genes of ubiquitously distributed macromolecules that have conserved primary and secondary structure and functional constancy. In contrast to geological and fossil evidence, analyses of macromolecules offer an almost unlimited source of invaluable information about the genealogy of living organisms (Zuckerkandl & Pauling, 1965). In particular, estimation of the natural relationships among organisms presently alive can be by sequence analysis of ribosomal (r)RNAs and their genes, genes coding for certain enzymes (ATPases) and regulatory proteins (tuf-factors), and by nucleic acid hybridization studies. These methods are able to span the full range of relationships, from the hypothetical ancestor of life on earth to most recently evolved strains. In his superb reviews Woese (1987, 1991) discussed the rationale for using rRNA as a molecular clock in phylogenetic studies, rather than the traditional classification system which failed to delineate phylogenetic relationships, and discussed the power of sequences and nucleotide signatures to unravel phylogenetic trees.

Introduction

The evolution of virus diseases is distinct from, although related to, the evolution of viruses in general. The emergence of a virus disease can reflect the ‘evolution’ of the causal agent, but a disease can emerge in the absence of any change in the agent. To maintain this distinction we will use a special vocabulary and refer to the ‘emergence, epidemicity, and control’ of virus diseases (Nathanson, 1990).

Propagated infections

In some instances, a new virus disease is the direct consequence of the appearance of an agent which is truly new to the population affected. Recent striking instances are the appearance of canine parvovirus and of human immunodeficiency virus (HIV), both of which were signalled by a global pandemic of disease. It appears that canine parvovirus represents an authentic instance of virus evolution, in which a pre-existing agent, feline panleukopenia virus, underwent a few key point mutations which made it very infectious and pathogenic for the canine population (Parish, 1990). These mutations presumably led to the emergence of canine parvovirus disease. Likewise, it seems probable that HIV evolved from a viral ancestor, such as simian immunodeficiency virus (SIV), which was circulating in subhuman primates. It is likely that this highly plastic agent has undergone some evolution since originally infecting humans, which has enhanced its ability to replicate in human CD4-positive mononuclear cells. A mass of circumstantial data strongly suggests that the virus first invaded the human population in Africa, and that it has spread worldwide only in the last 15 years (Desrosiers, 1990; Getchell et al, 1987; Karpas, 1990; Levy et al, 1986).

Introduction

In this chapter, we describe the biological, ger.omic and genetic diversity of the herpesviruses and then discuss the mechanisms that have been used to generate their different genetic complements. We consider how recent work has expanded our view of the possible origins of the family, and finish by sketching out the limitations that studies of present-day herpesviruses impose on our understanding of herpesvirus evolution. We have limited citations of the literature to appropriate reviews and particularly pertinent research papers.

Herpesviruses are complex viruses of higher eukaryotes which have large linear double-stranded DNA genomes and replicate in the nuclei of host cells (Matthews, 1982; Minson, 1989). They have a characteristic appearance in the electron microscope: an icosahedral capsid of 162 capsomeres embedded in an amorphous protein layer (the tegument) which is surrounded by a protein-containing lipid envelope. Agents of this type have been isolated from a wide range of vertebrates, including bony fish, amphibians, reptiles, birds, marsupials and placental mammals. It is possible that herpesviruses also infect invertebrates such as oysters (Farley et at., 1972), but this has yet to be confirmed. Known hosts in addition to humans are largely those subjected to husbandry, and the best studied are infected by several different herpesviruses. For example, humans are hosts to at least seven herpesviruses, and horses to at least five. The ubiquity of members of this large virus family, coupled with the very high degree of host specificity exhibited by individual members, indicates that the herpesviruses have a long history of evolution in close association with their hosts.

Introduction

Two major groups of immunodeficiency-associated retro viruses are presently known to infect man. These are human immunodeficiency virus type 1 (HIV-1) which is the recognized agent of AIDS in Central Africa, Europe, the United States, and most countries worldwide (Barre-Sinoussi et ai, 1983; Popovic et aL, 1984), and the more geographically restricted human immunodeficiency virus type 2 (HIV-2), which is most predominant in West Africa (Barin et ai, 1985; Clavel et al., 1987). Although a causative relationship between HIV-1, HIV-2 and clinical AIDS is well established (Fauci, 1988), the pathogenic mechanisms by which these viruses induce immunosuppression and disease remain unknown. Ten million individuals are currently infected with HIV worldwide and this number is expected to rise to 40 million by the year 2000 (Mann, 1992). Given the magnitude of the AIDS pandemic, new insights into the natural history of HIV-1 and HIV-2 infection as well as a better understanding of the events responsible for their recent epidemic spread are critically needed for a rational drug design and the development of effective vaccines.

Molecular characterization of HIV-1 and HIV-2, including cloning and sequence analysis of several full-length genomes, has revealed features that distinguish human AIDS viruses from the traditional RNA tumour viruses. First, the HIV-1 and HIV-2 genomes are relatively complex, each including at least six genes (in addition to the common gag, pol and env genes) termed vif, vpr, vpu (HIV-1 only), vpx (HIV-2 only), tat, rev and nef, which collectively regulate viral transcription, translation, latency and other properties that contribute to viral pathogenesis (Cullen, 1991).

Introduction

Membership in the retroid family (Fuetterer & Hohn, 1987) is defined by the shared amino acid sequence identity to the conserved motifs in the reverse transcriptase (RT) segment of the RNA-directed DNA polymerase. The retroid family is composed of retro viruses, two different classes of DNA viruses, two distinct types of retrotransposons, retroposons, group II introns and plasmids of cellular organelles, an orphan group, the retrons (Temin, 1989) of bacteria (Inouye et ai, 1989; Lampson, Inouye & Inouye, 1989; Lim & Maas, 1989) and the telomere elongation protein (EST-1) of yeast (Table 27.1) (Lundblad & Blackburn, 1990).

The variability of gene content and sequence similarity in extant retroid elements (Table 27.1) can be used to infer a model of the evolutionary history of the retroid family (Fig. 27.1). The phylogenetic tree topology, based on RT similarities, indicates an initial bifurcation leading to lineages I and II. Independently derived phylogenies for each set of homologous proteins in the capsid/ribonuclear protein/protease/ reverse transcriptase/ribonuclease H/histidine-cysteine motif/integrase (CA/NC/PR/RT/RH/H-C/IN) element and capsid/reverse transcriptase/ tether (CA/RT/T) element produce trees that are congruent with the RT tree, suggesting that the ancestral units evolved as linked genes (Doolittle et ai, 1989; McClure, 1992; McClure, unpublished data). The hypothetical ancestral unit of lineage I is further supported by the congruency of the phylogenetic tree for the H-C/IN segment, even though it is found in a position in the copia-likt retrotransposons different from its position in all other retroid elements. Subsequent acquisition or deletion of gene units may have occurred as indicated along the various branches leading to the tree tips (Fig. 27.1).