Virology Midterm Transe PDF

LECTURE 10: whether the nucleic acid is DNA or RNA CLASSIFICATION AND whether the nucleic acid is single NOMENCLATURE OF VIRUSES...

LECTURE 10: whether the nucleic acid is DNA or RNA CLASSIFICATION AND whether the nucleic acid is single NOMENCLATURE OF VIRUSES stranded or double stranded whether or not the genome is segmented the size of the virion whether the capsid has helical symmetry or icosahedral symmetry whether the virion is naked or enveloped. Various combinations of these criteria produced some useful virus groups, but there was no single approach to the naming of the groups, and names were derived in a variety of ways: small, icosahedral, single-stranded 10.1 History of virus classification and DNA viruses of animals were called nomenclature parvoviruses (Latin parvus = small); Virologists are no different to other scientists nematode-transmitted polyhedral in that they find it useful to classify the (icosahedral) viruses of plants were objects of their study into groups and called nepoviruses; sub-groups. phages T2, T4 and T6 were called T In the early days, when little was known even phages. about viruses, they were loosely grouped on the basis of criteria such as the type of host, Serological relationships between viruses the type of disease caused by infection and were investigated, and distinct strains whether the virus is transmitted by an (serotypes) could be distinguished in arthropod vector. serological tests using antisera against purified virions. As more was learnt about the characteristics of virus particles some of Serotypes reflect differences in virus these began to be used for the purposes of proteins and have been found for many classification, for example: types of virus, including rotaviruses and foot and mouth disease 10.1.1 International Committee on Some virus families have been Taxonomy of Viruses grouped into orders, but higher taxonomic groupings, such as class By 1966 it was decided that some and phylum, are not used. Only order had to be brought to the some virus families are divided into business of naming viruses and subfamilies. classifying them into groups, and the International Committee on Each order, family, subfamily and Taxonomy of Viruses (ICTV) was genus is defined by viral formed. The committee now has characteristics that are necessary many working groups and is advised for membership of that group, by virologists around the world. whereas members of a species have characteristics in common but The ICTV lays down the rules for the no one characteristic is essential for nomenclature and classification of membership of the species. viruses, and it considers proposals for new taxonomic groups and virus Many species contain variants names. known as virus strains ○ Those that are approved are published in book form serotypes (differences are detected (Please see Sources of by differences in antigens) further information at the end of this chapter.) and on the genotypes (differences are detected web; these sources should by differences in genome be consulted for definitive sequence). information. The web site for this book Many of the early names of virus (www.wiley.com/go/carter) groups were used to form the names has links to relevant websites of families and genera, Ex. the picornaviruses became the family 10.2 Modern virus classification and Picornaviridae. nomenclature Each taxonomic group has its own For a long time virologists were suffix and the formal names are reluctant to use the taxonomic printed in italic with the first letter in groups such as family, subfamily, upper case (Table 10.1), Ex. the genus and species that have long genus Morbillivirus. been used to classify living ○ When common names are organisms, but taxonomic groups of used, however, they are not viruses have gradually been in italic and the first letter is accepted and are now established in lower case (unless it is the (Table 10.1). first word of a sentence), e.g. the morbilliviruses.  In many cases analysis of the sequence and organization of virus genomes has supported earlier classifications of viruses, e.g. the genera of the family Reoviridae. Another example is the rhabdoviruses, which were originally grouped together because of their bullet-shaped morphology, but it turns out that they are also related genetically. 10.2.1 Classification based on genome sequences Now that technologies for sequencing virus genomes and for determining genome organization are readily available, the modern approach to virus classification is based on comparisons of genome sequences and organizations. The degree of similarity between virus genomes can be assessed using computer programs, and can be represented in diagrams known as phylogenetic trees because they show the likely phylogeny (evolutionary development) of the viruses. Phylogenetic trees may be of various types Rooted - the tree begins at a root which is assumed to be the ancestor of the viruses in the tree. Unrooted - no assumption is made about the ancestor of the viruses in the tree. The branches of a phylogenetic tree indicate how sequences are related. The branches may be scaled or unscaled; - if they are scaled, their lengths represent genetic distances between sequences. 10.2.2 Nomenclature of viruses and taxonomic groups The naming of individual viruses has been a rather haphazard business, with somewhat different approaches taken for viruses of different host types. Bacterial viruses were simply allotted codes, such as T1, T2 and ΦX174. Viruses of humans and other vertebrates were commonly named Many insect viruses were named after the diseases that they cause, after the insect, with an indication of - Ex. measles virus, smallpox the effect of infection on the host. A virus, foot and mouth disease virus was isolated from Tipula virus, though some were paludosa larvae that were named after the city, town or iridescent as a result of the large river where the disease was quantities of virions in their tissues. first reported - Ex. Newcastle disease virus, Another virus was isolated from Norwalk virus, Ebola virus. Autographa californica larvae that Some of these original had large polyhedral structures in names have been adopted the nuclei of infected cells. These as the formal names of the viruses were named Tipula viruses. iridescent virus and Autographa californica nuclear polyhedrosis Some of the place names where virus. viruses were first found have become incorporated into the names Most plant viruses were given of virus families and genera (Table names with two components: the 10.2). host and signs of disease ○ Ex. potato yellow dwarf virus, tobacco rattle virus. Some of these names have been used as the bases for family and genus names As in other areas of biology, many names of virus taxonomic groups are based on Latin words, while some have Greek origins; a sample is given in Table 10.4. The student of virology thus gains some 10.3 Baltimore classification of viruses grounding in the classical languages! We have seen how viruses can be grouped We can note that both Latin and into seven classes on the basis of the type Greek translations of "thread' have of genome and the way in which the been used to name the filoviruses genome is transcribed and replicated and the closteroviruses, (Sections 6.2 and 7.1). respectively. Both of these families have thread-shaped virions. This approach to virus classification was first suggested by David Similarly, Latin and Greek Baltimore, after whom the scheme translations of 'small' have been is named. used to name the parvoviruses (animal viruses) and the Differentiation of Plus-Strand RNA microviruses (phages). Viruses: ○ Class VI viruses carry out The word for "small' from a third reverse transcription. language was used when devising a ○ Class IV viruses do not carry name for small RNA viruses; the out reverse transcription. Spanish 'pico' was linked to 'RNA' to form 'picornaviruses'. Differentiation of dsDNA Viruses: ○ Class VII viruses carry out reverse transcription. ○ Class I viruses do not carry out reverse transcription. Advantage: The Baltimore classification provides clarity in understanding the replication mechanisms of various viruses. In the chapters that follow we shall examine in depth a representative family of viruses from each of the seven Baltimore classes. Learning outcomes By the end of this chapter you should be able to evaluate the traditional criteria used to classify viruses into families and genera; write family and genus names in the correct format; explain how genome sequence data are used to classify viruses; evaluate phylogenetic trees; explain the basis of the Baltimore classification of viruses. Classification and whether or not the genome is segmented nomenclature of viruses the size of the virion whether the capsid has helical symmetry or icosahedral symmetry whether the virion is naked or enveloped. Various combinations of these criteria produced some useful virus groups, but there was no single approach to the naming of the groups, and names were derived in a variety of ways: 10.1 History of virus small, icosahedral, classification single-stranded DNA and nomenclature viruses of animals were called parvoviruses (Latin Virologists are no different to parvus = small); other scientists in that they find it useful to classify the objects of nematode-transmitted their study into groups and polyhedral (icosahedral) sub-groups. viruses of plants were called nepoviruses; In the early days, when little was known about viruses, they were phages T2, T4 and T6 loosely grouped on the basis of were called T even criteria such as the type of host, phages. the type of disease caused by infection and whether the virus Serological relationships between is transmitted by an arthropod viruses were investigated, and vector. distinct strains (serotypes) could be distinguished in As more was learnt about the serological tests using antisera characteristics of virus particles against purified virions. some of these began to be used Serotypes reflect differences in for the purposes of classification, virus proteins and have been for example found for many types of virus, including rotaviruses and foot whether the nucleic acid is and mouth disease virus. DNA or RNA whether the nucleic acid is 10.1.1 International Committee single stranded or double on Taxonomy of Viruses stranded  By 1966 it was decided that some Only some virus order had to be brought to the families are divided into business of naming viruses and subfamilies. Each order, family, classifying them into groups, and subfamily and genus is defined the International Committee on by viral characteristics that are Taxonomy of Viruses (ICTV) necessary for membership of that was formed. group, whereas members of a species have characteristics in The committee now has many common but no one working groups and is advised by characteristic is essential for virologists around the world. membership of the species. The ICTV lays down the rules for Many species contain variants the nomenclature and known as virus strains, classification of viruses, and it serotypes (differences are considers proposals for new detected by differences in taxonomic groups and virus antigens) or names. genotypes (differences are detected by differences in Those that are approved are genome sequence). published in book form (Please see Sources of further Many of the early names of virus information at the end of this groups were used to form the chapter.) and on the web; these names of families and genera, sources should be consulted for e.g. the picornaviruses became definitive information. The web the family Picornaviridae. site for this book (www.wiley.com/go/carter) has Each taxonomic group has its links to relevant web sites. own suffix and the formal names are printed in italic with the first letter in upper 10.2 Modern virus classification case (Table 10.1), e.g. the and nomenclature genus Morbillivirus. For a long time virologists were When common names are reluctant to use the taxonomic used, however, they are not in groups such as family, subfamily, italic and the first letter is in genus and species that have long lower case (unless it is the first been used to classify living word of a sentence), e.g. the organisms, but taxonomic groups morbilliviruses. of viruses have gradually been accepted and are now established (Table 10.1). Some virus families have been grouped into orders, but higher taxonomic groupings, such as class and phylum, are not used.  10.2.1 Classification based Another example is the on genome sequences rhabdoviruses (Chapter 15), which were originally grouped together because of their Now that technologies for bullet-shaped morphology, but it sequencing virus genomes turns out that they are also and for determining genome related genetically. organization are readily available, the modern approach to virus classification is based on comparisons of genome sequences and organizations. The degree of similarity between virus genomes can be assessed using computer programs, and can be represented in diagrams known as phylogenetic trees because they show the likely phylogeny (evolutionary development) of the viruses. Phylogenetic trees may be of various types (Figure 10.1). ○ Rooted – the tree begins at a root which is assumed to be the ancestor of the viruses in the tree. ○ Unrooted – no assumption is made about the ancestor of the viruses in the tree. 10.2.2 Nomenclature of viruses The branches of a phylogenetic and taxonomic groups tree indicate how sequences are related. The branches may be The naming of individual viruses scaled or unscaled; if they are has been a rather haphazard scaled, their lengths represent business, with somewhat different genetic distances between approaches taken for viruses of sequences. different host types. In many cases analysis of the Bacterial viruses were simply sequence and organization of allotted codes, such as T1, T2 virus genomes has supported and ϕX174. earlier classifications of viruses, e.g. the genera of the family Viruses of humans and other Reoviridae. (Figure 10.1(b)). vertebrates were commonly named after the diseases that  they cause, e.g. measles virus, smallpox virus, foot and mouth Another virus was isolated from disease virus, though some Autographa californica larvae were named after the city, town or that had large polyhedral river where the disease was first structures in the nuclei of infected reported, e.g. Newcastle cells. disease virus, Norwalk virus, Ebola virus. These viruses were named Tipula iridescent virus and Some of these original names Autographa californica nuclear have been adopted as the formal polyhedrosis virus. names of the viruses. Most plant viruses were given Some of the place names where names with two components: the viruses were first found have host and signs of disease, e.g. become incorporated into the potato yellow dwarf virus, names of virus families and tobacco rattle virus. genera (Table 10.2). Some of these names have been used as the bases for family and genus names (Table 10.3). As in other areas of biology, many names of virus taxonomic groups are based on Latin words, while some have Greek origins; a sample is given in Table 10.4. The student of virology thus gains some grounding in the classical languages! We can note that both Latin and Greek translations of ‘thread’ have been used to name the filoviruses and the closteroviruses, respectively. Both of these families have thread-shaped virions. Similarly, Latin and Greek translations of Many insect viruses were named ‘small’ have been used to name after the insect, with an indication the parvoviruses (animal of the effect of infection on the viruses) and the microviruses host. (phages). A virus was isolated from Tipula The word for ‘small’ from a third paludosa larvae that were language was used when iridescent as a result of the large devising a name for small RNA quantities of virions in their viruses; the Spanish ‘pico’ was tissues (see photograph in linked to ‘RNA’ to form Chapter 1, at a glance). ‘picornaviruses’. 10.3 Baltimore classification of viruses We have seen how viruses can be grouped into seven classes on the basis of the type of genome and the way in which the genome is transcribed and replicated (Sections 6.2 and 7.1). This approach to virus classification was first suggested by David Baltimore, after whom the scheme is named. An advantage of the Baltimore classification is its differentiation between plus-strand RNA viruses that do (class VI) and do not (class IV) carry out reverse transcription, and between dsDNA viruses that do (class VII) and do not (class I) carry out reverse transcription. In the chapters that follow we shall examine in depth a representative family of viruses from each of the seven Baltimore classes.  There are eight herpesviruses Herpesviruses known in man, and most adults in (and other dsDNA the world are persistently infected with most of them. viruses) 11.2.1 Herpes simplex viruses 1 and 2 Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) initially infect epithelial cells of the oral or genital mucosa, the skin or the cornea. The virus may enter neurones and may be transported to their nuclei, 11.1 Introduction to where they may establish latent infections. herpesviruses HSV-1 commonly infects via the lips The herpesviruses derive their name or the nose between the ages of 6 from the Greek word herpein, and 18 months. A latent infection meaning to creep. More than 100 may be reactivated if, for example, herpesviruses have been isolated the host becomes stressed or from a range of hosts that includes immunosuppressed. mammals, birds, fish, reptiles, amphibians and molluscs. Eight of Reactivation results in the these viruses are human viruses production of virions, which in about (Section 11.2). 20–40 percent of cases are transported within the neurone to the A notable characteristic of initial site of infection, where they herpesviruses is that, once they cause productive infection in have infected a host, they often epithelial cells, resulting in a cold remain as persistent infections for sore. the lifetime of the host. Occasionally there may be serious These infections are often latent complications such as encephalitis, infections, which can be reactivated especially in immunocompromised from time to time, especially if the hosts. host becomes immunocompromised. HSV-2 is the usual causative agent Both primary and reactivated of genital herpes, which is a sexually herpesvirus infections can either be transmitted disease. In newborn asymptomatic or can result in babies infection can result in serious disease of varying severity. disease, with a mortality rate of about 54 percent. The outcome depends on the interplay between the particular virus Although the face and the genitals and its host, and especially on the are the normal sites of infection for immune status of the host HSV-1 and HSV-2, respectively there are increasing numbers of 11.2 The human herpesviruses cases where HSV- 1 infects the  genitals and HSV-2 infects the consequences may be serious. In face (Figure 11.1). the US about one per cent of babies are born infected with the virus (about 40 000 per year). 11.2.2 Varicella-zoster virus In about seven percent of these Infection with varicella-zoster virus there is evidence of virus-induced usually occurs in childhood and damage at birth, including small causes varicella (chickenpox), brain size and enlargement of the when the virus spreads through the liver and spleen. In other blood to the skin, causing a rash. It individuals damage develops at a may also spread to nerve cells, later stage; the damage may be where it may establish a latent manifest in a number of ways, such infection. The nerves most often as hearing loss and mental affected are those in the face or the retardation. trunk, and these are the areas most commonly affected in zoster Human cytomegalovirus can also (shingles) when a latent infection is cause severe disease (e.g. reactivated. pneumonitis, hepatitis) in immunocompromised patients such as those with AIDS, those who have 11.2.3 Epstein-Barr virus received treatment for cancer and those who are immunosuppressed Epstein-Barr virus (EBV) is because they have received an transmitted in saliva. Epithelial organ transplant. cells are infected first then the infection spreads to B cells, which are the main host cell type for this 11.2.5 Human herpesvirus 6 virus. More than 90 per cent of people become infected with EBV, There are two types of human usually during the first years of life, herpesvirus 6, known as HHV-6A when infection results in few or no and HHV-6B. symptoms. Infection of a child with the latter can In developed countries some cause a fever and the sudden individuals do not become infected appearance of a rash known as until adolescence or adulthood. A exanthem subitum. proportion of these individuals develop infectious mononucleosis (glandular fever), commonly 11.2.6 Human herpesvirus 7 called ‘the kissing disease’ by doctors. EBV is associated with a Human herpesvirus 7 was first number of tumours in man (Chapter isolated from a culture of CD4 T 22). cells that developed a cytopathic effect; the cells were from a healthy person. 11.2.4 Human cytomegalovirus The virus has been associated with In the vast majority of infections with some cases of exanthem subitum. human cytomegalovirus symptoms are either absent or they are mild. In a pregnant woman, however, the 11.2.7 Kaposi’s sarcoma-associated virus can infect the placenta and herpesvirus then the foetus, for whom the  Kaposi’s sarcoma-associated pentons and the remainder of herpesvirus was discovered in which are hexons (Figure 11.3). 1994 and is named after the tumour with which the virus is associated In HSV-1 the capsomeres are (Chapter 22). constructed from VP5: a penton is made from five molecules of VP5 and a hexon from six molecules. 11.3 The herpesvirus virion Other proteins make up structures called triplexes, which connect the Herpesviruses have relatively capsomeres. complex virions composed of a large number of protein species organized into three distinct structures: capsid, tegument and envelope (Figure 11.2). The virus genome is a linear dsDNA molecule, which varies in size within the herpesvirus family from 125 to 240 kbp. The DNA is housed in the capsid, which is icosahedral, and the capsid is surrounded by the tegument. 11.4 HSV-1 genome organization The HSV-1 tegument contains at organization least 15 protein species and some virus mRNA molecules. The envelope contains a large number of HSV-1 is one of the most-studied spikes (600–750 in HSV-1) herpesviruses; we shall look at its composed of ten or more genome organization and then at its glycoprotein species. replication. There are several different sizes of The genome consists of two unique spike. A number of schemes have sequences each flanked by repeat evolved for the nomenclature of sequences (Figure 11.4(a)). The herpesvirus proteins, with the result unique sequences are not of equal that an individual protein may be length: the longer is designated UL referred to in the literature by two or and the shorter is designated US. more different names. The HSV-1 genome encodes at least Most of the structural proteins are 74 proteins plus some RNAs that are commonly named VP (virus not translated (Figure 11.4(b)). Both protein). In HSV-1 the most strands of the DNA are used for abundant proteins in the capsid and coding. The inverted repeats contain the tegument are VP5 and VP16, some genes, so the genome respectively. In the envelope there contains two copies of these genes, are at least 12 species of one in each strand. glycoprotein, each of which is prefixed ‘g’, for example gB, gCand gD. 11.5 HSV-1 replication The capsid is constructed from 162 Although HSV-1 infects only humans capsomeres, 12 of which are in nature, a variety of animal species and cell cultures can be infected in  the laboratory. The replication cycle nucleocapsid to reach the nucleus of the virus has been studied in cell by passive diffusion. cultures from a number of species, including humans, monkeys, mice In fact, the nucleocapsid is rapidly and dogs. transported along microtubules to the vicinity of a nuclear pore (Figure Red- Pentons 11.6). Blue- Hexons Green- Triplexes The virus DNA is released into the nucleus, where the linear molecule The Major Regions of HSV-1 Genome is converted into a covalently closed circular molecule, which becomes U- unique sequence associated with cell histones. R- repeat sequence L- long Studies with antibodies specific for S- short tegument proteins have provided T- terminal evidence that these proteins are I- inverted transported to several sites in the cell. At these sites tegument proteins play a variety of roles, including the down-regulation of host DNA, RNA and protein synthesis. 11.5.1 Attachment and entry One tegument protein known as The sequence of events at the cell virion host shutoff (vhs) protein surface usually involves the HSV-1 degrades cell mRNA. Other virion binding initially to heparan tegument proteins are involved in sulphate, and then to the main the activation of virus genes, in receptor. particular the major tegument protein, VP16, which is transported The latter can be one of several to the nucleus, where it becomes types of cell surface molecule associated with the virus DNA. including some nectins, which are cell adhesion molecules. The virion envelope then fuses with the plasma membrane (Figure 11.5). Infection may also occur by endocytosis, followed by fusion between then virion envelope and the endosome membrane. At least five of the glycoprotein species in the envelope are involved in these processes (Table 11.1). The nucleocapsid and the tegument 11.5.2 Transcription and translation proteins are released into the cytoplasm and the nucleocapsid must then be transported to the Herpesvirus genes are expressed in nucleus, where virus replication three phases: immediate early (IE), takes place. When the host cell is a early (E) and late (L) (Figure 11.7). neurone this journey is a long one; it has been estimated thatit would take Some authors refer to these phases at least 200 years for the by the Greek letters α, β and γ.  There are introns in a few of the 11.9). Copies of an origin-binding HSV-1 genes, mainly in the IE protein bind at one of three ori sites genes. in the virus DNA. The IE genes are activated by VP16. The protein has a helicase activity, It was noted above that VP16 from causing the double helix to unwind infecting virions associates with the at that site, and it has an affinity for virus DNA. It does this by binding to the resulting single strands of DNA. a complex of cell proteins including Oct-1, which binds to the sequence The double helix is prevented from TAATGARAT present in the re-forming by the binding of copies promoter of each of the IE genes of a ssDNA-binding protein. The ori (Figure 11.8). site is then bound by a complex of three proteins, which act as a VP16 then acts as a transcription helicase, further unwinding the factor to recruit the host RNA double helix to form a replication polymerase II and associated fork. initiation components to each IE gene. On one of the strands a complex of the same three proteins (now acting There are five IE proteins and all are as a primase) synthesizes a short transcription factors with roles in sequence of RNA complementary to switching on E and L genes and in the DNA. This RNA acts as a primer, down-regulating the expression of and the DNA polymerase complexed some of these genes.NAt least some with a polymerase processivity factor of the IE proteins have more than starts to synthesize the leading one role. strand of DNA. HSV- 1 Transcription and Translation On the other genome strand Phases primases synthesize short RNAs, which are the primers for the IE- intermediate early synthesis of the Okazaki E- early fragments of the lagging strand of L- late DNA. Some of the E proteins have roles in In addition to the activities of the virus DNA replication (next section), seven proteins just described, other which takes place in discrete regions virus proteins, such as a thymidine of the nucleus known as replication kinase, may also be involved in DNA compartments. replication. It is thought that the circular DNA is first ampli- fied by θ Virus DNA and proteins accumulate replication, and that later the in these compartments along with replication mode switches to σ, also cell RNA polymerase II, which known as rolling circle (Section transcribes the L genes. Most of the 7.5). L proteins are the virus structural proteins. The latter is the predominant mode of herpesvirus DNA replication, and the products are long DNA 11.5.3 Genome replication molecules known as concatemers (Figure 11.10), each of which The virus DNA is replicated by E consists of multiple copies of the proteins, seven of which are virus genome. essential for the process (Figure 11.5.4 Assembly and exit of virions sequence of events is as follows from the cell (Figure 11.13): The virus envelope glycoproteins are budding through the inner synthesized in the rough membrane of the nuclear endoplasmic reticulum and are envelope, giving the transported to the Golgi complex. nucleocapsid a temporary envelope (Figure 11.13(b)); The other structural proteins, such as VP5, accumulate in the nuclear fusion of the temporary replication compartments, where envelope with the outer procapsids are constructed. A membrane of the nuclear procapsid is more rounded than a envelope, releasing the mature capsid and its structural nucleocapsid into the integrity is maintained by the cytoplasm; incorporation of scaffolding proteins. acquisition of VP16 and other components of the tegument; Before or during DNA packaging the scaffolding proteins are removed acquisition of the virion by a virus-encoded protease. envelope by budding into a vesicle derived from the Each procapsid acquires a Golgi complex (Figure genome-length of DNA, which is cut 11.13(c), (d)); from a concatemer (Figure 11.11). Each cleavage occurs at a fusion of the vesicle packaging signal at the junction of membrane with the plasma two copies of the genome. The DNA membrane, releasing the enters the procapsid via a portal at virion from the cell (Figure one of the vertices of the 11.13(e)). icosahedron. Although the virion envelopes are There is evidence from electron derived from membranes within the microscopy of capsids treated with cell, virus glycoproteins are also antibody specific for pUL6 (the expressed at the cell surface. These protein encoded by the UL6 gene) glycoproteins can cause fusion that this protein forms the portal between infected cells and (Figure 11.12). It is likely that the non-infected cells, resulting in the DNA passes through the portal both formation of giant cells known when entering the procapsid during as syncytia, which can be observed packaging and on leaving the capsid both in infected cell cultures (Figure during the infection process, the 2.11) and in HSV lesions. Infected portal playing a similar role to the cell cultures are normally destroyed head–tail connector in a tailed phage 18–24 hours after inoculation. particle (Section 3.4.2.d). 11.5.5 Overview of HSV-1 replication Once the nucleocapsid has been constructed it must acquire its The HSV-1 replication cycle is tegument and envelope and then the summarized in Figure 11.14. resulting virion must be released from the cell; these are complex 11.6 Latent herpesvirus processes and many of the details infection are still unclear. It is thought that the  When infection of a cell with a pUL6 at one vertex of the HSV-1 herpesvirus results in latency rather capsid. The preparation was treated than a productive infection, multiple with antibody specific for pUL6 genome is switched off during followed by an antiantibody latency, but a few regions are conjugated to gold beads. The bar transcribed and a few RNAs are represents 100 nm. From Newcomb synthesized; some viruses also et al. (2001) Journal of Virology, 75, synthesize a few proteins. No virus 10923. Reproduced by permission of proteins are required to maintain the American Society for latency in cells that do not divide, so Microbiology and the author. none are produced in neurones latently infected with HSV-1. Papillomaviruses are the causative agents of warts (papillomas) and Virus RNAs, however, are some of them cause human synthesized; these are known as cancers. The dsDNA phages are latencyassociated transcripts considered further in Section 19.5. (LATs). Primary transcripts are synthesized from the LAT gene, Most dsDNA viruses, like the which is located in the terminal herpesviruses, encode genes in both repeats of the genome (Figure 11.4). strands of the DNA, so the strands The LATs undergo splicing, and at cannot be designated as plus and least one of them plays a role in minus. There are some dsDNA inhibiting apoptosis, thereby viruses, however, such as the ensuring the survival of the neurone papillomaviruses and phage T7, that with its latent HSV-1 infection. encode all of their genes in one strand of the DNA. EBV, in contrast, becomes latent in memory B cells, which divide from time to time; the virus therefore synthesizes proteins needed to maintain the copy number of its genome when the host cell divides. The likelihood of a latent herpesvirus infection becoming reactivated is increased if the host becomes immunocompromised; the greater the degree to which the host is immunocompromised, the greater the likelihood of reactivation. 11.7 Other dsDNA viruses Some further examples of viruses with dsDNA genomes in Baltimore class I are given in Table 11.2. Baculoviruses infect insects and other invertebrates. Some of them are used as insecticides and some are used as gene vectors in protein expression systems. Figure 11.12 Evidence for  The first dependovirus to be Parvoviruses (and other discovered was observed in the ssDNA viruses) electron microscope as a contaminant of an adenovirus preparation (Figure 12.1). The contaminant turned out to be a satellite virus (Section 9.3.1): a defective virus dependent on the help of the adenovirus for replication. The satellite virus was therefore called an adeno-associated virus. Other dependoviruses (distinct serotypes) have since been found in adenovirus preparations and in infected humans and other species. 12.1 Introduction to Results of surveys using serological parvoviruses methods and PCR detection of virus DNA indicate that dependovirus Parvoviruses are amongst the infections are widespread. smallest known viruses, with virions in the range 18–26 nm in diameter. Not all dependoviruses have an They derive their name from the absolute requirement for the help of Latin parvus (= small). an adenovirus. Other DNA viruses (e.g. herpesviruses) may sometimes The family Parvoviridae has been act as helpers, and some divided into two subfamilies: the dependoviruses may replicate in the Parvovirinae (vertebrate viruses) absence of a helper virus under and the Densovirinae (invertebrate certain circumstances. viruses). Dependoviruses are valuable gene Some of the genera and species of vectors. They are used to introduce the two subfamilies are shownin genes into cell cultures for Table 12.1. The subfamily massproduction of the proteins Parvovirinae includes the genus encoded by those genes, and they Dependovirus, the members of are being investigated as possible which are defective, normally vectors to introduce genes into the replicating only when the cell cells of patients for the treatment of isco-infected with a helper virus. various genetic diseases and cancers. Other parvoviruses that do not require helper viruses are known as One of the advantages of autonomous parvoviruses. dependoviruses for such applications is the fact that they are not known to cause any disease, in contrast to other viruses under 12.2 Examples of parvoviruses investigation, such as retroviruses (Section 16.5). 12.2.1 Dependoviruses  silkworm (Bombyx mori), and can cause economic damage to the silk industry. 12.3 Parvovirus virion 12.2.2 Autonomous Parvoviruses are small viruses of parvoviruses simple structure with the ssDNA genome enclosed within a capsid A parvovirus that does not require a that has icosahedral symmetry helper virus was discovered in (Figure 12.3). serum from a healthy blood donor. The virus, named after a batch of blood labelled B19, infects red blood 12.3.1 Capsid cell precursors. Many infections with B19 are without signs or symptoms, The parvovirus capsid has but some result in disease, such as icosahedral symmetry and is built fifth disease (erythema infectiosum), from 60 protein molecules. One in which affected children develop a protein species forms the majority of ‘slapped-cheek’ appearance (Figure the capsid structure and there are 12.2). small amounts of between one and three other protein species, Other diseases caused by B19 virus depending on the virus. The proteins include are numbered in order of size, with VP1 the largest; the smaller proteins acute arthritis are shorter versions of VP1. aplastic anaemia in persons Each protein species contains an with chronic haemolytic eight-stranded β-barrel structure that anaemia is common to many viral capsid proteins, including those of the hydrops foetalis (infection picornaviruses (Chapter 14). may be transmitted from a pregnant woman to the The virion is roughly spherical, with foetus and may kill the surface protrusions and canyons foetus). (Figure 12.3(c)). At each of the vertices of the icosahedron there is a In 2005 a new human parvovirus protrusion with a pore at the centre. was discovered using a technique for molecular screening of nasopharyngeal aspirates from children with lower respiratory tract disease. The virus is related to known parvoviruses in the genus Bocavirus. Viruses in the subfamily Densovirinae cause the formation of 12.3.2 Genome dense inclusions in the nucleus of the infected cell. Some of these Parvoviruses have genomes viruses are pathogens of the composed of linear ssDNA in the  size range 4–6 kb. At each end of a 12.4 Parvovirus replication DNA molecule there are a number of short complementary sequences that can base pair to form a The small genome of a parvovirus secondary structure (Figure 12.4). can encode only a few proteins, so the virus depends on its host cell (or Some parvovirus genomes have another virus) to provide important sequences at their ends known as proteins. Some of these cell proteins inverted terminal repeats (ITRs), (a DNA polymerase and other where the sequence at one end is proteins involved in DNA replication) complementary to, and in the are available only during the S opposite orientation to, the phase of the cell cycle (Figure 4.5), sequence at the other end (Section when DNA synthesis takes place. 3.2.6). This restricts the opportunity for As the sequences are parvovirus replication to the S complementary, the ends have phase. Contrast this situation with identical secondary structures that of the large DNA viruses, such (Figure 12.4(a)). Other parvoviruses as the herpesviruses (Chapter 11), have a unique sequence, and which encode their own therefore a unique secondary DNA-replicating enzymes, allowing structure, at each end of the DNA them to replicate in any phase of the (Figure 12.4(b)). cell cycle. During replication, parvoviruses with This account of parvovirus ITRs generate and package equal replication is based on studies with numbers of (+) and (−) strands of several parvoviruses. Some aspects DNA, while most viruses with unique specific to the dependoviruses are sequences at the termini do not. covered in Section 12.4.6. The percentages of virions containing (+) DNA and (−) DNA 12.4.1 Attachment and entry therefore vary with different viruses (Table 12.2). In a (−) DNA the genes for non-structural proteins are A virion attaches to receptors on the towards the 3 end and the structural surface of a potential host cell protein genes are towards the 5 end (Figure 12.6). In the case of B19 (Figure 12.5). virus the host cell is a red blood cell precursor and the receptor is the blood group P antigen. The virion enters the cell by endocytosis and is released from the endosome intothe cytoplasm, where it associates with microtubules and is transported to a nuclear pore. With a diameter of 18–26 nm, the parvovirus virion is small enough to pass through a nuclear pore, unlike the herpesvirus nucleocapsid (Section 11.5.1), though there is evidence that the virion must undergo some structural changes  before it can be transported into the structural proteins (see genome nucleus. organization, Figure 12.5). Nuclear localization signals have The non-structural proteins are been found in the capsid proteins of phosphorylated and play roles in the some parvoviruses. control of gene expression and in DNA replication. 12.4.2 Single-stranded DNA to double-stranded DNA 12.4.4 DNA replication In the nucleus the single-stranded After and virion assembly conversion virus genome is converted to dsDNA of the ssDNA genome to dsDNA by a cell DNA polymerase (Figure (Figure 12.7), the DNA is replicated 12.7). The ends of the genome are by a mechanism called double stranded as a result of base rolling-hairpin replication. This is a pairing (Figure 12.4), and at the 3 leading strand mechanism and sets end the –OH group acts as a primer parvoviruses apart from other DNA to which the enzyme binds. viruses, which replicate their genomes through leading and lagging strand synthesis (Section 7.5). Procapsids are constructed from the structural proteins and each is filled by a copy of the virus genome, either a (+) DNA or a (−) DNA as appropriate. One of the non-structural proteins functions as a helicase to unwind the dsDNA so that a single strand can enter the procapsid (Figure 12.9). 12.4.3 Transcription and translation The cell RNA polymerase II transcribes the virus genes and cell transcription factors play key roles. The primary transcript(s) undergo various splicing events to produce two size classes of mRNA (Figure 12.4.5 Overview of parvovirus 12.8). replication The larger mRNAs encode the non-structural proteins and the The parvovirus replication cycle is smaller mRNAs encode the summarized in Figure 12.10. 12.4.6 Dependovirus replication When a cell is co-infected with a dependovirus and an appropriate helper virus there is a productive infection with both viruses (Figure 12.11(a)). In nature it is perhaps more common for a dependovirus to infect a cell in the absence of a helper virus, in which case the virus genome, after it has been converted to dsDNA, may be integrated into a cell chromosome (Figure 12.11(b)). Integration occurs as a result of recombination between the cell and viral DNAs and results in a latent infection. In human cells the virus DNA is integrated at a specific site in chromosome 19. Latent dependovirus infections have been found in a number of cell lines of human and monkey origin. If a cell with a latent dependoviral genome becomes infected with an appropriate helper virus then a productive infection with both viruses can ensue (Figure 12.11(c)). 12.5 Other ssDNA viruses Some further examples of viruses with ssDNA genomes are given in Table 12.3. These viruses, and indeed the majority of the known ssDNA viruses, have circular genomes. The only viruses known with ssDNA linear genomes are the parvoviruses, the main subjects of this chapter. The ssDNA phages are considered further in Section 19.4 VIROLOGY TRANSES MIDTERM Chapter 13: Avian viruses are important Reoviruses disease agents, but most (and other dsRNA viruses orthoreovirus infections in mammals are asymptomatic. The majority of humans are infected with orthoreoviruses early in life and have specific serum antibodies by early adulthood. Plant-infecting reoviruses Most plant-infecting reoviruses are transmitted between plants by insect vectors (Chapter 4). The viruses replicate in both the plant and the insect, generally causing disease in the plant, but little or no harm to the infected insect. Rotaviruses The main focus of this chapter is on rotaviruses, which have been subjects of intensive study. 13.1 Introduction to reoviruses Rotaviruses are among the most important agents of Icosahedral viruses with gastroenteritis in humans and dsRNA genomes isolated from animals. the respiratory tracts and enteric tracts of humans and 13.2 Rotavirus virion animals. Initially, no disease could be Rotaviruses were first described associated with these viruses, so in 1963 during electron they were termed orphan viruses microscopy of faecal samples and became known as from monkeys and mice. reoviruses. Spherical virions about 75 nm in A large number of similar viruses diameter, with structures have been found in: resembling the spokes of a ○ Mammals wheel, were described (Figure ○ Birds 13.1). ○ Fish ○ Named after the Latin ○ Invertebrates, including word rota (= wheel). insects Similar viruses were observed 10 ○ Plants years later during electron ○ Fungi microscopy of faecal samples Many of these viruses are from children with diarrhoea. causative agents of disease, but the original name has been Virion structure preserved in the family name Reoviridae. The virion has icosahedral The name Reoviridae has been symmetry and is known as a incorporated into the names of triple-layered particle due to its several genera within the family capsid having three layers, each (Table 13.1). constructed from a distinct virus protein (VP): Orthoreovirus ○ Inner layer: Constructed from VP2, perforated by The original reoviruses are channels. incorporated into the genus ○ Middle layer: Constructed Orthoreovirus. from VP6, contains the Prepared by: DOLAR ,GUARDAPIES, PADERNAL VIROLOGY TRANSES MIDTERM 'spokes' of the 'wheel' and the plus strand (coding strand) is the major component from the minus strand. of the virion. ○ Outer layer: Constructed from VP7, which is glycosylated. VP7 is associated with a membrane within the cell before being incorporated into the virion (Section 13.3.3). Virion proteins Three other proteins found in the virion: ○ VP1 and VP3: Located in the core. ○ VP4: Forms 60 spikes at the surface. The proteins are numbered based on their sizes. The three largest proteins are found towards the center of the virion: ○ Within the inner capsid layer (VP2), associated with the genome, are 12 copies of VP1 and VP3, which are enzymes. ○ VP1: RNA-dependent RNA polymerase. ○ VP3: Has guanylyl transferase and methyl transferase activities. ○ One copy each of VP1 and VP3 is attached to the inner capsid layer at each of the 12 vertices of the icosahedron. Rotavirus genome The genome consists of 11 dsRNA segments, which can be separated by electrophoresis in a sodium dodecyl sulphate–polyacrylamide gel (Figure 13.2). Each RNA segment encodes one protein, except for one segment that encodes two proteins. A total of 12 proteins are Figure 13.1 The rotavirus virion. (b) From Baker et al. (1999) Microbiology and Molecular Biology Reviews, encoded: 63, 862, by permission of the American Society for ○ Six structural proteins Microbiology and the author. (c) By permission of (VP). Professor M. Stewart McNulty, The Queen’s University of Belfast. (d) From: L´opez and Arias ○ Six non-structural (2004) Trends in Microbiology, 12, 271, courtesy proteins (NSP). of Dr. B.V.V. Prasad, Baylor College of Medicine, In diagrams, the RNA strands Houston, TX, US. Reproduced by permission of Elsevier Limited. are colour-coded to distinguish Prepared by: DOLAR ,GUARDAPIES, PADERNAL VIROLOGY TRANSES MIDTERM Two possible ways a virion can enter the cell (Figure 13.5): 1. Direct penetration across the plasma membrane. Thought to be mediated by a hydrophobic region of VP5*. This region is hidden in uncleaved VP4, so virions with uncleaved spike proteins cannot use this mechanism. 13.3 Rotavirus replication Rotaviruses infect cells called enterocytes located at the ends of the villi (finger-like extensions) in the small intestine (Figure 13.3). 13.3.1 Attachment and entry The mechanisms by which rotaviruses attach to and enter host cells are complex, with many details still uncertain. Cleavage of the spike protein VP4 into its products VP8* and VP5* by proteolytic enzymes such as trypsin (Figure 13.4) results in faster entry into the cell. Binding of the virion to a cell occurs through: 1. Spike proteins (VP4, VP8*, VP5*). 2. Capsid surface via the glycoprotein VP7. Likely interaction with several cell surface proteins: 1. Evidence suggests VP5* and VP7 bind to integrins. Prepared by: DOLAR ,GUARDAPIES, PADERNAL VIROLOGY TRANSES MIDTERM ○ NSP5 is phosphorylated and O-glycosylated. Virus proteins accumulate in the cytoplasm in discrete regions known as viroplasms. ○ NSP2 and NSP5 play roles in viroplasm formation. ○ Transient expression of genes for these proteins leads to the formation of viroplasm-like structures. ○ Reduced expression of NSP5 by RNA interference (Section 2.9.3) results in fewer and smaller viroplasms. In the viroplasms, virion cores are assembled from VP1, VP2, and VP3. Newly synthesized (+) RNAs enter the cores, and a rigorous selection procedure ensures each core receives one of each of the 11 RNA species, forming a full genome complement. ○ This procedure involves the recognition of a unique sequence in each genome segment. 13.3.2 Early events Synthesis of (−) RNA takes place during the entry of the (+) The outer layer of the virion is strands into the core, with VP1 removed, leaving a acting as the RNA polymerase. double-layered particle (Figure ○ The dsRNA of the 13.1(b)), which activates infecting virion remains transcription (Figure 13.6). intact, and the mode of It is likely that each of the 11 replication is genome segments is associated conservative. with: VP6 is added to the core, forming ○ A molecule of VP1, which the second layer of the capsid, synthesizes a new copy of resulting in a double-layered the (+) RNA. particle similar to the one ○ A molecule of VP3, which derived from the infecting virion. caps the 5′ end of the new RNA. 13.3.2 Early events Nucleotides for RNA synthesis enter the particles through The outer layer of the virion is channels in the protein layers, removed, leaving a and the transcripts are double-layered particle (Figure extruded through the same 13.1(b)), which activates channels. transcription (Figure 13.6). The transcripts are not Each of the 11 genome polyadenylated. segments is likely associated Some virus proteins undergo co- with: and post-translational ○ VP1, which synthesizes a modifications: new copy of the (+) RNA. ○ VP2 and VP3 are ○ VP3, which caps the 5′ myristylated. end of the new RNA. Prepared by: DOLAR ,GUARDAPIES, PADERNAL VIROLOGY TRANSES MIDTERM Nucleotides enter the particles The virus requires varying through channels in the protein amounts of each of its 12 layers, and transcripts are proteins: extruded through the same ○ Large amounts of VP6 channels. (main capsid protein) are The transcripts are not required. polyadenylated. ○ Relatively smaller amounts Some virus proteins undergo co- of VP1 are needed. and post-translational Despite equimolar amounts of 11 modifications: dsRNAs, mRNA species are not ○ VP2 and VP3 are produced in equal quantities, and myristylated. translation control ○ NSP5 is phosphorylated mechanisms further regulate and O-glycosylated. protein production. Virus proteins accumulate in Final virion assembly involves viroplasms in the cytoplasm. adding the outer capsid layer ○ NSP2 and NSP5 are and spikes: essential for viroplasm ○ VP7 and NSP4 are formation. synthesized and ○ RNA interference N-glycosylated in the reducing NSP5 expression rough endoplasmic results in fewer and reticulum (ER), where smaller viroplasms. they remain Virion cores are assembled from membrane-localized. VP1, VP2, and VP3 in ○ NSP4 binds both VP4 and viroplasms. double-layered particles Newly synthesized (+) RNAs (Figure 13.7, inset). enter the cores, ensuring each ○ The immature virion buds core receives one of each of the through the membrane 11 RNA species, forming a into a vesicle within the complete genome. ER. Synthesis of (−) RNA takes The vesicle membrane forms a place as (+) strands enter the temporary 'envelope' containing core, with VP1 as the RNA VP7. polymerase. ○ Cleavage of VP7 releases ○ The dsRNA of the it from the membrane to infecting virion remains form the outer layer of intact, with a conservative the virion. replication mechanism. ○ VP4 is added to form the VP6 is added to the core, forming spikes of the virion. the second layer of the capsid, ○ It remains uncertain creating a double-layered whether the spikes are particle similar to the one from added within the ER or the infecting virion. elsewhere. Virions are released from the cell 13.3.3 Late events either by lysis or exocytosis. A further round of transcription 13.3.4 Overview of rotavirus takes place within the replication double-layered particles. ○ Unlike early transcripts, The rotavirus replication cycle is late transcripts are not summarized in Figure 13.8 capped (Figure 13.7). The cell's translation machinery shifts to select uncapped transcripts, shutting down cell protein translation while continuing virus protein translation. Prepared by: DOLAR ,GUARDAPIES, PADERNAL VIROLOGY TRANSES MIDTERM 13.4 Other dsRNA Viruses Virions of most dsRNA viruses have icosahedral symmetry and are mostly naked (non-enveloped). ○ An exception is the family Cystoviridae, which are enveloped bacteriophages (Section 19.3). Examples of viruses with dsRNA genomes can be found in Table 13.2. A major challenge for dsRNA viruses is that dsRNA is a potent inducer of cell defense mechanisms, including: ○ Apoptosis ○ Interferon production ○ RNA silencing (Chapter 13.3.5 Rotavirus Disease 9) Most dsRNA viruses, including Enterocytes on the villi are rotaviruses, overcome this by destroyed as a result of rotavirus ensuring that the viral dsRNA is infection. always enclosed within virus This leads to reduced absorption protein structures, preventing of water, salts, and sugars from the dsRNA from being free in the the gut. cytoplasm and triggering these Evidence suggests that tight defenses. junctions between cells are damaged by the non-structural protein NSP4, allowing fluid leakage into the gut. These effects of virus infection, along with the secretion of water and solutes by secretory cells, result in diarrhoea and can lead to dehydration. Treatment involves rehydrating the patient with a solution of salts and sugar. ○ However, this treatment may not be available in some parts of the world. It is estimated that there are around half a million deaths of infants and young children each year due to rotavirus infections. Although most rotavirus infections are confined to the gut, there is evidence that, on occasion, the virus may cross the gut and infect other tissues. Prepared by: DOLAR ,GUARDAPIES, PADERNAL VIROLOGY TRANSES MIDTERM transcription of virus genes must Chapter 14 occur before virus Picornaviruses (and other plus-strand protein synthesis RNA viruses) can start. 14.2 Some Important Picornaviruses 14.2.1 Hepatitis A Virus Hepatitis A is especially prevalent in developing countries with poor sanitation. In most infants and young children, infection is asymptomatic or mild and leads to life-long immunity. When adults are infected: ○ About 75% develop jaundice. ○ Severe hepatitis is rare but can be fatal. 14.2.2 Poliovirus 14.1 Introduction to Poliovirus has been extensively Picornaviruses researched due to the paralysis it can cause. Members of the family Most poliovirus infections are Picornaviridae are found in harmless and occur in the mammals and birds. oropharynx and gut. Some genera in the family and Serious disease occurs when: important viruses are listed in ○ The virus infects other Table 14.1. tissues, resulting in Poliovirus was one of the first viraemia (virus in the viruses to be: blood) and spread to the ○ Propagated in cell central nervous system. culture (Enders, Weller, Babies rarely develop serious and Robbins, 1949). disease due to anti-poliovirus ○ Plaque purified antibodies acquired from their (Dulbecco and Vogt, mothers. 1954). ○ As hygiene and sanitation Most picornaviruses: improve, poliovirus ○ Grow readily in cell infections occur later in culture. life, increasing the ○ Are easy to purify. likelihood of central ○ Are stable, making them nervous system popular for laboratory infection. studies. Poliovirus infection of the Picornaviruses are classified as central nervous system can class IV viruses: cause: ○ Their genome is a ○ Meningitis, from which plus-strand RNA that most patients recover functions as mRNA once completely. released into a host cell. ○ Encephalitis and/or ○ The first virus molecules paralytic poliomyelitis. synthesized in an infected Paralysis is caused cell are proteins. by virus replication This contrasts with in motor neurons other viruses where of the spinal cord Prepared by: DOLAR ,GUARDAPIES, PADERNAL VIROLOGY TRANSES MIDTERM or brain stem, 14.2.5 Foot and Mouth Disease Virus affecting limbs or breathing Foot and mouth disease virus muscles. infects a wider range of hosts The fear of paralysis led to the than other picornaviruses, development of polio vaccines including cattle, sheep, goats, in the mid-20th century: and pigs. ○ Inactivated vaccines and ○ It causes lesions on the live attenuated vaccines feet and in the mouth. have proven highly Outbreaks can have serious effective. economic consequences: ○ By the early 21st century, ○ Milk yields drop, young the number of global polio infected animals may die. cases had dropped to ○ In developing countries, 3500, just 1% of cases infected animals become compared to 1988. unfit for ploughing and ○ Polio has been eradicated transport. in many parts of the world, ○ Restrictions on trade of and complete eradication susceptible animal species is hoped for soon. cause further economic damage. 14.2.3 Coxsackieviruses In 2001, a massive outbreak in the UK was controlled by In 1948, faecal specimens from measures including the suspected polio cases were slaughter of over 6 million injected into suckling mice in the animals. town of Coxsackie, USA, leading ○ The estimated cost of the to the discovery of outbreak exceeded 8 coxsackieviruses. billion pounds. Coxsackieviruses cause a range of medical conditions, including: ○ Myocarditis (heart disease) ○ Meningitis ○ Rashes 14.2.4 Rhinoviruses Rhinoviruses are the most common agents of upper respiratory tract infections in humans. ○ By age 2, most children have had at least one rhinovirus infection. ○ In adults, rhinoviruses account for about 50% of common colds. Rhinoviruses replicate in the epithelium of the upper respiratory tract, where the temperature is around 33–35°C. ○ Some human rhinoviruses can replicate at 37°C, possibly causing disease in the lower respiratory tract. Prepared by: DOLAR ,GUARDAPIES, PADERNAL VIROLOGY TRANSES MIDTERM cryo-electron microscopy. ○ They are approximately 2 nm deep, which, for a virion of this size, is a significant depth, being approximately seven percent of the virion diameter. ○ This is relatively much greater than the depth of the Grand Canyon on the surface of the Earth! ○ The canyons, which are lined by the C termini of VP1 and VP3 molecules, contain the virus attachment sites. Evolution of picornaviruses 14.3 Picornavirus Virion has generated a lot of variability in the capsid proteins, some of Picornaviruses are small RNA which is reflected in the existence viruses of relatively simple of distinct serotypes (Table structure (Figure 14.4). 14.2). ○ The RNA is enclosed by a ○ This antigenic variability capsid, which is roughly