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Baron S, editor. Clinical Microbiology. Fourth edition. Galveston (TX): university of Texas clinical Branch in ~ Galveston; 1996.


Structure and also Function

Viruses are small obligate intracellular parasites, which by meaning containeither a RNA or DNA genome surrounded by a protective, virus-coded protein coat.Viruses might be perceived as mobile hereditary elements, most most likely of cellularorigin and characterized through a lengthy co-evolution of virus and host. Forpropagation viruses depend on dedicated host cells providing the complexmetabolic and biosynthetic machine of eukaryotic or prokaryotic cells. Acomplete virus fragment is referred to as a virion. The main duty of the virion isto deliver its DNA or RNA genome into the host cell so the the genome have the right to beexpressed (transcribed and translated) by the hold cell. The famous genome, oftenwith associated simple proteins, is packaged within a symmetric protein capsid.The nucleic acid-associated protein, dubbed nucleoprotein, along with thegenome, forms the nucleocapsid. In sheathe viruses, the nucleocapsid issurrounded by a lipid bilayer obtained from the modified host cell membrane andstudded v an external layer that virus envelope glycoproteins.

Classification the Viruses

Morphology: Viruses are grouped ~ above the basis of size and also shape,chemical composition and also structure the the genome, and mode the replication.Helical morphology is seen in nucleocapsids of plenty of filamentous and pleomorphicviruses. Helical nucleocapsids covers a helical variety of capsid proteins(protomers) wrapped about a helical filament of main point acid. Icosahedralmorphology is properties of the nucleocapsids the many“spherical” viruses. The number and also arrangement that thecapsomeres (morphologic subunits the the icosahedron) are useful inidentification and also classification. Numerous viruses additionally have an outer envelope.

Chemical Composition and also Mode of Replication: The genome of a virusmay covers DNA or RNA, which might be solitary stranded (ss) or dual stranded(ds), linear or circular. The whole genome may occupy one of two people one main point acidmolecule (monopartite genome) or number of nucleic mountain segments (multipartitegenome). The different varieties of genome necessitate different replicationstrategies.


Aside from physical data, genome structure and also mode that replication are criteriaapplied in the classification and also nomenclature the viruses, including thechemical composition and configuration the the nucleic acid, whether the genomeis monopartite or multipartite. The genomic RNA strand that single-stranded RNAviruses is referred to as sense (positive sense, plus sense) in orientation if it canserve as mRNA, and also antisense (negative sense, minus sense) if a complementarystrand synthesized through a famous RNA transcriptase serves as mRNA. Also consideredin viral classification is the site of capsid assembly and, in envelopedviruses, the site of envelopment.

Structure and also Function

Viruses space inert external the organize cell. Tiny viruses, e.g., polio and tobaccomosaic virus, can also be crystallized. Viruses room unable to create energy. Asobligate intracellular parasites, throughout replication, they fully depend on thecomplicated biochemical machinery of eukaryotic bio or prokaryotes cells. The mainpurpose that a virus is to supply its genome right into the host cell to enable itsexpression (transcription and translation) by the host cell.

A totally assembled transmittable virus is dubbed a virion. The simplest virions consistof two simple components: nucleic mountain (single- or double-stranded RNA or DNA) and aprotein coat, the capsid, which features as a shell to defend the viral genomefrom nucleases and which during infection attaches the virion to details receptorsexposed on the prospective host cell. Capsid proteins are coded for by the virusgenome. Due to the fact that of its limited size (Table41-1) the genome codes for just a few structural protein (besidesnon-structural regulatory proteins connected in virus replication). Capsids areformed as single or double protein shells and also consist of only one or a fewstructural protein species. Therefore, many protein copies must self assemble toform the constant three-dimensional capsid structure. Me assembly the viruscapsids follows two basic patterns: helical symmetry, in i m sorry the protein subunitsand the nucleic acid are arranged in a helix, and also icosahedral symmetry, in i m sorry theprotein subunits assemble into a symmetric covering that consist of the nucleicacid-containing core.


Some virus families have second covering, called the envelope, i beg your pardon isusually derived in part from modified host cell membranes. Viral envelopes consistof a lipid double layer that closely surrounds a covering of virus-encodedmembrane-associated proteins. The exterior the the double layer is studded withvirus-coded, glycosylated (trans-) membrane proteins. Therefore, enveloped virusesoften exhibit a fringe of glycoprotein spikes or knobs, also called peplomers. Inviruses that obtain their envelope by budding v the plasma or anotherintracellular cabinet membrane, the lipid composition of the famous envelope closelyreflects the of the particular host membrane. The outer capsid and also the envelopeproteins the viruses room glycosylated and important in identify the host selection andantigenic composition of the virion. In addition to virus-specified envelopeproteins, budding viruses lug also specific host cell proteins together integralconstituents the the famous envelope. Virus envelopes have the right to be taken into consideration an additionalprotective coat. Larger viruses regularly have a complicated architecture consists of bothhelical and isometric symmetries confined to different structural components. Smallviruses, e.g., hepatitis B virus or the members the the picornavirus or parvovirusfamily, room orders that magnitude an ext resistant than are the larger complicated viruses,e.g. Members of the herpes or retrovirus families.

Classification that Viruses

Viruses space classified top top the communication of morphology, chemical composition, and mode ofreplication. The viruses that infect human beings are at this time grouped into 21 families,reflecting only a small part of the spectrum that the multitude of various viruseswhose organize ranges prolong from vertebrates to protozoa and also from plants and also fungi tobacteria.

Helical Symmetry

In the replication of viruses with helical symmetry, the same proteinsubunits (protomers) self-assemble into a helical variety surrounding thenucleic acid, which adheres to a comparable spiral path. Such nucleocapsids formrigid, very elongated rods or flexible filaments; in either case, detailsof the capsid framework are often discernible by electron microscopy. Inaddition to classification as flexible or rigid and also as nude or enveloped,helical nucleocapsids are defined by length, width, pitch of thehelix, and number of protomers every helical turn. The many extensivelystudied helical virus is tobacco mosaic virus (Fig. 41-1). Numerous important structural functions ofthis plant virus have actually been detected by x-ray diffraction studies. Figure 41-2 shows Sendai virus, anenveloped virus v helical nucleocapsid symmetry, a member the theparamyxovirus family members (see Ch.30).


Figure 41-1

The helical structure of the strictly tobacco mosaic virusrod. Around 5 percent that the size of the virion is depicted.Individual 17,400-Da protein subunits (protomers) rally in ahelix v an axial repeat that 6.9 nm (49 subunits per threeturns). Each (more...)


Figure 41-2

Fragments of flexible helical nucleocapsids (NC) the Sendaivirus, a paramyxovirus, room seen either in ~ the protectiveenvelope (E) or free, after rupture the the envelope. The intact nucleocapsid is about 1,000 nm long and also 17 nm indiameter; its key (more...)

Icosahedral Symmetry

An icosahedron is a polyhedron having 20 equilateral triangular faces and also 12vertices (Fig. 41-3). Lines throughopposite vertices specify axes that fivefold rotational symmetry: allstructural features of the polyhedron repeat five times within each360° the rotation around any of the fivefold axes. Lines v thecenters of opposite triangular faces type axes that threefold rotationalsymmetry; twofold rotational symmetry axes are formed by currently throughmidpoints of the opposite edges. An icosaheron (polyhedral or spherical) withfivefold, threefold, and also twofold axes of rotational symmetry (Fig. 41-3) is characterized as having 532symmetry (read together 5,3,2).


Figure 41-3

Icosahedral models seen, left to right, ~ above fivefold,threefold, and also twofold axes of rotational symmetry. This axes space perpendicular come the airplane of the page and passthrough the centers of every figure. Both polyhedral (upper) andspherical (lower) creates (more...)

Viruses were very first found to have actually 532 the contrary by x-ray diffraction studiesand subsequently by electron microscopy v negative-staining techniques.In many icosahedral viruses, the protomers, i.e. The structure polypeptidechains, room arranged in oligomeric clusters referred to as capsomeres, which arereadily delineated by negative staining electron microscopy and kind theclosed capsid shell (Fig. 41-4 a/b). The plan of capsomeres into an icosahedral shell (compare Fig. 41-4 through the upper appropriate modelin Fig. 41-3) permits theclassification of such viruses by capsomere number and pattern. Thisrequires the identification of the nearest pair of vertex capsomeres (calledpenton: those with which the fivefold symmetry axes pass) and also thedistribution the capsomeres in between them.

Figure 41-4

Adenovirus after negative stain electron microscopy. (A) The capsid expose the typical isometric shell made up from20 equilateral triangular faces. The 252 capsomeres, 12 pentonsand the 240 hollow hexon capsomeres space arranged in a T= 25 symmetry (more...)

In the adenovirus version in Figure41-4, among the penton capsomeres is arbitrarily assigned theindices h = 0, k = 0 (origin), wherein h and also k are theindicated axes the the inclined (60°) network of capsomeres. The net axesare created by lines of the closest-packed neighboring capsomeres. Inadenoviruses, the h and k axes also coincide with the edge of thetriangular faces. Any 2nd neighboring peak capsomere has indices h= 5, k = 0 (or h = 0, k = 5).The capsomere number (C) can be figured out to be 252 from the h and also kindices and the equation: C = 10(h2 +hk+ k2) + 2. This symmetry and also number ofcapsomeres is typical of every members that the adenovirus family.

Virus main point Structure

Except in helical nucleocapsids, little is known about the packaging ororganization that the viral genome in ~ the core. Tiny virions space simplenucleocapsids include 1 to 2 protein species. The larger viruses containin a main point the nucleic acid genome complexed with an easy protein(s) andprotected by a single- or twin layered capsid (consisting of much more than onespecies that protein) or by an envelope (Fig.41-5).

Figure 41-5

Two-dimensional diagram of HIV-1 correlating (immuno-)electron microscopic findings v the recent nomenclature forthe structural contents in a 2-letter code and also with themolecular weights that the virus structure (glyco-)proteins. SU means (more...)

RNA Virus Genomes

RNA viruses, consisting of 70% of all viruses, differ remarkably in genomestructure (Fig. 41-6). Since ofthe error price of the enzymes involved in RNA replication, this virusesusually display much greater mutation prices than perform the DNA viruses. Mutationrates that 10-4 bring about the consistent generation that virus variantswhich show an excellent adaptability to brand-new hosts. The famous RNA may besingle-stranded (ss) or double-stranded (ds), and the genome might occupy asingle RNA segment or be dispersed on two or an ext separate segments(segmented genomes). In addition, the RNA strand of a single-stranded genomemay be either a sense strand (plus strand), i beg your pardon can function as messengerRNA (mRNA), or an antisense strand (minus strand), i m sorry is safety tothe sense strand and cannot duty as mRNA protein translation (see Ch. 42). Feeling viral RNA alonecan replicate if injected right into cells, since it can function as mRNA andinitiate translation of virus-encoded proteins. Antisense RNA, ~ above the otherhand, has actually no translational function and cannot every se produce viralcomponents.

Figure 41-6

Schemes of 21 virus families infecting humans showing anumber of distinctive criteria: presence of an envelope or(double-) capsid and also internal nucleic acid genome. +, feeling strand; -, antisense strand; ±,dsRNA or DNA; 0, one DNA; C, number (more...)

DsRNA viruses, e.g., members that the reovirus family, save on computer 10, 11 or 12separate genome segment coding because that 3 enzymes associated in RNA replication, 3major capsid proteins and a variety of smaller structural proteins. Eachsegment consists of a safety sense and antisense strand the ishydrogen bonded into a linear ds molecule. The replication of these virusesis complex; just the sense RNA strands space released indigenous the infectingvirion come initiate replication.

The retrovirus genome comprises 2 identical, plus-sense ssRNA molecules,each monomer 7–11 kb in size, that space noncovalently attached over ashort terminal region. Retroviruses save on computer 2 envelope protein encoded bythe env-gene, 4–6 nonglycosylated main point proteins and 3non-structural practical proteins (reverse transcriptase, integrase,protease: RT, IN, PR) mentioned by the gag-gene (Fig. 41-5). The RT transcribes the famous ssRNA intodouble-stranded, circular proviral DNA. This DNA, mediated by the viralintegrase, i do not care covalently bonded right into the DNA that the organize cell come makepossible the succeeding transcription that the feeling strands the eventuallygive increase to retrovirus progeny. After ~ assembly and budding, retrovirusesshow structural and functional maturation. In immature virions thestructural proteins of the main point are current as a large precursor proteinshell. After proteolytic processing by the famous protease the protein ofthe mature virion space rearranged and form the dense isometric or cone-shapedcore usual of the mature virion, and also the bit becomes infectious.

DNA Virus Genomes

Most DNA viruses (Fig. 41-6) containa single genome of direct dsDNA. The papovaviruses, consisting of the polyoma-and papillomaviruses, however, have circular DNA genomes, around 5.1 and also 7.8kb bag in size. DsDNA serves as a design template both because that mRNA and also forself-transcription. 3 or 2 structural proteins consist of the papovaviruscapsid: in addition, 5-6 nonstructural proteins space encoded that arefunctional in virus transcription, DNA replication and also celltransformation.

Single-stranded straight DNA, 4–6 kb in size, is found with themembers of the Parvovirus family members that comprises the parvo-, the erythro- andthe dependoviruses. The virion has 2–4 structure proteinspecies which room differently obtained from the very same gene product (see Ch. 64). The adeno-associatedvirus (AAV, a dependovirus) is incapable of developing progeny virions exceptin the presence of helper viruses (adenovirus or herpesvirus). That istherefore stated to be replication defective.

Circular single-stranded DNA of only 1.7 to 2.3 kb is discovered in members the theCircovirus family which make up the smallest autonomously propagatedviruses. The isometric capsid procedures 17 nm and also is composed of 2 proteinspecies only.

Virus Classification

On the communication of shared properties viruses are grouped at different hierarchicallevels the order, family, subfamily, genus and also species. Much more than 30,000 differentvirus isolates are recognized today and also grouped in more than 3,600 species, in 164 generaand 71 families. Viral morphology offers the basis for grouping viruses intofamilies. A virus household may consists members the replicate just in vertebrates,only in invertebrates, just in plants, or only in bacteria. Particular families containviruses that replicate in more than one of these hosts. This section involves onlythe 21 families and genera of medical importance.

Besides physical properties, several components pertaining to the setting of replicationplay a role in classification: the construction of the nucleic mountain (ss or ds,linear or circular), whether the genome consists of one molecule of nucleic acid oris segmented, and also whether the strand the ss RNA is sense or antisense. Alsoconsidered in group is the website of famous capsid assembly and, in envelopedviruses, the site of nucleocapsid envelopment.Table 41-1 list the major chemical and morphologic properties of thefamilies the viruses that cause condition in humans.

The use of Latinized names finishing in -viridae because that virus families and also ending in -virusfor famous genera has actually gained broad acceptance. The surname of subfamilies finish in-virinae. Vernacular names continue to be provided to explain the viruses in ~ agenus. In this text, Latinized endings for families and also subfamilies usually space notused. Table 41-2 reflects the currentclassification the medically significant viruses.

In the at an early stage days that virology, viruses were called according to usual pathogenicproperties, e.g. Body organ tropism and/or modes of transmission, and also often additionally aftertheir discoverers. From the early on 1950s till the mid-1960s, when many new viruseswere being discovered, it was famous to create virus names by using sigla(abbreviations obtained from a few or initial letters). Therefore the name Picornaviridaeis acquired from pico (small) and RNA; the name Reoviridae is acquired fromrespiratory, enteric, and also orphan viruses since the agents were discovered in bothrespiratory and also enteric specimens and also were not related to other classified viruses;Papovaviridae is indigenous papilloma, polyoma, and also vacuolating agent (simian virus 40); retrovirus is from reverse transcriptase; Hepadnaviridaeis native the replication the the virus in hepatocytes and their DNA genomes, as seenin hepatitis B virus. Hepatitis A virus is classified now in the familyPicornaviridae, genus Hepatovirus. Although the current rules because that nomenclature donot prohibit the arrival of new sigla, they need that the siglum bemeaningful to workers in the field and also be recognized by international studygroups.

The name of the other households that save on computer viruses pathogenic for humans arederived as follows: Adenoviridae (adeno, “gland”; describes theadenoid organization from i m sorry the viruses were very first isolated); Astroviridae (astronmeans star); Arenaviridae (arena “sand”) defines the sandyappearance the the virion. Bunyaviridae (from Bunyamwera, the ar in Africa wherethe type strain to be isolated); Calicivirus (calix, “cup” or“goblet” native the cup-shaped depressions on the viral surfaces);Coronaviridae (corona, “crown”) describes the illustration of thepeplomers protruding from the viral surface; Filoviridae (from the Latin filum,“thread” or “filament”) describes themorphology of these viruses. Herpesviridae (herpes, “creeping”)describes the nature that the lesions; Orthomyxoviridae (ortho,“true,” plus myxo “mucus,” a problem forwhich the viruses have an affinity; Paramyxoviridae acquired from para,“closely resembling” and also myxo; Parvoviridae (parvus means,“small”); Poxviridae (pock means,“pustule”); Rhabdoviridae (rhabdo, “rod”describes the form of the viruses and Togaviridae (toga,“cloak”) describes the tight viral envelope.

Several viruses of clinical importance still remain unclassified. Some room difficultor impossible to propagate in traditional laboratory host systems and also thus can not beobtained in adequate quantity to permit much more precise characterization. Hepatitis Evirus, the Norwalk virus and comparable agents (see Ch. 65) that cause nonbacterial gastroenteritis in humansare now assigned to the calicivirus family.

The fatal transmissible dementias in humans and other pets (scrapie in lamb andgoat; bovine spongiform encephalopathy in cattle, transmissible mink encephalopathy;Kuru, Creutzfeldt-Jakob disease, and Gerstmann-Straussler-Scheinker syndrome inhumans) (see Ch. 71) are brought about by theaccumulation the non-soluble amyloid fibrils in the main nervous systems. Theagents resulting in transmissible subacute spongiform encephalopathies have been linkedto viroids or virinos (i.e. Plant pathogens consisting of naked, but very stablecircular RNA molecules of about 3-400 bases in size, or transmittable genomes enwrappedinto a organize cell coat) since of their resistance come chemical and also physical agents.According come an different theory, the term “prion” has beencoined to allude to an essential nonviral infectious cause for this fatalencephalopathies—prion standing because that self-replicating proteinaceous agentdevoid that demonstrable nucleic acid. Few of the transmissible amyloidoses present afamilial pattern and also can be defined by identified mutations which render a primarysoluble glycoprotein insoluble, which consequently leads come the pathognomonicaccumulation the amyloid fibers and plaques. The pathogenesis of the sporadicamyloidoses, however, is tho a issue of very ambitious research.

Caspar DLD: architecture principles in virus particleconstruction. In Horsfall FL, Tamm i (eds): Viral and also Rickettsial epidemic inMan. 4th Ed. JB Lippincott, Philadelphia, 1975 .
Mattern CFT: the opposite in virus architecture. InNayak DP (ed): molecule Biology of pet Viruses. Marcel Dekker, brand-new York,1977 .

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Murphy FA, Fauquet CM, Bishop DHL, et al. (eds):Virus Taxonomy: sixth Report of the global Committee on Taxonomy ofViruses. Springer-Verlag, brand-new York, 1995 .