Viruses

Viruses are extremely small infectious agents that invade cells of all types. Once inside another cell, viruses become hijackers, using the cells' machinery to produce more viruses. Whether viruses constitute living organisms or merely conglomerations of molecules has been a source of debate for many years. Are they alive? One of the fundamental hallmarks of life is the ability to reproduce. Whether viruses have this ability is key to a debate over their status as living things. Some argue that since viruses cannot reproduce independently, they are not alive. However, similar to viruses, there are a few prokaryotes that are obligate parasites and cannot reproduce without a host. But these prokaryotes show another hallmark of life that viruses lack: growth. Once assembled, a virus does not change in size or chemical composition. They lack the machinery for producing energy to drive such biological processes. This makes them radically different from any known organism. Viruses do, however, show some characteristics of living things. They are made of proteins and glycoproteins like cells are. They contain genetic information needed to produce more viruses in the form of DNA or RNA. They evolve to adapt to their hosts. So while it is doubtful viruses are truly alive, they are clearly very similar to living organisms. Virus Diversity There is more diversity among viruses than among all groups of living organisms combined. New varieties are constantly being described. It would be nearly impossible to describe all of the groups of viruses and their characteristics briefly. Instead, we will look at the characteristics shared by all viruses, such as their basic structure and general replicative cycle. Then we will discuss the features used to classify new viruses, such as shape and form of genetic material.

Terms
Capsid - The protein coat that surround the genetic material of a virus. Envelope - A membranous covering found on some virus capsids that allows the virus to enter a host cell by fusing with the host's cell membrane. Enzymes - Proteins that act as catalysts for chemical reactions. Genes - A unit of genetic material containing the information needed to produce and regulate a single protein. Lysogenic - The phase found in some viruses in which the virus's genetic material becomes incorporated into the host cell and no new viruses are produced. Compare with lytic. Lytic - In viruses with a lysogenic phase, the opposing phase in which virus replication takes place.

General Characteristics of Viruses

Structure Because most viruses are extremely well adapted to their host organism, virus structure varies greatly. However, there are some general structural characteristics that all viruses share.

Figure %: General virus structure All viruses have a capsid or head region that contains its genetic material. The capsid is made of proteins and glycoproteins. Capsid contruction varies greatly among viruses, with most being specialized for a particular virus's host organism. Some viruses, mostly of the type infecting animals, have a membranous envelope surrounding their capsid. This allows viruses to penetrate host cells through membrane fusion. The virus's genetical material rests inside the capsid; that material can be either DNA, RNA, or even in some cases a limited number of enzymes. The type of genetic material a virus contains is used in classification, and is discussed in Virus Classification. In addition to the head region, some viruses, mostly those that infect bacteria, have a tail region. The tail is an often elaborate protein structure. It aids in binding to the surface of the host cell and in the introduction of virus genetic material to the host cell. Virus "Life" Cycles

Figure%: Generalized Replication of Viruses Though the details of virus infection and replication vary greatly with host type, all viruses share 6 basic steps in their replication cycles. These are: 1) attachment; 2) penetration; 3) uncoating; 4) replication; 5) assembly; 6)release. As shown in , the virus must first attach itself to the host cell. This is usually accomplished through special glycoprotiens on the exterior of the capsid, envelope or tail. Next, penetration occurs, either of the whole virus or just the contents of the capsid. If the entire capsid enters, the genetic material must be uncoated to make it available to the cell's replication machinery. Replication of genetic material takes place, as well as the production of capsid and tail proteins. Once all of the necessary parts have been replicated, individual virus particles are assembled and released. Release often takes place in a destructive manner, bursting and killing the host cell. Some viruses have a slightly more complicated replication cycle involving lytic and lysogenic phases. The lytic phase is similar to that described above, with virus particles infecting and being replicated. In the lysogenic phase, however, viral genetic material that has entered the host cell becomes incorportated in the cell and lies dormant. It is passed on to the progeny of the infected cells. Eventually, the lytic phase will start again, and cells that were never infected themselves, but carry the viral genetic material will begin to produce new virus particles.

Classification of Viruses
In 1962, Lwoff, Horne and Tournier proposed a classification system in which viruses were grouped by shared characteristics among the particles themselves rather than the host cells. While their classification system is no longer used, this basic premise is the foundation of modern classification systems. Some of the main features of viruses used in their classification are type of genetic material and capsid shape. Genetic Material Viruses may carry DNA or RNA as their genetic material. DNA may be single- or double-stranded (ssDNA and dsDNA), and it may be circular or linear. The code found in viral genetic material is usually very complex, with many genes overlapping each other to conserve space in the tiny capsid. Capsid Shape Though capsid shape varies greatly, there are two main categories: helical and icosahedral. Helical capsids are formed by a helix of structural proteins, forming a long tube in which the genetic material resides. Icosahedral

capsids are shaped like polygons, forming a ball around the genetic material. The geometry of the polygons is used for further classification. In addition, viruses are capsids are grouped into those with envelopes and those without. /PARGRAPH

Classification
Main article: Virus classification Classification seeks to describe the diversity of viruses by naming and grouping them on the basis of similarities. In 1962, Andr Lwoff, Robert Horne, and Paul Tournier were the first to develop a means [116] of virus classification, based on the Linnaean hierarchical system. This system bases classification on phylum, class, order, family, genus, and species. Viruses were grouped according to their shared [117] properties (not those of their hosts) and the type of nucleic acid forming their genomes. Later the International Committee on Taxonomy of Viruses was formed. However, viruses are not classified on the basis of phylum or class, as their small genome size and high rate of mutation makes it difficult to determine their ancestry beyond Order. As such, the Baltimore Classification is used to supplement the more traditional hierarchy.

ICTV classification
The International Committee on Taxonomy of Viruses (ICTV) developed the current classification system and wrote guidelines that put a greater weight on certain virus properties to maintain family uniformity. A unified taxonomy (a universal system for classifying viruses) has been established. The 7th lCTV Report formalised for the first time the concept of the virus species as the lowest taxon [118] (group) in a branching hierarchy of viral taxa. However, at present only a small part of the total diversity of viruses has been studied, with analyses of samples from humans finding that about 20% of the virus sequences recovered have not been seen before, and samples from the environment, such as from seawater and ocean sediments, finding that the large majority of sequences are [119] completely novel. The general taxonomic structure is as follows: Order (-virales) Family (-viridae) Subfamily (-virinae) Genus (-virus) Species (-virus) In the current (2011) ICTV taxonomy, six orders have been established, the Caudovirales, Herpesvirales, Mononegavirales, Nidovirales, Picornavirales and Tymovirales. A seventh order Ligamenvirales has also been proposed. The committee does not formally distinguish between subspecies, strains, and isolates. In total there are 6 orders, 87 families, 19 subfamilies, [120][121][122] 349 genera, about 2,284 species and over 3,000 types yet unclassified.

Baltimore classification
Main article: Baltimore classification

The Baltimore Classification of viruses is based on the method of viral mRNA synthesis.

The Nobel Prize-winning biologist David Baltimore devised the Baltimore [31][123] classification system. The ICTV classification system is used in conjunction with the [124][125][126] Baltimore classification system in modern virus classification. The Baltimore classification of viruses is based on the mechanism of mRNA production. Viruses must generate mRNAs from their genomes to produce proteins and replicate themselves, but different mechanisms are used to achieve this in each virus family. Viral genomes may be singlestranded (ss) or double-stranded (ds), RNA or DNA, and may or may not use reverse transcriptase(RT). In addition, ssRNA viruses may be either sense (+) or antisense (). This classification places viruses into seven groups: I: dsDNA viruses (e.g. Adenoviruses, Herpesviruses, Poxviruses) II: ssDNA viruses (+)sense DNA (e.g. Parvoviruses) III: dsRNA viruses (e.g. Reoviruses) IV: (+)ssRNA viruses (+)sense RNA (e.g. Picornaviruses, Togaviruses) V: ()ssRNA viruses ()sense RNA (e.g. Orthomyxoviruses, Rhabdoviruses) VI: ssRNA-RT viruses (+)sense RNA with DNA intermediate in life-cycle (e.g. Retroviruses) VII: dsDNA-RT viruses (e.g. Hepadnaviruses)

As an example of viral classification, the chicken pox virus, varicella zoster (VZV), belongs to the order Herpesvirales, familyHerpesviridae, subfamily Alphaherpesvirinae, and genus Varicellovirus. VZV is in Group I of the Baltimore Classification because it is a dsDNA virus that does not use reverse transcriptase.