Virus

Physical Description and Classification

Viruses are distinguished from free-living microbes, such as bacteria and fungi, by their small size and relatively simple structures. Diminutive viruses such as parvovirus may have a diameter of only 25 nanometers (nm, 10^-9 meters). Poxviruses, the largest known viruses, are about 300 nanometers across, just at the detection limits of the light microscope. Typical bacteria have diameters of 1,000 nanometers or more. Information on the structure of viruses has been obtained with several techniques, including electron

Nucleic Acid	Polarity	Family	Examples	Host	Diseases/pathologies
ss DNA	+	Parvoviridae	parvovirus B19	humans	erythema infectiosum (fifth disease)
ds DNA	+/-	Myoviridae	Bacteriophage T4	E. coli	bacterial lysis
		Papillomaviridae	HPV types 2, 16, 18, 33	humans	warts, cervical and other cancers
		Herpesviridae	herpes zoster virus	humans	chicken pox, shingles
		Poxviridae	variola virus	humans	smallpox
ss RNA non-seg.	+	Picornaviridae	poliovirus types 1-3	humans	poliomyelitis
			rhinovirus (100+ serotypes)	humans	common cold
		Togaviridae	equine encephalitis virus	insects/horses	CNS disease in horse and humans
ss RNA non-seg.	-	Rhabdoviridae	rabies virus	mammals	rabies
		Paramyxoviridae	measles virus	humans	measles
ssRNAt segmented	-	Orthomyxoviruses	influenza virus	mammals, birds	influenza
ssRNA segmented	-and/or ambi	Bunyaviridae	Sin Nombre virus	rodents	hanta fever
		Arenaviridae	Lassa fever virus	primates	hemorrhagic fever
ds RNA	+/-	Reoviridae	Rice dwarf virus	plants	stunting
ssRNA DNA rep. int.	+	Retroviridae	HIV types 1, 2	humans	AIDS
			HTLV type I	humans	adult T-cell leukemia
ds DNA +/-RNA rep. int.	+/-	Hepadnaviridae	hepatitis B virus	humans	hepatitis, hepatocellular carcinoma
ss=single-stranded;ds=doublestranded; non-seg.=non-segmented; ambi = ambisense;rep. int = replicativeintermediate; HPV= human papillomavirus;CNS = centralnervous system.

microscopy (EM). The limit of resolution of traditional EM is about 5 nm. With advanced EM techniques, such as cryogenic EM (cryoEM, in which the sample is rapidly frozen instead of exposed to chemical fixatives), coupled with computer image processing, smaller structures (1-2 nm) can be resolved. However, X-ray crystallography is the only method that allows for atomic-level resolution. Small viruses that produce uniform particles can be crystallized. The first atomic-level structure of a virus, tomato bushy stunt virus, was solved in 1978.

There is great diversity among viruses, but a limited number of basic designs. Capsids are structures that contain the viral genomes; many have icosahedral symmetry. An icosahedron is a three-dimensional, closed shape composed of twenty equilateral triangles. Viral proteins, in complexes termed "capsomers," form the surface of the icosahedron.

Other viruses, such as the virus that causes rabies, are helical (rod shaped). The length of helical viruses can depend on the length of the genome, the DNA or RNA within, since there are often regular structural interactions between the nucleic acids of the genome and the proteins that cover it.

A lipid-containing envelope is a common feature of animal viruses, but uncommon in plant viruses. Embedded in the envelope are surface proteins, usually glycoproteins that help the virus interact with the surface of the cell it is infecting. A matrix layer of proteins often forms a bridge between the surface glycoproteins and the capsid. Some viruses, such as the picornaviruses, are not enveloped, nor do they have a matrix layer. In these viruses, cell-surface interactions are mediated by the capsid proteins.

Some viruses have compound structures. The head of the T4 bacterial virus (bacteriophage) is icosahedral and is attached via a collar to a contractile

Molecule	Sequence	Polarity or Sense
Complementary RNA	A U U G G G C U C	negative
Coding strand DNA	T A A C C C G A G	positive
Complementary DNA	A T T G G G C T C	negative
mRNA	U A A C C C G A G	positive

tail with helical symmetry. Large viruses, such as the herpesviruses and poxviruses, can have higher-ordered and more complex structures.

Classification of viruses considers the genome characteristics, virion shape and macromolecular composition, and other properties, such as antigenicity and host range. A scheme for classification of viruses based on the type of nucleic acid (DNA or RNA) present in the virus particle and the method of genome replication was devised by David Baltimore, co-discoverer of reverse transcriptase (see Table 1). Reverse transcriptase is an enzyme that converts retroviral genomic single-stranded (ss) RNA into doubled-stranded (ds) DNA.

Viral genomes can be RNA or DNA, positive or negative in polarity, ss or ds, and one continuous (sometimes circular) molecule or divided into segments. By convention, messenger RNA (mRNA) that can be directly translated to protein is considered positive sense (or positive in polarity). DNA with a corresponding sequence (that is, the coding strand of double-stranded DNA) is also a positive-sense strand. An RNA or DNA molecule with the reverse complementary sequence to mRNA is a negative-sense strand. A few viruses have been identified that contain one or more "ambisense" genomic RNA segments that are positive sense in one part of the molecule (this part can be translated directly into protein) and negative sense (reverse complement of coding sequence) in the rest of the molecule.

Virus Replication Cycle

For a virus to multiply it must infect a living cell. All viruses employ a common set of steps in their replication cycle. These steps are: attachment, penetration, uncoating, replication, assembly, maturation, and release.

Attachment and Penetration.

A virion surface protein must bind to one or more components of the cell surface, the viral receptors. The presence or absence of receptors generally determines the type of cell in which a virus is able to replicate. This is called viral tropism. For example, the poliovirus receptor is present only on cells of higher primates and then in a limited subset of these, such as intestine and brain cells. While called virus receptors, these are actually used by the cell for its own purposes, but are exploited by the virus for entry.

Entry of the viral genome into the cell can occur by direct penetration of the virion at the cell surface or by a process called endocytosis, which is the engulfment of the particle into a membrane-based vesicle. If the latter, the virus is released when the vesicle is acidified inside the cell. Enveloped viruses may also fuse with the cellular surface membrane, which results in release of the capsid into the cytoplasm. Surface proteins of several viruses contain "fusion peptides," which are capable of interacting with the lipid bilayers of the host cell.

Uncoating and Replication.

After penetration, viral capsid proteins must be removed, at least partly, to express and replicate the viral genome. In the case of most DNA viruses, the capsid is routed to the nucleus prior to uncoating. An example can be seen in the poxviruses, whose large DNA genomes encode most of the proteins needed for DNA replication. These viruses uncoat and replicate completely in the cytoplasm. RNA viruses typically lose the protective envelope and capsid proteins upon penetration into the cytoplasm. In reoviruses, only an outer protein shell is removed and replication takes place inside a structured subviral particle.

Viral genomes must be expressed as mRNAs in order to be translated into structural proteins for the capsids and, in some cases, as replicative proteins for replicating the virus genome. Viral genomes must also provide templates that can be replicated to produce progeny genomes that will be packaged into newly produced virions. Replication details vary among the different types of viruses.

The ss positive-sense DNA of parvoviruses is copied by host DNA polymerase (the enzyme that replicates DNA) in the nucleus into a negative-sense DNA strand. This in turn serves as a template for mRNA and progeny DNA synthesis. The genomes of larger DNA viruses, with the exception of the poxviruses, are also transcribed and replicated in the nucleus by a combination of viral and host enzymes (for example, DNA-dependent RNA polymerses for transcription of mRNAs, DNA-dependent DNA polymerase for genome replication).

Positive-polarity RNA virus genomes can be translated directly, but for effective progeny production additional rounds of RNA replication via a negative-stranded intermediate are required. This is accomplished by a viral transcriptase (RNA-dependent RNA polymerase) and associated cofactors. Single-stranded negative-sense RNA viruses of animals must also carry a viral transcriptase to transcribe functional mRNAs and subsequently produce proteins, since this RNA-to-RNA enzymatic activity is typically lacking in animal cells.

Retroviruses are unique among viruses in that the genome is diploid, meaning that two copies of the positive-polarity RNA genome are in each virus particle. The genomic RNA is not translated into protein, but rather serves as a template for reverse transcription, which produces a double-stranded DNA via a viral reverse transcription enzyme. The DNA is subsequently integrated into the host cell chromosomal DNA. Hepadnaviruses also encode a reverse transcriptase, but replication occurs inside the virus particle producing the particle-associated genomic DNA.

Assembly, Maturation, and Release.

As viral proteins and nucleic acids accumulate in the cell, they begin a process of self-assembly. Viral self-assembly was first demonstrated in a seminal series of experiments in 1955, wherein infectious particles of tobacco mosaic virus spontaneously formed when purified coat protein and genomic RNA were mixed. Likewise, poliovirus capsomers are known to self-assemble to form a procapsid in the cytoplasm. Progeny positive-strand poliovirus RNAs then enter this nascent particle. "Chaperone" proteins (chaparonins) of the cell play a critical role in facilitating the assembly of some viruses. Their normal role is to help fold cellular proteins after synthesis.

The maturation and release stages of the replication cycle may occur simultaneously with the previous step, or may follow in either order. Many viruses assemble their various components into "immature" particles. Further intracellular or extracellular processing is required to produce a mature infectious particle. This may involve cleavage of precursors to the structural proteins, as in the case of retroviruses.

Viruses that are not enveloped usually depend upon disintegration or lysis of the cell for release. Enveloped viruses can be released from the cell by the process of budding. In this process the viral capsid and usually a matrix layer are directed to a modified patch of cellular membrane. Interactions between the matrix proteins and/or envelope proteins drive envelopment. In the case of viruses that bud at the cell surface, such as some togaviruses and retroviruses (including HIV), this also results in release of the virus particles. If the virus acquires a patch of the nuclear membrane (as is the case with herpesviruses), then additional steps involving vesicular transport may be required for the virus to exit the cell.

Infection Outcomes

Viral infection can result in several different outcomes for the virus and the cell. Productive infection, such that each of the seven steps outlined above occurs, results in the formation of progeny viruses. Cells productively infected with poliovirus can yield up to 100,000 progeny virions per cell, although only a small fraction (fewer than 1 per 1,000) of these are capable of going on to carry out a complete replication cycle of their own. Productive infection may induce cell lysis, which results in the death of the cell. Nonenveloped viruses typically induce cell lysis to permit release of progeny virions. Many enveloped viruses also initiate events that result in cell death by various means, including apoptosis, necrosis, or lysis.

Viral infection may be abortive, in which one or more necessary factors, either viral or cellular, are absent and progeny virions are not made. Infection may be nonproductive, at least transiently, but viral genomes may still become resident in the host cell. Herpesviruses and retroviruses can establish latent infections. Latently infected cells may express a limited number of viral products, including those that result in cell transformation. Latent infections can often be activated by various stimuli, such as stress in the case of herpesviruses, to undergo a productive infection.

Viral Cancers

Infection with certain viruses can also result in cell transformation, stable genetic changes in the cell that result in disregulated cell growth and extended growth potential (immortalization). In animals, such virally induced cellular changes can result in cancer. This correlation was first made by Harry Rubin and Howard Temin in the 1950s, when they observed that Rous sarcoma virus, a retrovirus capable of inducing solid tumors in chickens, could also cause biochemical and structural changes and extend the proliferative potential of cultured chicken cells.

Viruses are perhaps second only to tobacco as risk factors for human cancers. DNA tumor viruses include papillomaviruses and various herpes viruses (such as HHV-8, which causes Kaposi's sarcoma). More than sixty strains of human papillomaviruses (HPV) have been identified. HPV cause warts, which are benign tumors, but are also the causes of malignant penile, vulval, and cervical cancers. Infection with hepatitis B or C viruses is associated with increased incidence of liver cancer. Adenoviruses have been shown to induce cancers in animals, but not in humans. Retroviruses can also cause cancer in various animal species, including humans. HTLV-1 causes adult T-cell leukemia in about 1 percent of infected humans.

Viruses can cause cancer through their effects on two important cellular genes or gene products: tumor suppressors and oncogenes. These genes are critical players in cell-cycle regulation. One protein product from HPV binds to the retinoblastoma (Rb) tumor suppressor protein. HPV E6 protein binds p53 tumor suppressor protein and promotes its degradation. Acutely transforming retroviruses, which induce tumors in a short time period of weeks to months, carry modified versions of cellular oncogenes, called viral oncogenes. Slowly transforming retroviruses also subvert cellular oncogenes, but by integrating into or near the oncogene, thereby altering its expression, a process that can take years because of the apparently random nature of retrovirus integration.

Vaccines

Many viral infections can be prevented by vaccination. Several classes of vaccines are currently in use in humans and animals. Inactivated vaccines, such as the poliovirus vaccine developed by Jonas Salk, are produced from virulent viruses that are subjected to chemical treatments that result in loss of infectivity without complete loss of antigenicity (antigenicity is the ability to produce immunity). Another approach is the use of weakened variants of a virus with reduced pathogenicity to induce a protective immune response without disease. While vaccines are usually given before exposure to a virus, postexposure vaccines can cure some virus infections with extended incubation periods, such as rabies.

Vaccines against smallpox eradicated the illness in 1980. It is believed that it may also be possible to eliminate polio. A recombinant vaccine against hepatitis B virus is now produced in yeast. However, developing effective vaccines to some viruses, including the common cold viruses, HIV-1, herpesviruses, and HPV, is proving very difficult principally due to the existence of many variants. Public health measures, such as mosquito control programs to curb the spread of viral diseases transmitted by these vectors, and safe-sex campaigns to slow the spread of sexually transmitted diseases, can also be effective. Because viruses replicate in cells, drugs that target viruses typically also affect cell functions. These therapeutic agents must be active against the virus while having "acceptable toxicity" to the host organism. The majority of the specific antiviral drugs currently in use target viral enzymes. For example, nucleoside analogues that target viral polymerases are active against HIV and certain herpesviruses.

SEE ALSO BIOTECHNOLOGY; CANCER; CELL, EUKARYOTIC; DNA POLYMERASES; GENE THERAPY; HIV; ONCOGENES; RETROVIRUS; TRANSFORMATION; TUMOR SUPPRESSOR GENES; VIROIDS AND VIRUSOIDS.

Robert F. Garry

Bibliography

Garrett, Laurie. The Coming Plague: Newly Emerging Diseases in a World out of Balance. New York: Penguin Books, 1994.

Kolata, Gina B. Flu: The Story of the Great Influenza Pandemic of 1918 and the Search for the Virus That Caused It. New York: Farrar, Straus and Giroux, 1999.

Preston, Richard. The Hot Zone. New York: Random House, 1994.

Internet Resource

Sanders, David M., and Robert F. Garry. "All the Virology on the World Wide Web." <www.virology.net>.