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 Papillomaviridae Herpesviridae Poxviridae

Bacteriophage T4 HPV types 2, 16, 18, 33 herpes zoster virus variola virus

E. coli humans humans humans

bacterial lysis warts, cervical and other cancers chicken pox, shingles smallpox

ss RNA non-seg.

+

Picornaviridae Togaviridae

poliovirus types 1-3 rhinovirus (100+ serotypes) equine encephalitis virus

humans humans insects/horses

poliomyelitis common cold

CNS disease in horse and humans

ss RNA

Rhabdoviridae

rabies virus

mammals

rabies

non-seg.

Paramyxoviridae

measles virus

humans

measles

ssRNA segmented

Orthomyxoviruses

influenza virus

mammals, birds

influenza

ssRNA segmented

- and/ or ambi

Bunyaviridae Arenaviridae

Sin Nombre virus Lassa fever virus

rodents primates

hanta fever hemorrhagic fever

ds RNA

+/-

Reoviridae

Rice dwarf virus

plants

stunting

ssRNA DNA rep. int.

+

Retroviridae

HIV types 1, 2 HTLV type I

adult T-cell leukemia

ds DNA +/-RNA rep. int.

+/-

Hepadnaviridae

hepatitis B virus

humans

hepatitis, hepatocellular carcinoma

ss=single-stranded; ds=double stranded; non-seg.= non-segmented; ambi = ambisense; rep. int CNS = central nervous system.

= replicative intermediate; HPV= human papillomavirus;

Table 1. Classification of selected viruses by nucleic acid replication strategy (Baltimore Scheme).

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 picor-naviruses, 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

Table 1. Classification of selected viruses by nucleic acid replication strategy (Baltimore Scheme).

lipid fat or waxlike molecule, insoluble in water glycoproteins proteins to which sugars are attached

Table 2. The polarity, or sense, of a strand is an indication of how its sequence relates to messenger RNA (mRNA).

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

response enzyme that copies RNA into DNA

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 antigenicity ability to shape and macromolecular composition, and other properties, such as anti-provoke an immune genicity 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-reverse transcriptase 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 seg-

?ments. 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.

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