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Viruses are considered simple forms of life, consisting of a nucleic acid surrounded by protein. They are much smaller than bacteria (<0.5 μm) and are obligate intracellular parasites that depend on host cells, both prokaryotes and eukaryotes, for replication. They can be classified by a variety of methods, including size, structure, presence or absence of a lipid-containing envelope, type of nucleic acid, diseases they cause, and cell types they infect. In the consideration of biocides, viruses can be classified as being nonenveloped (or naked) or enveloped (Fig. 1.10).

Nonenveloped viruses consist of a nucleic acid surrounded by a protein-based capsid and are considered hydrophilic. Enveloped viruses also contain an external lipid bilayer envelope, which can include proteins (usually glycoproteins, or proteins with linked carbohydrate groups). Central to all viral structures is the nucleocapsid, consisting of the nucleic acid (which can be single- or double-stranded DNA or RNA) protected by a protein capsid. The capsid is made of individual capsomeres, which consist of single or multiple protein types. Examples of nonenveloped viruses are the parvoviruses. Parvoviruses consist of 50% DNA and 50% protein, and the capsid is composed of three proteins that are responsible for their considerable resistance to disinfection. In addition, some viruses contain proteins, associated within the capsid or externally within an outer envelope, which play a role in the infection or replication of the virus particle in a susceptible host. An example is the adenoviruses, which are nonenveloped DNA viruses with a capsid containing 252 capsomeres of at least 10 different proteins, which are involved in viral structure, cell binding, and penetration; in addition, they have slender glycoproteins projecting from the capsid. Enveloped viruses are more complicated in their structure. Herpesviruses, for example, have an inner core consisting of DNA wound around a proteinaceous scaffold and surrounded by a capsid of 162 capsomeres, a protein-filled tegument, and finally an outer lipophilic envelope containing numerous glycoproteins and evenly dispersed surface spikes. Another group is the enveloped orthomyxoviruses, which contain two envelope-associated surface proteins that are involved in virus infectivity: hemagglutinins, which bind the virus to the recipient cell, and neuraminidases, which break down muramic acid in the protective mucopolysaccharide layer, which is found on the surfaces of target epithelial cells and allows contact with sensitive cellular receptor proteins. Additional proteins can be associated with the viral nucleic acid, including nucleic acid polymerases; for example, retroviruses are RNA viruses that contain reverse transcriptases that allow the generation of DNA from the viral RNA molecule, which is subsequently transcribed and translated to produce viral proteins in the host.

FIGURE 1.10 Basic viral structure.

Based on these basic viral structures, a variety of virus families which vary in shape and composition have been described. Examples of virus families are given in Table 1.13, but this list is not complete. For example, at least 20 families of viruses that are of medical importance and that vary in size, shape, and chemical composition have been identified; additional virus families have been described for plants, fungi, protozoa, and bacteria.

Viruses are dependent on host cells for survival and multiplication. Despite the range of viruses described, viral infection occurs in a similar series of steps: attachment, penetration, synthesis of biomolecules, assembly, and release (Fig. 1.11). The first stage is attachment of the virus to the cell surface. This is mediated by specific proteins on the capsid or envelope surface that specifically interact with molecules on the cell surface known as receptors. Receptors can be cell membrane or cell wall proteins, lipids, carbohydrates, and even combinations of these. Therefore, the presence of specific receptors on the cell surface determines sensitivity or resistance to virus infection. Examples of receptors include the HIV receptor CD4 protein on the surfaces of human T cells and the binding of influenza virus to sialic acid, a carbohydrate linked to a cell membrane protein.

The next stage is penetration of the virus into the target cell, which can occur by different mechanisms. The nucleocapsid or nucleic acid, as the source genetic material that encodes the viral structure, can be injected or released into the cell. Similarly, the whole virus can be endocytosed into the cell or, in the case of enveloped viruses, by fusion with the cell membrane, which is subsequently uncoated to allow nucleic acid release. Endocytosis is typical for penetration of many vertebrate viruses. As mentioned above, some enzymes that are associated with the virus capsid are required for viral multiplication (e.g., reverse transcriptase in retroviruses, such as HIV) and are released into the target cell. In some viruses, the nucleic acid is modified (e.g., by methylation) to protect it from damage (by nucleases) when it is free in the cell. Once the cell is infected, the virus uses the available cell metabolic processes to replicate its nucleic acid and to allow the synthesis of specific viral proteins during the multiplication stage. Multiplication depends on the transcription and translation of viral mRNA. For DNA viruses, this can be achieved by the use of existing host enzymes, such as DNA-dependant RNA polymerases; in the case of RNA viruses, it may require specific viral proteins. An example already mentioned is the use of reverse transcriptase in retroviral multiplication, which generates DNA from a single-stranded RNA virus template. The viral proteins that are subsequently produced can be involved in the multiplication process (e.g., viral replication) or as structural parts of the virus. If viral multiplication continues, the cell will eventually burst or lyse to release the viral particles (Fig. 1.11, step 4a); an example is poliovirus. Lysing, however, does not occur with all viruses. A further mechanism of virus release is budding from the cell surface, which produces a persistent infection in a cell. Examples include influenza virus and HIV; it should be noted that both of these are enveloped viruses and that the viral envelope is actually formed around the viral nucleocapsid during the budding release from the cell surface. Some viruses can remain dormant in their host cells; these are referred to as latent infections, which can reactivate at a later stage to cause disease. During dormancy, the virus may not affect the normal cellular functions. An example of a virus causing latent infection is the varicellazoster virus, which can remain dormant in neurons; varicella-zoster virus can cause chickenpox, commonly in children, and can reactivate to cause shingles, which is more prevalent in adults. In some cases, the presence of the virus may also trigger the uncontrolled growth of cells, leading to the development of cancers. Strong associations of viruses with cancers include papillomaviruses with skin and cervical cancers and some herpesviruses with lymphomas and carcinomas.

TABLE 1.13 Viral families, with examples of classifications, including size, presence of a lipophilic envelope, and nucleic acid type

Viral family	Structure	Size (nm)	Envelope	Nucleic acid	Example(s)
Parvoviridae		18–26	No	DNA	Mouse parvovirus, parvovirus B 19
Flaviviridae		40–50	Yes	RNA	Ebola virus, Marburg virus
Adenoviridae		70–90	No	DNA	Adenovirus serotypes
Retroviridae		90–120	Yes	RNA	HIV type 1
Herpesviridae		180–200	Yes	RNA	Epstein-Barr virus, herpes simplex virus
Poxviridae		250–400	Yes	DNA	Monkeypox virus, variola (smallpox) virus

FIGURE 1.11 Typical viral life cycle. The stages include (1) attachment, (2) penetration into the cell, and (3) multiplication. Depending on the virus type, viral particles can be released by cell lysis (4a) or by budding (4b); alternatively, the virus can remain dormant in the cell (4c).

Viruses have been identified as the causes of a variety of plant, human, and animal diseases, including respiratory, sexually transmitted, neurological, and dermatological diseases (Table 1.14). The traditional difficulty of isolation and identification of viruses limits their study; however, it is thought that many more viruses remain to be identified and implicated in diseases by developing molecular biology and electron microscopy techniques.

Separate families of plant viruses have also been described, including tobamoviruses (nonenveloped RNA viruses; e.g., tomato-tobacco mosaic virus is a significant agricultural and horticultural concern, because it infects vegetables, flowers, and weeds, leading to leaf, flower, and fruit damage), Comoviridae (nonenveloped RNA viruses), and Geminiviridae (nonenveloped DNA viruses). Viruses that infect fungi (e.g., the nonenveloped RNA viruses barnavirus and chryovirus) and bacteria (bacteriophages) (Fig. 1.12) have also been described.

TABLE 1.14 Examples of viral diseases

Family and virus	Disease(s)
Parvoviridae (DNA, nonenveloped)
Human parvovirus B19	Erythema infectiosum (fifth disease)
Minute virus of mice	Cell line contamination, oncolysis
Papovaviridae (DNA, nonenveloped)
Human papillomavirus	Cervical cancer, genital warts
Picornaviridae (RNA, nonenveloped)
Poliovirus	Poliomyelitis
Rhinoviruses	Common cold
Coxsackievirus A16	Foot-and-mouth disease
Retroviridae (RNA, enveloped)
HIV type 1	AIDS
Human T-cell leukemia virus type 1	Human T-cell leukemia
Orthomyxoviridae (RNA, enveloped)
Influenza viruses A, B, and C	Influenza, pharyngitis
Hepadnaviridae (DNA, enveloped)
Hepatitis B virus	Hepatitis
Poxviridae (DNA, enveloped)
Variola virus	Smallpox
Vaccinia virus	Smallpox vaccine
Rhabdoviridae (RNA, enveloped)
Rabies virus	Rabies, paralysis
Vesicular stomatitis virus	Similar to foot-and-mouth disease; flu-like
Coronaviridae (RNA, enveloped)
Human coronavirus	Severe acute respiratory syndrome, colds
Mouse hepatitis virus	Wasting syndrome
Herpesviridae (DNA, enveloped)
Herpesvirus (herpes simplex virus types 1 and 2)	Conjunctivitis, gingivostomatitis, genital herpes, meningitis
Varicella-zoster virus	Chickenpox/shingles

Bacteriophages (commonly known as phages) are mostly DNA viruses (e.g., the T3, T7, and lambda [λ] phages are E. coli viruses), although some RNA viruses have been described (e.g., nonenveloped MS2 and enveloped ϕ6 E. coli phages). Bacteriophages have been studied for many years as genetic-engineering tools, but they have other practical applications, including uses in typing of bacteria and as indicators of fecal contamination in water and limited medical applications (such as antibacterials). Lactobacillus phages are a significant contamination concern in the dairy industry. Phages are considered to be resistant to biocides, like other animal and plant viruses, and are therefore used to investigate biocidal activities (e.g., MS2 phage) and modes of action. They can be routinely cultured and purified in most bacteriology laboratories.

FIGURE 1.12 E. coli bacteriophages. The T-phages are complex DNA viruses; MS2 and ϕ6 are RNA viruses, with ϕ6 enveloped.

Two other groups of infectious agents are also considered “viruses” but have unique morphologies. The first are viroids, which are devoid of protein and appear to consist of naked RNA molecules. The second are proposed to be devoid of a nucleic acid and are termed “prions”; these are discussed in further detail in section 1.3.6. Viroids are known to infect only higher plants and have been identified as the causes of a number of crop diseases. Examples are potato spindle tuber viroid, coconut cadang-cadang viroid, and tomato apical stunt viroid. They consist only of small, circular RNA sequences that range in size from 246 to 375 nucleotides. It is interesting that their sequences do not encode proteins and that they are dependent on the host for replication in the cell nucleus. Although at first it would seem that these agents would not survive well in the environment, their structures are somewhat protected by forming double-stranded portions (by base pairing) within their circular, single-stranded structures. Although no human viroids have been identified, hepatitis D (delta) virus is similar to a viroid and is known as a satellite virus. A satellite virus is an agent that consists of a nucleic acid and that depends on the coinfection of a host with another virus, which is required for its replication. Hepatitis delta virus appears to be a defective transmissible pathogen that is dependent on hepatitis B virus. It consists of a circular RNA molecule (~1,680 bp), but unlike a true viroid, it does encode a capsid protein. The virus consists of a nucleocapsid of 60 proteins surrounding the RNA molecule and an external envelope of lipid and hepatitis B surface antigens.