Chapter 43Viral Genetics

Fleischmann WR Jr.

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General Concepts

Genetic Change in Viruses

Viruses are continuously changing as a result of genetic selection. They undergo subtle genetic changes through mutation and major genetic changes through recombination. Mutation occurs when an error is incorporated in the viral genome. Recombination occurs when coinfecting viruses exchange genetic information, creating a novel virus.


Mutation Rates and Outcomes

The mutation rates of DNA viruses approximate those of eukaryotic cells, yielding in theory one mutant virus in several hundred to many thousand genome copies. RNA viruses have much higher mutation rates, perhaps one mutation per virus genome copy. Mutations can be deleterious, neutral, or occasionally favorable. Only mutations that do not interfere with essential virus functions can persist in a virus population.

Phenotypic Variation by Mutations

Mutations can produce viruses with new antigenic determinants. The appearance of an antigenically novel virus through mutation is called antigenic drift. Antigenically altered viruses may be able to cause disease in previously resistant or immune hosts.

Vaccine Strains from Mutations

Mutations can produce viruses with a reduced pathogenicity, altered host range, or altered target cell specificity but with intact antigenicity. Such viruses can sometimes be used as vaccine strains.


Recombination involves the exchange of genetic material between two related viruses during coinfection of a host cell.

Recombination by Independent Assortment

Recombination by independent assortment can occur among viruses with segmented genomes. Genes that reside on different pieces of nucleic acid are randomly assorted. This can result in the generation of viruses with new antigenic determinants and new host ranges. Development of viruses with new antigenic determinants through independent assortment is called antigenic shift.

Recombination of Incompletely Linked Genes

Genes that reside on the same piece of nucleic acid may undergo recombination. The closer two genes are together, the rarer is recombination between them (partial linkage).

Phenotypic Variation from Recombination

Development of viruses with new antigenic determinants by either type of recombination may allow viruses to infect and cause disease in previously immune hosts.

Vaccines through Recombination

Vaccine strains of viruses can be used to create recombinant viruses that carry extra genes coding for a specific immunogen. During viral vaccination, the replicating virus will express the specific immunogen. Specific antibody production will be stimulated, and the host will be protected from the immunogen as well as from the vaccine virus.


Viruses are simple entities, lacking an energy-generating system and having very limited biosynthetic capabilities. The smallest viruses have only a few genes; the largest viruses have as many as 200. Genetically, however, viruses have many features in common with cells. Viruses are subject to mutations, the genomes of different viruses can recombine to form novel progeny, the expression of the viral genome can be regulated, and viral gene products can interact. By studying viruses, we can learn more about the mechanisms by which viruses and their host cells function.

Genetic Change in Viruses

This chapter covers the mechanisms by which genetic changes occur in viruses. Two principal mechanisms are involved: mutation and recombination. Alterations in the genetic material of a virus may lead to changes in the function of viral proteins. Such changes may result in the creation of new viral serotypes or viruses of altered virulence.


Mutations arise by one of three mechanisms: (1) by the effects of physical mutagens (UV light, x-rays) on nucleic acids; (2) by the natural behavior of the bases that make up nucleic acids (resonance from keto to enol and from amino to imino forms), and (3) through the fallibility of the enzymes that replicate the nucleic acids. The first two mechanisms act similarly in all viruses; hence, the effects of physical mutagens and the natural behavior of nucleotides are relatively constant. However, viruses differ markedly in their mutation rates, which is due primarily to differences in the fidelity with which their enzymes replicate their nucleic acids. Viruses with high-fidelity transcriptases have relatively low mutation rates and vice versa.

Mutation Rates and Outcomes

DNA viruses have mutation rates similar to those of eukaryotic cells because, like eukaryotic DNA polymerases, their replicatory enzymes have proofreading functions. The error rate for DNA viruses has been calculated to be 10-8 to 10-11 errors per incorporated nucleotide. With this low mutation rate, replication of even the most complex DNA viruses, which have 2 × 105 to 3 × 105 nucleotide pairs per genome, will generate mutants rather rarely, perhaps once in several hundred to many thousand genome copies. The RNA viruses, however, lack a proofreading function in their replicatory enzymes, and some have mutation rates that are many orders of magnitude higher—10-3 to 10-4 errors per incorporated nucleotide. Even the simplest RNA viruses, which have about 7,400 nucleotides per genome, will generate mutants frequently, perhaps as often as once per genome copy.

Not all mutations that occur persist in the virus population. Mutations that interfere with the essential functions of attachment, penetration, uncoating, replication, assembly, and release do not permit misreplication and are rapidly lost from the population. However, because of the redundancy of the genetic code, many mutations are neutral, resulting either in no change in the viral protein or in replacement of an amino acid by a functionally similar amino acid. Only mutations that do not cripple essential viral functions can persist or become fixed in a virus population.

Phenotypic Variation by Mutations

Mutations that alter the viral phenotype but are not deleterious may be important. For example, mutation can create novel antigenic determinants. A mutation in the hemagglutinin gene of influenza A virus can give rise to a hemagglutinin molecule with an altered antigenic site (epitope) (Fig. 43-1). Provided the attachment function of the new hemagglutinin is intact, the mutant virus may be able to initiate an infection in an individual immune to viruses expressing the previous hemagglutinin. For example, from 1968 to 1979, mutations altered 10 percent of the amino acids in the influenza virus hemagglutinin serotype H3 molecule. This relatively modest mechanism of antigenic change through mutation, called antigenic drift, may allow a virus to outflank host defenses and cause disease in previously immune individuals.

Figure 43-1. Mutation causing phenotypic (antigenic) variation.

Figure 43-1

Mutation causing phenotypic (antigenic) variation. . Mutation of the codon for the hydrophilic amino acid serine to the codon for the hydrophobic amino acid phenylalanine can change an epitope on the viral hemagglutinin protein and thereby alter its recognition (more...)

Vaccine Strains from Mutations

Mutation has been a principal tool of virologists in developing attenuated live virus vaccines (Table 43-1). For example, the Sabin vaccine strains of poliovirus were developed by growing polioviruses in monkey kidney cells. Mutation and selection produced variant polioviruses that were adapted for efficient replication in these cells. Some of the mutations in these variants affected the genes coding for the poliovirus coat proteins in such a way as to produce mutants unable to attach to human neural cells but still able to infect human intestinal cells. Infection of human intestinal cells does not produce paralytic disease but does induce immunity. Poliovirus vaccine strains 1 and 2 have multiple mutations in the coat proteins and are very stable. The type 3 vaccine strain is less stable and is subject to back-mutations (reversions) that restore neural virulence. This vaccine strain therefore causes paralytic disease in one out of every several million vaccinated individuals. Despite the possibility of back-mutations, the generation and selection of attenuated viral mutants remains an important mechanism for producing viral vaccines.

Table 43-1. Live Attenuated Virus Vaccines.

Table 43-1

Live Attenuated Virus Vaccines.


Viral recombination occurs when viruses of two different parent strains coinfect the same host cell and interact during replication to generate virus progeny that have some genes from both parents. Recombination generally occurs between members of the same virus type (e.g., between two influenza viruses or between two herpes simplex viruses). Two mechanisms of recombination have been observed for viruses: independent assortment and incomplete linkage. Either mechanism can produce new viral serotypes or viruses with altered virulence.

Recombination by Independent Assortment

Independent assortment occurs when viruses that have multipartite (segmented) genomes trade segments during replication (Fig. 43-2). These genes are unlinked and assort at random. Recombination by independent assortment has been reported, for example, for the influenza viruses and other orthomyxoviruses (8 segments of single-stranded RNA) and for the reoviruses (10 segments of double-stranded RNA). The frequency of recombination by independent assortment is 6 to 20 percent for orthomyxoviruses. Independent assortment between an animal and a human strain of influenza virus (see Ch. 58) during a mixed infection can yield an antigenically novel influenza virus strain capable of infecting humans but carrying animal-strain hemagglutinin and/or neuraminidase surface molecules. This recombinant can infect individuals that are immune to the parent human virus. This mechanism results in an immediate, major antigenic change and is called antigenic shift. Antigenic shifts in influenza virus antigens can give rise to pandemics (worldwide epidemics) of influenza. Such antigenic shifts have occurred relatively frequently during recent history (Table 43-2). Because the number of different serotypes of hemagglutinin and neuraminidase are limited, a given strain reappears from time to time. For example, the H1N1 influenza virus strain was responsible for the 1918 to 1919 influenza pandemic that caused 20 million deaths. The same virus also caused pandemics in 1934 and in 1947, then disappeared after 1958 and reappeared in 1977. The reappearance of virus strains after an absence is believed to be the result of recombinational events involving the independent assortment of genes from two variant viruses.

Figure 43-2. Recombination by independent assortment during dual infection.

Figure 43-2

Recombination by independent assortment during dual infection. After infection of a cell with two viruses with two or more genetic segments (“chromosomes”), reassortment of the replicated segments can occur. Independent assortment results (more...)

Table 43-2. Antigenic Shifts Resulting from Reassortment of Genome Segments.

Table 43-2

Antigenic Shifts Resulting from Reassortment of Genome Segments.

Recombination of Incompletely Linked Genes

Recombination also occurs between genes residing on the same piece of nucleic acid (Fig. 43-3). Genes that generally segregate together are called linked genes. If recombination occurs between them, the linkage is said to be incomplete. Recombination of incompletely linked genes occurs in all DNA viruses that have been studied and in several RNA viruses.

Figure 43-3. Recombination by break-rejoin of incompletely linked genes.

Figure 43-3

Recombination by break-rejoin of incompletely linked genes. . The genetic interaction of DNA viruses can result in break-rejoin recombination, in which the two DNA molecules of different viruses break and then cross over. Break-rejoin recombination results (more...)

In DNA viruses, as in prokaryotic and eukaryotic cells, recombination between incompletely linked genes occurs by means of a break-rejoin mechanism. This mechanism involves the actual severing of the covalent bonds linking the bases of each of the two DNA strands in a DNA molecule (Fig. 43-3). The severed DNA strands are then rejoined to the DNA strands of a different DNA molecule that has been broken in a similar site. Recombination rates for herpesviruses, which are DNA viruses that replicate in the nucleus of infected cells, approximate those expected for a eukaryotic genome of the size of the herpesvirus genome. Herpesviruses have an average recombination frequency of 10 to 20 percent for any two loci. However, the rate of recombination between a specific pair of genetic loci depends on the distance between them and varies from less than 1 percent to approximately 50 percent. Measurement of the recombination frequencies for different loci can be used to map the virus genome. In this type of genetic map, loci with high recombination frequencies are far apart and loci with low recombination frequencies are close together.

Recombination has been shown to occur in several positive-sense single-stranded RNA virus groups: retroviruses, picornaviruses, and coronaviruses. That is initially surprising, as recombination between RNA molecules has not been observed in prokaryotic or eukaryotic cells. In retroviruses, recombination actually occurs at the point in replication when the retrovirus genome is in a DNA form and takes place by the same break-rejoin mechanism as in cells and DNA viruses. Recombination can occur both between two related retroviruses and between the retrovirus DNA and the host cell DNA. Recombination between two retroviruses gives rise to novel viral progeny with reassorted genes. Recombination between retroviruses and the host cell can give rise to novel viral progeny that carry nonviral genes. If these host genes code for growth factors, growth factor receptors, or a number of other specific cellular proteins, the recombinant retroviruses may be oncogenic (see Ch. 47).

In picornaviruses and coronaviruses, recombination takes place at the level of the interaction of the viral RNA genomes and is not believed to occur by a break-rejoin mechanism. The mechanism is currently believed to be a copy-choice mechanism (Fig. 43-4). Copy-choice may occur in these RNA viruses because the viral RNA polymerase binds to only a few bases of the template RNA at any one time. Such a weak interaction of the polymerase with the template RNA would permit the polymerase, carrying its RNA strand, to disassociate from the original template nucleic acid strand and then associate with a new template RNA strand. Recombination frequencies in the range of 0.2 to 0.4 percent have been reported. Therefore, the efficiency of this mechanism of recombination is low.

Figure 43-4. Recombination by copy-choice of incompletely linked genes. The genetic interaction of certain RNA viruses can result in copy-choice recombination.

Figure 43-4

Recombination by copy-choice of incompletely linked genes. The genetic interaction of certain RNA viruses can result in copy-choice recombination. In this mechanism, the polymerase begins replicating RNA template. By an unknown mechanism, which may involve (more...)

Phenotypic Variation from Recombination

As mentioned above, viral recombination is important because it can generate novel progeny viruses that express new antigenic and/or virulence characteristics. For example, the novel progeny viruses may have new surface proteins that permit them to infect previously resistant individuals; they may have altered virulence characteristics; they may have novel combinations of proteins that make them infective to new cells in the original host or to new hosts; or they may carry material of cellular origin that gives them oncogenic potential.

Vaccines and Gene Therapy through Recombination

Recombination is being used experimentally by virologists to create new vaccines. Vaccinia virus, a DNA virus of the poxvirus group, was used as a live vaccine in the eradication of smallpox. Recombinant vaccinia viruses are being developed that carry vaccinia virus DNA recombined with DNA from other sources (exogenous DNA) (Fig. 43-5). For example, vaccinia virus strains carrying DNA coding for bacterial and viral antigens have been produced. It is expected that after vaccination with the recombinant vaccinia virus, the bacterial or viral antigen (immunogen) will be produced. The presence of this immunogen will then stimulate specific antibody production by the host, resulting in protection of the host from the immunogen. Studies with these live, recombinant vaccinia viruses are currently under way to determine whether inoculation of the skin with the recombinant virus can induce a protective host antibody response to the bacterial or viral antigens. Other studies are investigating the use of live, recombinant adenoviruses containing bacterial or viral genes to infect the gastrointestinal tract and induce both mucosal and systemic immunity.

Figure 43-5. Development of recombinant vaccinia virus for immunization against cholera toxin.

Figure 43-5

Development of recombinant vaccinia virus for immunization against cholera toxin. Vaccinia virus genomic DNA is cut with an endonuclease. A specific sequence of DNA (with appropriate regulatory sequences) coding for a protein (e.g., cholera toxin) to (more...)

In a similar manner, recombinant viruses are also being developed that carry normal human genes. It is envisioned that such recombinant viruses could be useful for gene therapy. Target diseases for gene therapy span a wide range, including diabetes, cystic fibrosis, severe combined immunodeficiency syndrome, etc. Indeed, treatment of cystic fibrosis patients with replication deficient, recombinant adenoviruses bearing a normal copy of the cystic fibrosis transmembrane regulator gene has already been approved.

If these studies give positive results, such directed generation of recombinant viruses may become an important tool in the development of vaccines and for gene therapy.


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