Viral Mutation Rates

The quasispecies model defines an optimal mutation rate for evolving populations (Eigen et al., 1988). At the critical mutation rate pmml (referred to as the error threshold), the distribution becomes too broad for selection to withstand the dispersion and it wanders stochastically on the fitness landscape. The optimal mutation rate for evolvability should be as close to pm Crit as possible without exceeding it. Indeed, it was found that viral mutation rates are very close to pm m,. By assuming that the mutation probability is the same at each residue, the error threshold in terms of mutation rate pm ai, was derived as... 

Like most viral RNA polymerases, NS5B does not possess 3 -5 exonuclease editing capability and is relatively error prone. This results in a mutation rate of approximately 1.4 x 10 nucleotide changes per site per year [18, 19]. Combined with the estimated production of up to 10 virions per day in an infected individual [20], HCV sequences clearly have the potential to evolve rapidly. This results in the appearance of multiple sequence variants or quasi-species in each infected individual [21]. 

Single agents are seldom used to treat HIV infection. Instead, multidrug therapy is used to counteract the rapid mutation rate of HIV and to minimize drug toxicity. Highly active antiretroviral therapy (HAART) uses combinations of reverse transcriptase inhibitors and protease inhibitors (Table 51.1). In this system, drugs working by different mechanisms produce a sequential blockade of steps required for viral reproduction. It is... 

Artificially enhanced error rates needed for the creation of sequence diversity in a population can be achieved readily with PCR. Reverse transcription and transcription are also susceptible to increase of mutation rates. These two and other new techniques for RNA amplification provide universal and efficient tools for the study of molecular evolution under laboratory conditions and make the usage of viral replicases with their undesirable sequence specificities obsolete. 

Unlike E. coli DNA polymerases, there is no 30 to 50 exonuclease proofreading activity in the E. coli RNA polymerase and, therefore, the error rate is relatively higher (-10-410-5). Since RNA represents only a transient copy of DNA, and is not inherited through the germ line, this error frequency is tolerable. As discussed in Chapter 30, viral RNA polymerases and another enzyme, reverse transcriptase, which also lacks proofreading activity, have error frequencies in the same range as the bacterial RNA polymerase. This mutation rate is most likely beneficial to some viruses because it results in frequent alterations in viral protein sequences and thus allows the virus to escape immune-system defenses in the host (Chapter 30). 

Role of RNA intermediates (Herbert and Rich, 1999). The mutation rate of a genome is likely to increase when genetic information is passed through RNA whether RNA is a viral genome or a retrotransposon because RNA polymerase reaction is neither edited nor subject to post-replicative repair. In addition, hotspots of a genetic chain in RNA retrotransposons can result from nomandom patterns of a decreased fidelity strand transfer to other templates and untemplated extensions. 

The emergence of HIV drng resistance against Pis is associated with accumulation of numerous mutations (mainly) in the HIV PR. The mutation rate of the HIV is very high due to the lack of proofreading activity of the viral reverse transcriptase, and the rapid viral replication in infected persons lead to a selection of viral species resistant to the virostatics that are currently available. The pattern of mutations associated with viral resistance is very complex, and a proper description of the mechanism of resistance development is outside the scope of this chapter (see Weber, 2009 and the references therein). The mutations are selected not only in the protease substrate-binding cleft, but also outside the active site of the enzyme (Figure 3.3). 

The reverse transcriptase enzyme (RT) is the primary enzyme responsible for the conversion of the viral single-strand RNA to the double-strand DNA. The reverse transcriptase enzyme is a component of the virion and is encoded by the pol gene. The RT is manufactured in the HIV-infected cells as a gag-pol fusion polyprotein. The RT is not the only enzyme necessary for the translation of RNA to DNA. The other enzymes for this conversion include RNA-dependent DNA polymerase, DNA-dependent DNA polymerase, and RNase H (Gilboa and Mitra, 1978 Prasad and Gogg, 1990). The reverse transcriptase enzyme has a high error rate (1 in 2000 bases), which produces higher incidents of mutation. Some of these mutations make the virus resistant to NNRTI treatment. 

Mechanism of Action An antiviral agent that incorporates into DNS causing increased rate of mutation and errors in protein formation. T herapeutic Effect Prevents viral replication. 

After reaching the lymph nodes, CD4+ cells are rapidly infected and replication of the virus continues. During the initial phase of infection, the virus is spread throughout the body via blood that contains many viral particles. The flu-like symptoms are first observed in about 70% of the patients 2-A weeks after HIV infection. At this stage, HIV titer is reduced due to the development of virus-specific CD8+ cells and due to humoral immune response, which generally causes a return to the normal numbers of CD4+ cells. As the HIV continues to replicate, a person may stay free of HIV-related symptoms for years. The high rate of mutation makes it impossible for the body to completely eliminate the HIV. Independent of mutation, certain subsets of HIV-recognizing killer T cells are not present or lack optimal function, and there is an inhibition of IFN secretion and cytotoxic T-cell activity due to impairment in the function of CD4+ cells. The HIV is also protected from immune surveillance when it hides within the chromosomes of the infected cells. 

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