Mechanisms of viral mutation

Abstract

The remarkable capacity of some viruses to adapt to new hosts and environments is highly dependent on their ability to generate de novo diversity in a short period of time. Rates of spontaneous mutation vary amply among viruses. RNA viruses mutate faster than DNA viruses, single-stranded viruses mutate faster than double-strand virus, and genome size appears to correlate negatively with mutation rate. Viral mutation rates are modulated at different levels, including polymerase fidelity, sequence context, template secondary structure, cellular microenvironment, replication mechanisms, proofreading, and access to post-replicative repair. Additionally, massive numbers of mutations can be introduced by some virus-encoded diversity-generating elements, as well as by host-encoded cytidine/adenine deaminases. Our current knowledge of viral mutation rates indicates that viral genetic diversity is determined by multiple virus- and host-dependent processes, and that viral mutation rates can evolve in response to specific selective pressures.

Keywords: Evolution; Genetic diversity; Hyper-mutation; Mutation rate; Post-replicative repair; Replication fidelity; Virus.

Fig. 1

Mutation rate definition. a Basic processes determining population genetic diversity. The observed population frequency of a mutation depends on the rate at which it is produced (mutation rate), but also on natural selection, random genetic drift, and recombination, among other processes. Most mutations are deleterious and tend to be removed from the population by selection, whereas beneficial mutations or combinations of mutations can be maintained/favored. Recombination can also contribute to the maintenance of genetic diversity. Random genetic drift leads to allele fixation and hence reduces population genetic diversity. b Basic processes determining viral mutation rates. Mutations originate from replication errors, nucleic acid damage, and editing of the genetic material by host-encoded proteins or by specialized molecular systems such as diversity-generating retro-elements (DGRs). If these changes are not corrected, they will be passed to the viral progeny and hence will contribute to elevating the viral mutation rate. Expression of host error-prone polymerases may also contribute to creating new mutations in viruses. Recombination can also enhance the ability of some viruses to create new mutations by increasing gene copy number or by producing genome rearrangements

Fig. 2

Mutation rate variation across viruses. a Range of variation of mutation rates for the seven Baltimore classes of viruses (ss single-strand, ds double-strand; +/− genome polarity, RT retroviruses, pRT para-retroviruses). In the RT group, all mutation rates fall in the non-hatched arrow region except the HIV-1 mutation rate measured in cellular DNA, which is orders of magnitude higher than the rate measured in plasma. This is because many APOBEC-edited viral genomes fail to produce viable progeny and hence do not reach plasma (see text for details). b Negative correlation between genome size and mutation rate in viruses. Baltimore groups are indicated. The observed correlation can be explained in terms of differences between RNA and DNA viruses and between ss and ds viruses. In the RT group, the extremely high mutation rate of HIV-1 in cellular DNA is indicated with an arrow. In contrast, the HIV-1 mutation rate measured in plasma falls within the usual RT range

Fig. 3

Viral replication modes and mutation accumulation. a Stamping machine versus semi-conservative replication. As opposed to cells, which use only semi-conservative replication, viruses can adopt a variety of replication modes. In the stamping machine model, a single template strand is used to synthesize all progeny genomes within a given cell. However, this is not possible in practice because replication requires synthesis of complementary strands or “anti-genomes” (blue). Under this model, the mutation frequency after one cell infection cycle will equal the mutation rate except if mutations occur during the first round of copying (from genome to anti-genome), in which case they will be present in all of the viral progeny. Under semi-conservative replication, multiple rounds of copying are required to produce enough progeny, thus allowing for the intra-cellular accumulation of mutations. b Relationship between lysis time and mutation accumulation. Longer cell infection cycles (late burst) can allow for the production of more progeny viruses. Under semi-conservative replication, this will require more rounds of copying but, if replication follows the stamping machine model, the number of rounds of copying will not change (more progeny genomes will be produced from the same template). Hence under this model, a late-burst virus variant will undergo fewer total rounds of copying at the population scale than early-burst variants and will tend to accumulate fewer mutations

Fig. 4

Cell culture systems for the accumulation of mutations in the absence of selection. a HIV-1 shuttle vector. The vector contains only cis-acting HIV-1 sequences such as the Rev-responsive element (RRE), the encapsidation signal (Ψ), and the long terminal repeats (LTR). A resistance gene (RES, red) is inserted to allow for the selection of cells containing the vector. Any (short) sequence of interest (SEQ, blue), including HIV sequences, can be cloned in the shuttle vector and propagated in the absence of selection. The shuttle vector DNA is co-transfected with helper plasmids encoding the Gag (capsid) and Pol (RT, integrase) proteins as well as a viral glycoprotein suited for transducing a given cell line (here vesicular stomatitis G protein, VSV-G, which has a broad tropism). Pseudotyped viruses are produced, used for transduction, and cells carrying the retroviral shuttle vector are selected with the appropriate antibiotic. The infection cycle can be restarted at any time by transfecting the two helper plasmids. The SEQ DNA is then extracted, PCR-amplified, and sequenced to score mutations. b HCV replicon. Two cistrons are separated by an internal ribosome entry site (IRES). The right cistron encodes HCV non-structural (NS) proteins required for replication, but lacks the envelope proteins and hence does not support viral budding. The left replicon carries a resistance gene to select cells carrying the replicon. Reporters such as luciferase can be also cloned in this cistron. Since these play no function, they can be replaced with any short sequence of interest (SEQ), including HCV sequences. Replicon RNA is obtained by in vitro transcription and transfected into Huh7 hepatoma cells. Cells are selected using the appropriate antibiotic and passaged before confluence to allow vigorous replication of the viral RNA. The SEQ RNA is reverse-transcribed, PCR-amplified, and sequenced to score mutations