The Three Faces of Riboviral Spontaneous Mutation: Spectrum, Mode of Genome Replication, and Mutation Rate

Abstract

Riboviruses (RNA viruses without DNA replication intermediates) are the most abundant pathogens infecting animals and plants. Only a few riboviral infections can be controlled with antiviral drugs, mainly because of the rapid appearance of resistance mutations. Little reliable information is available concerning i) kinds and relative frequencies of mutations (the mutational spectrum), ii) mode of genome replication and mutation accumulation, and iii) rates of spontaneous mutation. To illuminate these issues, we developed a model in vivo system based on phage Qß infecting its natural host, Escherichia coli . The Qß RT gene encoding the Read-Through protein was used as a mutation reporter. To reduce uncertainties in mutation frequencies due to selection, the experimental Qß populations were established after a single cycle of infection and selection against RT − mutants during phage growth was ameliorated by plasmid-based RT complementation in trans . The dynamics of Qß genome replication were confirmed to reflect the linear process of iterative copying (the stamping-machine mode). A total of 32 RT mutants were detected among 7,517 Qß isolates. Sequencing analysis of 45 RT mutations revealed a spectrum dominated by 39 transitions, plus 4 transversions and 2 indels. A clear template•primer mismatch bias was observed: A•C>C•A>U•G>G•U> transversion mismatches. The average mutation rate per base replication was ≈9.1×10 −6 for base substitutions and ≈2.3×10 −7 for indels. The estimated mutation rate per genome replication, μ g , was ≈0.04 (or, per phage generation, ≈0.08), although secondary RT mutations arose during the growth of some RT mutants at a rate about 7-fold higher, signaling the possible impact of transitory bouts of hypermutation. These results are contrasted with those previously reported for other riboviruses to depict the current state of the art in riboviral mutagenesis.

Experimental selection reveals a trade-off between fecundity and lifespan in the coliphage Qß

“…Although the experimental population displaying the highest average B was TC 25 , the difference in average B between TB 25 and TC 25 is probably not significant considering the variability in burst size usually observed for Qß [27]. Overall, these results seem to suggest that the less the amount of time that Qß needs to invest in progeny production (due, for instance, to a faster but less stable folding of the progeny genome), the shorter is the lifespan of the progeny.…”

Contribution of Silent Mutations to Thermal Adaptation of RNA Bacteriophage Qβ

“…In addition to the four proteins covering 95.5% of the whole genome, the secondary and tertiary structures of the Q␤ RNA genome are essential for its amplification (25)(26)(27). The genome is 4,217 bases in length (25) and has a high error rate of 10 Ϫ3 to 10 Ϫ5 per base per replication (28)(29)(30)), thus facilitating genome-level experimental evolution.…”

Immunogenicity in mice of human metapneumovirus with a truncated SH glycoprotein

“…The virus recovered from mouse lung, particularly in the later stages of infection was predominantly in possession of a full SH open reading frame but one which was extensively mutated predominantly by U to C transitions. Although a predominance of U to C transitions has previously been reported in spectra of RNA virus mutations [Garcia‐Villada and Drake, ] this hypermutation is unusual and contrasts with the A to G hypermutation of the G gene among antibody escape mutants of HRSV reported by Martinez et al []. Whether these mutations modify the function of the SH glycoprotein or are responsible for the success of this unusual variant in the infection of mice in this experiment remains to be determined.…”