Population Disequilibrium as Promoter of Adaptive Explorations in Hepatitis C Virus

Abstract

Replication of RNA viruses is characterized by exploration of sequence space which facilitates their adaptation to changing environments. It is generally accepted that such exploration takes place mainly in response to positive selection, and that further diversification is boosted by modifications of virus population size, particularly bottleneck events. Our recent results with hepatitis C virus (HCV) have shown that the expansion in sequence space of a viral clone continues despite prolonged replication in a stable cell culture environment. Diagnosis of the expansion was based on the quantification of diversity indices, the occurrence of intra-population mutational waves (variations in mutant frequencies), and greater individual residue variations in mutant spectra than those anticipated from sequence alignments in data banks. In the present report, we review our previous results, and show additionally that mutational waves in amplicons from the NS5A-NS5B-coding region are equally prominent during HCV passage in the absence or presence of the mutagenic nucleotide analogues favipiravir or ribavirin. In addition, by extending our previous analysis to amplicons of the NS3- and NS5A-coding region, we provide further evidence of the incongruence between amino acid conservation scores in mutant spectra from infected patients and in the Los Alamos National Laboratory HCV data banks. We hypothesize that these observations have as a common origin a permanent state of HCV population disequilibrium even upon extensive viral replication in the absence of external selective constraints or changes in population size. Such a persistent disequilibrium—revealed by the changing composition of the mutant spectrum—may facilitate finding alternative mutational pathways for HCV antiviral resistance. The possible significance of our model for other genetically variable viruses is discussed.

Standing Genetic Diversity and Transmission Bottleneck Size Drive Adaptation in Bacteriophage Qβ

“…Recent studies carried out with the hepatitis C virus propagated under constant conditions in cell cultures showed a similar diversification of the mutant spectrum, which included some variants that were resistant to particular antiviral drugs to which the virus had not been exposed [ 21 , 62 , 63 ]. These results, like ours, show how the process of viral replication in a constant environment may lead to the emergence of mutants with selective advantages under new conditions.…”

SARS-CoV-2 Point Mutation and Deletion Spectra and Their Association with Different Disease Outcomes

“…Controls to establish the basal error, the frequency of PCR-induced recombination, and the similarity of the results with different amplifications and sequencing runs were performed previously ( 38 , 41 , 89 ). Therefore, mutations identified with a frequency above the 0.5% cutoff value and with coverage greater than 10,000 reads were considered for the analyses, based on different controls carried out with hepatitis C virus (HCV), as detailed elsewhere ( 38 , 90 ).…”

Mutation Rates, Mutation Frequencies, and Proofreading-Repair Activities in RNA Virus Genetics

“…The range of mutation rates and frequencies exhibited by RNA viruses, with or without a functional proofreading-repair activity in their replication complexes, is compatible with the rapid development of mutant spectra that are an asset for adaptability. So great is the tendency towards diversification that, at least according to studies with HCV, long-term, monotonous replication in a cell culture environment does not deter the system from continuous exploration of sequence space via expansion of the mutant spectrum [ 115 , 116 , 117 , 118 ]. An unknown in viral population dynamics is the time required for a set of infected cells to produce a sufficiently diverse population of infectious particles so as to confer adaptive value to the mutant swarm.…”

“…Either with repair activity or not, some important problems for disease control that arise from viral population dynamics are likely to apply to many viral pathogens. One is a sustained population disequilibrium even when a virus replicates extensively in an invariant biological environment (reviewed in [ 118 ]). The second problem is that limited attention has been paid to mutant spectrum dynamics in comparison with temporal variations of consensus sequences.…”