Research Article: Evolution and Emergence of Enteroviruses through Intra- and Inter-species Recombination: Plasticity and Phenotypic Impact of Modular Genetic Exchanges in the 5’ Untranslated Region

Date Published: November 12, 2015

Publisher: Public Library of Science

Author(s): Claire Muslin, Marie-Line Joffret, Isabelle Pelletier, Bruno Blondel, Francis Delpeyroux, Adam Lauring.


Genetic recombination shapes the diversity of RNA viruses, including enteroviruses (EVs), which frequently have mosaic genomes. Pathogenic circulating vaccine-derived poliovirus (cVDPV) genomes consist of mutated vaccine poliovirus (PV) sequences encoding capsid proteins, and sequences encoding nonstructural proteins derived from other species’ C EVs, including certain coxsackieviruses A (CV-A) in particular. Many cVDPV genomes also have an exogenous 5’ untranslated region (5’ UTR). This region is involved in virulence and includes the cloverleaf (CL) and the internal ribosomal entry site, which play major roles in replication and the initiation of translation, respectively. We investigated the plasticity of the PV genome in terms of recombination in the 5’ UTR, by developing an experimental model involving the rescue of a bipartite PV/CV-A cVDPV genome rendered defective by mutations in the CL, following the co-transfection of cells with 5’ UTR RNAs from each of the four human EV species (EV-A to -D). The defective cVDPV was rescued by recombination with 5’ UTR sequences from the four EV species. Homologous and nonhomologous recombinants with large deletions or insertions in three hotspots were isolated, revealing a striking plasticity of the 5’ UTR. By contrast to the recombination of the cVDPV with the 5’ UTR of group II (EV-A and -B), which can decrease viral replication and virulence, recombination with the 5’ UTRs of group I (EV-C and -D) appeared to be evolutionarily neutral or associated with a gain in fitness. This study illustrates how the genomes of positive-strand RNA viruses can evolve into mosaic recombinant genomes through intra- or inter-species modular genetic exchanges, favoring the emergence of new recombinant lineages.

Partial Text

Two driving forces are implicated in the variability of RNA viruses: high mutation rates, which generate a population of related sequences named quasispecies, and genomic RNA recombination [1–3]. By allowing the exchange of genetic information and incorporating viral RNA fragments into new genomic contexts, recombination can eliminate lethal mutations or other genetic alterations [4–9], and increase viral pathogenicity [10–12] and fitness [7, 8, 13, 14]. Genetic recombination has shaped the genetic diversity of RNA viruses and in particular that of enteroviruses (EVs), which often show mosaic genomes [15–22].

In this study, we used an in vitro system targeting recombination to the 5’ UTR to evaluate how the PV genome tolerates 5’ UTRs from other EVs to improve our understanding of the natural evolution of cVDPVs through recombination. Surprisingly, a cVDPV genome made defective by mutagenesis of the 5’UTR could be rescued following transfection of cells with 5’ UTR sequences from the four different human EV species. In this model, we cannot determine whether recombinants were produced by the nonreplicative recombination mechanism (breakage-ligation of genomic RNAs) or the replicative one (template switching of the RNA polymerase), or both. In any case, most recombinants were nonhomologous, consistent with previous studies by our group and others using experimental models based on the rescue of defective viral genomic RNA fragments following the co-transfection of cells [5–7].




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