Recombination in Enteroviruses Is a Biphasic Replicative Process Involving the Generation of Greater-Than Genome Length 'Imprecise' Intermediates

PLoS Pathog. 2014 Jun 12;10(6):e1004191. doi: 10.1371/journal.ppat.1004191. eCollection 2014 Jun.


Recombination in enteroviruses provides an evolutionary mechanism for acquiring extensive regions of novel sequence, is suggested to have a role in genotype diversity and is known to have been key to the emergence of novel neuropathogenic variants of poliovirus. Despite the importance of this evolutionary mechanism, the recombination process remains relatively poorly understood. We investigated heterologous recombination using a novel reverse genetic approach that resulted in the isolation of intermediate chimeric intertypic polioviruses bearing genomes with extensive duplicated sequences at the recombination junction. Serial passage of viruses exhibiting such imprecise junctions yielded progeny with increased fitness which had lost the duplicated sequences. Mutations or inhibitors that changed polymerase fidelity or the coalescence of replication complexes markedly altered the yield of recombinants (but did not influence non-replicative recombination) indicating both that the process is replicative and that it may be possible to enhance or reduce recombination-mediated viral evolution if required. We propose that extant recombinants result from a biphasic process in which an initial recombination event is followed by a process of resolution, deleting extraneous sequences and optimizing viral fitness. This process has implications for our wider understanding of 'evolution by duplication' in the positive-strand RNA viruses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Capsid Proteins / genetics
  • Cell Line, Tumor
  • Cricetinae
  • Genetic Variation / genetics*
  • Genome, Viral / genetics*
  • HeLa Cells
  • Humans
  • Mice
  • Molecular Sequence Data
  • Nocodazole / pharmacology
  • Poliovirus / classification
  • Poliovirus / genetics*
  • Poliovirus / growth & development
  • RNA Replicase / genetics
  • RNA, Viral / genetics
  • Recombination, Genetic / genetics*
  • Sequence Analysis, RNA
  • Serial Passage
  • Tubulin Modulators / pharmacology
  • Untranslated Regions / genetics
  • Virus Replication / drug effects
  • Virus Replication / genetics


  • Capsid Proteins
  • RNA, Viral
  • Tubulin Modulators
  • Untranslated Regions
  • RNA Replicase
  • Nocodazole

Associated data

  • GENBANK/V01149
  • GENBANK/X00925