Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing

Andrew Routh, Phillip Ordoukhanian, John E. Johnson

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Next-generation sequencing has been used in numerous investigations to characterize and quantify the genetic diversity of a virus sample through the mapping of polymorphisms and measurement of mutation frequencies. Next-generation sequencing has also been employed to identify recombination events occurring within the genomes of higher organisms, for example, detecting alternative RNA splicing events and oncogenic chromosomal rearrangements. Here, we combine these two approaches to profile RNA recombination within the encapsidated genome of a eukaryotic RNA virus, flock house virus. We detect hundreds of thousands of recombination events, with single-nucleotide resolution, which result in diversity in the encapsidated genome rivaling that due to mismatch mutation. We detect previously identified defective RNAs as well as many other abundant and novel defective RNAs. Our approach is exceptionally sensitive and unbiased and requires no prior knowledge beyond the virus genome sequence. RNA recombination is a powerful driving force behind the evolution and adaptation of RNA viruses. The strategy implemented here is widely applicable and provides a highly detailed description of the complex mutational landscape of the transmissible viral genome.

Original languageEnglish (US)
Pages (from-to)257-269
Number of pages13
JournalJournal of Molecular Biology
Issue number5
StatePublished - Dec 14 2012
Externally publishedYes


  • deep sequencing
  • defective RNAs
  • flock house virus
  • virus-like particles

ASJC Scopus subject areas

  • Structural Biology
  • Molecular Biology


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