Estimation of the in vivo recombination rate for a plant RNA virus

[EN] Phylogenomic evidence suggested that recombination is an important evolutionary force for potyviruses, one of the larger families of plant RNA viruses. However, mixed-genotype potyvirus infections are marked by low levels of cellular coinfection, precluding template switching and recombination events between virus genotypes during genomic RNA replication. To reconcile these conflicting observations, we evaluated the in vivo recombination rate (r(g)) of Tobacco etch virus (TEV; genus Potyvirus, family Potyviridae) by coinfecting plants with pairs of genotypes marked with engineered restriction sites as neutral markers. The recombination rate was then estimated using two different approaches: (i) a classical approach that assumed recombination between marked genotypes can occur in the whole virus population, rendering an estimate of r(g)=7.762x10(-8) recombination events per nucleotide site per generation, and (ii) an alternative method that assumed recombination between marked genotypes can occur only in coinfected cells, rendering a much higher estimate of r(g)=3.427x10(-8) recombination events per nucleotide site per generation. This last estimate is similar to the TEV mutation rate, suggesting that recombination should be at least as important as point mutation in creating variability. Finally, we compared our mutation and recombination rate estimates to those reported for animal RNA viruses. Our analysis suggested that high recombination rates may be an unavoidable consequence of selection for fast replication at the cost of low fidelity.We thank Francisca de la Iglesia and Angels Prosper for excellent technical assistance, Jose A. Dare's for methodological advice, Jose M. Cuevas for critical reading of the manuscript, and other lab members for helpful discussions. This work was supported by the Spanish Secretaria de Estado de Investigacion, Desarrollo e Innovacion (grants BFU2009-06993 and BFU2012-30805). N. T. was supported,by a pre-doctoral fellowship from the former Spanish Ministerio de Ciencia e Innovacion.Tromas, N.; Zwart, MP.; Poulain, M.; Elena Fito, SF. (2014). Estimation of the in vivo recombination rate for a plant RNA virus. Journal of General Virology. 95:724-732. https://doi.org/10.1099/vir.0.060822-0S7247329