Recombination every day: abundant recombination in a virus during a single multi-cellular host infection

Abstract

Viral recombination can dramatically impact evolution and epidemiology. In viruses, the recombination rate depends on the frequency of genetic exchange between different viral genomes within an infected host cell and on the frequency at which such co-infections occur. While the recombination rate has been recently evaluated in experimentally co-infected cell cultures for several viruses, direct quantification at the most biologically significant level, that of a host infection, is still lacking. This study fills this gap using the cauliflower mosaic virus as a model. We distributed four neutral markers along the viral genome, and co-inoculated host plants with marker-containing and wild-type viruses. The frequency of recombinant genomes was evaluated 21 d post-inoculation. On average, over 50% of viral genomes recovered after a single host infection were recombinants, clearly indicating that recombination is very frequent in this virus. Estimates of the recombination rate show that all regions of the genome are equally affected by this process. Assuming that ten viral replication cycles occurred during our experiment-based on data on the timing of coat protein detection-the per base and replication cycle recombination rate was on the order of 2 x 10(-5) to 4 x 10(-5). This first determination of a virus recombination rate during a single multi-cellular host infection indicates that recombination is very frequent in the everyday life of this virus.

Figure 1. Genetic Map of CaMV

The CaMV genome is a circular double-stranded DNA of 8,024 bp, represented in the figure by a double line. The thick arrows with different textures represent the organization of open reading frames I to VI, encoding proteins detected in planta. Markers a, b, c, and d were engineered at the positions indicated (see Materials and Methods for precise positions). The inner black arrows represent monocistronic 19S RNA and polycistronic 35S RNA produced by the cellular machinery. The nucleotide position 0 (numbering according to [44]) indicates the origin of replication via reverse transcription, which occurs in the direction indicated by the dotted outermost circle-like arrow. Reverse transcription is accomplished by the viral reverse transcriptase, using the 35S RNA as template [49].