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 × 10−5 to 4 × 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.

Risks from GMOs due to Horizontal Gene Transfer

“…Using Cauliflower mosaic virus as a model, over 50% of viral genomes recovered after a single host infection were recombinant with an estimated baseline recombination frequency of 2−4 × 10 −5 per base each replication cycle (Froissart et al, 2005). Other studies support these findings of recombination amongst many groups of viruses (Aaziz and Tepfer, 1999;Banner and Lai, 1991;Bruyère et al, 2000;Revers et al, 1996;Rokyta et al, 2006) and viroids (Keese and Symons, 1985;Rezaian, 1990).…”

“…One study that measured the rate of recombination demonstrated frequent HGT between viruses during every infection, higher than the rate of mutations per base (Froissart et al, 2005). Using Cauliflower mosaic virus as a model, over 50% of viral genomes recovered after a single host infection were recombinant with an estimated baseline recombination frequency of 2−4 × 10 −5 per base each replication cycle (Froissart et al, 2005).…”

Diversity of Plant Virus Populations: A Valuable Tool for Epidemiological Studies

“…However, in spite of the relevant epidemiological role of genetic exchange, till date, little information is available on the rates with which it occurs in plant viruses in the absence of selection. Recombination rates have been experimentally estimated in coinfections of different genotypes of Brome mosaic virus [28,29], Cauliflower mosaic virus (CaMV) [30] and TEV [31]. Although results obtained should be compared with caution, they are similar (particularly those of CaMV and TEV) and as high as mutation rates (at least for TEV), indicating that recombination may be as relevant as mutation in creating variability [31].…”

Risks from GMOs due to Horizontal Gene Transfer

“…Furthermore, to give rise to increased risk, the recombinant virus that acquires a viral transgene should also be more harmful than the parental virus and arise more frequently than background levels of viral HGT. Although recombination events in viruses have sometimes contributed to greater disease burden (Legg and Thresh, 2000), these cases represent only a minute fraction of all HGT events (Froissart et al, 2005).…”