Recombination in natural populations of watermelon mosaic virus: new agronomic threat or damp squib?

Abstract

Since their introduction in southeastern France around 1999, new, 'emerging' (EM) strains of watermelon mosaic virus (WMV) coexist with the 'classic' (CL) strains present for more than 40 years. This situation constitutes a unique opportunity to estimate the frequency of recombinants appearing in the few years following introduction of new strains of a plant RNA virus. Molecular analyses performed on more than 1000 isolates from epidemiological surveys (2004-2008) and from experimental plots (2009-2010), and targeting only recombinants that became predominant in at least one plant, revealed at least seven independent CL/EM or EM/EM recombination events. The frequency of recombinants involving at least one EM parent in the natural populations tested was on the order of 1 %. No new recombinant was detected for more than 1 year, and none but one in more than one location. In tests comparing host range and aphid transmissibility, the new recombinants did not display a better fitness than their 'parental' isolates. No recombinant was detected from artificial mixed infections of CL and EM isolates of various hosts after testing more than 1500 subcultures obtained after single-aphid transmission. These results constitute one of the first estimations of the frequency of recombinants in natural conditions for a plant RNA virus. This suggests that although viable recombinants of WMV are not rare, and although recombination may potentially lead to new highly damaging strains, the new recombinants observed so far had a lower fitness than the parental strains and did not emerge durably in the populations. The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this study are shown in Table 1.

Evidence for positive selection and recombination hotspots in Deformed wing virus (DWV)

“…The advantage of recombination has largely been debated. Usually, recombinants are thought to be less fit than their parents, on average, and this has been demonstrated in several RNA viruses4748. The fact that we observed recombination hotspots close to the frontiers of the three proposed modules of the DWV genome suggests that these hotspots may result from selective pressure favoring these recombinants because they globally preserve the three functional modules that are essential for virus survival and dispersal49.…”

Distribution and partial properties of three viruses infecting cucumber in West Iran and their reservoir weed hosts

“…AJ420019). Some recombinants tend to invade populations (Desbiez et al 2011), but since the timing of contact between the parental strains is usually unknown, the real recombination frequency and kinetics of recombinant emergence in natural conditions remains an open question.…”

The evolution of soybean mosaic virus: An updated analysis by obtaining 18 new genomic sequences of Chinese strains/isolates

“…They had occurred in ancestral SMV isolates and were well-inherited by multiple descendent sequences. Frequent intraspecific recombination has been observed in many potyviruses such as WMV (Desbiez et al, 2011), PVY (Cuevas et al, 2012), TuMV (Nguyen et al, 2013), and BCMV (Revers et al, 1996;Zhou et al, 2014). On the other hand, interspecific recombination was also likely to happen in potyviruses (Ali et al, 2006;Larsen et al, 2005).…”