Recombination events are frequently inferred from the increasing number of sequenced viral genomes, but their impact on natural viral populations has rarely been evidenced. TYLCV-IS76 is a recombinant (Begomovirus,Geminiviridae) between the Israel strain of tomato yellow leaf curl virus (TYLCV-IL) and the Spanish strain of tomato yellow leaf curl Sardinia virus (TYLCSV-ES) that was generated most probably in the late 1990s in southern Morocco (Souss). Its emergence in the 2000s coincided with the increasing use of resistant tomato cultivars bearing the Ty-1 gene, and led eventually to the entire displacement of both parental viruses in the Souss. Here, we provide compelling evidence that this viral population shift was associated with selection of TYLCV-IS76 viruses in tomato plants and particularly in Ty-1-bearing cultivars. Real-time quantitative PCR (qPCR) monitoring revealed that TYLCV-IS76 DNA accumulation in Ty-1-bearing plants was significantly higher than that of representatives of the parental virus species in single infection or competition assays. This advantage of the recombinant in Ty-1-bearing plants was not associated with a fitness cost in a susceptible, nearly isogenic, cultivar. In competition assays in the resistant cultivar, the DNA accumulation of the TYLCV-IL clone - the parent less affected by the Ty-1 gene in single infection - dropped below the qPCR detection level at 120 days post-infection (p.i.) and below the whitefly vector (Bemisia tabaci) transmissibility level at 60 days p.i. The molecular basis of the selective advantage of TYLCV-IS76 is discussed in relation to its non-canonical recombination pattern, and the RNA-dependent RNA polymerase encoded by the Ty-1 gene.

Recombinant viruses are increasingly being reported but the dynamics of their emergence is rarely documented. A new recombinant Tomato yellow leaf curl virus (TYLCV-IS76) was detected for the first time in 2010 in Southern Morocco (Souss). An original diagnostic tool was needed to fit its unusual recombination profile. Although IS76 was detected following the appearance of Tylc symptoms on tolerant tomato plants, symptoms could not be associated to IS76 or to a synergy with criniviruses. According to infection profiles of Tylc-associated viruses determined on 879 plant samples collected between 1998 and 2014 and a Bayesian inference applied to genomic sequences of representatives of TYLCV, IS76 emerged in Southern Morocco at the end of the 1990s, replaced the parental viruses between 2004 and 2012 in Souss and is spreading towards the North of Morocco. The emergence of IS76 coincides with the increasing use of tolerant cultivars in the 2000s.

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Tomato yellow leaf curl virus (TYLCV) and tomato yellow leaf curl Sardinia virus (TYLCSV) (genus Begomovirus, family Geminiviridae) as well as their whitefly vector Bemisia tabaci were reported from the south-west and central regions of Morocco. To establish a more comprehensive view of tomato begomoviruses and B. tabaci biotypes throughout Morocco, 32 tomato fields were surveyed for tomato yellow leaf curl disease (TYLCD) symptoms in southern and northern regions, and 54 samples of leaves from cultivated plants or weeds and 35 B. tabaci individuals were collected and analysed by PCR, randomly amplified polymorphic DNA and sequencing. Only TYLCV or TYLCSV were detected. TYLCV was detected in 15 plant samples whereas TYLCSV only in 4. Sequence analyses revealed the presence of the 'Spanish' strain of TYLCSV and distinguished two genetically distinct strains of TYLCV. The begomovirus infections were unevenly distributed throughout Morocco. In the north-west and northcentral regions where tomato plants exhibiting TYLCD symptoms were rarely observed, only 1 sample out of 13 tested positive for the presence of a begomovirus. In the north-east region, the ratio of begomovirus-positive samples was higher, 6/13, and in the south-west region, it was the highest, 13/14. Consistently the frequency of plants exhibiting TYLCD-like symptoms in the northern regions was lower than that in the south-west region. B. tabaci biotype Q is present throughout the country and in Algeria, whereas biotype B, identified for the first time in Morocco, was detected only in the north-east region.