Diversité génétique et variabilité du pouvoir pathogène du Sugarcane yellow leaf virus, agent causal de la feuille jaune de la canne à sucre
Sugarcane yellow leaf virus (SCYLV) is a Polerovirus of the family Luteoviridae and the causal agent of yellow leaf, an emerging disease of sugarcane. Four genotypes of SCYLV (BRA for Brazil, CUB for Cuba, PER for Peru and REU for Reunion) were identified by phylogenetic analyses of the genome of 14 virus isolates from Brazil, China, Colombia, Cuba, Florida, India and Reunion Island. Specific primers were designed to differentiate these genotypes by RT-PCR, and a unique fragment was amplified from each, with the exception of genotypes BRA and PER which are phylogenetically close and which were named genotype BRA-PER. Genotyping by RT-PCR of 245 virus isolates from 18 sugarcane production areas showed that genotype BRA-PER is widespread in the world. In contrast, genotypes CUB and REU were found in only four locations each. In Guadeloupe, the coexistence of genotypes BRAPER, CUB and REU revealed local transmission of these three genotypes by the aphid vector Melanaphis sacchari. However, nearly exclusive presence of genotype BRA-PER in Brazil and genotype REU in Reunion Island also suggested the existence of strong interactions between SCYLV genotypes and their environment, and therefore different evolution events within this virus. The high percentage of diversity between genotype CUB isolates and isolates of the other genotypes led us to propose the reclassification of CUB isolates within a new species called Sugarcane yellow leaf Cuba virus (SCYLCV). The evolution history of SCYLV was traced by phylogenetic studies and analysis of evolutionary events in the viral genome (recombinations, deletions, insertions) specific to some isolates, and detection of selective pressures on ORFs and positive selection of codons. The occurrence of several strains of SCYLV was demonstrated by inoculation of eight sugarcane varieties with genotypes BRA-PER, CUB and REU via M. sacchari, as well as comparison of virus populations and growth characteristics of two sugarcane varieties naturally infected by genotypes BRA-PER and REU. The genetic origin of these variations in pathogenicity remains to be elucidated.