Detection by high-throughput sequencing and molecular characterization of complexes of fabaviruses infecting ‘Staccato(R)’ sweet cherry (Prunus avium) in Canada

Abstract

High throughput sequencing (HTS) revealed the existence of complexes of fabaviruses infecting two ‘Staccato(R) ’ sweet cherry plants (Prunus avium). Species classified as members of the genus Fabavirus are positive sense RNA viruses that possess bipartite genomes. The cherry plants Stac-3B (symptomatic) and Stac-4B (asymptomatic) were each determined to be infected with multiple RNA1 and RNA2 segments of Prunus virus F (PrVF) and the putative cherry virus F (CVF). The RNA1 and RNA2 segments Stac-3B_C3 and Stac-3B_c11, respectively, are proposed to represent an isolate identified as PrVF-CP1; while the RNA1 and RNA2 segments Stac-3B_C4 and Stac-3B_c7 are proposed to represent an isolate CVF-CC1. The termini of these four RNA segments were confirmed by RACE revealing that the first 28 nucleotides of the 5ʹuntranslated region (UTR) of all four RNA segments is conserved and is predicted to form a hairpin structure. The 3ʹUTRs possess various repeat sequences. Very interestingly, a group of PrVF sequences, exemplified by SwC 74_2c, were identified as the products of an interspecies recombination event, with PrVF 8816_s1 as a possible major parent and an isolate of CVF being the minor parent. This was supported by all methods in the RDP4 program. No association was made of any of the fabavirus complexes with any disease symptoms. This is the first description of the detection of CVF in Canada.