Genomic, Phylogenetic, and Functional Characterization of Novel Resistance-Breaking Tomato Spotted Wilt Virus Strains

Abstract Text:

The emergence of resistance-breaking (RB) strains of tomato spotted wilt virus (TSWV) that overcome single-gene resistance conferred by Sw-5b (tomato) and Tsw (pepper) threatens global vegetable production. However, a comprehensive genomic and phylogenetic analysis integrating full-genome sequences of RB strains with key TSWV effector proteins, NSm and NSs, is still lacking. In this study, we sequenced six TSWV strains—four RB strains from tomato and one RB and one non-resistance-breaking (NRB) strain from pepper—and analyzed their genomic and phylogenetic relationships. We further characterized these strains functionally by quantifying virus accumulation via qRT-PCR and assessing phenotypic effects in resistant and susceptible tomato and pepper cultivars. Tomato-infecting RB strains overcame Sw-5b-mediated resistance but failed to break Tsw resistance, while the pepper RB strain uniquely overcame both resistance genes, producing distinct symptoms in each host. Virus titers, symptom onset, and severity varied across cultivars. Several novel point mutations were identified in RB strains and are being validated for their role in resistance breaking. By integrating mutation profiling, comprehensive phylogenetic analysis—including all reported RB strains to date—and host phenotype analysis, this study provides critical insights into RB strain evolution and establishes a foundation for future research on host-virus interactions.