Deep Sequence Characterization of Tomato Spotted Wilt Virus (TSWV) in Cultivated and Wild-Derived Allotetraploid Peanuts in Georgia, USA.

Tomato spotted wilt virus (TSWV) is a globally important pathogen of peanut, characterized by rapid evolution, broad host range, and capacity to overcome resistance. In this study, we performed deep sequencing of TSWV isolates from two peanut cultivars (GA-06G and Bailey II) and two induced allotetraploids derived from four wild Arachis species ([A. gregoryi × A. stenosperma]⁴ˣ and [A. vallsii × A. williamsii]⁴ˣ) grown in Georgia, USA. Complete genomes of TSWV and co-infecting peanut mottle virus (PMV) were assembled for all samples. Despite the phylogenetic distance among hosts, TSWV isolates showed high sequence identity and clustered tightly, suggesting limited host-driven divergence. However, segment-wise analysis revealed differential variation: conserved regions included RdRp, G_N/G_C, and N proteins, while NSm and NSs-linked to host adaptation and immune suppression-were more variable. This inference is based solely on the TSWV isolates used in this study. Phylogenetic comparison with 113 global isolates confirmed that clustering was driven more by geography than host, with southeastern USA isolates forming a distinct clade. Notably, peanut-associated TSWV isolates showed the highest nucleotide diversity among hosts, illustrating their potential to generate resistance-breaking variants. PMV, once thought nearly absent, was detected in all samples, raising new questions about low-level persistence or resurgence. This study reports the first full-genome sequences of TSWV and PMV from U.S. peanuts, including wild-derived genotypes, and highlights the need for sustained genomic surveillance. The results have direct implications for resistance breeding and disease management, particularly as wild genetic resources are increasingly integrated into peanut improvement.