Mapping the Enigma of Cryptic Tomato Yellow Stunt Disease: A Synergistic Viral Infection Threatening Global Tomato Health

A quite prevalent cryptic tomato yellow stunt disease (ToYSD) has recently emerged, caused by mixed infection of tomato yellow leaf curl virus (TYLCV), tomato chlorosis virus (ToCV), southern tomato virus (STV), tomato brown rugose fruit virus (ToBRFV), and tomato infectious chlorosis virus (TICV). However, the pathological and epidemiological impact of mixed viral infections-synergistic and/or antagonistic combinations-has rarely been investigated until recently. In this study, we report ToYSD with its associated viruses by small RNA sequencing of the nine pooled tomato samples collected from China, Pakistan, and Fiji. TYLCV, ToCV, TICV, ToBRFV, and STV were found exclusively in all samples. Furthermore, these viruses were also detected through RT-PCR assays from each tomato sample, showing the symptoms of ToYSD. In addition, seeds from these virus-infected plants were collected and sown in the glasshouse. ToBRFV was also mechanically inoculated into resulting seedlings, and viruliferous whiteflies (<i>Bemisia tabaci</i>) were collected from ToYSD symptomatic plants and released on these seedlings. Eventually, these plants developed symptoms of ToYSD, and RT-PCR assays confirmed the presence of TYLCV, ToCV, TICV, ToBRFV, and STV in leaf samples of these symptomatic plants. Subsequently, seed-borne viruses (TYLCV, ToBRFV, and STV) were also detected from the seed samples of these plants having mixed infection and confirmed by Sanger sequencing. The corresponding full-length genomes were assembled and submitted to GenBank (NCBI). The genetic diversities of these viruses were variable and, in some cases, comparable to that of global isolates of the same species. Consequently, the synergistic interactions and observed genetic variability among TYLCV, ToCV, TICV, ToBRFV, and STV, which collectively cause ToYSD, provide a solid foundation for further investigation into virus ecology, disease epidemiology, and their cumulative effect on tomato production.