Pervasive mixed infections and recurrent begomovirus co-detection in symptomatic pumpkin plants from Guangxi, China

Pumpkin production in Guangxi, China, is increasingly affected by complex viral diseases, but the regional viral spectrum and mixed-infection structure in symptomatic pumpkin plants remain insufficiently characterized.

We analyzed 289 symptomatic pumpkin samples collected across Guangxi during 2022-2025 using small-RNA sequencing for virus discovery and targeted PCR/RT-PCR assays for individual-sample confirmation. Virus prevalence, mixed-infection profiles, regional and host-associated differences, and virus-virus and symptom-virus associations were evaluated.

Small-RNA sequencing identified 15 candidate virus species, and targeted assays confirmed 11 viruses. Among the 289 samples, 284 (98.27%) were positive for at least one confirmed virus and 279 (96.54%) carried two or more viruses. The dataset was dominated by PuYmMV, SLCPHV, TLCCNV, ToLCNDV, and SLCCNV, which were detected in 87.89%, 87.89%, 83.39%, 78.89%, and 68.86% of samples, respectively. The most frequent infection profile was simultaneous detection of these five begomovirus species, occurring in 35.64% of samples. After Benjamini-Hochberg correction, ZTMV and PRSV were enriched in northern Guangxi, whereas TLCCNV and ToLCNDV were enriched in southern Guangxi. Host-species differences were not significant after correction. Pairwise analysis revealed a strong begomovirus-rich co-detection module, whereas symptom-virus associations were comparatively weak.

Symptomatic pumpkin viral disease in Guangxi is characterized by broad virus diversity, pervasive mixed infection, and recurrent begomovirus-rich co-detection. These findings provide a regional baseline for multiplex diagnosis, begomovirus-oriented surveillance, and future plant-vector-reservoir studies in pumpkin production systems.