Widespread occurrence of cassava torradovirus 2 and cassava frogskin associated oryzavirus characterized the 2020–2023 outbreak of severe cassava frogskin disease in the Orinoquia region of Colombia

Severe root symptoms of Cassava Frogskin Disease (CFSD) remerged in Colombia during 2020–2023 significantly impacting cassava yield in Orinoquia, one of the main cassava producing regions. Using a finite population sampling strategy (ca. 136 fields with ~30 observations per field = 4620 observations), field surveys in the main cassava-producing provinces showed high prevalence values of severe root symptoms. The upper limits of prevalence values were observed in Fuente de Oro (66.67%), Granada (63.33%), Vista Hermosa (56.67%), Puerto Lleras (46.67%), and El Castillo (23.33%). Molecular diagnostics of a subsample (n=149) identified torradovirus species 2 (CsTLV-2) and the oryzavirus CsFSaV as the most frequent pathogens (27.63% and 57.89%, respectively) in this region. The overall prevalence of CsTLV was 27.63%. Notably, among the torradoviruses, CsTLV-2 (100%) showed a clear dominance over CsTLV-1 (9.52%). In contrast, samples collected in the Department of Cauca—where the disease has been endemic and reported since the early 1970s—exhibited a distinct torradovirus profile. The total prevalence of CsTLV was 46.58%, with CsTLV-1 and CsTLV-2 detected at frequencies of 52.94% and 85.29%, respectively. In contrast, the incidence of CsFSaV was approximately threefold lower than that observed in Orinoquia. It is noteworthy that the diversity of torradoviruses was higher in Cauca and that in Orinoquia CsTLV-2 showed characteristics consistent with a recent population expansion. Altogether, the data presented here indicate that the 2020–2023 outbreak of CFSD was characterized by a high prevalence of severe roots symptoms and widespread infections by CsTLV-2 and the oryzavirus CsFSaV, in comparison with other pathogens detected in the analyzed samples.