A survey of whitefly-transmitted viruses on tomato crops in South Africa

Whitefly-transmitted viruses are a growing threat to modern day agriculture. Their impact on South Africa's vegetable industry results in unprecedented economic losses. Tomatoes are important vegetable crops that are highly susceptible to whiteflies and an almost indispensable part of meal preparation in many South African homes. Against this background, tomato crops and nearby weed species in South Africa were surveyed for whitefly-transmitted viruses. In addition, some pepper crops in adjacent tomato fields were also included in this study. Field and greenhouse crops were inspected for the development of virus-like symptoms in the presence of whitefly infestations. Leaf samples exhibiting virus-like symptoms were collected and analyzed for whitefly-transmitted crini-, torrado-, begomo-, ipomo- and carla viruses using molecular assays. The identity of each virus positive sample was confirmed by Sanger sequencing and used in subsequent phylogenetic studies. Tomato chlorosis crinivirus (ToCV), Tomato torrado virus (ToTV) and Tomato curly stunt begomovirus (ToCSV) were three major viruses identified in the study. ToCV was the most abundant whitefly-transmitted virus in South Africa with an overall prevalence of 47.1% (tomatoes) and 21% (weeds). ToCV isolates from South Africa matched >= 97% to isolates from Spain and Sudan. ToTV outbreaks emerged on tomato crops in the northern parts of South Africa in the presence of abnormally high whitefly populations. ToTV infections of tomatoes were restricted to the Limpopo province, however, a second isolate was identified on an unknown arable weed that did not infect nearby tomato crops. ToTV isolates from South Africa matched 99% and 92.8% to Polish and Italian isolates and had an overall incidence of 7.5% (tomatoes) and 11% (weeds). ToCSV isolates from South Africa matched 100% with Mozambican isolates. Phylogenetic analysis showed that current ToCSV isolates in South Africa were distantly related to a previously identified South African ToCSV isolate. The disease was identified on tomatoes in three provinces and had an overall incidence of 9.4%. On the contrary, whitefly-transmitted viruses were not identified on pepper crops exhibiting virus-like symptoms. In this study, whitefly-transmitted viruses infecting tomatoes, and some weed species in South Africa were elucidated. These findings are intended to raise awareness on the impact of whitefly-transmitted viruses in South Africa's tomato industry.