Weeds : reservoirs of vector-borne viral pathogens in South Africa.
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Weeds have the potential to alter the function of ecosystems either as pests themselves or by harbouring vectors and vector-borne diseases. Their role as reservoirs of viral pathogens has had a significant bearing on viral epidemiology in many parts of the world. However past scientific research has largely overlooked the impact of weeds on viral ecology. Only in recent years has virological research shifted to include the role of weeds in viral epidemiology and ecology. While there is an increasing number of reports on viruses identified on weeds globally, there is a significant lack of information on the distribution of weeds and the viruses they harbour in South Africa. Therefore, a survey was conducted across major tomato growing areas located throughout various provinces in South Africa to identify weed species that harbour vectors and vector-borne viral diseases. Fifteen weeds species growing around tomato crop fields were found exhibiting virus-like symptoms in the presence of excessively high aphid, thrip and whitefly populations. Symptoms observed on weeds and tomato crops ranged from mosaics, mottling, necrotic spots, leaf curling, interveinal chlorosis and purple discoloration of leaves. Tomato spotted wilt virus (TSWV), Potato virus Y, Tomato torrado virus and Tomato chlorosis virus were positively identified using reverse transcription polymerase chain reaction (RT-PCR), and confirmed using BLAST, on Amaranthus thunbergii, Physalis peruviana, Datura stramonium and Solanum nigrum respectively. These viruses were also detected on tomato crops. These results confirm that weeds act as reservoirs of viral pathogens which may cause serious repercussions for crop production. The density and distribution of weeds in South Africa emphasise their role in viral epidemiology. Therefore stringent control measures should be employed to reduce the rate of vector transmitted viruses. TSWV is ranked among the most destructive and complex viral pathogens globally. It has an extensive host range and global distribution, yet very few TSWV isolates have been completely sequenced. Most sequences of TSWV isolates have only been partially characterised. Therefore the aim of this study was to conduct a complete genome analysis of a South African TSWV isolate. Next-generation sequencing technology was used to obtain the complete genome of TSWV. The complete genome (LK-1), as well as the genome organisation of TSWV, was obtained and subjected to phylogenetic and recombination analysis. Phylogenetic analysis showed geographically diverse phylogenetic relationships of each open reading frames of TSWV. One recombination event on the NSs ORF of S segment was detected. It seems that most recombination events are limited to this particular region. In this study, the first complete genome of a South African TSWV isolate is reported. Additional full genome sequences of other South African TSWV isolates will enable a comprehensive population study of TSWV in South Africa. This information will contribute to the understanding of the emergence and evolution of TSWV and its adaptation to new hosts.