Potato Virus Y in South Africa: Isolate Characterization and Assessment of Potato Cultivar Resistance

Potato virus Y (PVY) is one of the most serious viral threats to potato production worldwide and throughout Africa, resulting in severe yield reduction. Management of this virus is key to sustainable potato production. The virus is spread by infected tuber material and aphid vectors. In South Africa, the pathology of PVY infections has changed in recent years. Disease diagnosis based on leaf symptoms became problematic, and diagnosis by means of ELISA testing was the only way to eliminate diseased mother tuber material. The PVYNTN strain has recently been found in South Africa which can cause potato tuber necrotic ringspot disease (PTNRD) and this can lead to crop failure as tubers showing necrosis are unacceptable to the consumer. In this study we characterized the PVY strains which are currently responsible for infections in South Africa using whole genome sequencing and a novel approach to the phylogenetic analysis of these sequence data. We were able to determine that the older PVY ordinary (PVYO) and PVY necrotic (PVYN) strains had largely been replaced by PVYN-Wilga and PVYNTN strains since 1995. Presently, approximately 75% of the PVY isolates in South Africa are of the PVYN-Wilga and PVYNTN strains. To determine the resistance of potato cultivars commonly planted in South Africa against our local PVYN-Wilga and PVYNTN isolates, we assessed the speed of viral spread of selected isolates using the quantitative real-time reverse transcriptase PCR (qRT-PCR) in mechanically infected potato plants. Tubers were assessed for necrotic symptoms. This revealed that some cultivars show higher levels of resistance to PVY infection. Future assessments of the resistance of potato cultivars planted in South Africa will be conducted using this approach. Management of PVY in South Africa will in future be based on ongoing monitoring of PVY isolate mutation and recombination through whole genome sequencing and planting of PVY-resistant cultivars. Furthermore vector control by chemical means and planting during cooler seasons when aphid pressure is lower, and elimination of infected tubers by means of the certification scheme will together be used in a strategy to reduce the effects of PVY infections.