Detection and molecular characterization of Wheat stripe mosaic virus on wheat in South Africa

During the past few years, an unknown disease, which resulted in various degrees of chlorosis, mosaic and streaking of wheat leaves was commonly found in the irrigation wheat growing areas of South Africa (SA). The yellowing symptoms resembled a viral infection but were not consistent with previously reported wheat viruses in SA. The observed symptoms suggested that this disease was likely caused by soil-borne virus, which may be transmitted by soil inhabiting microorganisms such as Polymyxa graminis. Therefore, to identify any virus associated with leaves and determine the presence of P. graminis in roots, wheat plants exhibiting characteristic symptoms of the disease were collected during 2018 from farmers’ fields and/or experimental plots across major wheat growing regions of SA. While the roots of the samples were tested for P. graminis using light microscopy, polymerase chain reaction (PCR) and Sanger sequence analysis, the leaves were tested for the presence of viruses using Next generation sequencing (NGS), with the results being confirmed with reverse transcription (RT) PCR. Combined, the microscopic and PCR results confirmed P. graminis in 96% of the symptomatic samples tested. NGS analysis performed on a subset of 22 symptomatic leaf samples resulted in the identification of wheat stripe mosaic virus (WhSMV) in all the samples tested. RT-PCR confirmed the presence of WhSMV in similar samples suggesting that WhSMV is the most likely cause of the observed yellowing of wheat leaves. Twenty-one of the 22 samples which tested positive for WhSMV were also positive for P. graminis indicating that WhSMV is most probably transmitted by P. graminis. WhSMV is a novel virus that was recently described on wheat in Brazil and Paraguay. To our knowledge, this is the first report of WhSMV in South Africa and the third report in the world. As WhSMV has been detected only recently, information on the epidemiology and control of this disease is not yet available. •We investigate the cause of a virus-like disease recently observed in South Africa.•Symptomatic wheat plants exhibited various degrees of chlorosis, mosaic and streaking.•Wheat stripe mosaic virus (WhSMV) was detected in leaves of all tested samples.•Polymyxa graminis was found in the roots of symptomatic samples, hence the virus is most likely transmitted by P. graminis.•This is the first report of WhSMV in South Africa and the third report in the world.