Survey for viruses affecting maize along the major grain transport route between Gauteng and KwaZulu-Natal in South Africa

Abstract

The recent introduction of maize chlorotic mottle virus (MCMV) and spread of the resulting maize lethal necrosis disease (MLN) in East Africa presents a threat to maize production in all Southern African countries. As MLND is the result of the synergistic action of MCMV and various cereal-infecting potyviruses, the existing virus status of maize in KwaZulu-Natal, a province of South Africa bordering Mozambique and Eswatini, was determined. Additional viruses identified in MLND affected plants in East Africa previously were also tested for in this study, including maize streak virus (MSV), Morogoro maize-associated virus (MMaV), maize-associated pteridovirus (MaPV), and two maize-associated totivirus (MATV) variants. No MCMV or potyvirus infections were detected. MSV was identified in 29% of the pools (consisting of five plants each), MaPV was detected in three plants, while only a single plant tested positive for MMaV. The presence of MMaV and MaPV was confirmed with next generation sequencing (NGS) and their complete/near complete genome sequences assembled. MMaV was also further confirmed with additional PCR primer sets. This is the first time MMaV and MaPV have been reported in South Africa. Two distinct MATV variants and two Zea mays chrysovirus 1 strains were also detected using NGS but no further tests were conducted, hence, these findings remain preliminary. Future research is required to determine the incidence and distribution of these new viruses in South Africa, their mode(s) of transmission, and effects on maize yield to determine the possible risk they may pose to the South African maize industry.