Surveys in the Gauteng, Limpopo and Mpumalanga provinces of South Africa reveal novel isolates of sweet potato viruses

Previous surveys carried out between 2001 and 2003 in the Limpopo, Mpumalanga, Gauteng, Western Cape, Eastern Cape, Kwazulu Natal and North West Provinces of South Africa reported Sweet potato feathery mottle virus and Sweet potato virus G as the most common viruses of sweet potato. The two potyviruses were detected by indexing onto the indicator plant Ipomoea setosa Kerr. and by nitrocellulose enzyme linked immunosorbent assays (NCM-ELISA). In this study, surveys (2012/2013 and 2013/2014) were conducted in three Provinces in South Africa, Gauteng, Limpopo and Mpumalanga. Results showed the frequent occurrence of the russet crack (RC) strain of Sweet potato feathery mottle virus, Sweet potato virus G, Sweet potato virus C, and begomoviruses Sweet potato leaf curl Sao Paulo virus, Sweet potato leaf curl virus and Sweet potato mosaic virus in the three Provinces surveyed. Potyvirus identities were confirmed by partial sequencing of the part of nuclear inclusion body (NIb) protein, coat protein (CP) gene and the 3′-non-translated region (3′ NTR) of Sweet potato feathery mottle virus and Sweet potato virus C, and the NIb and CP-encoding region of Sweet potato virus G. The RC strain of Sweet potato feathery mottle virus from this study shared nucleotide (nt) identity of between 97% to 99% with the RC strains from Australia, Peru and China, and 94% to 98% with isolates from New Zealand and United States of America. Sweet potato virus C isolates from this study shared 91% to 94% (VER-7_SPVC and REF-26_SPVC) and 86% to 91% (GBD-12_SPVC and MAM-15_SPVC) nt identity with the previously reported Sweet potato virus C isolates reported in South Africa and other parts of the world. Similarly, Sweet potato virus G samples from the current study shared 94% to 97% nt identity with the South African CTB3-3 and isolates from other countries, and genetic diversity was observed when samples of the current study shared the nt identity of 85% to 87% with the Kwazulu Natal isolates. The presence of begomoviruses was confirmed by observing for typical symptoms such as the upward curling and rolling of leaves on Ipomoea setosa. Rolling circle amplification (RCA) and next generation sequencing (NGS) of the full-length genome revealed novel begomoviruses isolates, which were identified as Sweet potato leaf curl Sao Paulo virus isolate Tanz: ELLP_ZA and Sweet potato leaf curl Sao Paulo virus isolate Tanz: NMP-ZA since the two shared 94% and 95% nt identity with Sweet potato leaf curl Sao Paulo virus isolate TZ-SNG7:12 of Tanzania, respectively. TMBLP-ZA appears to be a novel isolate of Sweet potato leaf curl virus since it shared 91% nt identity with Sweet potato leaf curl virus isolates from different geographic regions of the world. Therefore, we propose that it is classified as Sweet potato leaf curl virus isolate South Africa (ZA): TMBLP-ZA.