Detection of SPV2 and SPCSV and their possible influence on the yield in multiple virus infections.

The prevalence of Sweet potato virus 2 (SPV2) and Sweet potato chlorotic stunt virus (SPCSV) in the Limpopo, Mpumalanga, and Gauteng provinces of South Africa was determined using serological and nucleic acid based methods. Cloning and sequencing part of the coat protein (CP) gene and the complete genome using next generation sequencing (NGS) were also conducted to characterize and determine the sequence variability in SPV2 isolates. Primers designed in the current study successfully detected and confirmed the prevalence of SPV2 in the three provinces surveyed. The pairwise comparison of the amino acid (aa) sequences encoding the CP gene region confirmed that isolates in this study are related to SPV2, sharing a 94% to 99% CP aa identity with those originally reported in South Africa. The East African (EA) strain of SPCSV was also detected in the three provinces surveyed. Phylogenetic analysis using part of the CP encoding nucleotide (nt) sequences showed that the South African isolates correspond to but are distinct from the other EA strains of SPCSV used as reference sequences. Assessment of varieties and breeding lines' response to multiple infection of potyviruses identified variety NC1560, breeding lines 2002‐21‐1 and 2006‐5‐4 as promising for inclusion in future breeding programs as sources of parent material for virus tolerance. Core Ideas: Sweet potato virus 2 and Sweet potato chlorotic stunt virus were confirmed to infect sweet potato in South Africa.The South African isolates of sweet potato chlorotic stunt virus were confirmed to belong to the East African serotype of the virus.Screening of varieties and breeding lines aid selection of potential tolerance varieties for inclusion in breeding programs. [ABSTRACT FROM AUTHOR]