Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

Abstract Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There little information on molecular properties in Kenya, hence we investigated population and genetic diversity Kenya. Methods samples virus-like symptoms were obtained from farmers’ field across country 2018 Illumina sequencing undertaken to determine begomoviruses. Additionally, selection pressure recombinant isolates within also evaluated. Results Twelve complete begomovirus genomes our an average coverage 99.9%. The sequences showed 95.7–99.7% identity among each other 95.9–98.9% similarities a virus Arusha (ToLCArV) isolate Tanzania. Analysis amino acid highest identities regions coding for coat protein gene (98.5–100%) isolates, 97.1–100% C4 ToLCArV. Phylogenetic algorithms clustered all Kenyan same clades ToLCArV, thus confirming be variant virus. was no evidence recombination isolates. Estimation revealed negative or purifying five out six sequences. Conclusions diseases Kenya possibly originating low this useful development appropriate management strategies disease country.