Genome characterisation of two complete coding sequences of tomato mild mottle virus from tree tomato and their distribution in Kenya

Summary We present here the first complete coding sequence of tomato mild mottle virus (TMMoV) infecting tree tomato in Kenya. A survey was conducted in three tree tomato-growing regions: Nairobi, Eastern, and Rift Valley. Leaf samples displaying mosaics, mottling, and malformation, were collected and analysed using high throughput RNA sequencing, which revealed the presence of TMMoV in the Eastern and the Rift Valley regions. Two coding sequences, MW537584 and MW537585 were assembled, and the HTS data were verified using RT-PCR and Sanger sequencing. Phylogenetic analysis revealed that both of these Kenyan isolates were highly similar to the Ethiopian isolate (NC038920) with 97 and 96% sequence identity, respectively. Samples from two farms that tested positive for TMMoV, also tested positive for potato virus Y (PVY), making it difficult to associate the symptoms observed with TMMoV, PVY, or a co-infection of both.