Characterization of A Divergent Strain of Moroccan watermelon mosaic virus (MWMV) from Tanzania Supports the Existence of Two Major Lineages
The focus of the research in this thesis is the characterization of a virus isolated from a cucurbit plant showing striking symptoms of virus infection including mosaic/mottle and dark green blisters in a commercial field on the outskirt of Dar es Salaam, Tanzania in 2016. Lateral flow tests were positive for potyvirus infection, and negative for Cucumber mosaic virus (CMV) and Squash mosaic virus (SqMV). With a degenerate primer pair in RT-PCR, the ~700 bp fragment of the potyvirus cylindrical inclusion (CI) gene was amplified and had highest identities (80-92%) to Moroccan watermelon mosaic virus (MWMV). This virus was mechanically transmitted to pumpkin and flexuous filamentous rod-like particles of ~820 nm long were purified from infected leaves. High throughput sequencing (HTS) analysis confirmed these symptoms were only due to the infection of an isolate of MWMV, named MWMV-TZ16. In a host range experiment, MWMV-TZ16 only infected species in the family Cucurbitaceae, different from MWMV isolates from North and South Africa and Southern Europe. The complete genome sequence of MWMV-TZ16 was determined with HTS and alignment of overlapping sequences of cloned RT-PCR fragments, with the 5’-end of the genome determined by 5’-RACE PCR. Sequence comparisons and phylogenetic analyses showed that MWMV-TZ16 is a genetically divergent strain that was placed in a strongly supported Central/East African clade, and less closely related to isolates in the North Africa and Southern European clade. General MWMV and East Africa strain-specific primer pairs were developed, and preliminary RT-PCR tests suggest these could be used to further investigate the distribution of these viruses.