Occurrence, Characterisation and Distribution of Viruses Infecting Tree Tomato (Solanum Betaceum Cav) in Kenya

Abstract

The tree tomato is a shrub belonging to the Solanaceae plant family that bears egg-shaped berries. Main production constraints include diseases, pests and drought. Diseases caused by fungi, bacteria and viruses are the largest contributor to farmer’s losses. Viruses are known to cause the heaviest economic losses. In Kenya, only two viruses, potato virus Y (PVY) and tomato mild mottle virus (TMMoV), have been previously detected infecting the crop. This study was conducted to identify and characterize the identified viruses infecting the crop, and determine their prevalence and distribution in the country. Two surveys were conducted in three agro-ecological zones (upper highlands, lower highland, and midlands) in the main tree tomato production counties of Machakos, Nairobi, Embu, Tharaka Nithi, Meru, Elgeyo Marakwet, Nandi, Baringo and Nakuru between 2018 and 2019. During the survey, 26 farms were visited and 358 tree tomato leaf samples showing symptoms of virus infection such as mosaics, vein clearing, vein banding, and leaf malformation were collected. It was observed that the severity of these symptoms was more pronounced in the midland and lower highland zones. Using next generation sequencing (NGS) three viruses, an RNA satellite, and a viroid were identified: potato virus Y (PVY), tomato mild mottle virus (TMMoV, 9243 bp, MW537585), Ethiopian tobacco bushy top virus (4199 bp, MW883068), and associated RNA satellite (522 bp, MW713579), and lastly potato spindle tuber viroid (359 bp, MZ054164). The PVY genome was not established. This is because the reads were from pooled sample, and plus the fact that the similarities in the recombination pattern and recombinant breakpoints among the genomes of recombinant strains would have led to the formation of a chimeric genome that does not exist. Results from NGS for all 3 viruses and the viroid were confirmed by RT-PCR using virus specific primers and Sanger sequencing. By pair-wise alignment, the sequences obtained from Sanger sequencing were all aligned to their respective NGS derived genomes and showed: 90% for ETBTV, 99% for satETBTV-E, 96% for TMMoV and 98 for PSTVd sequence identity. The PCR diagnostics were then used to determine the incidence and prevalence of each of the viruses. PVY was the most prevalent virus with 46% of all farms having samples which tested positive. Apart from Elgeyo Marakwet, all other counties had farms with samples had tested positive for PVY. Both TMMoV and PSTVd were present in two farms (from Embu and Meru), while ETBTV and its RNA satellite were present in one farm (from Tharaka Nithi). This is the first report of ETBTV and its RNA satellite infecting tree tomato, as well as the first report of a natural infection by PSTVd. Other viruses (pepper enomavirus, tobacco mottle virus, tomato chlorosis virus, Kenyan potato cytohabdovirus and tamarillo fruit ring virus) were also detected using NGS, however research is still ongoing in KALRO to characterise and validate their presence using RT-PCR. The results of this study have expanded the knowledge of the number of viruses infecting tree tomato in Kenya and developed primers and RT-PCR assays for quick diagnosis thereby allowing for consistent detection of viruses within commercial nurseries and farmers’ fields consistent with virus infection. The ability to perform routine diagnosis of these viruses is an essential tool for seed certification programs, breeding programmes, epidemiological monitoring and evaluation studies, and for development of management strategies.