Epidemiological studies of Begomoviruses in South African Region

Abstract

Begomoviruses belongs to group of plant viruses that possesses circular single stranded (ss) DNA genome(s) transmitted by Bemisia tabaci G. and only infects dicotyledonous plants. Begomoviruses affects a significant number of economically valuable number of plants including vegetables, weeds, and ornamental plants. Weeds and ornamental plants act as alternate reservoirs for economically important Begomoviruses, as source of inoculum and recombination sites. In addition, Begomovirus sequences submitted before updated classification in databases creates gray areas. The goal of this study was to examine the demarcation of species, geographic spread over the years and to disclose the alternate hosts of Begomoviruses in South African countries. FASTA and GenBank sequences of the full-length genome of Begomovirus are accessible in the database, were extracted and the parameters - host range, year of collection and geographic distribution of Begomoviruses were tabulated. The sequences were aligned by muscle alignments and species were identified through species demarcation tool (SDT) and confirmed by sequence distance. Graphs were generated using MS Excel, while Phylogenetic tree was constructed using MEGA X’s maximum likelihood. Till date 520 species of Begomoviruses are reported across the globe, among which 33 species and ~1096 isolates are present in South African countries. African cassava mosaic virus has the highest number of isolates (301) followed by East Africa cassava mosaic virus (230), South Africa cassava mosaic virus (137), East Africa cassava mosaic Kenya virus (104) and Cotton leaf curl Gezira has (79). Highest number of isolates are found in Madagascar (288), followed by Kenya (127), Burkina Faso (103), Ghana (84), Comoros (77), Central African Republic (67), Mayotte (38), Uganda (36) and Cameroon (34). Majority of begomoviruses isolates are found to infect Manihot esculenta (720), Solabun lycopersicum (104), Abelmoshus esculentus (46), and Jatropha curas (38) in South African countries. Begomoviruses have widened their choice of host, and they do have multiple alternative hosts. A single specie has potential to affect members of several groups of plants. Moreover, single plant is also the host to many types of Begomoviruses. The number of isolates that demands renaming is increased, and they move from one country to another. Chapter 1 Introductio