First Identification of Begomoviruses Infecting Tomato With Leaf Curl Disease in Burkina Faso

Leaf curl and yellow leaf curl are frequently affecting production of tomato (Solanum lycopersicum) in Burkina Faso, with an incidence of 60% in 1993 (2). However, the specific begomoviruses associated with the disease had not been identified. In January and February 2009, severe leaf curl symptoms coupled with heavy infestations of the whitefly Bemisia tabaci were observed in tomato plants in several parts of Burkina Faso. Leaf samples were collected from symptomatic tomato plants, and total DNA was extracted by CTAB method, or by FTA classic cards (4). PCR using universal coat protein (CP) gene primers (AC1048/AV494) followed by sequence analysis of cloned amplicons indicated infection with Tomato yellow leaf curl Mali virus (TYLCMLV), Tomato leaf curl Mali virus (ToLCMLV), and Pepper yellow vein Mali virus (PeYVMLV), with a mixed infection of the first two viruses in one tomato plant. Two tomato plant samples (Di-14 and Oua-20) from Di and Ouahigouya, respectively, were selected for rolling circle amplification (RCA) and the RCA product was subjected to restriction enzyme analysis. The linearized fragments (∼2.8 kb), which were obtained after digest with the EcoRV restriction enzyme, were cloned into pJET1.2/blunt (Thermo Scientific). Four clones for sample Di-14 (Tom-141, Tom-142, Tom-143b, and Tom-145b), and one clone (Tom-202b) for sample Oua-20 were fully sequenced in both directions and pairwise comparisons were carried out using the STD software (3). Four clones (Tom-141, GenBank accession number LM651400; Tom-142, LM651401; Tom-143b, LM651402; Tom-202b, LM651403) shared 97.7 to 100% identity with each other, and 97.6 to 99.2% with an isolate of TYLCMLV (EU847740) identified from tomato in Ghana. The clone Tom-145b (LM651404) shared 91.2% sequence identity with an isolate of ToLCMLV (AY502936) from Mali (5). All clones from tomato showed four open reading frames (ORFs) (Rep, C2, REn, and C4) on the complementary sense strand, and two ORFs (CP and V2) in the virion sense orientation, similar to previously characterized monopartite begomoviruses. According to the International Committee on Taxonomy of Viruses guidelines for species demarcation in the genus Begomovirus, Tom-141, Tom-142, Tom-143b, and Tom-202b belong to the Ghana strain of TYLCMLV, whereas Tom-145b is a member of a new Burkina Faso strain of ToLCMLV (ToLCMLV-BF). All five clones thus represent monopartite begomoviruses apparently of African origin, and belong to the family Gemini