First report of a distinct begomovirus associated with okra yellow crinkle disease in Mali

In November of 2004 and July of 2005, typical symptoms of begomovirus infection such as yellow veining, leaf yellowing, crinkling and cupping were observed in okra (Abelmoschus esculentus) variety trials near Bamako, Mali. Thirty-one symptomatic samples from seven varieties were collected and tested for the presence of begomovirus by polymerase chain reaction (PCR), using the begomovirus-specific degenerate primer pair PAL1v1978/PAR1c715 (Rojas et al., 1993). The expected 1.4-kb PCR product for begomoviruses was detected from seventeen samples from four varieties with yellow veining, leaf yellowing, crinkling or cupping symptoms. One PCR product from each of the 2004 and 2005 collection was cloned and sequenced. Based on the sequence of the 1.4-kb DNA product, specific primers were designed to complete the DNA-A sequence. DNA-B was not detectable in the two samples with DNA-B specific primer pairs (Green et al., 2001). However, a DNA-beta of 1.3-kb was detected in both samples with the DNA-beta primer pair Beta01/Beta02 (Briddon et al., 2002).

The DNA-A of the two virus isolates shared 99.2% sequence identity and are considered the same virus. Each consisted of 2792 nucleotides (Acc. Nos DQ902715 and DQ875879) and contained the six predicted open reading frames (ORFs V1, V2, C1, C2, C3 and C4). A BLAST analysis was conducted with geminivirus sequences available in the GenBank database and MegAlign software (DNASTAR, Madison) was used for further sequence comparisons. Highest sequence identity (76.7%) was found with Tobacco leaf curl Zimbabwe virus (AF350330). Only low sequence identities (70.9 to 72.5%) were obtained with full length DNA-A sequences of other okra-infecting begomoviruses available in the Genbank from African and Asian countries, including as Sudan (AY036006 and AY036008), Egypt (AY036010), India (AF241479) and Pakistan (AJ002451, AJ002453 and AJ002459). Even lower sequence identities (63.1 to 63.9%) were found with okra infecting begomoviruses from American countries, such as Mexico (AY751753 and DQ022611). Sequence identities with begomoviruses reported from other vegetable crops in Mali, including two from tomato (AY502934 and AY503936) and one from pepper (AY502935) were also low, ranging from 73.4 to 76.4.

To our knowledge, this is the first report of a begomovirus associated with okra yellow crinkle disease in Mali. Based on the DNA-A sequence comparison and the ICTV demarcation of species at 89% sequence identity, the okra begomovirus from Mali constitutes a distinct begomovirus and the name Okra yellow crinkle Mali virus is proposed.