A novel begomovirus with distinct genomic and phenotypic features infects tomato in Bangladesh

In Bangladesh, tomato is cultivated over c. 16 000 ha annually. Tomato leaf curl virus disease (ToLCVD) normally reduces tomato production significantly, often causing up to 100% yield loss. Diseased tomato plants were collected from Joydebpur, Bangladesh in September 2003 because they exhibited unusually mild ToLCVD symptoms of yellowing and leaf curling. In addition, mosaic-like symptoms developed on the older leaves of susceptible tomato cv. Moneymaker, which is atypical for leaf curl-inducing viruses. Total DNA was extracted from leaves with symptoms and putative viral genomes were amplified by PCR using degenerate primers specific to DNA-A and -B (Muniyappa et al., 2003), and DNA-β molecules (Briddon et al., 2002). Sequences generated from the amplicons were used either to design virus-specific primers, or to obtain directly complete viral sequences. A previously undescribed monopartite begomovirus, designated Tomato leaf curl Joydebpur virus-Mild (ToLCJV-Mld), was found associated with these mild symptoms. Based on DNA-A sequences (2761 nucleotides, EMBL accession no. AJ875159), ToLCJV-Mld was most similar to Pepper leaf curl Bangladesh virus (AF314531) at 87·1% nucleotide (nt) identity. ToLCJV-Mld satellite DNA-β molecule (1366 nt, AJ966244) shared highest (59·0%) nt identity with a molecule isolated from ToLCVD in India (AY438558). No DNA-B component was detected. The number and arrangement of ToLCJV-Mld DNA-A open reading frames (ORFs) was identical to monopartite begomoviruses, except that an additional ORF of 849 nt (282 amino acids) was predicted to occur on the complementary strand between nt positions 1139 and 291, encompassing the entire length of the coat protein gene. The association of a DNA-β molecule with begomoviruses is known to cause severe symptoms, but this is the first report where it is associated with mild symptoms. ToLCJV-Mld DNA-A shared 86·0 and 74·4% nucleotide identities with the previously reported Tomato leaf curl Bangladesh virus (AF188481) (Green et al., 2001) and Tomato leaf curl New Delhi virus-Severe[Jessore] (AJ875157) (Maruthi et al., 2005), respectively. These results confirm the occurrence of at least three begomovirus species in tomato in Bangladesh.