Pepper (Capsicum annuum) is an important crop worldwide. In Israel, approximately 2,500 ha are grown all year round for the local and export markets. Herein, we report the identification of a viral pathogen causing a new devastating disease in pepper crops. The disease syndrome includes shortening of stem internodes, interveinal yellowing, and upward rolling of the leaf blade, accompanied by fruit discoloration and size reduction. Virus purification from infected plants yielded isometric particles, 25 nm in diameter. The causal agent of the disease was tentatively named Pepper yellow leaf curl virus (PYLCV). The virus cross-reacted in DAS ELISA with antisera against Cucurbit aphid-borne yellows virus and Potato leafroll virus, members of the Polerovirus genus. The partial nucleotide sequence obtained from the cloned viral coat protein and movement protein genes indicated 92% identity at the amino acid level with Tobacco vein distortion virus (TVDV), another member of the Polerovirus genus. However, the host range of PYLCV is significantly different from the host range described for TVDV. Based on our findings, the taxonomic status of PYLCV is discussed.

We determined the complete sequence and organization of the genome of a putative member of the genus Polerovirus tentatively named Pepper yellow leaf curl virus (PYLCV). PYLCV has a wider host range than Tobacco vein-distorting virus (TVDV) and has a close serological relationship with Cucurbit aphid-borne yellows virus (CABYV) (both poleroviruses). The extracted viral RNA was subjected to SOLiD next-generation sequence analysis and used as a template for reverse transcription synthesis, which was followed by PCR amplification. The ssRNA genome of PYLCV includes 6,028 nucleotides encoding six open reading frames (ORFs), which is typical of the genus Polerovirus. Comparisons of the deduced amino acid sequences of the PYLCV ORFs 2-4 and ORF5, indicate that there are high levels of similarity between these sequences to ORFs 2-4 of TVDV (84-93%) and to ORF5 of CABYV (87%). Both PYLCV and Pepper vein yellowing virus (PeVYV) contain sequences that point to a common ancestral polerovirus. The recombination breakpoint which is located at CABYV ORF3, which encodes the viral coat protein (CP), may explain the CABYV-like sequences found in the genomes of the pepper infecting viruses PYLCV and PeVYV. Two additional regions unique to PYLCV (PY1 and PY2) were identified between nucleotides 4,962 and 5,061 (ORF 5) and between positions 5,866 and 6,028 in the 3' NCR. Sequence analysis of the pepper-infecting PeVYV revealed three unique regions (Pe1-Pe3) with no similarity to other members of the genus Polerovirus. Genomic analyses of PYLCV and PeVYV suggest that the speciation of these viruses occurred through putative recombination event(s) between poleroviruses co-infecting a common host(s), resulting in the emergence of PYLCV, a novel pathogen with a wider host range.