Molecular characterization of a new begomovirus infecting honeysuckle in Sapporo, Japan

A virus isolated from honeysuckle collected from Sapporo (SP1), Japan, showing symptoms of complete leaf yellowing and stunting was characterized. The complete DNA-A like molecules of SP1 was determined and found to comprise 2771 nucleotides (nts) with a typical begomovirus genome organization. Additionally, SP1 had a DNAβ deletion mutant molecule of 426 nts. A comparison of the complete DNA-A nt sequences revealed that SP1 shared 87-88% nt sequence identity with the other three isolates of Japanese Honeysuckle yellow vein mosaic virus (HYVMV) but 91% with HYVMV-[UK1], however, the isolate shared 95-98% of CP aa sequence identity with the Japanese isolates of HYVMV and only 86% with HYVMV-[UK1]. Phylogenetic analysis of full length DNA-A component clustered SP1 with Japanese tobacco begomoviruses but analysis of the aligned CP aa sequences clustered the virus with the Japanese honeysuckle begomoviruses. Molecular data show that P1 is an isolate of HYVMV.