Nucleotide sequence of the genome of a citrus isolate of olive latent virus 1

The 3699 nt genome of olive latent virus 1 (OLV-1), described years ago from Southern Italy as a putative sobemovirus, was completely sequenced. OLV-1 genomic RNA was not polyadenylated and had a structure virtually identical to that of species of theNecrovirus rather than theSobemovirus genus. Five open reading frames (ORFs) were identified, of which the 5′-proximal encoded a 23 K protein and ended with an amber codon whose readthrough could yield a putative 82 K product. This polypeptide had extensive sequence similarity with polymerases of serotypes A and D of tobacco necrosis necrovirus (TNV-A and TNV-D) and species of the familyTombusviridae and related genera (Dianthovirus andMachlomovirus). Two small ORFs followed, which encoded polypeptides of 8 K and 6 K, respectively. The 6 K product had extensive homology with the comparable 6 K protein of TNV-A and was also related to the 11 K protein of shallot latent carlavirus, one of the “triple block” polypeptides involved in cell-to-cell virus movement. The 3′-proximal ORF was in the same position as the coat protein (CP) cistron of necroviruses and encoded a 30 K product related to CP of both TNV-A and -D. Computer-assisted comparative analysis of structural and non-structural proteins of OLV-1, TNV-A and TNV-D disclosed an overall distant relationship between OLV-1 and TNV-D. OLV-1 genome appeared homologous to that of TNV-A, but differences from TNV-A were the absence of the small ORF downstream of the CP cistron and in the low degree of sequence identity in CP (39% aa identity). OLV-1 is serologically distantly related to TNV-A and even more distantly related to TNV-D. We propose that OLV-1 is a necrovirus species in its own right.