Deep-sequencing technology applied on double stranded RNA recovered from an apricot tree with vein clearing symptoms allowed the identification of a novel virus with a single-stranded RNA genome, for which the provisional name apricot vein clearing-associated virus (AVCaV) is proposed. Its genome comprises 7315 nucleotides, excluding the poly(A) tail, covering four open reading frames (ORFs). The putative virus-encoded proteins, i.e. replicase (REP), movement protein (MP), coat protein (CP) and nucleic acid-binding protein (NB), had an estimated molecular weight of 192.5 kDa, 32.15 kDa, 25.5 kDa and 16.1 kDa, respectively and shared the highest identity (ca. 40%) with citrus leaf blotch virus (CLBV) and with orthologs of other known members of the family Betaflexiviridae. The phylogenetic trees constructed with the sequences of the entire replication-associated polyproteins and the putative CP showed incongruent allocations of AVCaV within the genus Citrivirus or as an outgroup species close to the genus Vitivirus, respectively. The peculiar organization of its genome (4 ORFs), different from that typical of members of Citrivirus (3 ORFs) and Vitivirus (5 ORFs) genera, makes likely AVCaV a novel member of an unassigned genus of the family Betaflexiviridae. In RT-PCR assays, AVCaV was found to infect only one out of 39 varieties of apricot tested, thus suggesting to be limitedly spread.