Nucleotide sequence and genome organization of Apple latent spherical virus: a new virus classified into the family Comoviridae

A virus with isometric virus particles (ca, 25 nm) was isolated from an app le tree and named Apple latent spherical virus (ALSV). Virus particles puri fied from infected Chenopodium quinoa formed two bands with densities of 1. 41 and 1.43 g/cm(3) in CsCl equilibrium density-gradient centrifugation, in dicating that the virus is composed of two components. The virus had two ss RNA species (RNA1 and RNA2) and three capsid proteins (Vp25, Vp24 and Vp20) . The complete nucleotide sequences of RNA1 and RNA2 were determined to be 6815 nt and 3384 nt excluding the 3' poly(A) tail, respectively. RNA1 conta ins two partially overlapping ORFs encoding polypeptides of molecular mass 23 kDa ('23K'; ORF1) and 235 kDa ('235K'; ORF2); RNA2 has a single ORF enco ding a polypeptide of 108 kDa ('108K'). The 235K protein has, in order, con sensus motifs of the protease cofactor, the NTP-binding helicase, the cyste ine protease and the RNA polymerase, in good agreement with the gene arrang ement of viruses in the Comoviridae. The 108K protein contains an LPL movem ent protein (MP) motif near the N terminus. Direct sequencing of the N-term inal amino acids of the three capsid proteins showed that Vp25, Vp20 and Vp 24 are located in this order in the C-terminal region of the 108K protein. The cleavage sites of the 108K polyprotein were Q/G (MP/Vp25 and Vp25/Vp20) and E/G (Vp20/Vp24). Phylogenetic analysis of the ALSV RNA polymerase doma in showed that ALSV falls into a cluster different from the nepo-, como- an d fabavirus lineages.