Arch Virol (2004) 149: 2141–2154
A new potato virus in a new lineage of picorna-like viruses
J. R. Thompson
, K. L. Perry
, and W. De Jong
Department of Plant Pathology, Cornell University, Ithaca, New York, U.S.A.
Department of Plant Breeding, Cornell University, Ithaca, New York, U.S.A.
Received January 28, 2004; accepted April 30, 2004
Published online July 23, 2004
Summary. On constructing a cDNA library for potato, ‘contaminating’sequences
with a signiﬁcant identity to Apple latent spherical virus (ALSV) were found. De-
termination of the remaining genome sequence indicated the presence of a bipartite
virus with an RNA1 and 2 of 7034 and 3315 nucleotides, respectively, excluding
a poly(A)tail. RNA1 encodes a single polyprotein (233 kDa) and shares highest
amino acid identity with ALSV at 65%. Conserved amino acid motifs typical for
helicase, protease and RNA-dependent polymerase (RdRp) functions are present.
RNA2 encodes a single polyprotein (106 kDa) with amino acid identities to the ﬂat
apple isolate of Cherry rasp leaf virus (CRLV-FA) (97%) and ALSV (70%), sug-
gesting this is a potato strain of CRLV (CRLV-pot). Phylogenetic analysis using the
RdRp region shows that this virus falls within a group separate from the Comoviri-
dae that includes members of the Sequiviridae and the taxonomically unassigned
viruses ALSV, Strawberry mottle virus, Satsuma dwarf virus and Navel orange
infectious mottling virus. Other regions of the genome have highest identities with
both plant and animal infecting members of the picorna-like virus superfamily.
The evolutionary context of CRLV-pot and related viruses is discussed. Similar
viral sequences from an EST library of peppermint are also analysed.
Cultivated potato (Solanum tuberosum) is the world’s fourth and ﬁrst most impor-
tant food crop in terms of production and yield, respectively; no other foodstuff
provides as much energy per unit area of land [5, 36]. There are at least 36 viruses
known to infect potato, some of the most prominent being members of the species
Alfalfa mosaic virus, Potato leafroll virus, Potato virus A, Potato virus M, Potato
Sequences appear in the EBI database with accession numbers: AJ621357 (RNA1),