Molecular characterization of domestic and exotic potato virus S isolates and a global analysis of genomic sequences.

Five potato virus S (PVS) isolates from the USA and three isolates from Chile were characterized based on biological and molecular properties to delineate these PVS isolates into either ordinary (PVS(O)) or Andean (PVS(A)) strains. Five isolates - 41956, Cosimar, Galaxy, ND2492-2R, and Q1 - were considered ordinary strains, as they induced local lesions on the inoculated leaves of Chenopodium quinoa, whereas the remaining three (FL206-1D, Q3, and Q5) failed to induce symptoms. Considerable variability of symptom expression and severity was observed among these isolates when tested on additional indicator plants and potato cv. Defender. Additionally, all eight isolates were characterized by determining the nucleotide sequences of their coat protein (CP) genes. Based on their biological and genetic properties, the 41956, Cosimar, Galaxy, ND2492-2R, and Q1 isolates were identified as PVS(O). PVS-FL206-1D and the two Chilean isolates (PVS-Q3 and PVS-Q5) could not be identified based on phenotype alone; however, based on sequence comparisons, PVS-FL206-1D was identified as PVS(O), while Q3 and Q5 clustered with known PVS(A) strains. C. quinoa may not be a reliable indicator for distinguishing PVS strains. Sequences of the CP gene should be used as an additional criterion for delineating PVS strains. A global genetic analysis of known PVS sequences from GenBank was carried out to investigate nucleotide substitution, population selection, and genetic recombination and to assess the genetic diversity and evolution of PVS. A higher degree of nucleotide diversity (π value) of the CP gene compared to that of the 11K gene suggested greater variation in the CP gene. When comparing PVS(A) and PVS(O) strains, a higher π value was found for PVS(A). Statistical tests of the neutrality hypothesis indicated a negative selection pressure on both the CP and 11K proteins of PVS(O), whereas a balancing selection pressure was found on PVS(A).

Arabis mosaic virus in Grapevines in New York State.

In a limited survey of commercial vineyards and a germplasm repository in Ontario County, NY, 20 vines of Vitis sp. were tested in fall and spring 2010 to 2012 for viruses using a double-antibody sandwich (DAS)-ELISA and macroarray with oligonucleotide probes for grapevine viruses ((3) and unpublished). The plants selected for analysis included those showing atypical growth including leaf deformation, yellowing, cupping or spotting, vein clearing, shortening of internodes, and reduced vigor. Arabis mosaic virus (ArMV; genus Nepovirus, family Secoviridae) was detected in leaf tissue and wood scrapings in two vines using the DAS-ELISA with antibodies from Bioreba (Reinach, Switzerland). The ArMV positive vines were from Vitis hybrid cultivars Noah and Geisenheim 26. ArMV was also detected in these two vines using the macroarray, with hybridization observed to 24 of 32 oligonucleotide probes specific to this virus. To confirm the identification of the virus, total RNAs were extracted from leaf tissues, hybridized with random hexamers, and reverse-transcribed using MMLV reverse transcriptase (Life Technologies, Grand Island, NY). Complementary DNAs were amplified by PCR using an IQ supermix (BioRad, Hercules, CA), and two sets of generic primers for nepoviruses (1,4). Thermocycler conditions were 94°C 5 min (1×); 94°C 30 s, 50°C 30 s, and 69°C 2 min (35×), and 72°C for 5 min. The PCR products were sequenced directly. Sequences from the 340-bp products obtained from cultivars Geisenheim 26 (GenBank Accession No. HE984333) and Noah (HE984334) using the Wei et al. primers (4) had 76 to 84% sequence identity to ArMV RNA1 GenBank accessions GQ369528 and AY303786. Sequences from the 301-bp products obtained from cultivars Geisenheim 26 (HE984335) and Noah (HE984336) using the Digiaro et al. primers (1) had 87 to 91% sequence identity to ArMV RNA2 GenBank accessions AY017339 and X81814. ArMV was mechanically transmitted from Geisenheim 26 to Nicotiana tabacum cultivar Xanthi NN. Inoculation gave rise to necrotic local lesions on the inoculated leaves of five plants in each of two experiments (10 of 10 plants total). The presence of ArMV in tobacco was confirmed by DAS-ELISA. Thus, the presence of ArMV in New York grapevines has been confirmed by the detection of the coat protein antigen, virus specific oligonucleotide probes, and the sequencing of portions of both genomic RNAs. There are limited reports of ArMV in North America and in grapevine in particular (2), but with a wide host range and seed and nematode transmissibility, ArMV has the ability to become more widespread among grapevine and other crops. References: (1) M. Digiaro, et al. J. Virol. Methods 141:34, 2007. (2) B. N. Milkus et al. Am. J. Enol. Vitic. 50:56, 1999. (3) J. Thompson et al. J. Virol. Methods 183:161, 2012. (4) T. Wei et al. J. Virol. Methods 153:16, 2008.

A new potato virus in a new lineage of picorna-like viruses.

On constructing a cDNA library for potato, 'contaminating' sequences with a significant identity to Apple latent spherical virus (ALSV) were found. Determination 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%), suggesting 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 Comoviridae 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.