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The complete genomic sequence of a Pakistani isolate of Sugarcane streak mosaic virus (SCSMV-PAK) is determined to be 9782 nucleotides in length, excluding the 3' poly(A) tail, and it comprises a large open reading frame encoding a polyprotein of 3130 amino acid residues. The deduced polyprotein is likely to be cleaved at nine putative protease sites by three viral proteases to ten mature proteins. Conserved motifs of orthologous proteins of other potyviruses are identified in corresponding positions of SCSMV-PAK. The genomic organization is virtually identical to the genera Ipomovirus, Potyvirus, Rymovirus, and Tritimovirus in the family Potyviridae. Sequence analyses indicate that the SCSMV-PAK genomic sequence is different from those of Sugarcane mosaic virus and Sorghum mosaic virus, two viruses with very similar symptoms and host range to SCSMV-PAK. SCSMV-PAK shares 52.7% identity with Triticum mosaic virus (TriMV) and 26.4-31.5% identities with species of the existing genera and unassigned viruses in the Potyviridae at the polyprotein sequence level. Phylogenetic analyses of the polyprotein and deduced mature protein amino acid sequences reveal that SCSMV, together with TriMV, forms a distinct group in the family at the genus level. Therefore, SCSMV should represent a new genus, Susmovirus, in the Potyviridae.

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The presence of Gooseberry vein banding associated virus (GVBaV), a badnavirus in the family Caulimoviridae, is strongly correlated with gooseberry vein banding disease in Ribes spp. In this study, full-length genomic sequences of four GVBaV isolates from different hosts and geographic regions were determined to be 7649-7663 nucleotides. These isolates share identities of 96.4-97.3% for the complete genomic sequence, indicating low genetic diversity among them. The GVBaV genome contains three open reading frames (ORFs) on the plus strand that potentially encode proteins of 26, 16, and 216 kDa. The size and organization of GVBaV ORFs 1-3 are similar to those of most other badnaviruses. The putative amino acid sequence of GVBaV ORF 3 contained motifs that are conserved among badnavirus proteins including aspartic protease, reverse transcriptase, and ribonuclease H. The highly conserved putative plant tRNA(met)-binding site is also present in the 935-bp intergenic region of GVBaV. The identities of the genomic sequences of GVBaV and other badnaviruses range from 49.1% (Sugarcane bacilliform Mor virus) to 51.7% (Pelargonium vein banding virus, PVBV). Phylogenetic analysis using the amino acid sequence of the ORF 3 putative protein shows that GVBaV groups most closely to Dioscorea bacilliform virus, PVBV, and Taro bacilliform virus. These results confirm that GVBaV is a pararetrovirus of the genus Badnavirus in the family Caulimoviridae.

Four of 19 Prunus germplasm accessions hand carried from the Ukraine into the United States without authorization were found to be infected with Plum pox virus (PPV). Of the three isolates characterized, isolates UKR 44189 and UKR 44191 were confirmed to be isolates of PPV strain W, and UKR 44188 was confirmed to be an isolate of PPV strain D. UKR 44189 and UKR 44191 are very closely related to the PPV strain W isolate LV-145bt (HQ670748) from Latvia. Nucleotide and amino acid sequence identities between these three isolates were greater than 99%. This indicates that the isolates are very closely related and likely originated from a common source. The high genetic diversity among PPV-W strain isolates allowed the identification of potential recombination events between PPV isolates. It appears also that GF 305 peach and Prunus tomentosa are not hosts for the PPV isolate UKR 44189.

Nested polymerase chain reaction (PCR) assays were evaluated for use on a routine basis in a quarantine program to detect phytoplasmas in dormant fruit tree scionwood collected during the winter season. Phytoplasmas associated with peach yellow leaf roll, Western X, apricot chlorotic leaf roll, plum leptonecrosis, and apple proliferation diseases were detected in all known infected sources. Phytoplasmas in Prunus spp. were readily detected in both dormant bud and internodal tissues. Use of nested PCR versus a single primer pair resulted in electrophoresed PCR products that were easier to interpret. The nested PCR procedure has replaced 3-year tests with grafts on sensitive indicators to detect this group of pathogens.

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The 3 untranslated regions (UTRs) of RNA1 and RNA2 of Tomato ringspot virus (ToRSV) are 1.3 kb in size and virtually identical. In this study, sequences containing most of the 3 UTRs (1168-1265 bp) were determined from 18 ToRSV isolates collected from fruit trees, small fruits and grapevines in North America. Pairwise nucleotide sequence comparisons with sequences of two isolates available in GenBank showed identities ranging from 95.1 to 100% for the majority of ToRSV isolates. Most genetic variation occurs as point mutations and single insertions and/or deletions. Phylogenetic analysis showed that 17 of the 20 isolates grouped together into a major cluster and three isolates grouped into two minor clusters, with genetic divergence rates among the three clusters of 11.8% to 23.8%. No correlation was found between the 3 UTR sequences and symptom expression on Nicotiana benthamiana, host plant or geographic origin of ToRSV isolates. RT-PCR using primers designed within the highly conserved 3 UTR regions detected all 18 ToRSV isolates as well as two isolates from a vineyard. This assay can serve as a practical methodology for the sensitive detection of varied ToRSV isolates as it is more sensitive than a RT-PCR assay based on previously reported U1/D1 primers. Résumé:Les séquences non traduites (3 UTR) de l'ARN1 et de l'ARN2 du virus des taches annulaires de la tomate (ToRSV) mesurent 1,3 kb et sont essentiellement identiques. Dans cette étude, les séquences contenant la majorité des 3 UTR (1168-1265 bp) ont été déterminées á partir de 18 isolats de ToRSV collectés en Amérique du Nord sur des arbres fruitiers, des petits fruits et des vignes. Les comparaisons binaires de séquences de nucléotides avec les séquences de deux isolats de la GenBank ont montré des similarités variant de 95.1% á 100% en ce qui a trait á la majorité des isolats de ToRSV. La plupart des variations génétiques se produisent en tant que mutations ponctuelles et qu'insertions/délétions uniques. L'analyse phylogénétique a montré que 17 des 20 isolats étaient groupés en super-famille et que trois isolats l'étaient en deux familles mineures, dont les taux de divergence génétique, chez les trois familles, variaient de 11.8% á 23.8%. Nous n'avons trouvé aucune corrélation entre les séquences 3 UTR et l'expression des symptômes sur Nicotiana benthamiana, plante hôte ou origine géographique des isolats de ToRSV. Des amorces RT-PCR conçues dans les régions 3 UTR hautement conservées ont permis de détecter les 18 isolats de ToRSV ainsi que deux isolats provenant d'un vignoble. Ce test peut être utilisé comme méthode pratique pour la détection précise d'isolats de ToRSV puisqu'il est plus sensible qu'un test RT-PCR basé sur les amorces U1/D1 utilisées précédemment.