- Volume 76, Issue 8, 1995

The complete genomic sequence of a new virus, first found infecting oats in Wales, UK, has been determined. The genome is a positive-sense ssRNA molecule, 4114 nucleotides in length, examination of which indicates the presence of four ORFs. The first ORF initiating at the 5′ terminus (ORF1) encodes a protein with a predicted M r of 23476 (p23). ORF2 extends through the amber termination codon of ORF1 to give a protein with a predicted M r of 84355 (p84). The readthrough domain of p84 contains amino acid sequence similarities with a number of putative RNA-dependent RNA polymerases. ORF3 is in a different reading frame from ORF1/2 and encodes a protein with an M r of 48231 (p48), identified as the coat protein by direct peptide sequencing. ORF4 nests within ORF3 but is in a different frame from it and codes for a protein with a predicted M r of 8220 (p8). Comparisons of peptide sequence, particularly within the putative polymerase region and within the S domain of the coat protein, highlight similarities with members of both the tombusvirus and carmovirus groups. The coat protein region shows most similarity with members of the tombusvirus group, whilst the size and predicted strategy of the genome seem to be intermediate between that of the carmovirus and tombusvirus groups. These features highlight possible evolutionary links with each group whilst being distinct from both. We propose the name of oat chlorotic stunt for this new virus.

A virus isolate, designated as 11-Cal, originating from southern France has been identified as an isolate of the mite-transmitted brome streak mosaic rymovirus (BrSMV) by serological and morphological properties. BrSMV is a member of the genus Rymovirus of the family Potyviridae. The complete nucleotide sequence of the RNA genome of BrSMV has been determined. The assembled RNA is 9672 nucleotides in length, excluding a 3′-terminal poly(A)sequence. The RNA contains one open reading frame (ORF) of 9282 nucleotides coding for a polyprotein of 3093 amino acids. A comparison with typical potyviruses showed that BrSMV has a similar genome organization. The predicted cleavage sites of the polyprotein of BrSMV are similar to those of potyviruses. Nevertheless, unusual dipeptides are proposed in two cases. Based on the proposed location of the cleavage sites nine mature proteins are predicted. Specific motifs, described for potyviral polyproteins, are almost all present in the polyprotein of BrSMV, too. However, only an incomplete zinc-finger motif is present in the potential helper component and the motif for aphid transmission in the coat protein is not found. Several alignments of amino acid sequences showed less similarity between BrSMV and potyviruses than between different potyviruses.

The coat protein (CP) gene-containing circular DNA molecule of an isolate of tomato leaf curl geminivirus (ITmLCV; 2749 nt) obtained from southern India, and the CP genes of tomato yellow leaf curl geminivirus isolates from Nigeria and two regions of Saudi Arabia were sequenced. ITmLCV DNA had the same arrangement of ORFs, and the same pattern of repeats in the large intergenic region as is found in DNA-A of other whitefly-transmitted geminiviruses (WTGs) from the Old World. However, the sequence of ITmLCV DNA and the sequences of its predicted translation products differed substantially from those of other WTGs, including one isolate obtained from a tomato plant in northern India. Comparison of the four CP sequences deduced here with those of 18 WTGs previously studied indicated that their relationships can be represented by a tree with three branches that are unrelated to plant host species but which contain viruses from the Americas, Africa to the Middle East, and Asia to Australia, respectively. It is suggested that WTG CP evolution has proceeded along different paths in these three main regions, and that WTGs have adapted freely to new hosts in each region. Indeed, the virus isolates causing similar diseases of tomato plants in the different continents are, with few exceptions, not closely related and warrant recognition as separate species.

Single-strand conformation polymorphism analysis was found to be a powerful tool for rapidly assigning large numbers of beet necrotic yellow vein virus (BNYVV) isolates to a known strain group as well as for detecting mixed infections, minor variants or new strain groups. The prevalence of the B-type in Germany and France and the A-type in most other countries was confirmed. Minor variants with a very restricted distribution were detected occasionally. New rhizomania outbreaks in Great Britain were caused either by the A- or the B-type or mixtures of both suggesting introduction of BNYVV from several sites abroad. An entirely different BNYVV type (P-type) was identified in a small area in France. Evidence for further strain groups in China was also obtained.

The coat protein gene nucleotide sequences from eight previously uncharacterized strains of potato virus X (PVX) were determined. Comparison of the deduced amino acid sequences showed that two classes of PVX coat protein, designated types X and B, could be distinguished based on protein length and overall amino acid identities. In all there were 14 amino acid positions where all of the type X proteins differed from all of the type B proteins. The PVX coat protein is the principal viral determinant of the outcome of interactions between the virus and potatoes carrying either the Nx or Rx1 resistance genes. The different strains of PVX were tested for their ability to overcome resistance conferred by three potato resistance genes: Nx, Nb and Rx1. All of the strains that were avirulent on potato cultivars carrying the Nx resistance gene were found to have type X coat proteins whereas strains capable of overcoming the Nx resistance had type B coat proteins.