J. Allan Dodds

Molecular characterization of an isolate of citrus tristeza virus that causes severe symptoms in sweet orange.

The complete sequence (19,249 nucleotides) of the genome of citrus tristeza virus (CTV) isolate SY568 was determined. The genome organization is identical to that of the previously determined CTV-T36 and CTV-VT isolates. Sequence comparisons revealed that CTV-SY568, a severe stem-pitting isolate from California, has more than 87% overall sequence identity with CTV-VT, a seedling yellows isolate from Israel. Although SY568 has an overall sequence identity of 81% with CTV-T36, a quick decline isolate from Florida, the sequence identity in the 3′ half of the genome is over 90% while the sequence identity in the 5′ half of the genome is as low as 56%. Based on the sequence alignments of these three isolates, sequences in the 3′ half of the genome are generally well conserved, while the sequences in the 5′ half are relatively divergent. Sequence data of independent overlapping clones from the CTV-SY568 genome revealed two regions with highly divergent sequences. In open reading frame 1b (RNA dependent RNA polymerase), there were 118 nucleotide differences that lead to 16 amino acid changes. In the open reading frame of the divergent coat protein gene, 5 amino acid changes result from 48 nucleotide differences. Most differences occurred in the third position of the codons, and resulted in silent amino acid substitutions. RNase protection assays demonstrated that most of the clones obtained are representative of the major RNA species of this isolate. Northern analysis indicated that CTV-SY568 accumulated more viral RNA including genomic and certain subgenomic RNAs than isolates VT or T36 in sweet orange.

Analysis of genetic heterogeneity within the type strain of satellite tobacco mosaic virus reveals several variants and a strong bias for G to A substitution mutations

Satellite tobacco mosaic virus (STMV) is a small plant virus that is dependent for its replication on the presence of a helper tobamovirus. RNase protection analysis of genomic RNA of the STMV type strain revealed that it was composed of two major genome types which differed at a single detectable site near nucleotide 753. Analyses of 42 full-length STMV clones for sequence heterogeneity resulted in the identification of 16 variants distinguishable by unique RNase protection assay patterns. Characterization of these variants confirmed the presence of a major heterogeneity site at nucleotide 751 and identified several sites of sequence microheterogeneity typical of an RNA quasispecies population. Mapping of the heterogeneity sites revealed an apparently random distribution along the length of the STMV genome, with no significant clustering or preference for noncoding regions. Infectivity experiments in tobacco showed that RNA transcripts of 13 of the 16 variant clones were infectious, indicating that most of the variants represent functional genomes coexisting in the type strain with the two major genome types. Sequence analyses revealed that most of the heterogeneity sites detected, including the major site of heterogeneity, were single base differences. Assessment of all the heterogeneity sites found in the total of 10,545 nt sequenced allowed us to estimate that the RNase protection assays detected approximately 50% of the differences present in the 16 clones studied. The nature of these differences was highly biased in that 18 of the 29 single base differences characterized (62%) were G to A substitutions.

Cross-protection and interference between electrophoretically distinct strains of cucumber mosaic virus in tomato

Cucumber mosaic virus (CMV) was partially purified by polyethylene glycol precipitation from extracts of tomato leaflets. The presence and quantity of two strains with different electrophoretic mobilities was analyzed by polyacrylamide gel (2.5%) electrophoresis of preparations from as little as 50 mg of tissue. This method was used to analyze interference and cross-protection between the strains. Coinoculation resulted in local and systemic mixed infections and reductions in the synthesis of both strains. Systemic symptoms and accumulation of the strain with the more severe symptoms were not detected in up to 13 newly formed leaves in five of six plants preinfected with the mild strain and challenged with the severe strain. Systemic accumulation of the mild strain was not detected in each of six plants preinfected with the severe strain and challenged with the mild strain. Both strains could accumulate in challenge-inoculated leaves. The level or absence of interference in these leaves did not affect systemic cross-protection. Cross-protection between these strains of CMV involves considerable inhibition of virus accumulation in addition to absence of symptoms.

Natural Incidence of Mixed Infections and Experimental Cross Protection Between Two Genotypes of Tobacco mild green mosaic virus

ABSTRACT Isolates of Tobacco mild green mosaic virus (TMGMV), a member of the genus Tobamovirus, from Nicotiana glauca in southern California fall into two major genotypes, large (TMGMV-L) and small (TMGMV-S), distinguishable by the size of the coat protein (CP) subgenomic RNA. Mixed infections in the field were rare (1.6%), even at sites where both genotypes were common in single infections (62% for TMGMV-S; 37% for TMGMV-L). When plants experimentally protected by TMGMV-L were challenged by TMGMV-S, almost complete cross protection (90% of total plants challenged) was observed regardless of the protective time period (minimum 12 h and maximum 14 days). When plants protected by TMGMV-S were challenged with TMGMV-L, complete cross protection was observed when the protective time was 5 to 14 days. However, when the protective time was 3 days or less, protection by TMGMV-S was greatly reduced (11%), with mixed infections of TMGMV-S and -L predominating (69%), and single infections of the challenge virus TMGMVL were frequently observed (20%). When TMGMV-S and -L virions were co-inoculated, the virus progeny from individual plants most often contained only the TMGMV-L genome (61%) or, less frequently (39%), both genotypes. Therefore, TMGMV-L was more competitive than TMGMV-S and was able to displace TMGMV-S in experimental situations. The results obtained from cross-protection experiments in the greenhouse would explain the low frequency of natural mixed infections. It is possible that the experimental superior competitiveness of the novel L genotype has already or will play a role in its abundance in southern California.

Cytopathology of satellite tobacco mosaic virus and its helper virus in tobacco

Abstract Ultrastructural responses of tobacco cells infected with a newly discovered satellite virus (STMV) that has an isometric morphology and is associated with rigid rodshaped tobacco mosaic virus (TMV) were studied in situ . In cells infected with TMV alone,TMV particles occurred as crystalline arrays in the cytoplasm and were usually associated with TMV-characteristic X bodies. In cells infected with both TMV and STMV, particles of STMV occurred only in cells that contained TMV particles, which suggests a correlation between the satellite and helper virus presence. However, the replication and/or accumulation sites of STMV appear to be independent from its helper virus. Unlike TMV particles, STMV particles were associated with several cytopathic structures such as granular inclusions, membranous vesicles of 50–80 nm, and myelin-like bodies which were all bounded by a single common membrane, No X bodies occurred in cells containing STMV particles, and the mitochondria possessed abnormal tubular structures containing flocculent material.