Studies on the genome heterogeneity and its host passage effect of apple stem grooving capillovirus

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The 3'-terminal regions of the genomes of apple stem grooving virus (ASGV) isolated from apple, Japanese pear and European pear plants and citrus tatter leaf virus (CTLV) from citrus plants were amplified by the reverse transcription-polymerase chain reaction and then the DNA products were sequenced. The results indicated that all ASGV isolates from apple, Japanese pear and European pear comprise at least two to four 'sequence variants' which significantly differ in nucleotide sequence from each other. Comparison of the amino acid (aa) sequences of the ORF1 and ORF2 proteins among isolates or sequence variants including isolates of ASGV and CTLV reported previously showed that the aa sequences of the ORF2 protein (320 aa) and the putative coat protein (CP) (237aa) equivalent to aa positions 1868 to 2105 of the ORF1 protein of ASGV (P-209) were highly conserved among isolates or sequence variants.Similarities ranged from 92.8 to 100% for the ORF2 protein among 15 isolate or sequence variants and 93.2 to 100% for the CP among 21 isolates or sequence variants. On the contrary, the aa sequence similarities of a284 aa region (named 'V-region' in this paper) equivalent to aa positions 1584 to 1868 of the ORF1 protein which encodes ORF2 protein in another frame were highly variable (53.5 to 99.3%) among 15 isolates and sequence variants. The percentage of conserved V-region aa in all 15 was only 20.4%. Phylogenetic trees constructed from the aa sequences of CP,ORF2 or V-region proteins showed that isolates or sequence variants were separated into several clusters, regardless of the source host plant species (apple, Japanese pear, European pear, citrus and lily). In a tree constructed by V-region proteins, two CTLV isolates were grouped into two different clusters each of which contained isolates or sequence variants from apple and Japanese pear. These results demonstrate that CTLV from citrus cannot be distinguished from ASGV from Rosaceous plants at the molecular level.