Comparisons between sequenced and re-sequenced genomes of historical subterranean clover mottle virus isolates

Abstract We report comparisons between the complete genomic sequences of five historical Western Australian isolates subterranean clover mottle virus (SCMoV) from 1989–2000, and an infectious clone its 1989 isolate. Sanger Sequencing (SS) High Throughput (HTS), or both, were used to obtain these genomes. Four SCMoV sequenced by SS in 1999–2002, but re-sequenced again HTS 2020. The pairs obtained four differed only 18–59 nucleotides. This small difference resulted different sequencing methods, < 1–5 years each isolate was host passaged before freeze-drying prior sequencing, a combination both. Since has not been reported outside Australia, this similarity suggests population represents progeny either indigenous that spread native legume after introduction recent seed-borne incursion elsewhere. ORF1 most variable, phylogenetic tree constructed with ORF1s showed grouped according their symptom severity clover, indicating probability ORF1-encoded P1 protein is determinant. A satellite RNA associated all genomes none derived SS.