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

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