Genetic diversity of soybean dwarf virus in two regions of mainland Australia

• Published in: Archives of virology 2024-11, Vol.169 (11), p.216, Article 216
• Main Authors: Congdon, B. S., Sharman, M., Kehoe, M. A.
• Format: Article
• Language: English
• Subjects: Animals; Aphids - virology; Australia; Biomedical and Life Sciences; Biomedicine; Disease transmission; Epidemiology; Genetic analysis; Genetic diversity; Genetic Variation; Genome, Viral - genetics; Genomes; Genomic analysis; Host range; Host Specificity; Infectious Diseases; Luteovirus; Luteovirus - classification; Luteovirus - genetics; Luteovirus - isolation & purification; Medical Microbiology; Nucleotide sequence; Original; Original Article; Phylogenetics; Phylogeny; Plant Diseases - virology; Plant viruses; RNA viruses; RNA, Viral - genetics; Strains (organisms); Tombusviridae; Trifolium - virology; Trifolium subterraneum; Virology
• ISSN: 0304-8608; 1432-8798; 1432-8798
• DOI: 10.1007/s00705-024-06142-z

Soybean dwarf virus (SbDV; family Tombusviridae , genus Luteovirus , species Luteovirus glycinis ) is an RNA plant virus that is transmitted solely by aphids in a persistent, circulative and non-propagative manner. SbDV causes significant losses in cultivated Fabaceae, especially in subterranean clover ( Trifolium subterraneum ) pastures of mainland Australia. SbDV isolates are classified into four phenotypically distinguishable strains: YP, YS, DP, and DS. Y and D strains differ primarily in their host range, and P and S strains in their primary vector species. Genetically, Y and D strains separate into two clades in every genomic region except for the N-terminal region of the readthrough domain (N-RTD), in which P and S strains separate. SbDV diversity in Australia has yet to be investigated, so in this study, 41 isolates were collected from six different host species across two production regions of Australia: the south coast of Western Australia (‘south-west’) and northern New South Wales/southern Queensland (‘north-east’). A near-complete genome sequence of each isolate was obtained, and together with all 50 whole-genome sequences available in the GenBank database, underwent phylogenetic analysis of the whole genome nt and the N-RTD aa sequences. At the whole-genome level, the isolates separated into D and Y clades. At the N-RTD level, most of the isolates separated into P and S clades. All south-west isolates and 11 of the 31 north-east isolates were in the Y clade, and the remaining 20 north-east isolates were in the D clade. Except for one isolate that fell outside the P and S clades, all south-west and north-east isolates were in the P clade, suggesting that they are transmitted by Acyrthosiphon pisum and Myzus persicae . Available biological data largely supported the phenotypic inferences made from the phylogenetic analysis, suggesting that genetic data can provide critical epidemiological insights, provided that sufficient biological data have been collected.