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Title: Molecular analysis of Soybean dwarf virus isolates in the eastern United States confirms the presence of both D and Y strains and provides evidence of mixed infections and recombination

Author
item Schneider, William
item Damsteegt, Vernon
item Stone, Andrew
item KUHLMAN, MICKI - NONE
item BUNYARD, BRITT - NONE
item Sherman, Diana
item GRAVES, MICHAEL - UNIV OF MASS/LOWELL
item SMYTHERS, GARY - SAIC/NCI
item SMITH, ONEY - HOOD COLLEGE, FRED., MD
item HATZILOUKAS, EFSTATHIOS - UNIV OF IOANNINA

Submitted to: Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2011
Publication Date: 4/1/2011
Citation: Schneider, W.L., Damsteegt, V.D., Stone, A.L., Kuhlman, M., Bunyard, B., Sherman, D.J., Graves, M., Smythers, G., Smith, O., Hatziloukas, E. 2011. Molecular analysis of Soybean dwarf virus isolates in the eastern United States confirms the presence of both D and Y strains and provides evidence of mixed infections and recombination. Virology. 412: 46-54.

Interpretive Summary: Soybean dwarf virus (SbDV) causes two types of diseases in soybeans. One form of the disease, a near complete loss of color in the leaves, is caused by the yellowing strain of the virus (SbDV-Y). The other form of the disease, a severe stunting of the plant with little or no growth, is caused by the dwarfing strain of the virus (SbDV-D). Both forms of the disease have caused significant damage to soybean crops in Japan in the past. Recently, there have been reports of the dwarfing strain causing damage to soybean crops in the Midwest. A survey of several eastern US states determined that SbDV was also present there. An analysis of the genetic sequences of these eastern US SbDV populations determined that there were both dwarfing and yellowing strains present, sometimes in mixed infections, where both SbDV-Y and SbDV-D coexisted in the same plant. In one case, the genetic material of a SbDV-Y had recombined with the genetic material of a SbDV-D to make a hybrid virus. This is the first report of mixed infections of SbDV-Y and SbDV-D, as well as the first report of recombination between the two types of SbDV.

Technical Abstract: Soybean dwarf luteovirus (SbDV) has been identified in both Japan and the United States. Previous efforts determined that isolates representing both D-like and Y-like isolates exist in the eastern United States. These SbDV isolates tend to have host range limitations similar to their Japanese counterparts, but rarely develop symptoms as severe as the originally described Japanese strains. The eastern US isolates were analyzed by multiplex PCR and sequencing, revealing that some of the previously described single US isolates were in fact mixed infections of both Y and D isolates. In addition, one isolate contained a recombinant subisolate, where recombination had occurred between the D and Y components in the 3’ end of the coat protein (CP) gene. Phylogenetic analyses of the nucleotide sequences and the inferred amino acid sequences for CP and movement protein (nested within the CP gene) for the US isolates indicates that the nucleotide sequence phylogeny is most closely aligned with the inferred amino acid sequence phylogeny for the movement protein. A population level analysis determined that the US isolates demonstrated high levels of genetic diversity, consistent with levels noted for other plant RNA viruses.