GENETIC ANALYSIS OF A NOVEL ALASKA BARLEY YELLOW DWARF VIRUS IN THE FAMILY LUTEOVIRIDAE

Authors: ROBERTSON, NANCY; FRENCH, ROY

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/7/2006
Publication Date: 2/20/2007
Citation: Robertson, N.L., French, R.C. 2007. Genetic analysis of a novel Alaska barley yellow dwarf virus in the family Luteoviridae. Archives of Virology. 152(2):369-382.

Interpretive Summary: Barley yellow dwarf (BYD) disease is caused by Barley yellow dwarf virus (BYDV)-PAS, -PAV and Cereal yellow dwarf virus (CYDV)-RPV in barley and oat crops in south central Alaska. In 2003, an estimated one percent of the plants in an oat field contained discolored red leaves typical for BYD. Forty plants with symptoms were selected at random, and their leaves assayed for C/BYDVs. All were negative for BYDV-PAV, -MAV, -SGV, and CYDV-RPV by serological assays. Only one plant produced a RT-PCR (reverse transcriptase-polymerase chain reaction) product using standard “universal luteovirus” primers that was identified as BYDV-PAS. However when a new set of primers (described by Malmstrom and Shu in 2004) were used to assay the same 40 plants for C/BYDV, RT- PCR products were generated from over half the plants. Nucleotide sequences obtained from the coat protein gene were most similar to BYDV-MAV. However, the amino acid sequences were only 72-74 % identical to other BYDV-MAVs with little identity in key regions along the coat protein presumed to be serologically important. These defined amino acid differences not only accounted for the lack of specificity in the serological assays, but also introduced us to a new BYDV species with the proposed name, barley yellow dwarf virus-ORLV (oat red leaf virus).

Technical Abstract: A study on the occurrence and molecular diversity of a novel barley yellow dwarf virus (BYDV) in the family Luteoviridae in Alaska was carried out on 27 isolates. Forty plants from a field of oats (Avena sativa) with red leaves, typical of symptoms for BYD disease, gave negative results following enzyme-linked immunosorbent assays (ELISA) for BYDV-MAV, BYDV-PAV, BYDV-SGV, and Cereal yellow dwarf virus-RPV. Only one plant produced a RT-PCR (reverse transcriptase-polymerase chain reaction) product using standard “universal luteovirus” primers, Lu 1/Lu 4; subsequent sequence data indicated that it was closely related to BYDV-PAS (formerly BYDV-PAV-129). However, RT-PCR products were generated from over half of the plants with another set of primers, Yan-R/Shu-F primers. The fragments, ~830 bp, included the 3’-terminus of the polymerase gene (ORF 2), the intergenic region (~113 nt), and the coat protein gene (ORF 3). Sequences of these PCR products were most similar to BYDV-MAVs but had only 72-74 % amino acid identity. In particular, coat protein gene sequences of the Alaska isolates differed in several regions that otherwise are conserved among BYDV-MAV isolates which may explain the negative ELISA results. Based upon differences in serology and partial genomic sequences, we concluded that the Alaskan BYDV-MAV-like isolates were novel species in the genus Luteovirus, and proposed the name: barley yellow dwarf virus (BYDV)-ORLV (oat red leaf virus).