Beet curly top virus strains associated with sugar beet in Idaho, Oregon, and a Western U.S. collection

Curly top of sugar beet is a serious, yield limiting disease in semi-arid production areas caused by Beet curly top virus (BCTV) and transmitted by the beet leafhopper. One of the primary means of control for BCTV in sugar beet is host resistance but effectiveness of resistance can vary among BCTV strains. Strain prevalence among BCTV populations was last investigated in Idaho and Oregon during a 2006-2007 survey, but changes in disease severity suggested a need for reevaluation. Therefore, 406 leaf samples symptomatic for curly top were collected from sugar beet plants in commercial sugar beet fields in Idaho and Oregon from 2012 to 2015. DNA was isolated and BCTV strain composition was investigated based on polymerase chain reaction (PCR) assays with strain specific primers for the Severe (Svr) and California/Logan (CA/Logan) strains and primers that amplified a group of Worland (Wor)-like strains. The 2006-2007 ID/OR BCTV positive sugar beet samples (59% had mixed infections) included: 87% Svr, 7% CA/Logan, and 60% Wor-like. The BCTV strain distribution in the new survey (16% had mixed infections) averaged 2% Svr, 30% CA/Logan, and 87% Wor-like. Whole genome sequencing (GenBank accessions KT276895 to KT276920 and KX867015 to KX867057) with overlapping primers, found that the Wor-like strains included Wor, Colorado (CO), and a previously undescribed strain designated Kimberly1 (Kim1). Results confirm a shift from Svr being one of the dominant BCTV strains in commercial sugar beet fields in 2006-2007 to becoming undetectable at times during recent years