First report of Orthotospovirus iridimaculaflavi (Iris yellow spot virus) and Becurtovirus spinaciae (Spinach curly top Arizona virus) in sugarbeet in Idaho, United States.

Sugarbeet (Beta vulgaris L.), grown worldwide for sugar production, is susceptible to various viral diseases. Identifying the causal viral pathogen can be difficult due to mixed infections that might contribute to the disease symptoms. In the fall of 2022, widespread yellowing, chlorosis, vein clearing, and curling leaf symptoms were observed on sugarbeet plants across ~40 acres of commercial fields in southeast Parma, Idaho, with a disease incidence of 10 to 15%. Leaf symptoms resembled virus yellows, a known sugarbeet disease caused by a complex of viruses, Beet yellows virus, Beet western yellows virus, and Beet chlorosis virus (Wintermantel, 2005). To identify the causal viral pathogens responsible for the symptoms, total RNA was isolated from a pool of symptomatic leaves from four plants using the RNeasy Plant Mini Kit (Qiagen, CA). After depleting the ribosomal RNA, sequencing libraries were constructed and subjected to high throughput sequencing (HTS) using the Illumina NovaSeq 6000 with a 150-bp paired-end platform (Novogene, CA). After adapter trimming, a total of 71.67 million high-quality reads (Q>30) were obtained. Following the removal of reads mapped to host genome, the remaining 14.24 million reads were assembled into contigs using the SPAdes assembler (Bankevich et al. 2012; Prjibelski et al. 2020). The resulting 101513 contigs were aligned with the NCBI nonredundant database to identify contigs matching known viruses. The assembled contigs generated the complete genome of L, M, and S segments of Orthotospovirus iridimaculaflavi (Iris yellow spot virus, IYSV) with 98.08%, 98.98% and 96.65% identity with the corresponding reference sequences NC_029799, FJ361359 and OR526471 with 99 to 100% coverage. The full-length sequences of L (8863 nt), M (4823 nt), and S (3121 nt) segments of IYSV found in Idaho were deposited in GenBank with accession numbers PQ246270, PQ246271 and PQ246272, respectively. Additionally, a single 2860 nt contig exhibiting 98.57% identity and 100% coverage to Becurtovirus spinaciae (Spinach curly top Arizona virus, SpCTAV) HQ443515 identified in sugarbeet was deposited in GenBank with PQ246273. The SpCTAV was initially identified in spinach in AZ (Hernandez-Zepeda et al. 2013) and has recently been found in red table beet being grown in Idaho (Ramachandran et al. 2023) and in beet leafhopper (Circulifer tenellus) from Idaho (Strausbaugh et al. 2024). Accordingly, the current study identified SpCTAV in sugarbeet from Idaho. The IYSV incidence in the southeast Parma region of Idaho was further examined in additional sugarbeet samples collected in 2024. Total RNA was extracted from the leaves of 15 individual plants, and RT-PCR produced the expected amplicons of the L, M, and S segments of IYSV in all 15 plants. Sanger sequencing confirmed all the amplicons from 15 plants with 97.35% to 99.4% identity to the corresponding HTS of IYSV. To verify the presence of SpCTAV, genomic DNA was isolated and Sanger sequencing of the PCR product confirmed SpCTAV in 4 of 15 samples with 98.37% identity to the HTS sequence. Although virus yellows disease was suspected based on foliar symptoms, the HTS analysis revealed no known viruses in the analyzed sugarbeet samples. This is the first report of IYSV and SpCTAV in sugarbeet grown in Idaho. Monitoring the prevalence of IYSV, an RNA virus, and SpCTAV, a DNA virus, and their coexistence will clarify their role in the recently observed virus yellows-like disease symptoms in sugarbeet from Idaho.