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

Authors: Ramachandran, Vanitharani; CHINNADURAI, CHINNARAJA - North Dakota State University; HYON, CHO - US Department Of Agriculture (USDA); NEHER, OLIVER - Amalgamated Sugar Company; WEILAND, JOHN - US Department Of Agriculture (USDA); Bolton, Melvin

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/28/2025
Publication Date: N/A
Citation: N/A

Interpretive Summary: Sugar beet is affected by several diseases caused by viruses. Identification of the causal viral pathogen based on the disease symptoms often is difficult. In the fall 2022, widespread occurrence of leaf symptoms exhibiting yellowing, blotching, and curling were observed in commercial fields in the southeast of Parma, Idaho. These leaf symptoms were similar to those associated with virus yellows, a known disease of sugar beet caused by a complex of viruses typically including Beet yellows virus, Beet western yellows virus, and Beet chlorosis virus. To identify potential viral pathogen(s), we obtained RNA sequences from the leaf samples. Interestingly, two viruses, Iris yellow spot virus (IYSV) and Spinach curly top Arizona virus (SpCTAV) that were previously unknown to sugar beet were identified. Although, virus yellows disease was suspected based on disease symptoms, sequencing analysis did not reveal the presence of any of the viruses in these samples. To our knowledge, this is the first report of IYSV and SpCTAV in sugar beet grown in Idaho. Further monitoring of the frequency of these viruses and their coexistence in sugar beet from Idaho is important for developing disease management strategies.

Technical Abstract: Sugarbeet (Beta vulgaris L.) is grown for its sucrose production, a staple sugar used globally. Sugarbeet is susceptible to numerous virus diseases. During the fall of 2022, leaf symptoms of yellowing, blotching, and curling were observed on sugarbeet plants widespread in commercial fields in the southeast of Parma, Idaho. Leaf symptoms resemble to ‘virus yellows’, a known disease of sugarbeet caused by a complex of viruses including Beet yellows virus (Closterovirus), and the Poleroviruses Beet western yellows virus, and Beet chlorosis virus. To identify the causal viral pathogen(s) underlying the symptoms, total RNA was isolated from pooled symptomatic leaf samples and subjected to high-throughput sequencing (HTS) using the Illumina NovoSeq 6000. A total of 14.24 million reads were obtained after removing adapters and reads mapping to host genome. These reads were de novo assembled, and the contigs were aligned to NCBI nonredundant database. Interestingly, several contigs ranging from 1491 nt to 4064 nt that had sequence similarity to Iris yellow spot virus (IYSV) were identified. The nucleotide sequence of the obtained L-segment shared 97.79% identity with NC_029799, the M-segment shared 98.98% identity with FJ361350, and the S-segment shared 96.65% identity with OR526471, the reference genome of IYSV. In addition to IYSV, a single contig with 2860 nt representing the full-length genome of Spinach curly top Arizona virus (SpCTAV) was generated with 100% coverage and 98.57% identity to the reference genome of SpCTAV (HQ443515). To validate the HTS results of IYSV, RT-PCR was conducted using RNA samples to amplify multiple regions of L-segment, M-segment, and S-segment. Sanger sequencing of the RT-PCR products showed 97.35 to 99.4% nucleotide identity with the corresponding HTS-assembled IYSV L-, M-, and S-segments. To confirm the presence of SpCTAV, genomic DNA was isolated from symptomatic leaf tissue and sequencing of the PCR amplicon revealed 98.37% matching to the assembled HTS results for SpCTAV. This is the first report of Iris yellow spot virus (genus Tospovirus) and Spinach curly top Arizona virus (genus Becurtovirus) in sugarbeet grown in Idaho. Of note, virus yellows disease was suspected based on the foliar symptoms; however, HTS analysis did not reveal the presence of any of the viruses in these sugarbeet samples. Further monitoring the frequency of IYSV and SpCTAV and their coexistence in sugarbeet will elucidate their role in the recently observed disease symptoms in sugarbeet from Idaho.