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ARS Home » Northeast Area » Washington, D.C. » National Arboretum » Floral and Nursery Plants Research » Research » Publications at this Location » Publication #379009

Research Project: Detection, Identification, and Characterization of New and Emerging Viral and Bacterial Diseases of Ornamental Plants

Location: Floral and Nursery Plants Research

Title: First complete genome sequence of carnation latent virus, the type member of the genue Carlavirus

item Jordan, Ramon
item KOROLEV, ERICA - Biotechnology Academy
item Grinstead, Sam
item Mollov, Dimitre

Submitted to: Archives of Virology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/26/2020
Publication Date: 3/7/2021
Citation: Jordan, R.L., Korolev, E., Grinstead, S.C., Mollov, D.S. 2021. First complete genome sequence of carnation latent virus, the type member of the genue Carlavirus. Archives of Virology. 166:1501-1505.

Interpretive Summary: Carlavirus is a genus of plant viruses that includes 53 species recognized by the International Committee on Taxonomy of Viruses. Molecular sequences of many of these species are well-represented in the NCBI GenBank database. However, the type species for this genus, Carnation latent virus (CLV), had no full-length genomic sequences in the database. ARS scientists in Beltsville, MD determined the full-length genome sequence of CLV using high-throughput sequencing. The complete sequence was determined to be 8,513 nucleotides and was deposited in GenBank (accession #MN450069). The sequence data and analysis confirm that carnation latent virus is distinct from all other recognized carlaviruses. This is the first report of the full genome sequence of Carnation latent virus.

Technical Abstract: The genus Carlavirus [Family Betaflexiviridae, Order Tymovirales] includes 53 currently recognized species by ICTV. The NCBI GenBank database has 43 accessions of full-length (7,890 to 9,073 nt) carlavirus genomes. Surprisingly, the type species Carnation latent virus (CLV) only has accessions with 1313 or fewer nts. The goal of this study was to determine the full-length genome of CLV. Naturally infected greenhouse-grown ‘Kiwi Lace’ carnation plants that tested positive for CLV by ELISA and RT-PCR were used as source plants for high-throughput sequencing and completed by 5' and 3' RACE and validated by Sanger sequencing of CLV-specific RT-PCR generated amplicons. The complete CLV-KL sequence was determined to be 8,513 nt [MN450069]. In pairwise analysis, the genome shares 40-46% identity with recognized carlaviruses and the six in silico translated proteins have 15-62% amino acid identities with their respective carlavirus orthologs. The CLV-KL coat protein shares 98.4% identity with the CLV-UK NCBI Reference Sequence. In phylogenetic analysis, CLV clusters with Butterbur mosaic virus, Coleus vein necrosis virus, and Garlic common latent virus.