Molecular and biological characterization of a newly identified virus representing a novel taxon of Alphaflexiviridae infecting different accessions of seashore Paspalum, a turfgrass, widely grown in the United States

Authors: SAYANTA, BERA - Animal And Plant Health Inspection Service (APHIS); SCHULDEN, TAYLOR - Animal And Plant Health Inspection Service (APHIS); HU, XIAOJUN - Animal And Plant Health Inspection Service (APHIS); Abrahamian, Peter; YANG, YU - Animal And Plant Health Inspection Service (APHIS); PAULSON, ANNA - Animal And Plant Health Inspection Service (APHIS); HARVEY-WHITE, AMY - Animal And Plant Health Inspection Service (APHIS); PRADHAN, SHREENA - University Of Georgia; DEVOS, KATRIEN - University Of Georgia; DEVORSHAK, CHRISTINA - Animal And Plant Health Inspection Service (APHIS); FOSTER, JOSEPH - Animal And Plant Health Inspection Service (APHIS); ADHIKARI, BISHWO - Animal And Plant Health Inspection Service (APHIS)

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/22/2026
Publication Date: 6/25/2026
Citation: Sayanta, B., Schulden, T., Hu, X., Abrahamian, P., Yang, Y., Paulson, A., Harvey-White, A., Pradhan, S., Devos, K., Devorshak, C., Foster, J., Adhikari, B. 2026. Molecular and biological characterization of a newly identified virus representing a novel taxon of Alphaflexiviridae infecting different accessions of seashore Paspalum, a turfgrass, widely grown in the United States. International Journal of Molecular Sciences. 27(13). Article e5750. https://doi.org/10.3390/ijms27135760.
DOI: https://doi.org/10.3390/ijms27135760

Interpretive Summary: Seashore paspalum (Paspalum sp.) is a grass commonly used on golf courses, sports fields, and for landscaping in the United States. Paspalum plants from the USDA National Plant Germplasm System collection (NPGS) were examined using high throughput DNA sequencing. A novel virus, tentatively named Paspalum latent virus (PaLV) was discovered. PaLV does not cause obvious symptoms in Paspalum and thus is considered a latent virus. The full genome sequence of PaLV was determined using sequencing technologies. PaLV is related to Lolium latent virus and represents the second member of the genus Lolavirus. To evaluate the host range, PaLV was rub inoculated to different grass plants with positive infections subsequently detected in wheat, corn, sorghum and Lolium. An assay to detect the virus was developed and was used to screen the entire NPGS Paspalum collection (30 accessions), with 90% testing positive. Although the virus appears to be latent, this report raises awareness of this apparently widespread virus for grass breeders and researchers.

Technical Abstract: Seashore paspalum (Paspalum sp.), is an economically significant grass used in golf courses, sports fields, and landscaping in the United States. A novel Lolavirus, tentatively named paspalum latent virus (PaLV), was identified for the first time in seashore paspalum plants from the USDA National Plant Germplasm System (NPGS) using high-throughput sequencing. Three complete genome sequences of PaLV from different Paspalum accessions, with a length of around 6,995 nucleotides (nt), not including the poly(A) tail, were obtained by Rapid Amplification of cDNA Ends and Sanger sequencing. Phylogenetic analysis based on the replicase protein sequences from the Alphaflexiviridae family revealed that PaLV grouped with the Lolavirus genus, with the closest relative being Lolium latent virus (LoLV). PaLV shares less than 72% nt identity to the replicase and coat protein genes of LoLV, which demarks PaLV as a new species and the second member of the genus. Furthermore, the coat protein region showed intense negative selection pressure and moderate spatially structured diversity. Host range analysis of PaLV showed that wheat, corn, sorghum, and Lolium are systemic hosts of PaLV. A one-step RT-PCR technique was developed to reliably detect PaLV infection. Testing of the NPGS Paspalum collection revealed a 90% PaLV incidence among the 30 accessions. This suggests a high prevalence and widespread distribution of PaLV.