Identification of a novel isolate of Alfalfa virus S from China suggests a possible role of seed contamination in the distribution of the virus

Authors: Nemchinov, Lev; Grinstead, Sam

Submitted to: Plant Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/17/2020
Publication Date: 6/17/2020
Citation: Nemchinov, L.G., Mollov, D.S., Grinstead, S.C. 2020. Identification of a novel isolate of Alfalfa virus S from China suggests a possible role of seed contamination in the distribution of the virus. Plant Disease. https://doi.org/10.1094/PDIS-04-20-0906-SC.
DOI: https://doi.org/10.1094/PDIS-04-20-0906-SC

Interpretive Summary: Alfalfa is the most extensively cultivated forage legume in the world. Although viral infections of alfalfa are widespread in all major cultivation areas, their economic importance maybe underestimated. Contribution of viral pathogens to the severity of complex infections involving multiple pathogens is poorly understood. Recently, we have reported on the discovery of Alfalfa virus S (AVS), a new viral species that was identified in alfalfa from Sudan, Northern Africa, where commercial alfalfa fields were planted with seeds, imported from USA. In this study, we have identified and characterized a different isolate of the same virus in alfalfa plants originating from China. Our results suggest that AVS could be more widespread than previously thought. We have also detected the virus in alfalfa seeds and seedlings, which may indicate a potential role of seed transmission in the distribution of the virus. It is expected that data reported in this study can be used by plant pathologists and extension specialists for diagnostics and identification of this virus in alfalfa fields.

Technical Abstract: Alfalfa has recently become the third most valuable field crop in the United States with an estimated worth of over $9.3 billion, $1.2 billion more than wheat, according to the National Alfalfa and Forage Alliance. Alfalfa productivity is often limited by various biotic and abiotic components in the ecosystem. Viral infections of alfalfa are considered by producers, breeders, growers and research community as diseases of limited importance in spite of their wide distribution in all major alfalfa cultivation areas. In 2017, we have described a new species of the family Alphaflexiviridae provisionally named Alfalfa virus S (AVS). AVS was discovered in alfalfa samples received from Sudan, Northern Africa, where commercial pivot irrigated fields were planted with alfalfa seeds, imported from USA. A complete genome of AVS was obtained via RNA-sequencing and rapid amplification of cDNA ends and identity of the virus was confirmed by RT-PCR, molecular hybridization and serological assays. We have concluded that AVS represents a unique virus species with a general resemblance to the members of the genus Allexivirus. The AVS has been subsequently recognized by the ICTV as a species and a member of the genus Allexivirus. In this study, we have identified AVS in seedlings of the alfalfa variety “DRYLAND” that was acquired from China under APHIS quarantine permit. A complete genome of the Chinese isolate of AVS (AVS-C), obtained by a high throughput sequencing, 5'/3' RACE and sequencing of multiple RT-PCR products, consisted of 8,351 nucleotides, excluding the poly (A) tail. Comparison of the identity scores between computationally predicted proteins of AVS-C and AVS showed that AVS-C is a distinct isolate whose amino acid sequence differs from that of the reference virus. Our results suggest that AVS could be more widespread than originally thought. It is currently unknown if the virus was acquired in these countries locally or introduced through imported seed material. Detection of AVS in alfalfa seeds and seedlings developed from the virus-contaminated seeds may suggest a potential role of seed transmission in the distribution of the virus.