Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/10/2017
Publication Date: 5/30/2017
Citation: Nemchinov, L.G., Grinstead, S.C., Mollov, D.S. 2017. Alfalfa virus S, a new species in the family Alhapflexiviridae. PLoS One. 12(5):e0178222.
Interpretive Summary: Alfalfa is the most extensively cultivated forage legume in the world and the fourth most widely grown crop in the US, planted on more than 23 million acres in all 50 states. The estimated worth of alfalfa hay is $8.1 billion annually. Alfalfa productivity has often been affected and limited by different diseases, insect pests and abiotic stress factors. Minimizing these losses is a major area of concern in alfalfa industry. Alfalfa may serve as a natural reservoir for dissemination of viruses to other agriculturally important crops. In recent years, emerging viral diseases of alfalfa with the capacity to cause serious yield losses were described. Synergetic interactions of multiple viral infections can also threaten alfalfa production. In this work, we report discovery and characterization of a novel and unusual virus identified in alfalfa samples originating from Sudan. The virus, provisionally named Alfalfa virus S (AVS), was not previously described in alfalfa or any other plant species. Results of this study will be of interest to the researchers in academia and government organizations working in the fields of plant virology and alfalfa improvement.
Technical Abstract: A new species of the family Alphaflexiviridae provisionally named alfalfa virus S (AVS) was discovered in alfalfa samples originating from Sudan. A complete nucleotide sequence of the viral genome consisting of 8,349 nucleotides excluding the 3’ poly(A) tail was determined by high throughput sequencing (HTS) on an Illumina platform. An NCBI BLAST search revealed that the virus shares the greatest degree of sequence identity with members of the family Alphaflexiviridae, genus Allexivirus. The AVS genome contains six computationally-predicted open reading frames (ORF): viral replication protein, triple gene block protein 1 (TGB1), TGB2, TGB3-like protein, an unknown 38.4 kDa protein resembling serine-rich 40 kDa protein characteristic for allexiviruses, and coat protein (CP). It appears that AVS lacks a clear 3’ proximal ORF that encodes a nucleic acid-binding protein typical for allexiviruses. The identity of the virus was confirmed by RT-PCR with primers derived from the HTS-generated sequence, dot blot hybridization with DIG-labeled virus-specific RNA probes, and Western blot analysis with antibodies produced against a peptide derived from the CP sequence. Transmission electron microscopy observations of the infected tissues showed the presence of filamentous particles similar to allexiviruses in their length and appearance. To the best of our knowledge, this is the first report on the identification of a putative allexivirus in alfalfa (Medicago sativa). The genome sequence of AVS has been deposited in NCBI GenBank on 03/02/2016 as accession KY696659.