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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Molecular Plant Pathology Laboratory » Research » Publications at this Location » Publication #352367

Research Project: Regulation of Gene Expression in Alfalfa Development and Stress Tolerance

Location: Molecular Plant Pathology Laboratory

Title: Characterization of alfalfa virus F, a new member of the genus Marafivirus

Author
item Nemchinov, Lev
item Francois, Sarah - University Of Montpellier
item Roumagnac, Philippe - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)
item Hammond, Rosemarie
item Mollov, Dimitre
item Filloux, Denis - Centro De Cooperation Internationale En Recherche Agronomique Pour Le Development (CIRAD)

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/21/2018
Publication Date: 9/4/2018
Citation: Nemchinov, L.G., Francois, S., Roumagnac, P., Hammond, R., Mollov, D.S., Filloux, D. 2018. Characterization of alfalfa virus F, a new member of the genus Marafivirus. PLoS One. 13(9):e0203477.

Interpretive Summary: Viral infections of alfalfa are widespread in major cultivation areas and their impact on alfalfa production may be underestimated. We report the discovery of a new virus, originating from commercial alfalfa fields in Southern France. A new viral species, provisionally named alfalfa virus F (AVF), was diagnosed using metagenomics-based approach and its genomic sequence confirmed by laboratory investigations. Molecular method was developed for specific detection of the virus. Currently, newly identified virus represents an unknown risk and further research is necessary to establish its biological characteristics and geographical distribution. 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: Viral infections of alfalfa are widespread in major cultivation areas and their impact on alfalfa production may be underestimated. A new viral species, provisionally named alfalfa virus F (AVF), was identified using virion-associated nucleic acid (VANA) metagenomics-based approach in alfalfa (Medicago sativa L.) samples collected in Southern France. The nucleotide sequence of the viral genome was determined by de-novo assembly of VANA reads and by 5’/3’ RACE with viral RNA extracted from enriched viral particles or with total RNA, respectively. The virus shares the greatest degree of overall sequence identity (~78%) with Medicago sativa marafivirus 1 (MsMV1) recently deduced from alfalfa transcriptomic data. The tentative nucleotide sequence of the AVF coat protein shares ~83% identity with the corresponding region of MsMV1. A sequence search of the predicted single large ORF encoding a polyprotein of 235kDa in the Pfam database resulted in identification of five domains, characteristic of the genus Marafivirus, family Tymoviridae. The AVF genome also contains a conserved “marafibox”, a 16-nt consensus sequence present in all known marafiviruses. Phylogenetic analysis of the complete nucleotide sequences of AVF and other viruses of the family Tymoviridae grouped AVF in the same cluster with MsMV1. In addition to 5’ and 3’ terminal extensions, the identity of the virus was confirmed by RT-PCRs with primers derived from VANA-contigs, transmission electron microscopy with virus-infected tissues and transient expression of the viral coat protein gene using a heterologous virus-based vector. Based on the criteria demarcating species in the genus Marafivirus that include overall sequence identity less than 80% and coat protein identity less than 90%, we propose that AVF represents a distinct viral species in the genus Marafivirus, family Tymoviridae.