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First report and genomic sequence of a new alfalfa marafivirus from France

Nemchinov L.G., François S., Roumagnac P., Mollov D.S., Filloux D.. 2018. Phytopathology, 108 (10S) : p. S1.188. International Congress of Plant Pathology (ICPP2018). 11, 2018-07-29/2018-08-03, Boston (Etats-Unis).

DOI: 10.1094/PHYTO-108-10-S1.1

Viral infections of alfalfa are widespread in major cultivation areas. A new viral species, provisionally named alfalfa virus F (AVF), was diagnosed using VANA metagenomics-based approach (PMID:27764211) in alfalfa (Medicago sativa L.) samples collected in Southern France. Nucleotide sequence of the viral genome was determined by de-novo assembly of VANA reads and by 5'/3' RACE systems 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 (PMID:28974471). Tentative nucleotide sequence of the AVF coat protein shares ~83% identity with the corresponding region of MsMV1. Sequence search of a single ORF encoding a polyprotein of 235kDa in Pfam database resulted in identification of five domains, characteristic for the genus Marafivirus, family Tymoviridae: viral methyltransferase, tymovirus endopeptidase, viral (superfamily 1) RNA helicase, RNA dependent RNA polymerase and tymovirus coat protein. AVF genome contains a conserved ¿marafibox¿, a 16-nt consensus sequence present in all known marafiviruses. Phylogenetic analysis using MEGA 7 software with complete nucleotide sequences of AVF and other viruses of the family Tymoviridae grouped AVF in the same cluster with MsMV1. 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. Geographic distribution of the AVF will be further assessed using serological and molecular methods.

Mots-clés : virus des végétaux; marafivirus; séquence nucléotidique; medicago sativa; france; métagénomique; séquencage

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