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

Lev Nemchinov: USDA-ARS, BARC, Molecular Plant Pathology Laboratory

<div>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 (<em>Medicago sativa </em>L.) samples collected in Southern France. Nucleotide sequence of the viral genome was determined by <em>de-novo</em> 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 <em>Medicago sativa</em> 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 <em>Marafivirus</em>, family <em>Tymoviridae</em>: 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 <em>Tymoviridae</em> grouped AVF in the same cluster with MsMV1. Based on the criteria demarcating species in the genus <em>Marafivirus </em>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 <em>Marafiviru</em>s, family <em>Tymoviridae.</em> Geographic distribution of the AVF will be further assessed using serological and molecular methods.</p> <p><strong> </strong></div>