Complete Genome Sequence of a Novel Marafivirus Infecting Pearl Millet in Burkina Faso

Abstract Pearl millet (Pennisetum glaucum (L.) R. Br.) is a staple food that is widely cultivated in sub-Saharan Africa. In August 2018, a survey was conducted in the main producing regions of Burkina Faso and leaf samples were analyzed using virion-associated nucleic acid (VANA)-based metagenomic approach and Illumina sequencing. A new virus, tentatively named “pennisetum glaucum marafivirus” (PGMV), was detected and its complete nucleotide sequence of 6364 nucleotides was determined. The sequence contains a large open reading frame (ORF) encoding a polyprotein of 224.2 kDa with five domains (methyltransferase, papain-like protease, helicase, RNA-dependent RNA polymerase and coat proteins), typical of members of the marafiviruses. Additionally, a characteristic conserved marafibox domain was detected in the genome. The nucleotide sequence of the PGMV complete genome shares 68.5% identity with Sorghum bicolor marafivirus and its coat protein shares 58.5% identity with Oat blue dwarf virus. Phylogenetic analyses confirmed that the pearl millet virus is unambiguously grouped with members of the genus Marafivirus in the family Tymoviridae. This is the first report on the occurrence of a marafivirus on pearl millet.