Complete genome sequence of a novel marafivirus infecting pearl millet in Burkina Faso

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 marafiviruses. Additionally, a characteristic conserved marafibox domain was detected in the genome. The nucleotide sequence of the complete PGMV genome shares 68.5% identity with that of sorghum bicolor marafivirus, and its coat protein shares 58.5% identity with that of oat blue dwarf virus. Phylogenetic analysis 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 in pearl millet.

Automated summary

Pearl millet is a staple food widely cultivated in sub-Saharan Africa, and a new virus called Pennisetum glaucum marafivirus was discovered in Burkina Faso in 2018, belonging to the Marafivirus genus. The complete nucleotide sequence of PGMV shares 68.5% identity with sorghum bicolor marafivirus and its coat protein shares 58.5% identity with oat blue dwarf virus. Phylogenetic analysis confirms that the pearl millet virus is grouped with Marafivirus genus members in the Tymoviridae family.