Genomic Organization of the Newly Discovered Cassava Congo Cheravirus Reveals a Unique Maf/HAM1 Motif in the C-Terminal Region of the RNA1 Polyprotein and Suggests the Presence of Two Protein Domains Upstream of the Putative Helicase Domain

Cassava (<i>Manihot esculenta</i>) is a staple crop in sub-Saharan Africa threatened by several viral diseases. Here, we describe the genome sequence of a novel bipartite cheravirus (family <i>Secoviridae</i>) infecting cassava in the Democratic Republic of Congo and Tanzania. We designate the new virus "cassava Congo cheravirus". Each RNA segment encodes a single polyprotein (P1 and P2 for RNA1 and RNA2, respectively), embedded with various putative cleavage sites (six and three in P1 and P2, respectively), consistent with members of the genus <i>Cheravirus</i>. We note two new features in the P1: (i) the presence of two domains, X1 and X2, upstream of the putative helicase region, which we also predict in other cheraviruses and (ii) the presence of a Maf/HAM1-like inosine triphosphatase (ITPase) domain, a rare motif among viruses only previously detected in three potyviruses and a torradovirus, all of which infect plants from the Euphorbia family. Phylogenetic analyses placed the virus firmly within the genus <i>Cheravirus</i>, with amino acid identities in the Pro-Pol and coat protein regions well below existing ICTV species thresholds, supporting its classification as a virus belonging to a new species in the <i>Cheravirus</i> genus. Spatially distinct isolates from Bas-Congo, South-Kivu, and Tanzania form three genetic clusters, with evidence of recombination in both RNA segments. These results expand the known diversity of cassava viruses and suggest possible adaptation to the cassava host via ITPase acquisition.