Evolutionary and taxonomic insights into the genomic divergence of cowpea mild mottle virus: rapid evolution in replication-associated protein gene, but strong negative selection on coat protein gene.

Carlavirus vignae, with the common name cowpea mild mottle virus (CPMMV), has become a widespread carlavirus infecting economically important crops worldwide. CPMMV is transmitted by whiteflies, whereas other members of the Carlavirus genus are generally transmitted by aphids. Recently, the virus has been isolated from various host plants, including cucurbit plants in Brazil, exhibiting a wide genomic variation. Here, we present a comprehensive analysis of CPMMV genome diversity, focusing on the replication-associated protein (Rep) and coat protein (CP) genes, two key genomic regions for Betaflexiviridae classification. Cucurbit isolates of CPMMV from Brazil showed high divergent Rep but low CP aa sequences among them. Based on pairwise aa sequence identity of the Rep, the CPMMV available in public databases can be divided into at least four distinct genogroups. In contrast, CP sequences exhibited a remarkable sequence conservation across all analysed isolates, likely due to strong negative selection maintaining its functional or structural integrity. Furthermore, we concluded that the recombination is not the reason for the higher conservation of the CP relative to the Rep. These findings support the hypothesis that, in the family Betaflexiviridae, the Rep evolves at a more constant rate, whereas the CP evolves by 'leaps' of fast evolution. Since the differences in Rep aa sequence identities are well below the threshold defined by the Betaflexiviridae species demarcation criteria, we propose classifying the CPMMV isolates into four distinct species.