Detectable episodic positive selection in the virion strand a-strain Maize streak virus genes may have a role in its host adaptation.

Maize streak virus (MSV) has four genes: cp, encoding the coat protein; mp, the movement protein; and repA and rep, encoding two distinct replication-associated proteins from an alternatively spliced transcript. These genes play roles in encapsidation, movement, replication, and interactions with the external environment, making them prone to stimuli-driven molecular adaptation. We accomplished selection studies on publicly available curated, recombination-free, complete coding sequences for representative A-strain maize streak virus (MSV-A) cp and mp genes. We found evidence of gene-wide selection in these two MSV genes at specific sites within the genes (cp 1.23% and mp 0.99%). Positively selected sites have amino acids that are 60% hydrophilic and 40% hydrophobic in nature. We found significant evidence of positive selection at branches (cp: 0.76 and mp:1.66%) representing the diversity of MSV-A-strain in South Africa, which is related to the MSV-A-matA isolate (GenBank accession number: AF329881), well disseminated and adapted to the maize plant in sub-Saharan Africa. In the mp gene, selection significantly intensified for the overall diversities of the MSV-A sequences and those more related to the MSV-Mat-A isolate. These findings reveal that despite predominantly undergoing non-diversifying selection, the detectable diversifying positive selection observed in these genes may play a major role in MSV-A host adaptive evolution, ensuring sufficient pathogenicity for onward transmission without killing the host.