Evidence for Recombination in the Emerged Phylogroup SW6 of Prunus Necrotic Ringspot Virus and Estimate of Selection Pressure Acting on Capsid Protein of Affiliated Members

Recombination plays a key role in virus evolution. Except a limited number of works carried out so far on recombination in Prunus necrotic ringspot virus (PNRSV) genome, knowledge is still poor. Numerous phylogenetic studies particularly those based on capsid (CP) and movement protein (MP) of PNRSV showed that all accessions described so far split into three major phylogroups, i.e., PV96, PV32, and PE5. With the recent characterization of Chilean and Indian isolates which were phylogenetically closely related to the oldest member, i.e., SW6 (AF013287) from USA, a new phylogroup baptized SW6, emerged since it was outside of the evolutionary behavior of the classical PV96, PV32, and PE5 clusters. In order to understand how it evolved, six computerized methods were used to detect potential recombination in the CP sequences of nine components forming SW6 phylogroup. It was clearly demonstrated that various members underwent recombination. Additionally, networked relationships among them proved that numerous incompatibilities occurred in these sequences illustrated by the presence of boxes in the network implying therefore the possibility of recombination. According to inferred network, several sequences contained conflicting signals as illustrated by various splits and edges with special reference to Chilean (EF565255, EF565256), polish (AF332614) and Indian (AM494934) isolates. It is worth noting that the phylogenetic network provided a different clustering compared to the bifurcating tree. In fact, three distinct groups were delineated with SplitsTree4 software instead of a globally homogenous ensemble generated by MEGA7 algorithm. Furthermore, this study pointed out that members of SW6 phylogroup were the only recombinants among 205 tested accessions confirming that SW6 should be considered as the fourth phylogenetic group of PNRSV. On the other hand, CP was predominantly under purifying selection. However, positive selection was evidenced particularly in the C-terminal region of CP comprising part of dimerization region (DR). Such adaptive selection was exerted on a CP segment of AM494934 accession exchanged by recombination.