Time-dependent selection pressure on two arthropod-borne RNA viruses in the same serogroup

Understanding the genetic basis of viral adaptation to taxonomically diverse groups of host species inhabiting different eco-climatic zones is crucial for the discovery of factors underpinning the successful establishment of these infectious pathogens in new hosts/environments. To gain insights into the dynamics of nonsynonymous (dN) and synonymous substitutions (dS) and the ratio between the two (ω = dN/dS), we analyzed the complete nucleotide coding sequence data of the M segment, which encodes glycoproteins of two negative-sense RNA viruses, Akabane virus (AKV) and Schmallenberg virus (SBV) that belong to the same serogroup. While AKV is relatively older and has been circulating in ruminant populations since 1970s, SBV was first reported in 2011. The ω was estimated to be 1.67 and 0.09 for SBV and AKV, respectively, and the estimated mutation rate of SBV is at least 25 times higher than that of AKV. Given the different evolutionary stages of the two viruses, most of the slightly deleterious mutations were likely purged out or kept in low frequency in the AKV genome, whereas positive selection together with the accumulation of slightly deleterious mutations might contribute to such an inflated mutation rate of SBV. The evolutionary distance (d) is nonlinearly and negatively correlated with ω, but is positively correlated with dN and dS. Collectively, the different patterns in ω, dN, dS, and d between AKV and SBV identified in this study provide empirical evidence for a time-dependent selection pressure.