Molecular evolutionary and epidemiological dynamics of a highly pathogenic fish rhabdovirus, the spring viremia of carp virus (SVCV)

Abstract

Spring viremia of carp virus (SVCV), which causes an acute hemorrhagic and highly contagious disease in cyprinids, was first described in Europe and subsequently reported in parts of Asia and North America. SVCV can be classified into four genogroups: Ia, Ib, Ic, and Id. While Ia and Id have wide circulation and are reported to cause outbreaks in North America and Europe, respectively, Ib and Ic were last reported in the 1980s. We used a Bayesian framework to determine the nucleotide substitution rates, relative genetic diversity, and time to the most recent common ancestor (TMRCA) of SVCV using large sets of sequences of the phosphoprotein and glycoprotein (G) genes. The sampled genetic diversities of Ia and Id were found to have arisen during the year 1996 (95% Highest Posterior Density: 1986–1998) and 1957 (1926–1972), respectively, with consistent results across the two genes. The TMRCA for SVCV was estimated to have been around 1850 (1727–1938). The substitution rate for Ia is at least 5–7 times higher than that of Id. The rate of nonsynonymous (dn) to synonymous (ds) substitutions (dn/ds=ω) for the G gene of Ia (ω=0.608) is significantly higher than that of Id (ω=0.0749), indicating both exhibit distinct selection profiles. The SVCV population experienced a bottleneck during the early 1990s followed by a sudden rebound, primarily due to the sudden increase in genetic variants in Ia and Id, which coincided with the timing of a recent series of outbreaks reported in Europe and North America.