Discovery of a novel Sindbis virus from Chinese soft-shelled turtle, Pelodiscus sinensis

The Chinese soft-shelled turtle (Pelodiscus sinensis) is an economically important species in Chinese aquaculture. Recently, Chinese soft-shelled turtle water-floating disease (CSSTFD) outbreak caused almost 100% death in Chinese soft shelled turtle seedlings. The diseased turtles preferred to float to the surface of water and then died within four days. In this study, we charaterized the virus,which showed high similarity with Sindbis virus(SINV), in these turtles. We sequenced the viral genome using sequence independent single primer amplification(SISPA) and rapid amplification of cDNA ends(RACE). The whole genome, excluding the polyA tail, is 11700 nts in length and G + C content was 51.76%. BlastN analysis revealed that the isolate, designated SV-PsXY1, shares 99.24% nucleotide identity with Sindbis virus strain YN222. This virus genome contained a typical alphavirus organization and putatively encoded two large open reading frames(structural ORF and nonstructural ORF). Pairwise amino acid identities ranged between 82.86% and 100% with the corresponding proteins of SINV. To our knowledge, this is the first report of SINV in an aquatic reptile, which expands the known host range of this virus and highlights the need to investigate its origin, transmission routes, and zoonotic potential.