Synonymous SNPs of viral genes facilitate virus to escape host antiviral RNAi immunity

Abstract

24Synonymous single nucleotide polymorphisms (SNPs) are involved in codon 25 usage preference or mRNA splicing. Up to date, however, the role of synonymous 26 SNPs in immunity remains unclear. To address this issue, the SNPs of white spot 27 syndrome virus (WSSV) were characterized in shrimp in the present study. Our 28 results indicated that there existed synonymous SNPs in the mRNAs of wsv151 and 29 wsv226, two viral genes of WSSV. In the presence of SNP siRNA, wild-type siRNA, 30 wild-type mRNA and SNP mRNA of wsv151 or wsv226, RNAi was significantly 31 suppressed, showing that the synonymous SNPs of wsv151 and wsv226 played 32 negative roles in host siRNA pathway due to mismatch of siRNA with its target. In 33 insect cells, the mismatch, caused by synonymous SNPs of wsv151 or wsv226, 34 between siRNA and its target inhibited the host RNAi. Furthermore, the data revealed 35 that the co-injection of SNP siRNA and wild-type siRNA of wsv151 or wsv226 into 36 WSSV-infected shrimp led to a significant increase of WSSV copies compared with 37 that of SNP siRNA alone or wild-type siRNA alone, indicating that the synonymous 38 SNPs of viral genes could be a strategy of virus escaping host siRNA pathway in 39 shrimp in vivo. Therefore, our study provided novel insights into the underlying 40 mechanism of virus escaping host antiviral RNAi immunity by synonymous SNPs of 41 viral genes. 42Author Summary：Our results indicated that there existed synonymous SNPs in the 43 mRNAs of wsv151 and wsv226, two viral genes of WSSV. In the presence of 44 SNP siRNA, wild-type siRNA, wild-type mRNA and SNP mRNA of wsv151 or 3 45 wsv226, RNAi was significantly suppressed, showing that the synonymous SNPs of 46 wsv151 and wsv226 played negative roles in host siRNA pathway due to mismatch 47 of siRNA with its target. In insect cells, the mismatch, caused by synonymous SNPs 48 of wsv151 or wsv226, between siRNA and its target inhibited the host RNAi. 49 Furthermore, the data revealed that the co-injection of 50 SNP siRNA and wild-type siRNA of wsv151 or wsv226 into WSSV-infected shrimp 51 led to a significant increase of WSSV copies compared with that of SNP siRNA alone 52 or wild-type siRNA alone, indicating that the synonymous SNPs of viral genes could 53 be a strategy of virus escaping host siRNA pathway in shrimp in vivo. 54