Whole genome sequencing and evolutionary analysis of bovine ephemeral fever virus isolate JM 2020 in Guangdong Province

Objective  The purpose of this study was to analyze the evolutionary relationship between bovine ephemeral fever virus (BEFV) isolate JM 2020 in Guangdong Province and other strains from other regions, and clarify the characteristics of genetic evolution and whole genome, so as to provide information for the epidemic situation and prevention of bovine ephemeral fever disease in China and the world.

Method  According to the whole genome sequence information of BEFV strain downloaded from GenBank, primers were designed to amplify glycoprotein (G) gene by PCR. The 10 pairs of primers were designed to amplify the whole genome, and the gene sequences of 10 fragments were obtained by sequencing. The whole genome sequences were manually edited and spliced by EditSeq in DNAStar software. Using MEGA 6.0 to construct G gene and whole genome evolutionary tree respectively for evolutionary analysis.

Result  The G gene and whole genome of the JM 2020 strain had the highest nucleotide sequence similarity with the Thai strain, which were 94.9%−99.3% and 99.0% respectively. The evolutionary analysis showed that JM 2020 was in the same small branch with the 2013 to 2017 Thai strains, while there was a certain evolutionary distance from domestic virus strains such as JB76H and JT02L. Whole genome sequencing results showed that whole genome of JM 2020 was 14 902 nucleotides (nt) in length, including 50 nt leader sequence, 1 296 nt nucleoprotein (N) gene, and 837 nt phosphoprotein (P) gene, 672 nt matrixprotein (M) gene, 1 872 nt G gene, 1 812 nt non-structural glycoprotein II (G_NS) gene, 618 nt α1 and α2 gene, 444 nt β gene, 345 nt γ gene, 6 444 nt large multi-functional enzyme (L) gene and tail sequence of 73 nt, which was separated by 21, 47, 68, 67, 23, 64, 59, 79 and 35 nt intergenic regions. The P′ gene (polycistronic product of P gene) of JM 2020 was truncated like qy2017 and the Thai strain.

Conclusion  The JM 2020 strain is highly similar with the qy2017 strain isolated in 2017 and they are closely related to the evolution of the Thai strain. They have some evolutionary distance with JB76H strain etc. from other regions of China. This study enriches the genome information of BEFV epidemic strains in China and lays a foundation for the prevention and control of bovine ephemeral fever and the research of new vaccines.