Abstract：Abstract Goose hemorrhagic polyomavirus (GHPV) is a newly identified emerging infectious pathogen in ducks in recent years, China. In order to understand the genomic characterization of Cherry Valley duck (Anas platyrhynchos domestica) origin GHPV (designated as strain FJ201601), the whole genome of GHPV strain FJ201601 was amplified by PCR with five fragments by using specific primers. The obtained sequences were cloned and verified by Sanger sequence, and then the positive results were assembled. The results showed that the genome length of strain FJ201601 comprised of 5 254 nucleotides (GenBank accession number MG544856), with(G+C)% content at 48.01%, coding for 6 function genes with ORF-X (510 bp, 169 aa), VP2(981 bp, 326 aa), VP3(654 bp, 217 aa), VP1(1062 bp, 353 aa), Large T(1911 bp, 636 aa) and Small T(483 bp, 160 aa), respectively. Genomic nucleotide comparison demonstrated that GHPV strain FJ201601 shared nucleotide identity higher than 99.7% with other GHPV isolates, which were collected from different hosts and regions. The GHPV six functional genes were all showed high nucleotide and amino acids identity at ORF-X (99.4%~99.8% and 98.2%~99.4%), VP2 (99.7%~99.9% and 99.7%~100%), VP3 (99.7%~99.8% and 99.5%~100%), VP1 (99.5%~99.8% and 99.7%~100%), Large T (99.7%~100% and 99.8%~100%) and Small T (99.6%~100% and 99.4%~100%), respectively. Phylogenetic analysis indicated that GHPV isolates shared very closer evolution distance. However, there were subtle differences in genetic evolution different did not consistent with different hosts (different duck and goose species) and regions, the same as the Chinese Pekin ducks-origin GHPV and Cherry Valley ducks-origin GHPV. This study lays a good foundation for further epidemiological investigation and pathogenic mechanism study of the Goose hemorrhagic polyomavirus.
