Isolation and identification of a novel coronavirus from wild bird

Abstract

Abstract Abstract A novel coronavirus strain was isolated from laryngotracheal swab of wild partridge and designated as partridge GD S14 2003 (S14). Its whole genomic sequence was obtained (GenBank Accession number: AY646283) through RT-PCR amplification, cloning, nucleotide sequencing, and analysis by the DNASTAR program. To investigate the origin of the virus, we further analyzed the nucleotide homologies between the SI gene of S14 strain and those of nephrogenic-type strains JX1-99 and TJ2-96 were 94.6% and 93.4%, respectively. In addition, a relatively high genetic identity, 85% and 84.3%, respectively, was detected between SI gene of S14 and those of strains QXIBV and LX4. The results suggested that the S14 strain may be originated from or related to nephrogenic-type and proventriculus-type infectious bronchitis virus (IBV). The highest nucleotide homology between the S2 gene S14 strain and those of QXIBV and LX4 was 85% and 84.3%, respectively and all of them belonged to group II coronaviruses. The highest nucleotide homology between the M gene of S14 strain and those of strains SAIBV strains. Phylogenetic analysis of N gene indicated that group I strains might evolve from RNA recombination between strain H52 and Gray; while group II strains from strain H120 and D1466. S14 strain had the highest N gene homology with strain QXIBV which was 95.7%, thus classified as a group III member. Strains SAIB20 and GD6-98 which were closely related to the M gene of S14 strain belonged to group I and IV, respectively. A possible role of partridge S14 strain may play in the process of coronavirus evolution is discussed.