Discovery and genetic characterization of coronaviruses in Guangdong birds and poultry

This study aimed to surveillance the circulation of coronaviruses in birds and poultry in Guangdong Province. A total of 128 stool samples were collected from Guangzhou and Jiangmen regions in Guangdong Province. RT-PCR was used to screen for samples positive with coronaviruses. Metatranscriptome sequencing was performed on the positive samples, and complete genome sequences were assembled. Six samples were found positive for coronaviruses, and three complete genomes: Chinese Pond-Heron coronavirus XN11 (CPCoV XN11), Infectious bronchitis virus isolate Mallard feces/Guangdong/XN18/2022(IBV XN18), and Swan Goose coronavirus DWY40 (SGCoV DWY40)were assembled. CPCoV XN11 is a night heron coronavirus HKU19 with a nucleotide homology of 90%, IBV XN18 is a GI-13 type IBV, and SGCoV DWY40 is a new goose coronavirus CB17 member. Recombination analysis revealed that recombination occurred in the S gene of SGCoV DWY40. Three new strains of known viruses were identified, providing data for studying the evolution of animal coronaviruses.