Characteristics of Avian Coronaviruses in China From 2020 to 2023.

Abstract

Avian coronaviruses (CoVs) represent a significant threat to the poultry industry. To understand the epidemiological characteristics of avian CoVs in China, a nationwide surveillance was performed across 16 provinces from 2020 to 2023. More than 46,000 oropharyngeal/cloacal swab samples were collected and detected by RT-PCR using specific primers for the RdRp gene. A total of 7370 Gammacoronaviruses (γCoVs) and 39 Deltacoronaviruses (δCoVs) were detected. The individual positive rates of γCoVs and δCoVs were 15.71% and 0.08%, respectively. The detected γCoV included 5825 infectious bronchitis viruses (IBVs), 1023 duck CoVs (DuCoVs), 511 pigeon CoVs (PiCoVs), and 11 goose CoVs (GoCoVs). While the γCoVs detected in this study demonstrated host specificity, some isolates indicated the potential for cross-host transmission. The samples analyzed in this study were collected from 744 populations, including 191 poultry farms, 151 wholesale markets, 354 live poultry markets (LPMs), 38 slaughterhouses, 9 backyard flocks, and 1 wild bird observation point. Notably, wholesale markets (87.88%-95.96%) and LPMs (65.98%-95.77%) showed markedly high population positive rates. All avian CoV species detected in this study were identified in both wholesale markets and LPMs. Furthermore, concurrent circulation of two or more avian CoV species was detected in 48.10% (139/289) of positive LPMs and in 51.43% (72/140) of positive wholesale markets. The results indicate that LPMs and wholesale markets are key populations for the cross-species transmission and genetic recombination of avian CoVs. Subsequently, a total of 3065 representative IBV samples were selected for phylogenetic analysis based on the S1 gene. Four genotypes, including GI (1688 strains), GIII (4 strains), GVI (418 strains), and GVII (48 strains), were identified. Among these, the GI-19 (40.64%) and GVI-1 (19.37%) were the prevalent lineages circulating in the Chinese poultry population. This study reveals the epidemiology, distribution, genetic, and phylogenetic characteristics of avian CoVs in China, providing important data for the research on the biological characteristics and cross-host transmission mechanisms of avian CoVs.