Surveillance of coronaviruses in wild aquatic birds in Hong Kong: expanded genetic diversity and discovery of novel subgenus in the <i>Deltacoronavirus</i>

Migratory birds may carry emerging viruses over long distances. Regular surveillance and metagenomic analysis were employed to explore the diversity of avian coronaviruses at Hong Kong's Mai Po Wetland. We tested a total of 3239 samples collected from 2018 to 2024, among which the prevalence rate of viruses of the genus <i>Gammacoronavirus</i> (64.4%) was higher than that of <i>Deltacoronavirus</i> (35.6%). The host species were identified for 79.8% of the coronavirus-positive samples. Two deltacoronaviruses with full-genome sequences and one nearly complete gammacoronavirus genome were identified in faecal samples of three bird species. We also predicted putative transcriptional regulatory sequences and 3CLpro and PLpro cleavage sites for these viruses. Results from our phylogenetic analysis and pairwise amino acid identity comparisons, using the International Committee on Taxonomy of Viruses classification criteria based on the DEmARC framework, indicate that black-faced spoonbill coronavirus (BSCoV, strain MP22-1474) prototypes a new subgenus. Great cormorant coronavirus (GCCoV, strain MP18-1070) and falcated duck coronavirus (FDCoV, strain MP22-196) belong to two previously known species while diverging most profoundly from known viruses of these species. Two recombination events may have contributed to the evolution of FDCoV MP22-196 in genome regions from ORF1b to the S gene and from the M gene to the N gene. The cophylogenetic analysis between avian hosts and coronaviruses provides evidence for a strong linkage between viruses of the genus <i>Gammacoronavirus</i> and the birds of order <i>Anseriformes</i>. This study highlights the importance of ongoing surveillance for coronaviruses in wild migratory birds.