Detection of Coronaviruses and Genomic Characterization of Gammacoronaviruses from Overwintering Black-Headed Gulls (Chroicocephalus ridibundus) in Yunnan Province, China.

Black-headed gulls have been confirmed as the natural hosts of Deltacoronavirus (δ-CoV) and Gammacoronavirus (γ-CoV). A total of 59 CoV-PCR-positive fecal samples were identified among 509 fecal samples collected from overwintering black-headed gulls in Yunnan Province, China. The prevalence of black-headed gull deltacoronavirus (BHG-DCoV) was 3.54% (18/509), while that of black-headed gull gammacoronavirus (BHG-GCoV) was 8.06% (41/509). The prevalence of BHG-GCoV was significantly higher than that of BHG-DCoV (χ² = 9.518, p < 0.01). Two complete genome sequences of BHG-GCoVs were obtained, with lengths of 27,358 bp and 27,355 bp, respectively, from the fecal samples of black-headed gulls. The nucleotide similarity between the two complete genomes is 98.75%. Phylogenetic analysis based on the whole genome has confirmed that the two strains of BHG-GCoVs clustered into the species Gammacoronavirus anatis. Although BHG-GCoVs belong to the species Gammacoronavirus anatis, they are distantly related to the representative strain Duck_CoV 2714 and exhibit a closer genetic relationship with GCoVs from Xenus cinereus (AvXc-GCoV) and Numenius phaeopus (AvNp-GCoV). Similarity analysis of the five conserved domains revealed a high amino acid similarity not only with AvXc-GCoV and AvNp-GCoV but also with GCoVs from common gulls detected in Poland and those from ruddy turnstones identified in Australia. Additionally, we found that, except for the common gull, the amino acid sequences of the S protein of BHG-GCoVs showed a 88.69% to 96.44% similarity with those of GCoVs carried by Charadriiformes, while the similarity with GCoVs carried by Anseriformes ranged from 31.15% to 54.81%. Furthermore, recombination events were detected in BHG-GCoVs, suggesting that these strains are likely recombinant strains of common gull GCoV and the GCoV of Arenaria interpres (AvAi-GCoV), indicating that recombination events may occur frequently among GCoVs.