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 to be the natural hosts of Deltacoronavirus (δ-CoV) and Gammacoronavirus (γ-CoV). A total of 59 coronaviruses (CoVs) were detected in 509 fecal samples collected from overwintering black-headed gulls in Yunnan Province, China. Among them, the prevalence of black-headed gull Deltacoronavirus (BHG-DCoV) was 3.54% (18/509), and that of black-headed gull Gammacoronaviru (BHG-GCoV) was 8.06% (41/509). The prevalence of BHG-GCoV was higher than that of BHG-DCoV (χ² = 9.518, P < 0.01). It was obtained that two complete genome sequences of BHG-GCoVs with lengths of 27,358 nt and 37,355 nt respectively from the fecal samples of black-headed gulls. The nu-cleotide similarity between the two complete genomes is 98.75%. Phylogenetic analysis based on the whole genome has confirmed that the two stains 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 have a relatively close genetic relationship with the GCoV from Xenus cinereus (AvXc-GCoV) and the GCoV from Numenius phaeopus (AvNp-GCoV). Based on the similar-ity analysis of the five conserved domains, there is a high amino acid similarity not only with AvXc-GCoV and AvNp-GCoV, but also with the GCoV of the common gull detected in Poland and the GCoV from ruddy turnstone detected in Australia. We also found that the amino acids of the S protein of BHG-GCoVs had a relatively high similarity with GCoV from most of the Charadriiformes except for the common gull, while having a rela-tively low amino acid similarity with that from the Anseriformes. Meanwhile, we also de-tected recombination events in BHG-GCoVs, indicating that recombination events might occur frequently during the viral evolution process.