The spike (S) glycoprotein is a key virulence factor for coronaviruses (CoVs), and CoV variants are categorized through S gene analysis. In this study, we present the phylogenetic analysis of a newly isolated infectious bronchitis virus (IBV) strain in relation to available genome and protein sequences, based on network analysis, multiple sequence alignments, selection pressures, and evolutionary fingerprinting techniques, specifically in the People's Republic of China. We selected 111 CoV strains for analysis: Alphacoronaviruses (Alpha-CoVs; n = 12), Betacoronaviruses (Beta-CoVs; n = 37), Gammacoronaviruses (Gamma-CoVs; n = 46), and Deltacoronaviruses (Delta-CoVs; n = 16). Phylogenetic clustering showed that SARS-CoV-2 and SARS-CoVs grouped with Bat-CoVs and MERS-CoV within Beta-CoVs (C). The IBV HH06 strain from Avian-CoVs closely resembled Duck-CoV and partridge S14, LDT3 (from teal and chicken hosts). In contrast, Beluga whale-CoV (SW1) and Bottlenose dolphin-CoVs, of mammalian origin, were more distantly related but still fell under the Gamma-CoVs category with Avian-CoVs. Motif analysis revealed conserved domains in the S protein, which showed similarity within the same phylogenetic group but varied across different viral lineages. A recombination network tree demonstrated that SARS-CoV-2, SARS-CoV, and Bat-CoVs, while branching separately, shared common clades. MERS-CoVs from camel and human sources clustered into a distinct group but remained closely linked to SARS-CoV-2, SARS-CoV, and Bat-CoVs. In contrast, HCoV-OC43, of human origin, clustered with bovine CoVs but was more distantly related to other human-origin viruses like SARS-CoV-2 and SARS-CoV. These findings underline the ongoing genetic recombination and evolutionary processes of CoVs, which could maintain them as potential threats to both veterinary and human health.
