4.8. Epitope Sequence Similarity Analysis

Considering the homology between PDCoV and other coronaviruses, we conducted a sequence analysis of the epitope recognized by mAb 5-A11, focusing on PDCoV and δ coronaviruses. A total of 202 complete PDCoV genome sequences were retrieved from GenBank. Additionally, 18 δ coronavirus NS6 protein sequences homologous to the PDCoV NS6 protein were obtained from the InterPro database [43] (accession number: IPR044335) and the conserved domain database [44] (accession number: cd21629). The epitope and its flanking sequences of the NS6 protein were aligned with those of other selected coronavirus isolates using the MAFFT software [45] (version 7.525). Finally, the multiple sequence alignment results were visualized using the ggmsa package [46] (version 1.4.0) in R software [47] (version 4.4.0) to evaluate sequence conservation. The secondary structural elements of NS6 protein were analyzed using the online software ESPript (version 3.0) [48].