WTD ACE2 broadly binds to SARS-CoV-2 variantsAs of February 7, 2023, 583 SARS-CoV-2 sequences from WTD were uploaded to the Global Initiative on Sharing All Influenza Data (GISAID) (https://gisaid.org/). Phylogenetic analysis shows that these sequences form a highly divergent clade, covering multiple SARS-CoV-2 variants (Fig. 1A). Delta variant comprises the largest part, whereas relatively few sequences of the currently dominant Omicron variant are uploaded. However, the latest collection date is April 2022, when the Omicron variants only just started to gain dominance. Thus, the low proportion of Omicron variants might be due to sampling bias. Next, we analyzed the RBD of these SARS-CoV-2 sequences. We found that the RBDs of WTD-origin SARS-CoV-2 in GISAID are mainly classified as PT, Alpha, Gamma, Delta, Omicron BA.1, and Omicron BA.1.1 (Fig. 1B).
Fig 1
Fig 1 The subtypes of SARS-CoV-2 virus that infect WTD. (A) Phylogenetic analysis of 583 SARS-COV-2 genomes from WTD (Odocoileus virginianus) in the GISAID. The phylogenetic analysis was executed using iqtree2 (2.2.0-beta) with model UNREST + FO + R4, which was found by ModelFinder in iqtree2. (B) Schematic architecture of the SARS-CoV-2 S protein and substitution mapping of RBDs from different subtypes of SARS-CoV-2 related to this study.The binding of WTD ACE2 to various SARS-CoV-2 RBDs was evaluated by surface plasmon resonance (SPR) and flow cytometry assays. The assessed variants include VOCs, variants of interest (VOIs),