Researchers analyzed the structures of the receptor-binding domain (RBD) of the SARS-CoV-2 omicron variant and its receptor, angiotensin-converting enzyme 2 (ACE2), to gain insight into the variant’s potential animal reservoir.
Published in the journal ‘Proceedings of the National Academy of Sciences’ (PNAS), the study revealed that several key mutations in the omicron RBD are uniquely adapted to mouse ACE2 but are incompatible with human ACE2. The findings suggest that the SARS-CoV-2 omicron variant may have evolved in mice before adapting to humans, providing insight into the variant’s potential evolutionary origins, according to the authors.
The sudden emergence and rapid spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron variant has raised questions about its animal reservoir. Here, we investigated receptor recognition of the omicron’s receptor-binding domain (RBD), focusing on four of its mutations (Q493R, Q498R, N501Y, and Y505H) surrounding two mutational hotspots. These mutations have variable effects on the RBD’s affinity for human angiotensin-converting enzyme 2 (ACE2), but they all enhance the RBD’s affinity for mouse ACE2.
We further determined the crystal structure of omicron RBD complexed with mouse ACE2. The structure showed that all four mutations are viral adaptations to mouse ACE2: three of them (Q493R, Q498R, and Y505H) are uniquely adapted to mouse ACE2, whereas the other one (N501Y) is adapted to both human ACE2 and mouse ACE2. These data reveal that the omicron RBD was well adapted to mouse ACE2 before omicron started to infect humans, providing insight into the potential evolutionary origin of the omicron variant.
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) omicron variant emerged abruptly and spread rapidly around the globe (1-4). Tracking the animal reservoir of SARS-CoV-2 and its variants is important for understanding the current COVID-19 pandemic and preventing future pandemics. Speculations about the source of the omicron variant are abundant, yet experimental evidence has been scarce (5).
The interactions between the receptor-binding domain (RBD) of coronavirus spike proteins and their host receptor are among the best systems for understanding coronavirus evolution (6, 7).
Both SARS-CoV-2 and closely related SARS-CoV-1 recognize human angiotensin-converting enzyme 2 (ACE2) as their receptor (8-10). Previous research on the receptor recognition of SARS-CoV-1 has provided insight into the animal origin of SARS-CoV-1 (11-15). The RBD of the original SARS-CoV-2 strain (i.e., prototypic RBD) differs from the RBD of a bat coronavirus by only a few residues, supporting a bat origin of the prototypic RBD (16).
The omicron RBD (strain BA.2) differs from the prototypic RBD by 16 residues, seven of which are located in the receptor-binding motif (RBM) that directly contacts ACE2 (3). To recover the evolutionary traces left by these RBM mutations, this study compared the structural adaptations of the omicron RBD to ACE2 from human and mouse, two possible sources of omicron (5).
Three virus-binding hotspots have been identified at the interfaces between SARS-CoV-2 RBD and human ACE2 (hACE2) and between SARS-CoV-1 RBD and hACE2 (14, 17, 18). These hotspots center on Lys31 in hACE2 (i.e., hotspot-31), Lys353 in hACE2 (i.e., hotspot-353), and a receptor-binding ridge in the viral RBD (i.e., hotspot-ridge) (Fig. 1A). These virus-binding hotspots are also mutational hotspots for SARS-CoV-1: all of the RBM mutations occurred around the hotspots and impacted the structural stability of the hotspots (13, 14).
Establishment of the “hotspots” concept was instrumental in determining the molecular mechanisms by which SARS-CoV-1 was transmitted from palm civets to humans (11-15). The RBM mutations in the SARS-CoV-2 omicron variant are also around the hotspots (Fig. 1A). Curiously, only a few of these omicron mutations enhance the RBD’s affinity for hACE2, while some other mutations reduce it (Fig. 1B) (17).
Structural details of the interface between the omicron RBM (strain BA.1) and hACE2 elucidated the role of each of these mutations in binding hACE2 (17). The omicron mutations that reduce the RBD’s affinity for hACE2 are structurally incompatible with hACE2, raising questions about what other species may have mediated the evolution of omicron.
In this study, we provide biochemical and structural evidence demonstrating that the omicron mutations are better adapted to mouse ACE2 (mACE2) than to hACE2, suggesting that mice mediated the onset of the omicron variant. Our study helps clarify the animal reservoir of the omicron variant and contributes to the understanding of SARS-CoV-2 evolution. The findings may facilitate epidemiological surveillance of SARS-CoV-2 in animals to prevent future coronavirus pandemics.