Structural and biochemical mechanism for increased infectivity and immune evasion of Omicron BA.2 variant compared to BA.1 and their possible mouse origins

Abstract

The Omicron BA.2 variant has become a dominant infective strain worldwide. Receptor binding studies show that the Omicron BA.2 spike trimer exhibits 11-fold and 2-fold higher potency in binding to human ACE2 than the spike trimer from the wildtype (WT) and Omicron BA.1 strains. The structure of the BA.2 spike trimer complexed with human ACE2 reveals that all three receptor-binding domains (RBDs) in the spike trimer are in open conformation, ready for ACE2 binding, thus providing a basis for the increased infectivity of the BA.2 strain. JMB2002, a therapeutic antibody that was shown to efficiently inhibit Omicron BA.1, also shows potent neutralization activities against Omicron BA.2. In addition, both BA.1 and BA.2 spike trimers are able to bind to mouse ACE2 with high potency. In contrast, the WT spike trimer binds well to cat ACE2 but not to mouse ACE2. The structures of both BA.1 and BA.2 spike trimer bound to mouse ACE2 reveal the basis for their high affinity interactions. Together, these results suggest a possible evolution pathway for Omicron BA.1 and BA.2 variants via a human-cat-mouse-human circle, which could have important implications in establishing an effective strategy for combating SARS-CoV-2 viral infections.

Fig. 1. SARS-CoV-2 Omicron BA.2 spike protein with higher affinity to human ACE2.

a The infection frequency of SARS-CoV-2 Delta, Omicron BA.1, and Omicron BA.2 strains since January 2022 to April 2022. b Binding curves of the Omicron BA.2 spike trimer to human ACE2. K_D values were determined with Octet Data Analysis HT 12.0 software using a 1:1 global fit model. c Relative potency of WT, BA.1, and BA.2 with the ratio of their K_D values. d, e Cryo-EM density maps of the hACE2-Omicron BA.2 spike trimer complexes with hACE2 and BA.2 spike in 3:3 molar ratio (d) or in 2:3 molar ratio (e). f The locations of Omicron BA.2 mutations on the Spike trimer. Spike trimer is shown in surface. The shared mutations between BA.1 and BA.2 are colored in green and the BA.2 its own mutations are colored in red. g The locations of 16 Omicron BA.2 mutations on the RBD. RBD is shown in surface. The shared mutations between BA.1 and BA.2 are colored in green and for BA.2 its own mutations are colored in red, including S375F, T376A, D405N, R408S, and N440K.

Fig. 2. Structural analysis of Omicron BA.2 RBD and hACE2.

a Cryo-EM density map of Omicron BA.2 RBD bound to hACE2. Residues are shown in sticks with the correspondent cryo-EM density represented in mesh. hACE2 is colored in coral. The Omicron BA.2 RBD is colored in purple. b Interactions between Omicron BA.2 RBD and hACE2. c Comparison of Omicron BA.2 RBD-hACE2 and WT RBD-hACE2 interfaces. Up panels, Omicron BA.2 RBD-hACE2 with hydrogen bonds and salt bridges interactions. Down panels, WT RBD-hACE2 with hydrogen bonds and salt bridges interactions. Interactions of hydrogen bonds and salt bridges are in dotted lines. d Thermal stability shift analysis of the Omicron BA.2, Omicron BA.1, and WT spike trimer. e The mutation-induced conformation changes of Omicron BA.2 RBD compared with BA.1 RBD.

Fig. 3. Inhibition of ACE2 binding to the Omicron BA.2 spike trimer by the anti-Omicron antibody JMB2002.

a Binding of JMB2002 Fab and IgG to the Omicron BA.2 spike trimer. b Inhibition of the pseudovirus of Omicron BA.2 by JMB2002. c Cryo-EM density map of the Fab-bound Omicron BA.2 spike trimer shown as front and top views. d Top view of Fab-bound Omicron BA.2 spike trimer complex model with Fab and nanobody hidden. e Superposition of the ACE2-bound and Fab-bound Omicron BA.2 spike trimer showing that Fab binding to RBD inhibits ACE2 binding.

Fig. 4. Characterization of the binding affinity between mouse ACE2 and Omicron spike trimmers.

a–c Binding of Omicron BA.2 (a), Omicron BA.1(b) and WT (c) spike trimers to mouse ACE2 as determined by BLI. d The K_D values of tested pairs in this study as determined by BLI. e Amino acid alignment of the 16 key residues in hACE2 with 4 ACE2 orthologs from mouse, cat, rat, and dog. f Superposition of the structures of human ACE2 bound Omicron BA.2 spike trimer and the cat ACE2 bound original spike trimer. g, h The binding modes of dog (g) and rat (h) ACE2s with the BA.2 RBD, were generated based on the complex structure of human ACE2 bound Omicron BA.2 spike trimer. The different residues among ACE2 protein that are responsible for the interactions with SARS-CoV-2 spike protein are shown with detained interactions.

Fig. 5. Cryo-EM structure of the Omicron BA.2 and BA.1 spike trimers in complex with mACE2.

a, b Cryo-EM maps of the Omicron BA.2 spike protein-mACE2 complex with one RBD in “up” conformation at 3.2 Å resolution (a), and mACE2 complex with two RBDs in “up” conformation at 3.3 Å resolution (b), respectively. The three protomers are colored in purple, red and green, and the density for mACE2 is colored in coral. c, d Cryo-EM maps of the Omicron BA.1 spike protein-mACE2 complex with one RBD in “up” conformation at 3.1 Å resolution (c), and mACE2 complex with two RBD in “up” conformation at 3.2 Å resolution (d), respectively. The three protomers are colored in purple, red, and green, and the density for mACE2 is colored in coral. e, f Density maps and atomic models of the interaction interface in the BA.2 spike trimer-mACE2 (e) and BA.1-mACE2 complexes (f).

Fig. 6. Structural analysis of mACE2 and RBD.

a Overall structure of the BA.2-RBD and mACE2 complex. b Details of the binding between BA.2-RBD and mACE2. The binding between BA.2-RBM and mACE2 consists mainly of two interaction regions, marked in a red or a blue box. Residues involved in the interactions are shown as sticks. Hydrogen bonds are shown as dashed black lines. c, d Overall structure of the BA.1-RBD and mACE2 complex, with detailed hydrogen bond or salt bridge interactions in BA.1-RBD and ACE2 interface with the same view as in (a, b). e, f The superposition of the BA.2 RBD and mACE2 complex with SARS-CoV-2 WT-RBD alone (PDB: 6LZG). Detailed hydrogen bond or salt bridge interactions are highlighted with the same view as in a, b.

Fig. 7. Comparison of the binding mode of the BA.2 RBD to mACE2 and hACE2.

a The superposition of BA.2 RBD bound to mACE2 with BA.2 RBD bound to hACE2, with hydrogen bond or salt bridge interactions shown as dashed lines. Hydrogen bond or salt bridge interactions in hACE2-RBD and mACE2-RBD are shown as red and black dashed lines, respectively. b Residues involved in the interactions of BA.2 RBD with hACE2 and mACE2 are listed and connected by lines. Red dashed lines indicate one hydrogen bond or salt bridge and red solid lines indicate two hydrogen bonds, whereas the cyan solid line represents a π-π stacking interaction between the residues. c Infection selectivity of BA.1, BA.2, and WT strains to human, mouse, and cat.