New SARS-CoV-2 Sublineage RE.2.2 Shows Enhanced Binding and Unique Structural Features

Structural Features and Receptor Engagement of RE.2.2

The sublineage BA.3.2.2 descends from the omicron BA.3 variant and has demonstrated accelerated spread across several regions. Using surface plasmon resonance and cryo-electron microscopy, researchers in the laboratory of Prof. Gao George Fu at IMCAS determined that the receptor-binding domain of RE.2.2 displays high affinity for the human angiotensin-converting enzyme 2 receptor, as detailed in the study. Structural analyses revealed that a reverse mutation, designated as R493Q, forms an additional hydrogen bond with the human receptor residue K31, which serves as a primary determinant for heightened engagement. To understand host range characteristics, the research team tested the interaction of RE.2.2 with angiotensin-converting enzyme 2 proteins from various animal species. The results showed that the host species range of the sublineage is broadly comparable to the omicron variants used for comparison in the study.

Antibody Evasion and Immune Escape Profile

Pseudovirus neutralization and binding assays demonstrated a remodeled immune evasion landscape for the emerging variant, according to the published findings. While RE.2.2 successfully evaded multiple antibody classes, several broadly neutralizing antibodies that had previously lost activity against earlier omicron lineages—specifically S2K146 and L4.65—regained potent neutralizing capacity against RE.2.2. Cryo-electron microscopy ternary structures indicated that the key substitution G446D directly facilitates these antibody interactions. This dynamic demonstrates that viral antigenic evolution remains constrained by underlying structural requirements and cannot proceed without limits, the researchers noted.

Novel N-Linked Glycosylation Site Discovered

Comprehensive glycoproteomic profiling using liquid chromatography-tandem mass spectrometry and cryo-electron microscopy revealed up to 26 N-linked glycosylation sites on the spike trimer of RE.2.2. Among these, the variant harbors a previously unobserved N-linked glycosylation site at position N529 on the receptor-binding domain, an alteration not seen in SARS-CoV-2 variants. This specific modification forms inter-protomer hydrogen bonds that structurally stabilize the spike protein in a closed conformation. This mechanism balances high receptor affinity with regulated viral entry, while also supporting the established “O-follows-N” rule of protein glycosylation in coronavirus spike proteins, according to the research team.