A bispecific nanobody dimer broadly neutralizes SARS-CoV-1 & 2 variants of concern and offers substantial protection against Omicron via low-dose intranasal administration

Current SARS-CoV-2 Omicron subvariants impose a heavy burden on global health systems by evading immunity from most developed neutralizing antibodies and vaccines. Here, we identified a nanobody (aS3A) that strongly cross-reacts with the receptor binding domain (RBD) of both SARS-CoV-1 and wild-type (WT) SARS-CoV-2. The dimeric construct of aS3A (aS3A-Fc) tightly binds and potently neutralizes both SARS-CoV-1 and WT SARS-CoV-2. Based on X-ray crystallography, we engineered a bispecific nanobody dimer (2-3-Fc) by fusing aS3-Fc to aRBD-2, a previously identified broad-spectrum nanobody targeting an RBD epitope distinct from aS3A. 2-3-Fc exhibits single-digit ng/mL neutralizing potency against all major variants of concerns including BA.5. In hamsters, a single systemic dose of 2-3-Fc at 10 mg/kg completely protected against Omicron infection. More importantly, an even lower dose of 2-3-Fc (5.0 mg/kg, 2.3-Fc prophylactically administered through the intranasal route drastically reduced viral loads and completely eliminated Os1 virus titers in the trachea and lungs. Finally, we discovered that Y296-3-Fc containing a Y296 substitution in aRBD-2 showed better activity than 2-3-Fc in neutralizing BA.2.75, a recent omicron subvariant that emerged in India. This study expands the arsenal against SARS-CoV-2, providing potential therapeutic and prophylactic candidates that fully cover major SARS-CoV-2 variants, and may offer a simple preventive approach against Omicron and its subvariants.

Huan Ma, Xinghai Zhang, Weihong Zeng, Junhui Zhou, Xiangyang Chi, Shaohong Chen, Peiyi Zheng, Meihua Wang, Yan Wu, Dan Zhao, Fanwu Gong, Haofeng Lin, Hancong Sun, Changming Yu, Zhengli Shi, Xiaowen Hu, Huajun Zhang, Tengchuan Jin, Sandra Chiu