A viral fitness-constraint strategy exploits the structural and functional limitations of viral evolution

Despite the official end of the COVID-19 public health emergency, the continuous evolution of SARS-CoV-2 has rendered most reported monoclonal antibodies (mAbs) ineffective due to immune escape. The traditional “infection-first, screening-later” model can no longer keep pace with the virus’s rapid immune escape, creating an urgent need for broadly neutralizing antibodies (bnAbs) that remain effective against emerging variants.

In response to these challenges, a team of researchers from the Institute of Microbiology, Chinese Academy of Sciences (CAS), led by Professor George F. Gao, has revealed two innovative strategies for the development of durable and broadly neutralizing antibodies against SARS-CoV-2. Their study proposes the immune trajectory strategy and the viral fitness-constraint strategy, which provide new insights into how antibodies can be designed to remain effective despite viral mutations.

By analyzing receptor-binding domain (RBD) sequences from 16 post-Omicron variants, the team found that mutations have spread across all eight known antibody epitopes. This pattern suggests that previously conserved targets are eroded, making the discovery of truly broad antibodies increasingly difficult.

To evaluate antibody resilience, the researchers examined nearly 10,000 reported RBD-targeting antibodies and selected nine representatives with available structural data—eight mAbs (S2K146, BD55-1205, VIR-7229, SA55, S309, L4.65, BIOLS56, and S2H97) and one bispecific antibody(bsAb), Dia-19. Neutralization assays against 16 recent Omicron subvariants revealed that while antibodies such as S309, L4.65, and S2K146 gradually lost activity against the JN.1, BD55-1205, VIR-7229, SA55, and Dia-19 maintained strong cross-neutralizing potency.

Detailed sequence analysis showed that some mAbs tolerate up to 39% amino acid variation at their binding interfaces. Their heavy-chain variable regions carry 11–13 nucleotide substitutions, which is higher than the general average of 7–8, indicating that extensive affinity maturation contributes to improved tolerance against mutation. From these findings, the team developed two complementary design concepts. The immune trajectory strategy identifies antibodies that have undergone long-term natural maturation within individuals exposed to multiple coronaviruses, such as SARS-CoV-1 convalescents or people with breakthrough infections. The viral fitness constraint strategy focuses on exploiting viral structural and functional limits to restore or maintain neutralizing activity.

The bsAb Dia-19, composed of L4.65 and BIOLS56, exemplifies this approach. When one parental antibody loses activity due to escape mutations, the bispecific molecule cross-links the spike trimer and exposes hidden epitopes, recovering neutralization capacity. This mechanism leverages the virus’s evolutionary balance between infectivity and immune evasion, turning a biological limitation into a design opportunity.

Overall, these strategies provide a framework for developing durable, mutation-tolerant antibodies that can counter rapidly evolving pathogens. The study highlights new directions for rational antibody engineering and long-term antiviral preparedness.

About Author

Dr. Zhou Tong is an Associate Professor at the Institute of Microbiology, Chinese Academy of Sciences. He graduated with a bachelor’s degree from Ocean University of China in 2007. Supported by the China Scholarship Council, he completed his doctoral research in Microbiology at Auburn University, USA, focusing on phage display library technology and biosensors. After joining the Institute of Microbiology, his research focuses on the mechanisms underlying broad-spectrum antibody generation and the engineering of antibodies in vitro. He has established multiple microbial surface display and screening platforms based on phage, yeast, and bacterial systems, as well as a high-throughput microdroplet-based protein genotyping and functional screening system. Additionally, he has developed digitalized antibody libraries from humans and sharks, along with predictive algorithms for antibody evolution and optimization. To date, Dr. Tong has co-authored 27 SCI-indexed papers, including recent first or corresponding author publications in PNAS, Cell Reports, Nature Communications, and Nucleic Acids Research. He holds 18 authorized national invention patents, and his bispecific antibody “Dia-19” for broad coronavirus prevention entered clinical trials in 2024, completing Phase I in 2025.