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Updated: Aug 9, 2025
Author Spotlight: A Pseudotype Virus System for Assessing Omicron Subvariants and Neutralizing Antibodies in SARS-CoV-2 Research
Published on: September 8, 2023
Comparison of the replication and neutralization of different SARS-CoV-2 Omicron subvariants in vitro
Yaqing Zhang1,2, Qi Lv1,2, Feifei Qi1,2
1Beijing Key Laboratory for Animal Models of Emerging and Reemerging Infectious Diseases, NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
Background:
New Omicron subvariants are emerging rapidly from BA.1 to BA.4 and BA.5. Their pathogenicity has changed from that of wild-type (WH-09) and Omicron variants have over time become globally dominant. The spike proteins of BA.4 and BA.5 that serve as the target for vaccine-induced neutralizing antibodies have also changed compared to the previous subvariants, which is likely to cause immune escape and the reduction of the protective effect of the vaccine. Our study addresses the above issues and provides a basis for formulating relevant prevention and control strategies.
Methods:
We collected cellular supernatant and cell lysates and measured the viral titers, viral RNA loads, and E subgenomic RNA (E sgRNA) loads in different Omicron subvariants grown in Vero E6 cells, using WH-09 and Delta variants as a reference. Additionally, we evaluated the in vitro neutralizing activity of different Omicron subvariants and compared it to the WH-09 and Delta variants using macaque sera with different types of immunity.
Results:
As the SARS-CoV-2 evolved into Omicron BA.1, the replication ability in vitro began to decrease. Then with the emergence of new subvariants, the replication ability gradually recovered and became stable in the BA.4 and BA.5 subvariants. In WH-09-inactivated vaccine sera, geometric mean titers of neutralization antibodies against different Omicron subvariants declined by 3.7~15.4-fold compared to those against WH-09. In Delta-inactivated vaccine sera, geometric mean titers of neutralization antibodies against Omicron subvariants declined by 3.1~7.4-fold compared to those against Delta.
Conclusion:
According to the findings of this research, the replication efficiency of all Omicron subvariants declined compared with WH-09 and Delta variants, and was lower in BA.1 than in other Omicron subvariants. After two doses of inactivated (WH-09 or Delta) vaccine, cross-neutralizing activities against various Omicron subvariants were seen despite a decline in neutralizing titers.
Insights
New Omicron subvariants show reduced replication but can escape vaccine immunity. Cross-neutralizing antibodies offer some protection, but vaccine effectiveness may decrease against emerging SARS-CoV-2 variants.
Area of Science:
- Virology
- Immunology
- Epidemiology
Background:
- Emergence of new Omicron subvariants (BA.1, BA.4, BA.5) with altered pathogenicity and spike proteins.
- Omicron variants have become globally dominant, posing challenges to existing vaccine-induced immunity.
- Changes in spike proteins of BA.4/BA.5 may lead to immune escape and reduced vaccine efficacy.
Purpose of the Study:
- To analyze the replication ability of Omicron subvariants in vitro.
- To evaluate the neutralizing activity of sera from inactivated vaccines against Omicron subvariants.
- To provide data for developing prevention and control strategies against SARS-CoV-2 evolution.
Main Methods:
- Cultured Omicron subvariants (BA.1, BA.4, BA.5) in Vero E6 cells, measuring viral titers and RNA loads.
- Used wild-type (WH-09) and Delta variants as references for comparison.
- Assessed in vitro neutralizing antibody activity using macaque sera from WH-09 and Delta inactivated vaccines.
Main Results:
- In vitro replication ability decreased with Omicron BA.1 but recovered in BA.4/BA.5.
- Neutralizing antibody titers declined significantly (3.1–15.4-fold) against Omicron subvariants compared to original strains in vaccinated sera.
- Cross-neutralizing activity was observed, but with reduced efficacy.
Conclusions:
- Omicron subvariants exhibit reduced replication efficiency compared to WH-09 and Delta.
- Despite reduced neutralizing titers, inactivated vaccines (WH-09 or Delta) provide cross-neutralizing activity against Omicron subvariants.
- Findings highlight the need for updated strategies to address SARS-CoV-2 evolution and immune escape.
