A SARS-CoV-2 variant with the 12-bp deletion at E gene

Area of Science:

• Virology
• Immunology
• Vaccine Development

Background:

• The COVID-19 pandemic remains a significant global health challenge.
• Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent, with limited understanding of its genetic variations.
• Investigating viral genetic differences is crucial for understanding pathogenesis and developing countermeasures.

Purpose of the Study:

• To isolate and characterize SARS-CoV-2 strains with distinct genetic profiles from a single clinical sample.
• To evaluate the impact of a specific genetic mutation (E gene deletion) on viral properties and immunogenicity.
• To assess the potential of different viral strains in vaccine development.

Main Methods:

• Plaque purification was employed to isolate two distinct SARS-CoV-2 strains (F8 and 8X) from the same patient specimen.
• Viral titer and infectivity assays were performed to compare the biological activity of the isolated strains.
• Quantification of S protein content and assessment of IgG and neutralizing antibody titers post-vaccination with inactivated viral strains were conducted.

Main Results:

• Two SARS-CoV-2 strains were successfully isolated: F8 (with a 12-bp deletion in the E gene) and 8X (wild-type).
• No significant differences in viral titer or infectivity were observed between the F8 and 8X strains.
• The F8 strain exhibited significantly higher S protein content and elicited higher IgG and neutralizing antibody titers, sustained for at least 6 weeks, compared to the 8X strain.

Conclusions:

• Both E gene-mutant and wild-type SARS-CoV-2 strains can be isolated from the same clinical sample using plaque purification.
• A 12-bp deletion in the SARS-CoV-2 E gene plays a critical role in viral replication and enhances immunogenicity.
• The F8 strain, carrying the E gene deletion, demonstrates superior potential for developing effective inactivated COVID-19 vaccines.