In a recent study published on the bioRxiv* server, Boston University researchers made a chimeric recombinant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encoding the spike (S) glycoprotein gene of Omicron in the backbone of an ancestral SARS-. Isolated from CoV-2.
Study: Role of the spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1 Omicron. Image credit: Kateryna Kon/Shutterstock
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Omicron BA.1 is now the predominant SARS-CoV-2 variant of concern (VOC), which is highly transmissible in fully vaccinated populations and those with natural post-infection acquired immunity. Fortunately, it causes mild coronavirus disease 2019 (COVID-19). However, Omicron S differs from the ancestral isolate of SARS-CoV-2, Wuhan-Hu-1, by 59 amino acid mutations, and 37 of these reside in the S protein. Thus, the researchers investigated whether the protein The pathogenic and antigenic behavior of Omicrons is controlled.
About the study
In the present study, the researchers used a modified form of the cyclic polymerase extension reaction (CPER) to make a chimeric Omi-S virus. This method produced 0.5-5 x 106 plaque-forming units (PFU) per ml of virus stocks within two days of transfection.
For in vitro studies, the team infected angiotensin-converting enzyme 2 (ACE2)/transmembrane serine protease 2 (TMPRSS2)/Caco-2 and Vero E6 cells with Omi-S with a multiplicity of infections (MOI) of 0.01 and controlled viral spread. by flow cytometry and plaque assay. They then used lung alveolar epithelial type 2 (iAT2) cells derived from human induced pluripotent stem cells to monitor the secretion of viral progeny at the apical interface of the cells at 48 hours after the infections (hpi) and 96 hpi. iAT2 cells, grown as an air-liquid interface (ALI) culture, were infected by Omi-S at an MOI of 2.5.
In addition, the researchers evaluated the in vivo fitness of Omi-S compared to Omicron BA.1 in K18-hACE2 mice. They intranasally inoculated 12- to 20-week-old mice with 104 PFU of Omi-S. They collected lungs from mice at two and four dpi for virological and histological analysis. In addition, the team examined whether Omi-S exhibited an immune escape phenotype similar to natural Omicron. They performed a multicycle neutralization assay in an environment that mimicked an HIV-positive individual.
Results of the study
The main finding of the study was that although the S protein is the most mutated site of Omicron, it alone is not responsible for its attenuated infectivity. Thus, Omi-S, a chimeric recombinant with Omicron S in a Wuhan-Hu 1 backbone, developed vaccine resistance due to a cumulative effect of mutations distributed throughout the S protein, especially the motif of receptor binding 10 (RBM) mutations. The RBM resides within the receptor-binding domain (RBD) of the S1 domain of the S protein and makes direct contact with ACE2 receptors. Two point mutations within the RBM imparted Omicron S with the ability to resist neutralization. One was the E484A substitution and the other comprised a group of five substitutions, Q493R, G496S, Q498R, N501Y and Y505H.
In in vitro infection assays, Omi-S showed much higher replication efficiency than Omicron. Furthermore, in K18-hACE2 mice, Omi-S caused severe disease leading to about 80% mortality, indicating that mutations outside of S are the major determinants of the attenuated pathogenicity of Omicron. The authors emphasized the need for further studies to identify these mutations and elucidate their mechanisms of action. Infection with Omi-S, but not Omicron, resulted in neurological signs, such as hunched posture and unresponsiveness, in K18-hACE2 mice. It indicated that Omi-S preserved the property of neuroinvasion and the determinants of this property were outside S. Furthermore, Omi-S showed an increased propensity to replicate in the bronchiolar epithelium.
Sera from individuals vaccinated with two doses of an Omicron poorly neutralized COVID-19 messenger ribonucleic acid (mRNA) vaccine. Omi-S also showed similar mean maximum neutralizing dilution (ND50) values to Omicron, suggesting that the Omicron S protein, when incorporated into a WT virus, behaved similarly to Omicron.
Conclusions
Interestingly, the results of the study showed that the receptor binding capacity of Omicron S remained intact and higher relative to Wuhan-Hu-1 and Delta RBDs. It points to an evolving Omicron S that hinders antibody binding but preserves receptor engagement, opening new avenues of research. For example, next-generation broad-spectrum vaccines against COVID-19 should target the conserved and structurally restricted regions of S involved in ACE2 recognition.
Furthermore, the results of the study showed that mutations in the Omicron S protein were responsible for the ability of this VOC to evade infection-acquired and vaccine-induced immunity; however, they were not responsible for the decreased infectivity of Omicron. Determining the SARS-CoV-2 proteins that drive Omicron pathogenicity could help design better diagnostics and mitigation strategies for COVID-19.
*Important news
bioRxiv publishes preliminary scientific reports that are not peer-reviewed and therefore should not be considered conclusive, guide clinical practice/health-related behavior, or be treated as established information.
Journal reference:
- Chen, D., Kenney, D., Chin, C., Tavares, A., Khan, N., and Conway, H. et al. (2022). Role of the spike in the pathogenic and antigenic behavior of SARS-CoV-2 BA.1 Omicron. bioRxiv. doi: 10.1101/2022.10.13.512134