Study characterizes SARS-CoV-2 subvariants to inform development of next-generation COVID-19 vaccines

In a recent preprint posted to the bioRxiv* server, researchers characterized two novel XBB variants, EG.5.1 and XBB.2.3, with the former on track to become the dominant severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant.

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Background

The original Omicron variant arose globally in 2022 and soon became the dominant SARS-CoV-2 variant worldwide. The XBB sublineages of Omicron evolved in early 2023. XBB.2.3 evolved directly from the Omicron XBB sublineage, while EG.5.1 is an XBB.1.5 mutant. 

The former has two additional mutations in its spike (S), P521S in the receptor binding domain (RBD) and D253G in the N-terminal domain (NTD), while EG.5.1 has Q52H and F456L mutations in the NTD and RBD, respectively.

All XBB variants, including XBB.2.3 and EG.5.1, exhibited higher immune evasion capabilities than Omicron, in particular against neutralizing antibodies (nAbs) elicited by SARS-CoV-2 convalescence and coronavirus disease 2019 (COVID-19) vaccines based on the messenger ribonucleic acid (mRNA) technology.

Thus, the Food and Drug Administration (FDA) recommended including XBB subvariants in future iterations of COVID-19 mRNA vaccines.

However, immune imprinting can impair vaccine efficacy against evolving variants. Thus, a three-dose vaccination series based on S of wildtype virus biases vaccine-elicited nAbs toward earlier lineages and impairs immune responses towards recently emerged Omicron sublineages.

A bivalent mRNA booster vaccine based on wildtype and BA.4/5 spikes enhances the immune response toward Omicron sublineages, albeit to a limited extent compared to a three-dose monovalent vaccine series.

Some methods of counteracting immune imprinting include administering extra doses of Omicron S-based mRNA vaccines or exposure to Omicron infection. Nonetheless, there is a need to reconfigure current COVID-19 mRNA vaccination approaches.

In addition, continued surveillance efforts to characterize emerging SARS-CoV-2 variants are critical.

About the study

In the present study, researchers investigated S proteins of EG.5.1 and XBB.2.3 for infectivity, fusogenicity, and escape from nAbs in bivalent mRNA booster vaccinated sera, BA.4/5- and XBB.1.5-wave convalescent sera using HEK293T-ACE2 and CaLu-3 cells, and class III monoclonal antibody (mAb), S309.

Additionally, they compared these parameters to spikes from the ancestral D614G and Omicron subvariants BA.4/5, XBB, XBB.1.5, and XBB.1.16.

Results

As expected, bivalent mRNA vaccination elicited relatively low nAb titers against all XBB variants, especially EG.5.1 and XBB.2.3, than D614G and Omicron BA.4/5 despite the presence of BA.4/5 S in this vaccine formulation.

The nAb response mainly targeted D614G, providing additional evidence of immune imprinting elicited by the monovalent mRNA vaccines. 

SARS-CoV-2 acquired many mutations in its evolutionary journey. Antigenic cartography analysis has established antigenically distinct phenotypes of XBB sublineages, especially EG.5.1.

Yet, encouragingly, bivalent mRNA vaccination continues to confer better protection against reinfection than monovalent vaccinations and natural infection. The authors noted that XBB.1.5-F456L mutation enhanced the nAb escape of EG.5.1 compared to XBB.1.5.

Molecular modeling demonstrated that F456L did not impact S-binding to S309 but likely decreased S-binding to class 1 SARS-CoV-2 mAbs, S2E12, consistent with the findings from recent studies.

The majority of the bivalent vaccination cohort had breakthrough infections relative to the convalescent cohorts. XBB.1.5 infections broadened nAb titers against vaccines containing XBB.1.5 and XBB.1.16 spikes.

From that logic, EG.5.1 S-containing mRNA vaccines are more likely to overcome immune imprinting and confer more immunity against XBB sublineages. 

Although infectivity of XBB.2.3 and EG.5.1 was not significantly different from XBB variants in both cell lines tested, EG.5.1 infectivity was moderately higher in 293T-ACE2 cell lines but lesser in respiratory airway epithelial cell line CaLu-3.

This alleviates concerns regarding its increased pathogenesis in the lungs. Furthermore, the fusogenicity of their spikes was similar to other XBB variants. 

Molecular modeling revealed the effect of XBB.1.5-F456L mutation. The substitution of phenylalanine to leucine amino acid residue in XBB.1.5 S reduced the side chain size and increased the distance between its RBD and host ACE2 receptor, which resulted in diminished RBD-ACE2 affinity.

Conclusions

To conclude, the current study found no in vitro evidence of the enhanced pathogenic potential of newly emerged XBB variants, EG.5.1 and XBB.2.3. However, the need for in vivo and clinical evidence remains. 

The inclusion of XBB-lineage variant spikes in new mRNA vaccine formulations could enhance their effectiveness. There remains a need for continued surveillance efforts for these variants to inform decisions around next-generation COVID-19 vaccination strategies. 

Some pharmaceutical companies have already proposed new mRNA vaccine formulations containing XBB.1.5 S to the FDA, which may roll out in September 2023.

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Neha Mathur

Neha is a digital marketing professional based in Gurugram, India. She has a Master’s degree from the University of Rajasthan with a specialization in Biotechnology in 2008. She has experience in pre-clinical research as part of her research project in The Department of Toxicology at the prestigious Central Drug Research Institute (CDRI), Lucknow, India. She also holds a certification in C++ programming.