The coronavirus disease 2019 (COVID-19) pandemic was caused by the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Since then, several variants of SARS-CoV-2 have emerged in rapid succession, the most recent of which is the Omicron variant.
In a recent study in the journal PNAS, researchers describe the many mutations present in the Omicron variant and their impact on altered biological characteristics, such as neutralization and infectivity.
Study: Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-Cov-2 virus-like particles. Image credit: Kateryna Kon / Shutterstock.com
Introduction
Considerable research has been conducted on the pathogenicity of SARS-CoV-2, as this information is needed to determine the optimal approach to developing new therapeutic and prophylactic measures. Despite the global deployment of vaccines against COVID-19, several new variants such as Beta and Delta variants of concern (VOCs) have emerged that resist immunity induced by previous variants or vaccinations.
Investigating the infectivity and neutralizing capacity of SARS-CoV-2 variants is difficult due to the need to conduct such research in biosafety level III (BSL3) laboratories. To overcome this challenge, pseudoviruses such as vesicular stomatitis virus and lentivirus pseudotyped with the SARS-CoV-2 spike protein have been used.
Mutations in other regions of the SARS-CoV-2 genome can also affect its properties; however, these differences cannot be studied with these pseudoviruses. For this reason, researchers in the current study used SARS-CoV-2 virus-like particles (SC2-VLPs), which are capsids loaded with viral ribonucleic acid (RNA).
SC2-VLPs are produced by infecting cells in vitro with four specially designed plasmids. Three of these plasmids express the SARS-CoV-2 spike, nucleocapsid, membrane, and envelope antigens, while the fourth expresses a tagged messenger RNA (mRNA) that expresses a packaging signal. These plasmids allow researchers to quickly explore what happens after the mutation of these different structural genes.
The viral structural proteins used in this study originated from the B.1.1, Delta, and Omicron variants. The effects of these mutations were compared with the activity of B.1 (wild-type) genes.
For this study, the team of researchers designed virus-like particles, which are composed of the same proteins as the SARS-CoV-2 virus but without its viral genome, so they are safer to work with – there are live viruses. Shown here are Alison Ciling (left) and Abdullah Syed (right) working in a tissue culture room.
Results of the study
VLPs expressing SARS-CoV-2 Delta and Omicron spikes showed 60% reduced infectivity and higher infectivity, respectively, compared to B.1; however, spike expression was similar in all variants. This difference is likely due to the reduced efficiency of infection by Delta and the increased intrinsic efficiency of the Omicron spike protein.
However, lentiviral pseudoviral particles showed the opposite trend, with Delta and Omicron pseudoviruses showing higher and lower levels of viral entry, respectively. Spike cell interactions also differ with the specific membrane and nucleocapsid variants expressed.
These findings indicate that the entire genetic makeup of the virus affects the ability of the spike gene to infect cells. However, mutations in the Omicron spike are the main determinant of cellular infectivity.
Previous research has confirmed that the nucleocapsid gene in all three variants relative to B.1 contains R203 mutations that are associated with increased infectivity and RNA packaging. In the current study, both the Delta and Omicron nucleocapsid genes showed an increase in these two attributes as well as higher nucleocapsid expression. Thus, the nucleocapsid protein is essential for efficient infection and viral packaging.
If only the membrane or envelope mutations of the Omicron variant were replaced by other genes belonging to the ancestral B.1 strain, infectivity was reduced with lower nucleocapsid and spike expression. Therefore, some Omicron genes are associated with reduced efficiency of virion assembly and lower viral fitness.
However, other Omicron genes appear to compensate and ultimately contribute to the overall fivefold infectivity of this VLP compared to B.1. The infectivity of the Omicron VLP was comparable to that of Delta and B.1.1.
Neutralizing capacity
Antisera from vaccinated individuals, as well as convalescent sera from recovered patients with no history of vaccination, effectively neutralized B.1. The highest neutralizing antibody (nAb) titers to VLPs were from those receiving mRNA vaccines at around 500 each. In contrast, the antisera of those who received the viral vector vaccine, as well as the convalescents, showed lower titers of about 30 each.
These titers did not correlate with immunoglobulin G (IgG) titers, suggesting that binding antibodies are not always nAbs.
The neutralizing efficacy of mRNA vaccine antisera was lower against the Delta variant and was reduced 15- to 18-fold against Omicron. This escape from neutralization appeared to be mediated by multiple mutations.
Notably, a third dose of an mRNA vaccine elicited higher nAb titers against all variants tested. However, the neutralization of Omicron was still eight times less than that caused against B.1, thus indicating a partial escape.
Monoclonal antibodies
Commercial monoclonal antibodies (mAb) such as casirivimab (Regeneron), imdevimab (Regeneron), sotrovimab (Vir/GSK), and bebtelovimab (AbCellera/Eli Lilly) were tested for their neutralizing efficiency. All mAbs were highly effective against the ancestral spike protein; however, Omicron was only neutralized by sotrovimab and bebtelovimab.
Sotrovimab showed less efficacy against both Delta and Omicron than B.1. In comparison, bebtelovimab showed a low nanomolar 50% inhibitory concentration (IC50).
A VLP with Omicron mutations in the spike region but outside the receptor-binding domain (RBD), which interacts with the host cell angiotensin-converting enzyme 2 receptor, was also tested ( ACE2). This VLP had RBD mutations that have already been shown to escape binding by class 1 and class 3 antibodies (OmC1 and OmC3, respectively).
Furthermore, this VLP was not neutralized by casirivimab or imdevimab, although both readily neutralized B.1.1 and Delta VLPs. While casirivimab was found to neutralize OmC3, imdevimab was found to neutralize OmC1. However, the combination of Omicron mutations resulted in the two antibodies not neutralizing this variant.
Conclusions
The results of this study demonstrate the utility of SARS-CoV-2 VLPs for understanding how mutations in several structural proteins affect particle infectivity and antibody-mediated neutralization of different variants. An interesting finding is the reduced infectivity of Omicron envelope and membrane mutations, although this feature is offset by mutations in the spike and nucleocapsid genes that increase the viral fitness of this variant.
Tracking the evolution of the S and N genes and determining why the N gene has such a pronounced effect on the infectivity of viral particles may enable the development of better diagnostics, more broadly neutralizing the development of vaccines and potentially new therapeutics”.
The effectiveness of mRNA vaccines in neutralizing non-Omicron variants was confirmed, although the study did not take into account cellular immune responses that are thought to be effective in preventing and countering infection. Loss of efficacy of currently available mAbs against Omicron was also demonstrated, while a third dose of an mRNA vaccine appears to enhance nAb-specific responses to Omicron.
Our results suggest that Omicron has similar assembly efficiency and cellular entry compared to Delta and that its rapid spread is primarily due to reduced neutralization in sera from previously vaccinated subjects.”
The Omicron variant is also highly resistant to most mAbs in use today, except for bebtelovimab.
Journal reference:
- Syed, AM, Ciling, A., Taha, TY, et al. (2022). Omicron mutations enhance infectivity and reduce antibody neutralization of SARS-Cov-2 virus-like particles. PNAS. doi:10.1073/pnas.2200592119.