In a recent study published in the bioRxiv * prepress server, researchers evaluated the impact of epistatic interactions on the affinity of the angiotensin-2-converting enzyme (ACE2) in the Omicron variant of respiratory syndrome. severe acute coronavirus 2 (SARS-CoV-2).
Study: Compensatory epistaxis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1. Image credit: Kateryna Kon / Shutterstock
Fund
Several studies have investigated the effects of mutations in the Omicron SARS-CoV-2 variant on ACE2 affinity as well as antibody binding. These studies focus on the impact of individual mutations only on particular genetic backgrounds. However, extensive research is required to understand the interactions between combinations of mutations found in Omicron and their impact on immune evasion and ACE2 affinity.
About the study
In the present study, the researchers mapped the incident epistatic interactions between mutations present in the receptor-binding domain of the SARS-CoV-2 Omicron BA.1 subline in comparison with those of the Wuhan strain.
The team employed a combinatorial assembly approach to develop a plasmid library that included all probable combinations of the 15 mutations observed in BA.1 RBD. This library included all possible evolutionary intermediates between BA.1 and Wuhan RBDs. The team used a high-throughput sequencing and flow cytometry-based method called Tite-Seq to estimate the binding affinities (KD, app) of all possible viral variants of RBD to human ACE2. In addition, a standard biochemical model of epistaxis was suitable for the study data.
Results
The results of the study showed that all 32,768 possible SARS-CoV-2 RBD intermediates between the Wuhan strain and the Omicron BA.1 variant had a detectable affinity for ACE2 with a KD, application between 0.1 μM and 0 , 1 nM. The BA.1 RND had a three-fold increase in binding affinity compared to that of the Wuhan strain.
However, almost 60% of the RBD intermediate sequences showed a weaker ACE2 binding affinity than that observed for the Wuhan strain. This was because most BA.1 mutations had a neutral or detrimental effect on ACE2 affinity in most genetic antecedents. This was especially true for mutations such as G446S, K417N, Q493R, Y505H, and G496S, four of which were involved in the immune evasion of various classes of monoclonal antibodies.
Although many of the BA.1 mutations decrease the affinity for ACE2, the interactions observed between these mutations lead to an increase in the affinity of BA.1 for ACE2. These mutations were found to be more detrimental to ACE2 affinity in the presence of some other mutations; however, these mutations prove to be neutral or beneficial when many other mutations are present.
The team also observed that while most of the 15 RBD mutations decrease affinity with ACE2 at the bottom of the Wuhan strain, these mutations tend to be less harmful and more advantageous at the bottom of Omicron. This showed that Omicron BA.1 RBD showed a more robust ACE2 affinity although it included mutations that individually decrease ACE2 affinity due to the harmful effects of mutations mitigated by epistatic interactions between mutations.
The team found that the linear effects of the individual mutations were associated with the contact surface of ACE2 with the corresponding residue. The higher-order coefficients inferred from the biochemical method showed strong compensatory interactions that mitigated the affinity-reducing effects of individual mutations. The extent of these interactions was similar to that observed for linear effects, while the observed epistatic interactions were very positive. This indicated that mutations that reduced ACE2 affinity had become less harmful than in the background with other compensatory mutations.
Epistatic interactions also eliminated the strong harmful impact of mutations involved in antibody leakage. The team also found that the G446S, K417N, Q493R, Y505H, and G496S mutations had a negative linear effect on viral affinity for ACE2; however, this effect was found to be very rare in the SARS-CoV-2 phylogeny. This suggested that maintaining ACE2 affinity is probably an important feature of viral fitness; therefore, these mutations were probably selected against.
The team also found that mutations that had negative effects on ACE2 affinity mitigated by epistatic interactions with N501Y were enriched among all SARS-CoV-2 strains that also have N501Y. This further suggested that there were at least some couple epistatic interactions among other viral antecedents.
Conclusion
In summary, the results of the study showed that the evolution of antibody escape in the SARS-CoV-2 Omicron BA.1 subline was possible without reducing ACE2 binding due to the compensatory epistatic interactions that they occur with other mutations. The study showed that high-order epistaxis patterns were essential for viral evolution involving adaptive events such as immune evasion. Researchers believe that the generation of specific combinatorial landscapes can help to understand the general patterns of epistaxis responsible for viral evolution.
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