Compensatory epistasis maintains ACE2 affinity in SARS-CoV-2 Omicron BA.1

Abstract

The Omicron BA.1 variant emerged in late 2021 and quickly spread across the world. Compared to the earlier SARS-CoV-2 variants, BA.1 has many mutations, some of which are known to enable antibody escape. Many of these antibody-escape mutations individually decrease the spike receptor-binding domain (RBD) affinity for ACE2, but BA.1 still binds ACE2 with high affinity. The fitness and evolution of the BA.1 lineage is therefore driven by the combined effects of numerous mutations. Here, we systematically map the epistatic interactions between the 15 mutations in the RBD of BA.1 relative to the Wuhan Hu-1 strain. Specifically, we measure the ACE2 affinity of all possible combinations of these 15 mutations (215 = 32,768 genotypes), spanning all possible evolutionary intermediates from the ancestral Wuhan Hu-1 strain to BA.1. We find that immune escape mutations in BA.1 individually reduce ACE2 affinity but are compensated by epistatic interactions with other affinity-enhancing mutations, including Q498R and N501Y. Thus, the ability of BA.1 to evade immunity while maintaining ACE2 affinity is contingent on acquiring multiple interacting mutations. Our results implicate compensatory epistasis as a key factor driving substantial evolutionary change for SARS-CoV-2 and are consistent with Omicron BA.1 arising from a chronic infection.

Coordinated evolution at amino acid sites of SARS-CoV-2 spike

“…Mutations N440K and P681H are lineage-defining mutations of BA.1, but our analysis suggests that these mutations avoided each other before the appearance of Omicron due to negative epistasis. This indeed can be the case: despite the fact that the N440K mutation increases binding affinity to ACE2 and affects Ab neutralization efficiency ( Barnes et al, 2020 ; Harvey et al, 2021 ; Moulana et al, 2022 ), by the end of 2021 its frequency in BA.1 was relatively low (<75%), while P681H reached 98% frequency ( Gangavarapu, 2022c ). However, the worldwide prevalence of the mutation pattern N440K+P681H+N501 Y was increasing during the year and at the end of 2022, it was higher than 98% ( Gangavarapu et al, 2022e ).…”

“…The reasons for this change are unclear. Several non-exclusive explanations were proposed, including a distinct mode of evolution at variant origin, for example, in an immunosuppressed individual ( Corey et al, 2021 ; Kupferschmidt, 2021 ) or a different host species ( Wei et al, 2021 ) and/or cascades of substitutions at positively epistatically interacting sites ( Moulana et al, 2022 ). Here, we focus on the latter possibility.…”

“…For example, the Q498R mutation alone affected the affinity of Spike to ACE2 only slightly ( Zahradník et al, 2021 ), but on the background of N501Y, the affinity of binding increased by a factor of 4–25 ( Starr et al, 2022a ; Zahradník et al, 2021 ), with both mutations together increasing the affinity by up to 387-fold compared to the wild type ( Starr et al, 2022a ). The very strong binding provided by the double mutant allows accumulation, at Omicron origin, of multiple immune escape mutations at other sites which by themselves destabilize ACE2 binding ( Moulana et al, 2022 ; Starr et al, 2022a ).…”

Fitness effects of mutations to SARS-CoV-2 proteins

“…Although we derive this relationship, we do not adjust for sampling intensity and population dynamics when estimating mutation effects. Fourth, we make a single estimate for each mutation across all SARS-CoV-2, neglecting the epistasis that can affect some mutations [35,36]. Finally there are a few technical caveats to how we count mutations that are discussed in the Methods section.…”

“…The modest variation in estimates from different sequence subsets could have two causes: statistical noise due to finite mutation counts, or real shifts in mutation effects during SARS-CoV-2 evolution [35,36]. To test for statistical noise, we computed correlations with different thresholds for how many expected counts are required before making an estimate for a mutation (Figure 2C).…”