Neutralization of SARS-CoV-2 Variants of Concern Harboring Q677H

ABSTRACT The sensitivity of SARS-CoV-2 variants of concern (VOCs) to neutralizing antibodies has largely been studied in the context of key receptor binding domain (RBD) mutations, including E484K and N501Y. Little is known about the epistatic effects of combined SARS-CoV-2 spike mutations. We now investigate the neutralization sensitivity of variants containing the non-RBD mutation Q677H, including B.1.525 (Nigerian isolate) and Bluebird (U.S. isolate) variants. The effect on neutralization of Q677H was determined in the context of the RBD mutations and in the background of major VOCs, including B.1.1.7 (United Kingdom, Alpha), B.1.351 (South Africa, Beta), and P1-501Y-V3 (Brazil, Gamma). We demonstrate that the Q677H mutation increases viral infectivity and syncytium formation, as well as enhancing resistance to neutralization for VOCs, including B.1.1.7 and P1-501Y-V3. Our work highlights the importance of epistatic interactions between SARS-CoV-2 spike mutations and the continued need to monitor Q677H-bearing VOCs.

IMPORTANCE SARS-CoV-2, the causative agent of COVID-19, is rapidly evolving to be more transmissible and to evade acquired immunity. To date, most investigations of SARS-CoV-2 variants have focused on RBD mutations. However, the impact of non-RBD mutations and their synergy with studied RBD mutations are poorly understood. Here, we examine the role of the non-RBD Q677H mutation arising in many SARS-CoV-2 lineages, including VOCs. We demonstrate that the Q677H mutation enhances viral infectivity and confers neutralizing antibody resistance, particularly in the background of other SARS-CoV-2 VOCs. KEYWORDS Q677H, SARS-CoV-2, spike, neutralization, variant of concern S evere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve into new variants of concern (VOCs) with increased transmissibility, pathogenesis, and vaccine resistance (1). Such mutations can have drastic effects on viral spread, as illustrated by the D614G mutation, which emerged early in the pandemic and is now present in nearly all circulating SARS-CoV-2 strains (2, 3). As global vaccination efforts are under way, monitoring the immune escape of VOCs remains a critical priority. Neutralizing antibodies, or antibodies that directly block virus entry (4), are a key measure of protection against SARS-CoV-2 (5-7). Given that neutralizing antibodies often target the receptor binding domain (RBD) (8), recent studies on neutralizing antibody escape by VOCs, including the rapidly spreading B.1.1.7 (United Kingdom, Alpha), B.1.351 (South Africa, Beta), B.1.429 (United States), and P1 (P1-501Y-V3, Brazil, Gamma) variants (9)(10)(11)(12)(13), have focused on mutations in the RBD, including E484K, N501Y, and L452R, which have been shown to decrease the efficacy of mRNA vaccines to VOCs (14,15).
In comparison, emerging B.1.525 (Nigeria) and Bluebird (United States) variants containing Q677H have received less attention, despite maintaining a strong prevalence in some parts of the United States, especially the Midwest and Southeast areas, as well as Nigeria (16)(17)(18). Both the B.1.525 and Bluebird variants harbor a key S1 non-RBD mutation, Q677H, with the B.1.525 variant also possessing the E484K RBD mutation (Fig. 1a). Importantly, the Q677H mutation is also present in some isolates of VOCs, including B.1.1.7, B.1.351, and P1 (19). The possible role of Q677H in modulating viral infectivity and SARS-CoV-2 sensitivity to antibody neutralization is currently unknown, a particular concern if it emerges in an existing VOC. Here, we examine the infectivity and neutralization of non-RBD Q677H-bearing variants and define its synergistic effects in the context of key RBD mutations.
Q677H enhances resistance to neutralizing antibodies. To examine neutralizing activity against SARS-CoV-2 variants, we utilized our previously reported intron-Gaussia luciferase-bearing lentiviral pseudotype-based neutralization assay (20) (see Text S1 in the supplemental material). We first determined the neutralizing activity of sera from 9 intensive care unit (ICU) COVID-19 patients and 9 hospitalized non-ICU patients against SARS-CoV-2 USA-WA1/2020 (wild type [WT]), D614G, and a panel of variants harboring the Q677H mutation ( Fig. 1a to c). Sera were collected from both groups at least 14 days after symptom onset. For all neutralization assays, pseudotyped viruses were adjusted to comparable infectivity prior to neutralization-to prevent variations in infectivity from affecting virus neutralization. Notably, the single D614G mutant showed an increase in 50% neutralization titer (NT 50 ) compared to WT ( Fig. 1b and c), likely because the D614G mutation stabilizes the "open" (RBD-exposed) spike conformation (21). The Bluebird and B.1.525 variants exhibited ;2.2-fold (P , 0.01)-and ;3.6-fold (P , 0.01)-reduced NT 50 , respectively, compared with D614G for ICU patient samples (Fig. 1b), while non-ICU samples showed ;2.6-fold (P , 0.01)-reduced NT 50 for B.1.525 with only ;10% reduction for Bluebird (Fig. 1c), likely due to the ;8.7-fold-lower titer of the non-ICU samples or variations in disease state at time of serum collection.
Given the impact and epistasis of the non-RBD mutation Q677H on infectivity and neutralization escape, we hypothesized that it may induce conformational changes in the spike protein. To test this, we performed virus neutralization in the presence of an RBD-binding monoclonal antibody, 2B04 (22), which is known to bind the receptor binding motif of the RBD and serves as a conformation-dependent antibody. 2B04 exhibited an ;50% reduction in neutralization of Q677H relative to WT and of Q677H/D614G relative to D614G (Fig. 2c), potentially indicating an alteration to RBD conformation. Unsurprisingly, spike proteins bearing the E484K mutation in the epitope of 2B04 (22) were not neutralized by 2B04 (Fig. 2c).
Moderna versus Pfizer neutralization of Q677H-containing variants. We compared the effects of age-matched Moderna and Pfizer mRNA vaccines on neutralization of all variants used in this study, including VOCs ( Fig. 2d and e). Overall, the Moderna vaccine induced an ;52.7% higher NT 50 than did the Pfizer vaccine ( Fig. 2d; P , 0.001). In fact, the Moderna vaccine outperformed the Pfizer vaccine against each of the viruses tested in this study, in particular B.1.525, B.1.351, and P1 (P , 0.01) (Fig. 2e).
Discussion. Although the non-RBD mutation Q677H alone in SARS-CoV-2 spike led to only modest neutralization resistance, it increased viral infectivity and syncytium formation and, importantly, had an epistatic effect when paired with certain emerging RBD mutations present in VOCs. Q677 is situated in a disordered region near the critical RRAR furin-cleavage site of SARS-CoV-2 spike (16). Thus, it is possible that Q677H might alter protease processing or spike conformation, as suggested by the increased syncytium formation and reduced neutralization by 2B04 of the D614G/Q677H spike compared to D614G; however, no dramatic effect of Q677H on furin cleavage was observed. It is possible that the effect of Q677H is masked by the presence of other mutations, including D614G. Future structural studies are required to determine the exact mechanisms by which Q677H impacts infectivity and spike conformation.
In this study, we found that the E484K mutation had a greater impact on neutralization by convalescent-phase (;3.8-fold decrease) compared with vaccinee (;2fold decrease) sera, consistent with recent reports (14). Moreover, we found that Q677H increased the infectivity and neutralizing antibody resistance of B.1.1.7 and P1 spike. These conclusions are further strengthened by the neutralization profiles of K484E and H677Q reversion mutants made in the backbone of B.1.525 and Bluebird variants, where a modest effect was observed for Q677H mutants compared to K484E (Fig. S2). These findings are critical as SARS-CoV-2 VOCs continue to evolve to increase their transmissibility and resistance to vaccinee sera, including the Delta variants (2,(23)(24)(25). Interestingly, we did not find increased infectivity and neutralizing antibody resistance for Q677H in the context of the B.1.351 variant, which could be due to its preexisting strong resistance to neutralization (23) or due to the presence of other compensatory mutations. Overall, our findings underscore the need to better understand epistatic interactions between RBD and non-RBD mutations in the spike as SARS-CoV-2 evolves in the face of new immunologic challenges.