Study: Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity

  • Numerous variants of SARS-CoV-2-harboring mutations in spike have arisen globally
  • mRNA vaccines elicit potent neutralizing activity against homologous pseudovirus
  • Cross-neutralization of strains with receptor-binding domain (RBD) mutations is poor
  • Both RBD and non-RBD mutations mediate escape from vaccine-induced humoral immunity
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Vaccination elicits immune responses capable of potently neutralizing SARS-CoV-2. However, ongoing surveillance has revealed the emergence of variants harboring mutations in spike, the main target of neutralizing antibodies. To understand the impact of these variants, we evaluated the neutralization potency of 99 individuals that received one or two doses of either BNT162b2 or mRNA-1273 vaccines against pseudoviruses representing 10 globally circulating strains of SARS-CoV-2. Five of the 10 pseudoviruses, harboring receptor-binding domain mutations, including K417N/T, E484K, and N501Y, were highly resistant to neutralization. Cross-neutralization of B.1.351 variants was comparable to SARS-CoV and bat-derived WIV1-CoV, suggesting that a relatively small number of mutations can mediate potent escape from vaccine responses. While the clinical impact of neutralization resistance remains uncertain, these results highlight the potential for variants to escape from neutralizing humoral immunity and emphasize the need to develop broadly protective interventions against the evolving pandemic.

Since the first described human infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December of 2019, nine vaccines have been approved for use in humans (Craven, 2021). Two of the vaccines currently in use worldwide, BNT162b2 (manufactured by Pfizer) and mRNA-1273 (manufactured by Moderna), are based on lipid nanoparticle delivery of mRNA encoding a prefusion stabilized form of spike protein derived from SARS-CoV-2 isolated early in the epidemic from Wuhan, China. Both of these vaccines demonstrated >94% efficacy at preventing coronavirus disease 2019 (COVID-19) in phase III clinical studies performed in late 2020 in multiple countries (Polack et al., 2020Baden et al., 2021). However, the recent emergence of novel circulating variants has raised significant concerns about geographic and temporal efficacy of these interventions. Indeed, more recently completed trials of two adenovirus-based vaccines (AZD1222 from Astrazeneca and JNJ-78436735 from Johnson & Johnson), a nanoparticle-based vaccine (NVX-CoV2373 from Novavax), and an inactivated protein vaccine (Coronavac) have demonstrated reduced overall efficacy (Novavax, 2021AstraZeneca, 2020), and subset analyses suggest marked geographic variation with lower efficacy against mild-to-moderate disease in countries such as South Africa and Brazil, where the epidemic is dominated by variant strains. Taken together, these data suggest that neutralization-resistant variants may have contributed to these outcomes (Cohen, 2021Herper and Branswell, 2021).One of the earliest variants that emerged and rapidly became globally dominant was D614G. While several studies demonstrated that this strain is more infectious (Korber et al., 2020Yurkovetskiy et al., 2020aYurkovetskiy et al., 2020bPlante et al., 2020Zhou et al., 2020Hou et al., 2020), we and others found that sera from convalescent individuals showed effective cross-neutralization of both wild type and D614G variants (Garcia-Beltran et al., 2021Legros et al., 2021Hou et al., 2020). However, recent genomic surveillance in the United Kingdom has revealed rapid expansion of a novel lineage termed B.1.1.7 (also known as VOC-202012/01 or 501Y.V1). B.1.1.7 harbors three amino acid deletions and seven missense mutations in spike, including D614G as well as N501Y in the ACE2 receptor-binding domain (RBD), and has been reported to be more infectious than D614G (Santos and Passos, 2021Galloway et al., 2021Liu et al., 2021). Several studies have demonstrated that convalescent and vaccinee sera cross-neutralize B.1.1.7 variants with only slightly decreased potency, suggesting that prior infection or vaccination with wild-type SARS-CoV-2 may still provide protection against B.1.1.7 variants (Wu et al., 2021Muik et al., 2021Shen et al., 2021Rees-Spear et al., 2021Wang et al., 2021). There have also been reports of SARS-CoV-2 transmission between humans and minks in Denmark with a variant called mink cluster 5 or B.1.1.298, which harbors a two-amino acid deletion and four missense mutations including Y453F in RBD. Concerns relating to ongoing interspecies transmission resulted in the culling of over 17 million Danish minks to prevent further viral spread and evolution (Oude Munnink et al., 2021Oxner, 2020). Another variant that recently emerged in California, United States, designated as B.1.429, contains four missense mutations in spike, one of which is a single L452R RBD mutation. The ability of B.1.1.298 and B.1.429 variants to evade neutralizing humoral immunity from prior infection or vaccination has yet to be determined.Of particular concern is an E484K mutation in RBD, which was previously identified through in vitro selection experiments to escape from monoclonal antibodies (Baum et al., 2020) and was also recently identified through deep mutational scanning as a variant with the potential to evade monoclonal and serum antibody responses (Greaney et al., 2021aGreaney et al., 2021b). Novel variants arising from the B.1.1.28 lineage first described in Brazil and Japan, termed P.2 (with 3 spike missense mutations) and P.1 (with 12 spike missense mutations), contain this E484K mutation, and P.1 in particular also contains K417T and N501Y mutations in RBD. These strains have been spreading rapidly, and both P.2 and P.1 were recently found in documented cases of SARS-CoV-2 reinfection (Paiva et al., 2020Faria et al., 2021Resende et al., 2021Naveca et al., 2021Vasques Nonaka et al., 2021).Of greatest concern has been the emergence of multiple strains of the B.1.351 lineage (also known as 501Y.V2), which were first reported in South Africa and have since spread globally (Tegally et al., 2021). This lineage bears three RBD mutations, K417N, E484K, and N501Y, in addition to several mutations outside of RBD, and several reports have suggested that convalescent and vaccinee sera have decreased cross-neutralization of B.1.351 lineage variants (Wang et al., 2021Wibmer et al., 2021Wu et al., 2021Hu et al., 2021). A key limitation of several of these reports has been the use of single mutations or combinations of mutations that do not naturally occur. Regardless, the emergence of novel variants that appear to escape immune responses has spurred vaccine manufacturers to develop boosters for these spike variants (Jones, 2021).Here, we systematically assessed the neutralization potential of sera from a cohort of individuals who received one or two doses of the BNT162b2 (Pfizer) or mRNA-1273 (Moderna) vaccine against SARS-CoV-2 pseudoviruses that bear spike proteins found on circulating strains. We used our previously described high-throughput pseudovirus neutralization assay (Garcia-Beltran et al., 2021) to quantify neutralization against variants first arising in the United Kingdom (B.1.1.7), Denmark (B.1.1.298), United States (B.1.429), Brazil and Japan (P.2 and P.1), and South Africa (three variants of the B.1.351 lineage), as well as SARS-CoV from the 2002 Hong Kong outbreak and the pre-emergent bat coronavirus WIV1-CoV. We find that although neutralization is largely preserved against many variants, those containing the K417N/T, E484K, and N501Y RBD mutations, namely, P.1 and B.1.351 variants, have significantly decreased neutralization even in fully vaccinated individuals. Individuals that received only a single recent dose of vaccine had weaker neutralization titers overall and did not exhibit detectable neutralization of B.1.351 variants in our assays.Taken together, our results highlight that BNT162b2 and mRNA-1273 vaccines achieve only partial cross-neutralization of novel variants and support the reformulation of existing vaccines to include diverse spike sequences. Ultimately, development of new vaccines capable of eliciting broadly neutralizing antibodies may be necessary to resolve the ongoing pandemic.

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