Immunity to worrying SARS-CoV-2 variants

Candidate vaccines based on the peak, the essential glycoprotein for entry into the host cell by severe acute respiratory syndrome of coronavirus 2 (SARS-CoV-2), were being designed days after their reported sequence in January 2020. All vaccines target prevent disease primarily (but not exclusively) by inducing neutralizing antibodies that block the peak and therefore prevent the ability of SARS-CoV-2 to infect cells. The 95% efficacy of the messenger RNA (mRNA) vaccine BNT162b2 (from Pfizer / BioNTech) announced a series of results that show that the increase in neutralizing antibodies is strongly correlated with disease protection in clinical trials of various vaccines. Currently, there is concern about the reduction of immunological protection induced by the vaccine for emerging variants that have mutations in the peak protein. On page 1152 of this issue, Muik et al. (1) found reduced induction of neutralizing antibodies to BNT62b2. However, it is likely that there will be sufficient effectiveness remaining to provide protection against symptomatic diseases.

Coronaviruses are very large and complex compared to other RNA viruses (about four times the size of the hepatitis A virus genome), and therefore their replication fidelity must be increased. Despite this, since a pathogen can infect more than 100 million people, it is not surprising that sequence variants appear with a selective advantage. In late 2020, when regulators were granting approvals for a series of vaccines based largely on the wild-type “peak Wuhan” sequence antigen, several “worrying variants” of SARS-CoV-2 were detected. These variants have potentially improved transmission, pathogenicity, immune escape, or a combination of all three.

The first strings of a concern variant that emerged in the UK, B.1.1.7 (also called 501Y.V1), appeared in September 2020. It includes eight amino acid changes within the peak. One of these, N501Y (Asn⁵⁰¹→ Tyr), increases the peak affinity for its target cell angiotensin-converting enzyme 2 (ACE2) and, together with other less well characterized mutations, resulted in improved transmission (recognized since December) and possibly greater pathogenicity. Could this variant also escape antibody-mediated immunity? Muick et al. examined the immune sera ability of 40 older or younger two-dose BNT162b2 vaccine recipients to neutralize a pseudotype virus (a safe substitute virus designed to express peak) carrying a wild-type or all B-peak peak .1.1.7 mutations. The sera had a wide range of neutralizing antibody titers measured against the wild-type peak, from about 1/50 to about 1/1200. Although there was a significant reduction in mean geometric titers for the youngest (though not the oldest) cohort against variant B.1.1.7, the authors argue that, based on our knowledge of other respiratory viruses, such as the influenza, an overall reduced titer analysis of about 20% would not be expected to significantly reduce the vaccine’s effectiveness. However, such findings confirm that peak B.1.1.7 mutations affect not only transmission, but also immune recognition.

Another study analyzed in considerable detail the potential escape of the vaccine by B.1.1.7 (two) They considered immune sera from 23 vaccinees with an average age of 82, analyzed 3 weeks after a single dose of BNT162b2. The use of a peak-carrying virus pseudotype with all eight mutations led to a six-fold reduction in neutralization for most sera. In this older cohort, the ablation of functional neutralization was more apparent in those who started with lower antibody titers for the peak of the wild-type sequence. A parallel data set for neutralizing the wild type or peak B.1.1.7 sequence pseudotype by vaccinated sera from mRNA-1273 (Moderna) or NVX-CoV2373 (Novavax) detects a more marginal reduction in activity against the variant (3)

When population variation may mean that people develop several neutralizing antibody titers after vaccination, the extent to which a small drop in neutralization threatens protection against symptomatic diseases depends to some extent on the immunogenicity of the vaccine and how much margin it leaves for protection. This problem is beginning to be solved through analyzes of vaccinated ChAdOx1 nCoV-19 (University of Oxford / AstraZeneca) in the United Kingdom (4) Although the titer of neutralizing antibodies against B.1.1.7 was reduced by approximately nine times (from an average of about 1/500 of the titer of neutralizing antibodies against the wild-type virus), this did not affect the effectiveness of the vaccine because there was no increased susceptibility to infection [as determined with polymerase chain reaction (PCR) testing] attributable to the variant among the 499 participants who were infected.

Although variant B.1.1.7 has had a massive impact on the exacerbation of the number of cases and severity in many countries, there is an even greater concern about variants that carry additional immune avoidance mutations, notably the E484K (Glu⁴⁸⁴→ Lys) mutation found in variant B.1.351 (501Y.V2) that emerged in South Africa, variant P.1 found in Brazil and sporadic UK sequencing examples showing E484K in the background B.1.1.7 (5) That immune avoidance mutations – K417N (Lys⁴¹⁷→ Asn), E484K and N501Y – may appear in in vitro evolution experiments involving the culture of SARS-CoV-2 in the presence of immune sera offers caution against sub-optimal vaccination regimes (6)

The concern with variant B.1.351 derives from analyzes of its effects on the neutralization activity. The variant shows substantial ablation of any therapeutic monoclonal antibody (mAbs) neutralizing activity (7) Preliminary data suggest a reduced neutralizing response in the serum of vaccinated ChAdOx1 nCoV-19 and reduced efficacy in preventing mild to moderate COVID-19 (8) This supports the view that the neutralizing antibody titer is the key correlate of protection (CoP). Although analysis based on the loss of neutralizing activity in vitro by individual mAbs that represent the three dominant epitope classes at the peak offers strong evidence of immune evasion by the variants, the effect is less pronounced on the level of polyclonal immune serum after convalescence or vaccination. This suggests that the neutralizing repertoire is broader and more resistant than documented so far.

The findings of studies with mAbs offer caution when using them therapeutically, given their vulnerability to loss of individual epitopes and also their ability to drive the selection of variants that may escape immune recognition. Of course, the flip side of this argument is that detailed mapping of neutralizing antibody epitopes at the peak can facilitate the design of neutralizing vaccines and mAbs that can target multiple peak mutants (9) It has been postulated that SARS-CoV-2 may continue to accumulate mutations that prevent immune responses (10) But, as previously explored for other viruses, such as HIV, immune evasion often has a biological fitness cost for the virus, tending to impose an upper limit on the number of mutations that can be provided when confronted with a wide repertoire of neutralizing antibodies (11)

Furthermore, given that similar mutations recur at peak, presumably through convergent evolution in geographically distinct isolates, it is possible that peak variants that offer a survival advantage to the virus are restricted and finite. In addition, a peak protein that mutates residues A, B and C to avoid antibody recognition runs the structural risk of generating a new neutralizing epitope, D. Therefore, a finite number of iterative vaccines could target the main variants , but this would not necessarily have to be reassessed annually, as is the case with vaccines against the flu virus. Seasonal “common cold” human coronaviruses tend to appear with 2-year cycles, and recent data for one suggests that antigenic drift (mutations that impair immune recognition) may underlie the escape of acquired immunity (12)

T cell immunity is likely to present as an additional CoP against COVID-19 (13) CD4⁺ and CD8⁺ The T-cell response encompasses specificity for several hundred epitopes across the SARS-CoV-2 proteome, most of which are intact in the variants (14, 15) Even those T cell epitopes that are altered in the SARS-CoV-2 variants will, in most cases, bind to different human leukocyte antigen (HLA) molecules that present T cell antigenic peptides, although the affinities of connection can be changed. It would be useful to investigate whether T cell immunity is modified by SARS-CoV-2 variants.

The evaluation of variants in neutralization is complicated by the variability of the pseudotype assays used in these studies. It would be useful to have standardized in vitro neutralization assays for live viruses as internationally comparable benchmarks. As always, these are discussions that must be tied to some sense of CoP values. Although much debated, many researchers feel that people with a neutralizing IC antibody₅₀ (half of the maximum inhibitory concentration) greater than 1/100 the serum dilution would probably be protected against infection or, at least, against symptomatic infection. Since these are highly potent vaccines that often induce neutralizing antibody responses with HF₅₀ of at least 1/1000, it is expected that there is a reasonable safety margin before reduced variant recognition means that effective protection is lost (see figure). Ultimately, the best defense against the emergence of other worrying variants is a rapid, global vaccination campaign – in conjunction with other public health measures to block transmission. A virus that cannot transmit and infect other people has no chance of mutating.