Immune Imprinting, Comirnaty and Omicron (part 2)

More details emerge on why the mRNA vaccines are not preventing Omicron infection

Recently a series of high profile, “fully vaccinated” (four dose) pro-vaccine mandate politicians and bureaucrats have developed COVID-19 disease. In Part 1 of this two part series, a wide range of both primary data and mostly peer-reviewed academic publications relating to SARS-CoV-2 Omicron variant “breakthrough infections” were reviewed, multiple working hypotheses for what might be the cause of “negative effectiveness” of the genetic vaccines were described, and one of the hypotheses with the strongest supporting data (“Immune imprinting”) was discussed. This discussion was structured around the introductory section and references cited in a peer reviewed manuscript published in Science magazine, entitled:

Immune boosting by B.1.1.529 (Omicron) depends on previous SARS-CoV-2 exposure

Catherine J Reynolds, Corinna Pade, Joseph M Gibbons et al, Science, June 14 2022 doi: 10.1126/science.abq1841

This is not an easy paper, although not as challenging as the 17 June, 2022 Nature pre-print titled “BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection” which was briefly reviewed here. The Reynolds et al Science paper is well structured, with clearly labeled subsections throughout the overall results section, key findings of which will be briefly summarized below.

Results

B cell immunity after three vaccine doses

Health care workers (HCW) were identified with mild and asymptomatic SARS-CoV-2 infection by ancestral Wuhan Hu-1, B.1.1.7 (Alpha VOC), B.1.617.2 (Delta VOC) and then B.1.1.529 (Omicron VOC) during successive waves of infection and after first, second and third mRNA (BioNTech BNT162b2) vaccine doses. By three vaccine doses antibody responses had plateaued, regardless of infection history. We found differences in immune imprinting indicating that those who were infected during the ancestral Wuhan Hu-1 wave showed a significantly reduced anti-RBD (receptor binding domain) titer against B.1.351 (Beta), P.1 (Gamma) and B.1.1.529 (Omicron) compared to infection-naïve HCW.

Simplifying, if you were first infected with Wuhan Hu-1, then vaccinated, then infected with Omicron, your antibody levels against the important part of Spike (the receptor binding domain) were lower than those who had not been infected.

Memory B cell (MBC) frequency against ancestral Wuhan Hu-1, B.1.617.2 (Delta) and B.1.1.529 (Omicron) S1 (the extracellular part of Spike that includes the RBD) protein was boosted 2-3 weeks after the third vaccine dose compared to 20-21 weeks after the second vaccine dose. Irrespective of infection history, the MBC frequency against Wuhan Hu-1 and B.1.617.2 (Delta) S1 were similar, but significantly reduced against B.1.1.529 (Omicron) S1 2-3 weeks after the third vaccine dose and at 20-21 weeks after the second dose. Differences between VOC (variant of concern) RBD and whole spike binding and nAb (neutralizing antibody) IC50 with live virus indicated that antibody targeting regions outside RBD/spike or conformational epitopes exposed only during infection may contribute to neutralization.

Memory B cells are what gives rise to future ability to develop antibodies. MBC frequency is an indirect indicator of long term protection. The numbers of MBC capable of producing antibodies reactive against Spike S1 subunit were increased by a third injection relative to two injections, regardless of whether or not the patient was previously infected, but in the case of Omicron, these levels dropped after either two or three doses of vaccine. These effects were independent of prior virus infection history. Which is more evidence of immunologic escape of Omicron from B-cell mediated (antibody) control.

T cell immunity after three vaccine doses

We next compared T cell responses in triple-vaccinated HCW 2-3 weeks after the third dose, who were either infection- naïve or had been infected during the Wuhan Hu-1, B.1.1.7 (Alpha) or B.1.617.2 (Delta) waves. … for S1 B.1.1.529 (Omicron) protein we found a significantly reduced magnitude of response. Overall, more than half (27/50; 54%) made no T cell response against S1 B.1.1.529 (Omicron) protein, irrespective of previous SARS-CoV-2 infection history, compared to 8% (4/50) that made no T cell response against ancestral Wuhan Hu-1 S1 protein.

This is problematic. Half failed to generate T cells to Omicron. T cells are major contributors to the protection, and generating both B and T cell responses is the whole reason to use an mRNA vaccine.

To investigate T cell recognition of VOC (variant of concern) sequence mutations, we used a peptide pool specifically designed to cover all of the B.1.1.529 (Omicron) S1 and S2 spike mutations and a matched pool containing the Wuhan Hu-1 equivalent sequences. T cell responses against the B.1.1.529 (Omicron) peptide pool were reduced compared to the Wuhan Hu-1 pool, irrespective of previous infection history [fold-reduction in T cell response against B.1.1.529 (Omicron) peptide pool compared to equivalent ancestral Wuhan Hu-1 peptide pool was 2.7-fold for infection-naïve, 4.6-fold for previously Wuhan Hu-1 infected, 2.7-fold for previously B.1.1.7 (Alpha) infected and 3.8-fold for previously B.1617.2 (Delta) infected. In fact, 42% (21/50) of HCW make no T cell response at all against the B.1.1.529 (Omicron) VOC mutant pool. Overall, our findings in triple-vaccinated HCW with different previous SARS-CoV-2 infection histories indicated that T cell cross-recognition of B.1.1.529 (Omicron) S1 antigen and peptide pool was significantly reduced.

Not good. A large fraction of fully vaccinated (regardless of prior infection history) do not make good T cell responses. So now we have evidence suggesting both poor B and poor T responses to Omicron, or in other words Omicron has evolved to escape both B and T cell adaptive immunity (relatively speaking, compared to other variants).

But why and how?

B.1.1.529 (Omicron) spike mutations encompass gain and loss of T cell epitopes

Immunizing HLAII transgenic mice with either ancestral Wuhan Hu-1 or B.1.1.529 (Omicron) sequence specific peptide pools allowed us to investigate differential, sequence-specific T cell priming that occurs as a consequence of B.1.1.529 (Omicron) spike mutations. We showed that priming with one pool resulted in impaired responses to the other.

The G142D/del 143-5 mutation created a gain of function epitope, switching from a region not recognized by T cells, to one that induced a Th1/Th17 effector program. We have previously shown that the N501Y mutation converts a T cell effector-stimulating epitope to an inducer of immune regulation.

B cell immunity after B.1.1.529 (Omicron) infection

Next, we studied triple-vaccinated HCW 14-weeks after their third dose, who had suffered breakthrough infection during the B.1.1.529 (Omicron) wave. Previously infection-naïve triple-vaccinated HCW made significantly increased cross-reactive antibody binding responses against all VOC and B.1.1.529 (Omicron) itself after infection during the B.1.1.5129 (Omicron) wave: S1 RBD, whole spike and nAb IC50. However, antibody binding and nAb IC50 were attenuated against B.1.1.529 (Omicron) itself with a 4.5-fold reduction in S1 RBD binding (p = 0.001) and 10.1-fold reduction in nAb IC50 (p = 0.002) against B.1.1.529 compared to ancestral Wuhan Hu-1. Thus, infection during the B.1.1.529 (Omicron) wave produced potent cross-reactive antibody immunity against all VOC, but less so against B.1.1.529 (Omicron) itself. Importantly, triple-vaccinated, infection-naïve HCW that were not infected during the B.1.1.529 (Omicron) wave made no nAb IC50 response against B.1.1.529 (Omicron) 14 weeks after the third vaccine dose indicating rapid waning of the nAb IC50.

Omicron infection boosted immunity to prior strains in triple vaccinated HCW, but not so much against itself. For the triple vaccinated HCW who had not been infected by prior viral strains including Omicron, the neutralizing antibodies against Omicron were rapidly lost after third vaccination.

HCW with a history of prior Wuhan Hu-1 infection that were also infected during the B.1.1.529 (Omicron) wave showed no increase in cross-reactive S1 RBD or whole spike antibody binding or live virus nAb IC50 against B.1.1.529 (Omicron) or any other VOC, despite having made a higher N antibody response. Thus, B.1.1.529 (Omicron) infection can boost binding and nAb responses against itself and other VOC in triple-vaccinated previously uninfected infection naïve HCW, but not in the context of immune imprinting following prior Wuhan Hu-1 infection. Immune imprinting by prior Wuhan Hu-1 infection completely abrogated any enhanced nAb responses against B.1.1.529 (Omicron) and other VOC.

Basically, if the HCW were first infected by the original Wuhan strain (as I was), they do not make an increased neutralizing antibody response after Omicron infection (compared to those who are triple vaccinated but not previously infected by the original Wuhan strain). So, prior infection by Wuhan seems to block production of neutralizing antibody responses during/after Omicron infection. And that is pretty much proof of the immune imprinting effect.

In summary, B.1.1.529 (Omicron) infection resulted in enhanced, cross-reactive Ab responses against all VOC tested in the three-dose vaccinated infection-naïve HCW, but not those with previous Wuhan Hu-1 infection, and less so against B.1.1.529 (Omicron) itself.

So, we have immune imprinting with B cell/antibody responses, what about T cell responses?

T cell immunity after B.1.1.529 (Omicron) infection

We next explored T cell immunity following breakthrough infection during the B.1.1.529 (Omicron) wave. Fourteen weeks after the third dose (9/10, 90%) of triple-vaccinated, previously infection-naïve HCW showed no cross-reactive T cell immunity against B.1.1.529 (Omicron) S1 protein.

Post vaccination, rapid loss of any detectable T cell immunity against S1, which is the main antigen in the vaccines. Not good.

HCW infected during the B.1.1.529 (Omicron) wave showed similar T cell responses against spike MEP, ancestral Wuhan Hu-1 S1 and B.1.617.2 (Delta) S1 proteins, but significantly reduced T cell responses against B.1.1.529 (Omicron) S1 protein.

Although breakthrough infection in triple-vaccinees during the Omicron infection wave boosted cross-reactive T cell immune recognition against the spike MEP pool (p = 0.0117), ancestral Wuhan Hu-1 (p = 0.0039), B.1.617.2 (Delta) (p = 0.0003) and B.1.1.529 (Omicron) , the T cell response against B.1.1.529 (Omicron) S1 protein itself compared to spike MEP (p = 0.001), Wuhan Hu-1 (p = 0.001), and B.1.617.2 (Delta) (p = 0.001) was significantly reduced.

Fully vaccinated but post infection with Omicron, significantly reduced T cell responses against Omicron S1 protein, but still boosted responses to the preceding strains. This is basically a set up for either chronic Omicron infection or rapid Omicron re-infection.

Importantly, none (0/6) of HCW with a previous history of SARS-CoV-2 infection during the Wuhan Hu-1 wave responded to B.1.1.529 (Omicron) S1 protein (Fig. 5A). This suggests that, in this context, B.1.1.529 (Omicron) infection was unable to boost T cell immunity against B.1.1.529 (Omicron) itself; immune imprinting from prior Wuhan Hu-1 infection resulted in absence of a T cell response against B.1.1.529 (Omicron) S1 protein.

The findings show consistently that people initially infected by Wuhan Hu-1 in the first wave and then reinfected during the B.1.1.529 (Omicron) wave do not boost T cell immunity against B.1.1.529 (Omicron) at the level of nAb and T cell recognition.

In these HCW, if you were infected with the original Wuhan strain, then vaccinated, then reinfected with Omicron you do not make good neutralizing antibody or T cell responses to Omicron. Very bad news. Yet more evidence for initial immune imprinting reinforced by repeated vaccination with the original Wuhan virus-derived spike mRNA vaccine causing an inability to respond to Omicron. Really sounds like these sorts of patients may become the breeding ground for the next wave of Omicron variants.

Prior infection differentially imprints Omicron T and B cell immunity

To investigate in more detail the impact of prior SARS-CoV-2 infection on immune imprinting, we further explored responses in our longitudinal HCW cohort. We looked initially at the S1 RBD (ancestral Wuhan Hu-1 and Omicron VOC) antibody binding responses across the longitudinal cohort at key vaccination and SARS-CoV-2 infection timepoints, exploring how different exposure imprinted differential cross-reactive immunity and durability. This revealed that at 16-18 weeks after Wuhan Hu-1 infection or B.1.1.7 (Alpha) infection, unvaccinated HCW showed no detectable cross-reactive S1 RBD binding antibodies against B.1.1.529 (Omicron).

In other words, Omicron has evolved to completely evade any antibodies generated from natural infection by either the original Wuhan or the Alpha strains.

Hybrid immunity (the combination of prior infection and a single vaccine dose) significantly increased the S1 RBD binding antibodies against B.1.1.529 (Omicron) (p < 0.0001) compared to responses of infection-naïve HCW, which were undetectable after a single vaccine dose. This increase was significantly greater for prior Wuhan Hu-1 than B.1.1.7 (Alpha) infected HCW.

Good news. Prior infection with either original Wuhan or Alpha strains, followed by a single mRNA dose, resulted in detectable antibodies to Omicron, although this worked better if you were first infected with the original Wuhan rather than the Alpha strain.

However, 20-21 weeks after the second vaccine dose, differential B.1.1.529 (Omicron) RBD Ab waning was noted with almost all (19/21) of the HCW infected during the second B.1.1.7 (Alpha) wave no longer showing detectable cross-reactive antibody against B.1.1.529 (Omicron) RBD.

Oops. One dose of the mRNA vaccine after natural infection is good. Two doses not good.

This indicates a profound differential impact of immune imprinting on B.1.1.529 (Omicron) specific immune antibody waning between HCW infected by Wuhan Hu-1 and B.1.1.7 (Alpha) as this differential is not seen in Ab responses to ancestral WuhanHu-1 spike S1 RBD.

Fourteen weeks after the third vaccine dose previously infection-naïve HCW infected during the B.1.1.529 (Omicron) wave showed increased S1 RBD B.1.1.529 (Omicron) binding responses, but prior Wuhan Hu-1 infected HCW did not, indicating that prior Wuhan Hu-1 infected individuals were immune imprinted to not boost antibody binding responses against B.1.1.529 (Omicron) despite having been infected by B.1.1.529 (Omicron) itself.

Three doses of mRNA vaccine in people never infected with virus shows antibody production against Omicron spike protein, but not if the HCW were previously infected with the original Wuhan strain first.

In fact, infection during the B.1.1.529 (Omicron) wave imprinted a consistent relative hierarchy of cross-neutralization immunity against VOC across different individuals with potent cross-reactive nAb responses against B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta) (Fig. 6, D and E). Comparative analysis of nAb potency for cross-neutralization of VOC emphasized the impact of immune imprinting which effectively abrogates the nAb responses in those vaccinated HCW infected during the first wave and then reinfected during the B.1.1.529 (Omicron) wave.

If the HCW were first infected by the Wuhan strain, then vaccinated, then reinfected with Omicron, the immune imprinting associated with being first infected and then vaccinated pretty much destroyed their ability to respond effectively to Omicron.

Yes, Virginia, forcing HCW who were previously infected with Wuhan strain to take three doses of the mRNA vaccine actually pretty much destroyed their ability to mount a potent immune response against Omicron.

Unresolved is whether those fully vaccinated people who land in the hospitals and/or die from Omicron were first infected with another strain prior to becoming fully vaccinated.

What do the authors conclude about all of this?

Discussion

Molecular characterization of the precise mechanism underpinning repertoire shaping from a combination of Wuhan Hu-1 or B.1.1.7 (Alpha) infection and triple-vaccination using ancestral Wuhan Hu-1 sequence, impacting immune responses to subsequent VOCs, will require detailed analysis of differential immune repertoires and their structural consequences. The impact of differential imprinting was seen just as profoundly in T cell recognition of B.1.1.529 (Omicron) S1, which was not recognized by T cells from any triple-vaccinated HCW who were initially infected during the Wuhan Hu-1 wave and then re-infected during the B.1.1.529 (Omicron) wave. Importantly, while B1.1.529 (Omicron) infection in triple-vaccinated previously uninfected individuals could indeed boost antibody, T cell and MBC responses against other VOC, responses to itself were reduced. This relatively poor immunogenicity against itself may help to explain why frequent B.1.1.529 (Omicron) reinfections with short time intervals between infections are proving a novel feature in this wave. It also concurs with observations that mRNA vaccination carrying the B.1.1.529 (Omicron) spike sequence (Omicron third-dose after ancestral sequence prime/boosting) offers no protective advantage.

In summary, these studies have shown that the high global prevalence of B.1.1.529 (Omicron) infections and reinfections likely reflects considerable subversion of immune recognition at both the B, T cell, antibody binding and nAb level, although with considerable differential modulation through immune imprinting. Some imprinted combinations, such as infection during the Wuhan Hu-1 and Omicron waves, confer particularly impaired responses.

And we continue to have the government advise that all of our children, most of whom have already been infected and have cleared the virus with very little problem, should get vaccinated?

These data may help explain the negative effectiveness being observed with “full” mRNA vaccination in those who have been infected by Omicron.

For example, please see the latest clinical data from Canada and Portugal.