Research Review: COVID-19 mRNA Vaccine Immune Responses

Introduction

Conventional/historical vaccine design

Classically, vaccine design has been predicated on what is termed forward vaccinology, where surrogates of natural infection (e.g., killed pathogens, attenuated strains, toxoids, or protein subunits), have generated highly successful vaccines. Indeed, scourges, such as smallpox, polio, and measles that plagued humanity for millennia either have been rendered exceedingly uncommon or have, by-in-large, been eradicated and swept into the dustbin of history. Although cell-mediated responses (Th1) are almost definitely a component of traditional vaccines, the forward vaccinology gold standard correlate of vaccine protective efficacy is the generation of functional antibodies.

Need for new modalities

Success with traditional design strategies notwithstanding, the list of FDA-approved vaccines against human viruses is surprisingly short. Nontraditional, new technological approaches, such as mRNA-based strategies and reverse vaccinology, promise to augment the vaccine arsenal (Sharma S et al, 2019; Jackson NAC et al, 2020; Reichmuth AM et al, 2016).

COVID-19 and the rise of mRNA vaccines

Although the concept of mRNA vaccines dates back to the previous century (Ying H et al, 1999), 2020 saw mRNA vaccines abruptly thrust into the limelight because of the emergence of COVID-19, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

mRNA vaccines that have been designed to address COVID-19

Two mRNA vaccines, COMIRNATY^® (BNT162b2), which is made by Pfizer and BioNTech, and Spikevax^® (mRNA-1273), which is made by Moderna, have had their BLAs approved by the United States Food and Drug Administration but are still being manufactured and administered under Emergency Use Authorization status.

Immune responses generated by COVID-19 mRNA vaccines

Innate immune responses

The first step toward immunogenicity begins with the innate immune system. After injection and uptake by the myocyte, it is postulated that the antigen is transferred via a cross priming mechanism to bone marrow-derived antigen presenting cells that then induce MHC class-I restricted CD8⁺ T cells (Lazzaro S et al, 2015) in the periphery and in germinal centers (GCs). A certain portion of the vaccine must directly find its way to the lymph nodes as GCs contain vaccine mRNA and spike antigen up to 8 weeks postvaccination (Röltgen K et al, 2022).

The BNT162b2 SARS-CoV-2 mRNA vaccine modulates both monocytes and natural killer (NK) cells, the two main populations that are responsible for innate immune responses to pathogens. It has been shown that vaccination significantly increased: 1) classical and intermediate inflammatory monocytes, 2) CD56^bright, CD56^dim, and CD56^dim/CD16^dim NK cells, and 3) IFN-γ+ production as well as perforin and granzyme content by NK cells (Saresella M et al, 2022).

The innate immune response in response to vaccination likely is very different than that which occurs during an actual COVID-19 infection for the following reasons:

• Positron-emission tomography scans of recently mRNA vaccinated people showed what was described as an increased acute inflammatory reaction in deltoid muscle followed by immune reaction in the lymph nodes linked to humoral immunity (Kubota K et al, 2022).
• Viral single-stranded mRNA is inherently immunogenic as it is a pathogen-associated molecular pattern molecule that is detected by endosomal Toll-like receptors TLR7 and TLR8 (Zhang Z et al, 2016; Tanji H et al, 2015). However, modified RNAs have nonatural bases, such pseudouridine (Karikó K et al, 2008; Carlile TM et al, 2014) and 1-methylpseudouridine (Andries O et al, 2014) that facilitate translation but attenuate immunogenicity (Karikó K et al, 2011; Karikó K et al, 2008; Kariko K et al, 2008) and prevent the activation of TLR7, TLR8 and other innate immune sensors (Anderson BR et al, 2010; Anderson BR et al, 2011).
• COVID-19 mRNA vaccines disrupt and do not elicit immune responses through Type I interferon signaling, which has been demonstrated to be very important to overcoming COVID-19 infections (Seneff S et al, 2022).

Adaptive immune responses

T-cell -generated responses mRNA vaccines

COVID-19 mRNA vaccines have been shown to be capable of producing antigen protein along with concomitant innate immune responses that prime both CD8⁺ and CD4⁺ T-cells to differentiate into effector and memory subsets (Teijaro JR et al, 2021). Moreover, circulating spike protein-specific follicular helper T-cells (T_FH) cells, which represent a specialized subset of CD4⁺ T cells that provide critical signals for B cell maturation (Pardi N et al, 2018), correlate with neutralizing antibodies and increase during early convalescence (Boppana S et al, 2021). T_FH cells peak one week after the second immunization and are maintained for at least another six months (Mudd PA .et al, 2022); it remains to be deciphered how long spike protein-specific T_FH cells persist after vaccination.

Antibody-generated responses to mRNA vaccines

The importance of sustained humoral immunity is widely recognized, and with regard to established vaccines, humoral antiviral responses are extraordinarily stable (Amanna IJ et al, 2007) as many vaccines exhibit only a 5% to 10% yearly decrease in the neutralizing antibody levels (Davidkin I et al, 2008; Seagle EE et al, 2018). However, as shown in Table 1, the humoral responses generated in response to the COVID mRNA vaccination have not reached this level of durability.

Duration of antibody responses elicited by COVID-19 mRNA vaccines compared to established vaccines. EBV = Epstein-Barr virus; VZV = Varicella zoster virus. 1. Values were obtained from Amanna IJ et al, 2007. 2. Values were obtained from Shrotri M et al, 2021. 3. Values were obtained from Doria-Rose N et al, 2021 using an exponential decay model. 4. All binding antibodies. 5. Pseudovirus neutralization. 6. Live virus neutralization

The humoral response in response to mRNA vaccination likely is considerably different than that which occurs during an actual COVID-19 infection for the following reasons:

• In recovered individuals, both IgG and neutralizing antibody levels decrease only modestly at 8 to 10 months after the infection (Dan JM et al, 2021; Vanshylla K et al, 2021). In contrast, vaccine plasma and saliva spike and RBD-specific IgG concentrations decrease from their peak values by approximately 20-fold by 9 months after primary vaccination (Röltgen K et al, 2022).
• There is substantially lower incidence of breakthrough infection among previously infected persons than among vaccinated persons (Anderson M et al 2021; Hall VJ et al, 2021).
• Vaccination is heavily biased toward IgG responses, whereas infection is biased toward IgMs and IgAs. Antibody breadth against viral variants is lower after infection than mRNA vaccines but improves over several months (Röltgen K et al, 2022) and indicates ongoing clonal evolution (Wang Z et al 2021).
• Vaccines have not been demonstrated to generate long-lived plasma cells in a SARS-CoV-2 virus naïve population (Giannotta G. et al, 2021). In contrast, SARS-CoV-2 infection produces a memory compartment consistent with long-term persistence of germinal centers 12 months post infection (Wang Z et al 2021).
• SARS-CoV-2 protein and nucleic acids have been reported to remain in the gut for at least two months after infection (Gaebler C et al, 2021); to date, there is no evidence that COVID vaccine mRNAs or proteins persist in this tissue.
• SARS-CoV-2 spike-specific antibodies induce natural killer cell-mediated antibody-dependent cellular cytotoxicity (ADCC) in patients with natural infection and vaccinated persons. Although found at lower levels, antibodies elicited by natural infection induced a significantly stronger ADCC response compared to those induced by vaccination (Rieke GJ et al, 2022).

IgA — The forgotten immunoglobulin

IgA is the most abundantly produced Ig in humans (66 gm/kg/day) and the most abundant isotype at mucosal sites (Underdown BJ et al, 1998; Vidarsson G et al, 2014). Although not currently a correlate of vaccine protection, IgA production, both in serum and at the mucosa, should be for the following reasons:

• IgA possesses superior anti-viral properties vs. IgG for influenza and for SARS-CoV-2 (Muramatsu et al, 2014; Liew FY et al, 2014; Wang Z et al, 2021; Sterlin D et al, 2021; Chao YX et al, 2020).
• Serum IgA is 7-fold more potent than serum IgG in viral neutralization; temporal changes in circulating IgA+ plasmablasts with mucosal homing potential were detected during infection along with neutralizing IgA in airway fluid and saliva (Sterlin D et al, 2021).
   -Although SARS-CoV-2 spike-specific serum IgA levels decline quickly after infection, local concentrations at mucosal surfaces persist longer and include dimeric isoforms with potent neutralizing capacity, which are 15X greater than monomeric IgA (Wang Z et al, 2021; Sterlin D et al, 2021).
• IgA antibodies have been demonstrated to afford protection from a coronavirus, avian infectious bronchitis (Toro H et al, 1994).

Next generation COVID-19 mRNA vaccines—Back to the future

Limitations of the current COVID-19 mRNA vaccines

COVID-19 mRNA vaccines offered great hope of ending the pandemic as preliminary studies indicated that BNT162b2 was 94% to 95% effective in preventing symptomatic coronavirus COVID-19 7 days or more after receipt of the second dose of vaccine (Polack FP et al, 2020; Dagan N et al, 2021; Haas EJ et al, 2021; Chodick G et al, 2022) and that mRNA-1273 was 94% effective in preventing COVID-19 (Baden LR et al, 2021). Initial promise notwithstanding, as we approach 2023, COVID outbreaks and reinfections are still occurring, new variants are a constant cause of concern, and questions are rapidly accumulating about overall efficacy and potential unanticipated and unaddressed safety issues.

Next generation COVID-19 mRNA vaccines—Following the science

The following features are needed for the development of next-generation vaccines that can address the current set of challenges:

• Application of reverse vaccinology approaches, the central tenet of which is first identifying antigenic proteins and then finding immunodominant B-cell epitopes.
• Prolonged host immunity that both prevents individuals from being infected and from infecting others.
• More accurate recapitulation of an actual infection.
    -mRNA in the form of a self-amplifying construct delivered in a virus-like particle (Biddlecome A et al, 2019).
• True multivalent vaccines that incorporate other COVID-19 proteins, such as the N and M proteins, in addition to the Spike protein.
    -Mitigation against the evolution of new variants that give rise to vaccine resistance as a result of monovalency (Kennedy DA et al, 2018).
    -N proteins of many coronaviruses are highly immunogenic, expressed abundantly during infection (Cong Y et al, 2020), and accumulated fewer mutations over time than other coronavirus proteins (Grifoni A et al, 2020).
    -N antibodies neutralize SARS-CoV-2 intracellularly (Albecka A et al, 2021).
• Bias toward IgA and mucosal immunity.
• Assurance that the mRNA used is not immunogenic (does not generate anti-drug antibodies) and does not generate antibodies that disrupt extracellular RNA and its functionality (Kluever AK et al, 2019).
• Assurance that the antibodies generated are not anti-idiotypic (Murphy WJ et al, 2022).
• Design strategies to minimize GC content and G-quadraplex structures and eliminate nonatural bases in the mRNA (Seneff S et al, 2022).

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