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About viruses and viral disease

spike protein

An Intranasal SARS-CoV-2 Vaccine Candidate

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by Gertrud U. Rey

There are numerous advantages to administering a vaccine by the intranasal route: it is simple, painless, and does not require special training. The last time I discussed SARS-CoV-2 vaccine candidates for potential intranasal delivery, the idea was still fairly new. However, multiple new studies are now showing that delivery of a SARS-CoV-2 vaccine into the nose induces immune responses that are superior to those observed after delivery into the muscle.

The authors of one such recent study compared the efficacy of a single dose of two different adenovirus-based SARS-CoV-2 vaccine candidates after intramuscular injection to that after administration by the intranasal route. Both vaccines encoded three viral antigens: 1) the full-length S1 domain of the SARS-CoV-2 spike protein, which contains the region that binds to the host cell receptor ACE2; 2) the full-length nucleocapsid protein, which is essential for binding and packaging the viral genome; and 3) a truncated version of the RNA-dependent RNA polymerase (RdRp), the enzyme responsible for copying the viral genome during infection. The three antigens were inserted into either one of two adenovirus vectors: a virus of human origin to produce “Tri:HuAd” or a virus of chimpanzee origin to produce “Tri:ChAd.” Most currently approved SARS-CoV-2 vaccines only encode the full-length spike protein, but not nucleocapsid or RdRp. These two additional genes were likely included in the present study because nucleocapsid is the most abundant viral protein in infected cells, and because RdRp is well conserved among coronaviruses, thus potentially leading to broader immune responses.

To assess the antibody responses induced by either vaccine candidate, the authors immunized mice with a single dose of Tri:HuAd or Tri:ChAd into the nose or into the muscle and collected serum and lung wash samples 2, 4 and 8 weeks later. The collected samples were then tested for the presence of IgG antibodies, which provide the majority of antibody-based immunity. Analysis of sera collected at 4 weeks revealed that mice immunized intranasally with either vaccine had significantly higher levels of spike protein-specific IgG than did mice that were immunized intramuscularly, and these high levels were sustained through 8 weeks post-vaccination. However, only lung wash samples from mice immunized with either vaccine intranasally contained detectable levels of spike protein-specific IgG at the 4 week time point, suggesting that only intranasal immunization led to IgG production in the airways. Interestingly, the airways of Tri:ChAd recipients harbored almost twice as much spike-specific IgG as those of Tri:HuAd recipients, a difference that was not observed in the serum, suggesting that the vector of chimpanzee origin induced better local immune responses when administered via the nose. Additionally, only the lung wash samples from intranasal Tri:ChAd recipients contained any observable anti-spike IgA antibodies, which are prevalent in mucosal surfaces and represent a first line of defense against invasion by inhaled and ingested pathogens. These results suggested that both vaccines, but Tri:ChAd in particular, induced better immune responses when they were delivered intranasally.

Lung wash samples were also analyzed for vaccine antigen-specific T cells by detecting characteristic cell surface proteins on these T cells, and for specific cytokines produced by the T cells in response to their exposure to peptides encoding each of the three vaccine-encoded antigens: S1, nucleocapsid, or RdRp. This analysis revealed that when the vaccine was injected into the muscle, neither Tri:HuAd nor Tri:ChAd induced detectable airway antigen-specific cytotoxic T cells, which are capable of killing virus-infected cells. In contrast, both vaccines induced significant numbers of cytotoxic T cells in the airways when they were delivered intranasally. Although the detected T cells were specific for all three antigens, S1-specific cells were more abundant, and they were also multifunctional in that they produced more than one cytokine characteristic of cytotoxicity. However, in the context of intranasal vaccination, the Tri:ChAd vaccine induced higher total numbers of cytotoxic T cells than the Tri:HuAd vaccine, suggesting that a single dose of Tri:ChAd delivered intranasally is highly effective at inducing vaccine antigen-specific cytotoxic T cells in the respiratory tract.   

Interactions between lung macrophage cells and SARS-CoV-2 can increase the expression of the host-derived peptide MHCII on macrophage surfaces, allowing these cells to become a critical component of “trained innate immunity.” This altered innate immunity results from a functional modification of innate immune cells that leads to an antibody-independent temporary immune memory that is characterized by an accelerated response to a second challenge with the same pathogen. Neither Tri:HuAd nor Tri:ChAd induced detectable MHCII expression on macrophages in the lungs of mice when delivered intramuscularly. In contrast, both vaccines induced increased levels of MHCII-expressing lung macrophages 8 weeks after immunization when delivered intranasally, with a higher number of these cells in the lungs of Tri:ChAd recipients, suggesting that intranasal immunization with Tri:ChAd induces strong trained innate immunity.

The authors next tested the ability of the vaccines to protect mice from SARS-CoV-2 infection by intentionally infecting immunized mice with a lethal dose of SARS-CoV-2 at 4 weeks after immunization, and monitoring them for clinical signs of illness in terms of weight loss. Unvaccinated control animals and 80% of animals immunized intramuscularly with either vaccine were not protected from infection or disease and died by 5 days post-infection. In contrast, animals immunized with Tri:HuAd showed a temporary and slight weight loss, but rebounded over the course of two weeks, while animals immunized with Tri:ChAd did not lose weight at all for the duration of the two-week time course. This result correlated with reduced viral load and reduced lung pathology at 14 days post-infection in mice immunized intranasally compared to unvaccinated controls and intramuscular vaccine recipients, with Tri:ChAd recipients exhibiting the most reduced viral burden and lung pathology.   

Having determined that intranasal administration of Tri:ChAd induced the best immune responses, all subsequent experiments were carried out using this vaccination strategy. To assess the individual contributions of B cells and T cells in the vaccine-induced immune response, the authors immunized two groups of mice: one group that was genetically deficient in B cells and a second group of genetically wild type mice that were depleted of T cells by receiving injections of antibodies against T cell-characteristic cell surface molecules. Because T cells are needed for B cell stimulation and production of antibodies, the antibody injections were done on day 25 after immunization to ensure that vaccine-induced B cell functions and antibody production remained intact in the T cell-depleted mice. At 28 days after vaccination, both groups of animals were infected with SARS-CoV-2 and monitored for weight loss. Unvaccinated mice that were either B cell-deficient or T cell-depleted and control unvaccinated mice with normal B and T cell functions were subject to drastic weight loss. In stark contrast, neither B cell-deficient nor T cell-depleted mice that had been intranasally immunized with Tri:ChAd showed any weight loss throughout the 2-week experimental time course, despite the fact that both groups of animals had significantly elevated viral burden in the lung. This result suggested that Tri:ChAd was immunogenic enough to compensate for the lack of B or T cells and protect the mice from clinical disease after SARS-CoV-2 infection.

The authors next wanted to analyze the role of trained innate immunity in the absence of B and T cell immunity, so they immunized two groups of mice. The first group consisted of B cell-deficient animals that were depleted of T cells shortly after vaccination. Because T cells induce vaccine-mediated trained innate immunity early after vaccination, this strategy produced mice that lacked B cells, T cells, and trained innate immunity. The second group consisted of B cell-deficient animals that were depleted of T cells starting at day 25 post-vaccination to allow for induction of trained innate immunity and thus produce mice that lacked B cells and T cells, but possessed intact trained innate immunity. At 28 days after vaccination, both groups of animals were infected with SARS-CoV-2 and monitored for weight loss and lung pathology. Unvaccinated control mice with functional B cells, T cells, and trained innate immunity and unvaccinated mice lacking B cells, T cells, and trained innate immunity showed severe weight loss and severe lung pathology. In contrast, vaccinated mice lacking B cells and T cells but possessing trained innate immunity appeared healthy with no weight loss and no pathology in the lungs, suggesting that the immune protection observed in animals lacking B cells, T cells, or both, was likely mediated by trained innate immunity.

The study demonstrated similar results after infection of mice with alpha and beta variants of SARS-CoV-2; however, it would be interesting to see if these vaccines have similar efficacy against the later variants, including delta and omicron. Although these results are promising, it is important to remember that mice can be poor predictors of human disease outcomes. Nevertheless, I look forward to seeing the results of the clinical trial that is currently underway to compare the relative efficacies of Tri:HuAd and Tri:ChAd following intranasal delivery in humans.

[For a more detailed discussion of this paper, please check out TWiV 867.]

Spikevax Induces Durable Protection from the Delta Variant in Rhesus Macaques

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by Gertrud U. Rey

It is currently not clear how long SARS-CoV-2 vaccine-induced immunity lasts. The gold standard for determining the efficacy of a vaccine is the “challenge” study, which involves intentionally infecting immunized subjects with the pathogen against which they were immunized. Such studies are typically done in non-human primates, because it is unethical to deliberately infect humans with pathogens that cause serious morbidity and mortality.

A recent preprint by Kizzmekia Corbett and others describes experiments done to assess the efficacy of Moderna’s SARS-CoV-2 “Spikevax” vaccine in rhesus macaques one year after vaccination. The authors immunized eight animals with two doses of Spikevax at four-week intervals and then collected blood samples, nasal swabs, and lung wash samples at various time points over the course of the following year. The macaques were then challenged with the SARS-CoV-2 delta variant virus at 49 weeks, and more samples were collected at different time points after challenge.

Blood samples collected at 6, 24, and 48 weeks post-vaccination were used to analyze the ability of IgG antibodies in these samples to bind the receptor-binding domains of three different viruses: 1) “ancestral” SARS-CoV-2, which had the exact spike protein antigen encoded in the vaccine, 2) the delta variant, and 3) the beta variant. These latter two had variant spike proteins. IgG antibodies are mostly blood-resident and provide the majority of antibody-based immunity against invading pathogens. IgG levels were highest at 6 weeks after vaccination for all three viruses; they then declined rapidly between 6 weeks and 24 weeks, and more slowly between 24 weeks and 48 weeks. Most IgG detected at 6 weeks bound ancestral virus, with 5.4-fold and 8-fold fewer IgG molecules binding the delta and beta variants, respectively. However, when delta and beta variant-specific IgG antibodies were tested for their ability to block binding between SARS-CoV-2 and its cognate ACE2 receptor, they inhibited almost 100% of binding of both delta and beta variant viruses, suggesting that the antibodies were still functional in preventing infection, in spite of their diminished quantity.

The ability of blood-resident IgG antibodies to neutralize the three respective viruses followed a similar trend, with a gradual decline in neutralizing activity against all viruses by 48 weeks post-vaccination. Interestingly, even though the quantity of total binding and neutralizing antibodies targeting the delta variant decreased over time, the number of antibodies targeting regions associated with neutralization increased. In addition, the binding avidity of antibodies to ancestral virus increased significantly between week 6 and 24 and remained steady through week 48 post-vaccination. In contrast to affinity, which measures the strength of the binding interaction between antigen and antibody at a single binding site, avidity measures the total binding strength of an antibody at every binding site. These two shifts – the increase in the number of antibodies binding targets associated with neutralization and the increase in antibody avidity over time in spite of a decrease in total antibody levels – are suggestive of a maturing immune response that is more focused on viral regions of high immunological relevance. It is noteworthy to mention that the regions associated with neutralization are outside of areas where the variant viruses have accumulated changes in the spike protein, further implying that Spikevax and other SARS-CoV-2 vaccines are just as effective against viral variants as they are against ancestral virus.

Next, the authors analyzed lung wash samples and nasal swabs for delta-binding IgG and IgA antibodies. IgA antibodies are predominantly found in mucus membranes and their fluids, where they protect against invasion by inhaled and ingested pathogens. IgG kinetics in the lung were similar to those observed in the blood – both binding and neutralizing IgG to all three viruses were highest at 6 weeks after vaccination and decreased steadily over time until they were indistinguishable to those observed in unvaccinated animals. In contrast, IgG levels in the nose increased through week 25, plateaued, and remained stable through week 42 post-vaccination. IgA levels in the lung were highest at week 6 post-vaccination, but decreased to levels similar to those observed in unvaccinated animals by week 24. IgA levels in the nose were similar to those in unvaccinated animals at all time points. These results suggest that although SARS-CoV-2 vaccination may not induce a detectable mucosal immune response in the nose, it does induce good initial mucosal immunity in the lung, which is typically the site of severe COVID-19. This immunological difference between the lung and the nose might also explain why SARS-CoV-2 vaccines are more effective at preventing severe disease than at preventing infection.

The authors also analyzed blood samples from vaccinated animals for the presence of SARS-CoV-2-specific memory B cells, which can quickly produce spike-specific antibodies upon subsequent exposure to SARS-CoV-2. At week 6 post-vaccination, about 0.14% of all memory B cells were specific for the ancestral virus, and about 0.09% were specific for the delta variant. In comparison, about 2.5% of all memory B cells were specific for both the ancestral virus and the delta variant, and this high proportion of dual-binding to single-binding cells remained constant through week 42 post-vaccination.

To see whether these vaccine-induced immune parameters are protective after viral challenge, the authors infected the animals with delta variant virus at 49 weeks after the initial immunization. Lung washes and nasal swabs were collected on days 2, 4, 7, and 14 after challenge to monitor viral replication. On day 2 after challenge, vaccinated animals had about 11-fold fewer viral RNA copies per milliliter in their lungs than unvaccinated animals, and these RNA levels declined rapidly over the following days. In contrast, viral RNA levels in unvaccinated animals remained significantly elevated through day 7 post-infection. Viral RNA levels in the nose followed a similar trend; however, their decline in vaccinated animals was not as dramatic as that observed in the lung.

Antibodies to all three viruses in the lungs of vaccinated animals were significantly higher on day 4 after challenge than at week 42 after immunization, suggesting that memory B cell responses to infection were quick and robust. Viral challenge after vaccination also induced both T helper cells, which stimulate B cells to make antibodies, and cytotoxic T cells, which kill virus-infected cells. Analysis of lung tissue also revealed that vaccination prevented lung pathology and protected the lower respiratory tract from severe inflammation after infection.

Perhaps the most interesting observation in the study relates to whether vaccinated individuals who become infected replicate and transmit virus to others. When the authors analyzed lung wash samples for T cells specific for the SARS-CoV-2 N protein, which is not encoded in the Spikevax vaccine, they only found these cells in unvaccinated animals. This suggests that even though it had been one year since vaccination, immunized animals that were then infected did not replicate the challenge virus to a sufficient extent to produce T cells specific for the SARS-CoV-2 N protein – a response that would only be elicited by actual infection with whole virus. In other words, the memory response to the SARS-CoV-2 spike protein induced by the vaccine eliminated incoming virus so quickly that the immune system had no chance to mount a response to the viral N protein encoded in the challenge virus, presumably because the virus was cleared quickly.

In summary, vaccinated animals appear to be better protected from severe disease and to clear virus faster than unvaccinated animals. This result aligns with data published in a previous preprint, which showed that viral RNA levels in delta variant-infected people who had been vaccinated prior to infection declined more rapidly than in people who were not vaccinated. And although monkeys are not human, previous studies assessing the protective efficacy of Spikevax have shown that rhesus macaques are reliably predictive of outcomes in humans, making them a great model for determining the effects of waning antibody levels on long-term protection against SARS-CoV-2 infection.

[Kizzmekia Corbett, a viral immunologist at Harvard who was central to the development of the Moderna mRNA vaccine, was previously a guest on TWiV 670. The preprint described in this post was also discussed on TWiV 824.]

Dynamics of SARS-CoV-2 Vaccine-Induced Antibody Immunity

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Gertrud U. Rey

Vaccination against the vaccine-preventable diseases is preferable to natural infection because it prevents illness and the long-term effects associated with many infections; and in most cases, it also leads to better immunity. In the case of immunity induced by SARS-CoV-2 vaccination, it is slowly becoming clear that the immunity is of overall better quality than that induced by COVID-19.

Vaccination leads to production of polyclonal antibodies, which are derived from many different types of B cells and may target many different portions of an antigen (i.e., “epitopes”). Isolation of B cells from a blood sample allows one to artificially produce monoclonal antibodies, which are derived from a single type of B cell and target a single epitope. Using blood samples from 6 SARS-CoV-2 mRNA vaccine recipients and 30 COVID-19 survivors, the authors of a recent publication compared the dynamics of vaccine-induced antibody immunity to those resulting from natural infection. A comparison of total antibodies between the two groups of people revealed that polyclonal antibody levels in vaccinees were generally higher than those in COVID-19 survivors. However, when the authors tested the antibodies from vaccinees for SARS-CoV-2 neutralizing activity, only a minority were neutralizing, including antibodies that target the receptor-binding domain (RBD) on the SARS-CoV-2 spike protein.

To see whether any of the neutralizing antibodies from vaccinees were capable of binding to the RBD, the authors performed competition experiments, where they exposed the antibodies to the SARS-CoV-2 RBD alone, or to RBD pre-mixed with its binding target – the human ACE2 receptor. This experiment revealed that increasing concentrations of ACE2 led to decreased antibody binding, suggesting that the antibodies compete with the ACE2 receptor for binding to the RBD, and that they neutralize the virus by inhibiting its binding to ACE2.

A plasmablast is a type of B cell that differentiates from an immature B cell into a mature plasma cell, which can produce large amounts of a specific antibody. Although they are short-lived, plasmablasts also make antibodies, and are typically abundant and easy to isolate from peripheral blood. Analysis of monoclonal antibodies produced from the plasmablasts of vaccinated individuals showed that a substantial number of these antibodies also bound the N-terminal domain of the SARS-CoV-2 spike protein in addition to the RBD, suggesting that these two epitopes co-dominate as antibody targets.

“Original antigenic sin” is a phenomenon initially discovered with influenza viruses, where the immune system mounts the strongest response to the first version of one particular antigen encountered (i.e., the first virus variant with which one is infected in life). Similar observations have been made in the context of COVID-19, with natural SARS-CoV-2 infection purportedly also substantially boosting antibodies against seasonal β-coronaviruses OC43 and HKU1. To see if SARS-CoV-2 vaccination produces a similar effect, the authors analyzed the specificity of antibodies isolated from vaccine recipients before and after vaccination against the spike protein of α-coronaviruses 229E and NL63 and β-coronaviruses OC43 and HKU1. Although vaccination did not increase titers of pre-existing antibodies against 229E and NL63 viruses, it did increase titers against OC43 and HKU1, consistent with what happens during natural SARS-CoV-2 infection. These results suggest that some of the vaccine-induced antibody responses may be biased by pre-existing immunity to other circulating human β-coronaviruses.

The authors also determined whether plasmablast-derived monoclonal antibodies and polyclonal antibodies from the sera of COVID-19 survivors and vaccinated individuals could bind to the RBDs of different SARS-CoV-2 variants. Although complete loss of binding was rare, antibodies from COVID-19 survivors varied widely in their ability to bind to different variants. Antibodies isolated from vaccinees varied less, depending on the variant. However, for most plasmablast-derived monoclonal antibodies from vaccinees, there was no impact on binding to RBDs in the binding assay used, regardless of the variant.

This study raises several interesting points. First, the ability of SARS-CoV-2 vaccination to boost pre-existing antibodies against HKU1 and OC43 supports the premise for a universal β-coronavirus vaccine, several of which are already in development. Second, the ability of the RBD and N-terminal domain to co-dominate in eliciting spike-specific antibodies justifies the use of vaccines containing the entire spike protein, rather than just the RBD. Third, although it is surprising that vaccination induced so few neutralizing antibodies, the role of non-neutralizing antibodies in protection against disease and infection is currently unknown. Considering that vaccination is obviously so protective against disease and asymptomatic infection, the authors speculate that the antibodies induced by vaccination could have protective functions outside of neutralization. Lastly, the fact that vaccination-induced antibodies fluctuate little, if at all, in their ability to bind the RBDs of different variants compared to antibodies induced by natural infection, suggests that vaccination is more likely to protect from different variants than natural infection. Collectively, these findings further highlight the importance of vaccination for ending this pandemic.

One and Done

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by Gertrud U. Rey

On February 27, 2021, the FDA issued an emergency use authorization for a third SARS-CoV-2 vaccine. The vaccine was developed by Janssen Pharmaceutica, a Belgium-based division of Johnson & Johnson, in collaboration with Beth Israel Deaconess Medical Center in Boston. Perhaps the most exciting feature of this new vaccine is that it only requires one dose to be effective in inducing an immune response.

The vaccine is named Ad26.COV2.S because it consists of a human adenovirus vector, with a DNA genome, into which has been inserted the gene that encodes the full-length SARS-CoV-2 spike protein (pictured). Ad26.COV2.S is similar to AstraZeneca’s vaccine, based on a different adenovirus, and with a slightly different version of spike, which is not yet authorized in the U.S. The notion of using a virus as a vector to deliver vaccines to humans is based on the ability of viruses to enter cells by attaching to host cell receptors and releasing their genome into the cell. Upon injection into a vaccine recipient, the vaccine vector should enter cells and serve as a code for host proteins to synthesize the SARS-CoV-2 spike protein from the inserted gene. Ideally, the spike protein will then act as an antigen to prime the immune system to recognize SARS-CoV-2 if it infects the body at a later time. 

Adenoviruses are particularly suitable as vectors for delivering foreign genes into cells because they have a double-stranded DNA genome that can accommodate relatively large segments of foreign DNA, and because they infect most cell types without integrating into the host genome. However, because of the prevalence of adenovirus infections in humans, most people have adenovirus-specific antibodies that could bind and neutralize these vectors, thus rendering them less effective at stimulating antibodies to the inserted gene product. AstraZeneca circumvented this issue by using an adenovirus of chimpanzee origin that does not normally infect humans. The adenovirus used to make Ad26.COV2.S (Adenovirus 26) is of human origin; however, when tested, most people have very few antibodies that inactivate this adenovirus, compared to antibodies against other adenoviruses. Thus, potential Ad26.COV2.S recipients are less likely to have pre-existing antibodies to the adenovirus vector itself. To optimize Adenovirus 26 for use as a vaccine vector, Janssen investigators deleted the gene that regulates viral replication, thus ensuring that the virus vector cannot cause an infection in human cells.

During infection, the SARS-CoV-2 viral particle fuses with the host cell membrane; a process that is mediated by two main events: 1) a structural rearrangement of the spike protein from its pre-fusion conformation; and, 2) cleavage of the spike protein by a cellular enzyme called furin. Based on the knowledge that the pre-fusion, uncleaved form of spike is more stable and immunogenic, Janssen investigators also inserted two mutations into the spike gene: one that locks the translated spike protein into its pre-fusion conformation, and one that prevents its cleavage by furin.  

The FDA’s decision to issue an emergency use authorization for Ad26.COV2.S was based on safety and efficacy data from an ongoing Phase III clinical trial done in 39,321 participants who received either a single dose of Ad26.COV2.S or a placebo control. The trial was randomized, meaning that participants were randomly assigned to the experimental group receiving the Ad26.COV2.S vaccine, or the control group, so that the only expected differences between the experimental and control groups were the outcome variables studied (safety and efficacy). Randomizing trial participants eliminates unwanted effects that have nothing to do with the variables being analyzed. The trial was also double-blinded, meaning that neither the investigators nor the subjects knew who was receiving a particular treatment. Double-blinding leads to more authentic conclusions because they reduce researcher bias.

The basic findings of the trial were as follows:

  • side effects related to vaccination were mild to moderate; and
  • the vaccine was
    • 66% effective at preventing moderate to severe COVID-19 across all geographic areas and age groups (U.S., South Africa, and six countries in Latin America);
    • 72% effective at preventing moderate to severe COVID-19 across all age groups in the U.S.; 
    • 85% effective at preventing severe disease; and
    • 100% effective at preventing COVID-19-related hospitalization and death as of day 28 after vaccination.

The apparently reduced efficacy of Ad26.COV2.S compared to the Moderna and Pfizer vaccines has led to considerable public skepticism. However, this is an unfair comparison for several reasons. Ad26.COV2.S was tested at a time when more variants were in circulation, including in places where the Moderna/Pfizer vaccines are thought to be less effective against locally circulating variants. Some limited data also suggest that Ad26.COV2.S might protect from asymptomatic infection and may thus prevent transmission from vaccinated individuals to non-vaccinated individuals. Although there is some evidence to suggest that the Pfizer vaccine has a similar effect, no such data exist yet for the Moderna vaccine.

The most critical measure of a vaccine’s efficacy is how well it prevents severe disease, hospitalizations, and deaths, and in this regard, all three vaccines are comparable. Moreover, Ad26.COV2.S has at least two advantages over the Pfizer/Moderna vaccines: 1) it does not require a freezer and can be stored in a refrigerator for up to three months; and, 2) it can be administered in a single dose. This will increase vaccine uptake, because people won’t have to get two shots and/or remember to get the second shot.  It also makes it easier to immunize people with limited access to healthcare, such as the homeless and people living in remote areas. When all these factors are considered together, it is clear that Ad26.COV2.S will be a crucial additional tool in the fight against this pandemic.

RNA, in a Nutshell

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by Gertrud U. Rey

It is now a little more than a year since the emergence of SARS-CoV-2, and we already have several highly effective vaccines against this virus. Because of my previous research experience in vaccine science, I was very skeptical about the promise of a SARS-CoV-2 vaccine this soon. I was wrong, and I could not be happier about that.

Two of the leading vaccines were developed by Pfizer/BioNTech and Moderna and consist of a messenger RNA (mRNA) that encodes the full-length SARS-CoV-2 spike protein. Upon injection into a vaccine recipient, the mRNA would enter cells and be translated by the host protein synthesis machinery into the SARS-CoV-2 spike protein, which would then serve as an antigen to promote an immune response. mRNA vaccines are non-infectious and do not integrate into the genome, meaning that there is no risk of infection or mutations caused by inserted vaccine sequences. Although these vaccines are the first of their kind to be licensed for widespread use, the concept is not new. Reports of the first successful translation of a foreign mRNA in animals were published in 1990, and this technology has been refined ever since. Progress in the field has been hampered by concerns that the inherent instability of RNA would prevent its use for delivery as a therapeutic or vaccine. However, research has shown that the stability of RNA can be increased through various modifications and delivery methods.

One way a vaccine mRNA molecule can be modified is by placing it between two RNA sequences that don’t code for protein, i.e., untranslated regions (UTRs; see graphic), which stabilize the mRNA and optimize it for translation. The ends of the mRNA – also known as the 5′ and 3′ ends, respectively – can be further modified by addition of a “cap” and a “poly(A) tail.” The cap consists of a modified guanosine nucleotide followed by three phosphates (“G-PPP” in the graphic) and serves as a recognition signal for the cellular ribosome to bind and translate the mRNA. The poly(A) tail is a string of adenosine nucleotides (“AAA” in the graphic), which further stabilize the mRNA.

A common method for encapsulating and delivering the mRNA into cells is to encase it in a cocoon of phospholipids. For example, the mRNA molecule in both the Pfizer and Moderna vaccines is encapsulated in a lipid nanoparticle (pictured), which protects the mRNA from degradation and ensures proper delivery into cells. Addition of cholesterol molecules makes the nanoparticle more fluid and is thought to increase its ability to fuse with our cell’s membranes to deliver the mRNA into our cells. Addition of polyethylene glycol (PEG) increases the potency of the vaccine particle by hiding it from the host immune system, making it more water soluble, and slowing its degradation.

One of the reasons why SARS-CoV-2 mRNA vaccines could be produced so quickly is because all this basic science was already in place at the start of the pandemic. And although the SARS-CoV-2 vaccines are the first mRNA vaccines to be authorized by the FDA for emergency use, several mRNA vaccines have undergone clinical trials in humans before, for at least four infectious diseases: rabies, influenza, cytomegalovirus infection, and Zika virus infection.

Another factor that helped speed up the process of SARS-CoV-2 vaccine production is that, luckily, scientists were able to extrapolate the insight gained from the study of other coronaviruses to SARS-CoV-2. Like the spike protein of other coronaviruses, the SARS-CoV-2 spike protein is highly immunogenic and is targeted by neutralizing antibodies, which bind viral antigens to inactivate the virus and prevent infection of new cells. The spike protein also mediates binding of the virus to the ACE2 host cell receptor via spike’s receptor-binding domain and fusion of the viral particle with the host cell membrane via spike’s fusion domain. However, to mediate this fusion, the SARS-CoV-2 spike protein undergoes a structural rearrangement from its pre-fusion conformation. By 2017, scientists at the Vaccine Research Center of the National Institute of Allergy and Infectious Diseases had already determined that the pre-fusion form of Middle East respiratory syndrome coronavirus (MERS-CoV) is more immunogenic than its post-fusion form. Accordingly, they had spent several years engineering a mutation that locks the translated spike protein into its pre-fusion structure. When the SARS-CoV-2 genome sequence was published one year ago, scientists were able to compare it to the MERS-CoV sequence and identify the exact location where the pre-fusion stabilizing mutation had to be made. And luckily, making the mutation in the SARS-CoV-2 spike mRNA sequence stabilized the spike protein in its pre-fusion conformation. 

Conventional vaccine strategies have repeatedly failed to yield vaccines against challenging viruses like HIV-1, herpes simplex virus, and respiratory syncytial virus (RSV), while recent advances in mRNA vaccine technology show promise in immunizing against some of these viruses. For example, RSV poses a substantial public health threat due to its association with severe morbidity and mortality in infants and premature babies. Despite 60 years of continual efforts, we still don’t have a licensed RSV vaccine, in part because natural RSV infection does not induce a durable immune response. We do know that the RSV F (fusion) protein is highly conserved and elicits broadly neutralizing antibodies, and recent studies have shown that similar to the case of the SARS-CoV-2 spike protein, most neutralizing activity in human serum is directed against the pre-fusion form of the RSV F protein. This observation inspired scientists at Moderna to develop an RSV pre-fusion F protein mRNA vaccine, with Phase I clinical trial data showing promising results.

One of the exciting features of the mRNA vaccine platform is that it is not only applicable to preventing viral diseases but can also be used for treating cancer. Cancer mRNA vaccines would target tumor-associated antigens that are preferentially expressed in cancer cells.

Vaccination remains one of the most effective public health measures for preventing and controlling infectious diseases. However, conventional vaccine approaches using live-attenuated and inactivated virus vaccines are time-consuming and expensive. mRNA vaccines can be produced more quickly and cost-effectively than conventional vaccines because they obviate the need for growing and/or repeatedly passaging viruses in cell culture. Nonetheless, we would not know any of this without decades of prior studies, which further highlights the importance of regularly funding basic research.

SARS-CoV-2 UK variant: Does it matter?

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A variant of SARS-CoV-2 has been spreading within England, and it has been suggested that this virus is more transmissible. In this video Vincent explains the properties of the SARS-CoV-2 UK variant and why claims that it is more transmissible are not supported by experimental data.

This video was recorded on Monday, 21 December 2020. Since then additional data on the UK variant have been released but they do not change my view: there are no biological data in humans showing that the virus has increased transmissibility. The variant is certainly spreading in the population, but that could be due to other situations that have not been ruled out.