Immunity to SARS-CoV-2 induced by infection or vaccination
Immunity to SARS-CoV-2 induced by infection or vaccination
Antibodies (Abs) are produced by B cells in response to viral infection or vaccination.They provide a first line of defence against subsequent exposures to a pathogen. In addition to the robust Ab responses produced by short-lived plasma cells during an acute infection, lower levels of pathogen-specific Abs are produced by long-lived plasma cells in the bone marrow, providing serological memory for years after the pathogen has been cleared.
Most viral infections and vaccines provide protection against re-infection through the induction of neutralizing Abs that bind viral surface structures and block virus entry into target cells. During natural infection, CD8+ T cells play an important complementary role to contain the infection through their ability to eliminate already infected cells, while CD4+ helper T cells, amongst other functions, provide signals that support the development of Ab responses.
Since Covid-19 emerged in late 2019, much effort has been directed to the characterization of innate and adaptive immune responses to SARS-CoV-2 with the aim to understand the roles of different immune functions in viral clearance. As in other viral infections, T and B cells work in concert alongside the innate immune system to control SARS-CoV-2, with the adaptive arms displaying distinct response kinetics, mode of antigen recognition, effector functions and immunological memory. As the vast majority of SARS-CoV-2 cases result in asymptomatic or mild disease (with elderly cases developing disease more frequently), our immune system generally responds appropriately. However, longer-term consequences of COVID-19, such as potentially auto-reactive antibodies and persistent fatigue in post-acute COVID-19 syndrome, or ‘Long Covid’, affect a large number of people.
The B Cell Response to SARS-COV-2
Our immune response to viral infections engages functions that combat the invading pathogen in a series of steps. First engaged is the innate immune system, which recognizes and eliminates foreign viral material and activates a signaling cascade that limits the spread of the virus to neighbouring cells. The innate immune system may do a substantial part of the work to contain SARS-CoV-2 in some cases, such as asymptomatic or mild infections in children and young adults.
Soon thereafter, T cells are recruited to destroy infected cells and orchestrate the immune response, while the IgM antibody response develops in parallel. Anti-viral IgM plays a prominent role during the early stages of infection, and can remain stable for months. Memory T cells reactive to a diverse set of SARS-CoV-2 epitopes are detectable in convalescent individuals. Reports suggest that cross-reactive IgM memory B cells elicited by previous exposures to endemic coronaviruses (CoVs) may be engaged in the response to SARS-CoV-2 in a minority persons, while the IgG antibody response, especially to the spike glycoprotein, shows a high level of specificity for SARS-CoV-2.
De novo B cell responses to SARS CoV-2 are critical for generating effective neutralizing Abs against the virus. Following the initial IgM response, which wanes relatively quickly with viral clearance, primarily IgG and IgA antibodies are produced. After acute infections, IgG levels remain elevated and relatively stable for many months or years. How rapidly the response declines, sometimes beyond detection, depends on the magnitude of the peak response, the subtypes of antibodies involved, and the relative contribution of short-lived and long-lived plasma cells to the circulating IgG levels.
In the case of reinfection, antigen-specific memory B cells are quickly engaged improving immunological efficiency. It follows that repeated antigenic stimulation bolsters immunological protection; however, as mutations in key Ab epitopes in the S glycoprotein come into play, with different virus variants arising, the level of protective immunity may be compromised.
Therefore, the degree to which immunity induced by previous exposure to one strain protect against others, over longer timescales, remains to be determined.
Durability of immunity after natural infection
How long immunological protection lasts after SARS-CoV-2 infection is a critical metric that strongly impinges upon how the pandemic will play out, epidemiologically and in terms of public policy, since immune protection is sensitive to the emergence of viral immune escape variants. Moreover, many previously infected individuals would like to know their risk of acquiring COVID-19 a second time, and others would like to know how long the protective effect of their vaccination will last. Past-controlled human infection experiments with seasonal CoVs have demonstrated that infection-induced antibodies correlate with protection to re-challenge [114–118], although re-infection was possible. Indeed, it is important to appreciate that immunity represents a spectrum of protection that is dependent upon numerous cell types (e.g., B and T cells, NK cells [119, 120] and macrophages ) physical barriers that are more or less effective in different individuals, along with differences in environmental influences (e.g., medications with side-effects on the immune system ), general health status and age. Therefore, it is more useful to consider infection-induced immunity as measure of reduced risk upon re-infection, similarly to that induced by current SARS-CoV-2 vaccines that are highly effective at preventing severe COVID-19, but not necessarily viral transmission. It is hoped that the coming years will yield important advancements in quantitative immune profiling at population levels so that the relative contribution of different protective barriers and environmental factors can be estimated .
Although several studies have now shown that anti-SARS-CoV-2 Ab titers decline from peak levels with time [124–126], as Ab titers do for all cleared infections, neutralizing Ab responses and virus-specific memory B cells quantitated by flow cytometry were described to remain prevalent in the peripheral circulation up to 8 months or more post-infection – with most previously infected individuals still harboring good levels of circulating antibodies at this time point. One large study showed 13% of individuals lost detectable IgG titers 10 months post-infection . How this will play out in other cohorts, in the longer-term and after vaccination, remains to be seen. Some of the best empirical evidence for Ab-mediated protection from COVID-19 comes from a study of n = 12,541 healthcare workers in the United Kingdom, which reported a substantially reduced rate of re-infection over 6 months in persons previously antibody positive: for example, no symptomatic cases were detected in persons previously antibody positive to S or N in the study period . Smaller studies  in different contexts (e.g., a fishing vessel outbreak  and elderly care homes ) have also illustrated the highly protective effect of serum antibodies.
Evidence suggests that Ab immunity to endemic seasonal CoVs and SARS-CoV wanes within a 2- to 3-year period in the majority of those previously infected [79, 132–135], which represents a combination of lack of cross-protective immunity to mutating seasonal strains, rhythms in the circulation of different CoVs [136–138], and loss of antibody-producing cells over time with ageing . Several case studies of SARS-CoV-2 reinfection have been documented in the literature [140, 141], although it is not known at present whether these were caused by infection with a different strain, waning immunity or unique clinical features explained the occurrence. Indeed, early results indicate that the potency of engendered antibodies is generally reduced when faced with a new S variant strain [88, 142–144], suggesting less effective but not abolished immunity due to changes in neutralizing antibody epitopes in S. This is similar to what has been observed for vaccines based on the original Wuhan, China strain [145–148]. Neutralizing antibody titers after mild SARS-CoV-2 infection were reported to be comparable to those engendered by first-generation COVID-19 vaccines [149, 150].
Vaccine-induced immunity and protection
The correlate of protection for almost all clinically licensed vaccines is neutralizing Abs , and emerging data suggest that the current SARS-CoV-2 vaccines are no exception . As discussed above, evidence that the presence of neutralizing Abs is associated with protection against SARS-CoV-2 in humans was illustrated early in non-human primates receiving the neutralizing monoclonal Ab LY-CoV555 (Bamlanivimab) before a high dose SARS-CoV-2 exposure, which conferred protection , while adoptive transfer of purified IgG from convalescent non-human primates protected naive animals against challenge with SARS-CoV-2 .
Fortunately, SARS-CoV-2 is relatively easy to neutralize and even though variants that partly escape Ab responses have already evolved, the human neutralizing Ab response is quite effective at blocking infection if the antibody titers are of sufficient magnitude. As the S protein on the surface of SARS-CoV-2 is the target for neutralizing Abs, all currently licensed vaccines are based on this antigen. Once the original pandemic strain was identified, several vaccine companies initiated the development of different vaccine platforms with the goal to elicit anti-S Ab responses and protective immunity (Figure 2). The historical approach of producing vaccines, based on whole inactivated virus, was also used for SARS-CoV-2 vaccines, and several such vaccines are now approved for clinical use [155, 156]. However, the COVID-19 vaccines that have so far shown the best efficacy, and are most broadly distributed globally, are based on modern molecular biology-based technologies, in particular mRNA-based vaccines encoding the S protein [149, 157, 158]. Several genetically modified replication-incompetent adenovirus vectors encoding S are also approved [159, 160]. Furthermore, after highly successful clinical trials typified by strong anti-SARS-CoV-2 neutralizing antibody responses [148, 161, 162], vaccines based on recombinant S protein, in some cases produced as nanoparticle-like structures, given with adjuvant, are also expected to soon be approved for clinical use.
A common misperception is that the SARS-CoV-2 vaccine technologies are new concepts of which there is limited prior knowledge. However, the mRNA and adenovirus vector platforms have been studied already for a few decades in the development of vaccines against other pathogens, and multiple vaccine candidates based on these technologies have been evaluated in clinical trials [163, 164]. In addition, the human papilloma virus (HPV) and hepatitis B vaccines, which are successfully used in humans since many years, are examples of subunit vaccines that are based on modern recombinant protein technology. Being formulated for intra-muscular injection, these vaccines provoke mainly IgG responses, although lower levels of IgM and IgA are induced by mRNA vaccination , the degree to which may be influenced by host factors. From HPV vaccination, also delivered intra-muscularly, it is known that vaccine-induced IgG distributes to mucosal surfaces where it provides a high degree of protection against cervical cancer . COVID-19 vaccines given intra-nasally are under development , and future work will reveal if such vaccines have advantages, for example, for better curtailing transmission if a higher degree of neutralizing IgA antibodies are present within the respiratory tract .
Importantly, mRNA, adenovirus vector and recombinant protein vaccines are molecularly well-defined vaccines that are produced with a high degree of precision and reproducibility. The scale of the COVID-19 pandemic puts unprecedented demands on vaccine developers, production facilities and local infrastructure to administer vaccinations – requiring greater investment in public health to counter future threats. It also requires international cooperation to successfully distribute the vaccines to all countries of the world to control the pandemic. While equitable access is still far from a reality, mechanisms that are beginning to address such issues are now in operation (https://www.who.int/initiatives/act-accelerator/covax) and should be prioritized in future fights against pandemics.
Efficacy of SARS-CoV-2 vaccination
The current SARS-CoV-2 vaccines were approved after multiple successful clinical vaccine trials demonstrating high efficacy. Efficacy is determined as the percentage reduction of cases with symptomatic COVID-19 in those who were vaccinated compared with the number of cases observed in a placebo control group. It is not trivial to assess differences in efficacy between vaccine platforms or even vaccine products using similar platforms, since trials are performed at different locations, during different time periods, and sometimes, with different endpoints or criteria for scoring positive cases. However, in essence all approved vaccines have shown very good efficacy, demonstrating induction of Ab levels of similar or higher magnitude as those observed in convalescent individuals, and near complete protection against hospitalization and severe disease [152, 169]. As a comparison, vaccine efficacy for seasonal influenza is typically 30%–60%, depending on the year, and how well the vaccine matches the circulating virus strains.
In addition to the clinical phase 3 studies, very encouraging ‘real world’ data are now becoming available. Reports from the early initiated mass-vaccination using the Pfizer/BioNTech’s mRNA vaccine in Israel demonstrated 46%–74% efficacy after the first dose and 87%–95% after the second dose in terms of protection against symptomatic disease [170–172]. Another large study of healthcare workers in the UK (in which participants were PCR tested every second week), showed vaccine efficacy for protection against symptomatic infection to be 70% after the first dose and 85% 1 week after the second dose of the Pfizer/BioNTech’s mRNA vaccine . In a report issued by the UK government, the first dose was 78% and 75% effective at preventing hospitalizations after alpha or delta virus infection , while two doses conferred 92% and 94% protection, respectively. Future studies will also inform the duration of vaccine-induced protection. Interestingly, work from Israel suggests that mass-vaccination not only protected the vaccinated individuals, but also provided cross-protection to unvaccinated contacts, such as children under the age of 16 . Recent studies showed that the largest benefit of vaccination was obtained after two vaccine doses .
Additional reports from vaccine follow-up studies in different countries are likely forthcoming. It will be important to determine potential differences in vaccine efficacy between different age groups for different vaccines, if re-infections are more frequent in the elderly and, importantly, whether the frequency of breakthrough infections increases over time as vaccine-immunity wanes and/or new variants spread. Furthermore, a deeper understanding of adverse vaccine-induced responses, as reported for all platforms in use, is necessary to gain the public’s trust.
Protection against Variants of Concern
A major concern is that the vaccine efficacy will be reduced with the spread of viruses that carry mutations in key neutralizing Ab epitopes, allowing the virus to partially evade Ab recognition. If so, the vaccines may need to be updated to induce potent neutralizing Ab responses against new strains – as currently happens with seasonal flu vaccinations.
Recently, it was documented that neutralizing Ab responses induced by the current vaccines, which are based on the original Wuhan SARS-CoV-2 spike, are less active against the rapidly-spreading delta variant (B.1.617.2, originally isolated in India). Similar loss of neutralization potency in vaccinated sera were reported against alpha (B.1.1.7, originally isolated in the UK), beta (B.1.351, originally isolated in South Africa) and gamma (P.1, originally isolated in Brazil) variants. This means that the vaccines are less potent against these variants. Consistent with this, emerging data from the Israeli Health Ministry suggest that the current circulation of the delta variant there has already resulted in a reduction of vaccine efficacy in preventing symptomatic disease from above 90% to 64%, and this may drop further as individual antibody levels wane – suggesting the need for third doses before the winter season to protect the most vulnerable groups.
Given the high global transmission levels and the risk of new variants arising, continued virus surveillance will be needed for a foreseeable future. This is especially important as vaccine-induced Ab levels wane over time, in some cases below protective levels. So far, studies of breakthrough infections in vaccinated persons demonstrate that these are predominantly caused by Variants of Concern, like the Delta variant.
Therefore, boosting the immune response with a variant vaccine may be needed as soon as this falls, especially in the elderly population. However, it is important to note that, even if some classes of Abs lose reactivity, the overall anti-Spike protein Ab response, including to the RBD, is polyclonal and consists of Abs that also recognize the VoCs. Although virus-specific T cells are less affected by the mutations in the VoCs, it is known since many decades that cross strain-reactive T cells recognizing influenza virus, for example, are not sufficient to protect against reinfection and reduce disease burden. This is evident from the fact that updated seasonal influenza vaccines are required yearly to elicit Abs to the new circulating strains. The role of neutralizing Abs as a correlate of protection for COVID-19 vaccines is becoming increasingly clear.
An interesting study demonstrated that Abs elicited in individuals infected with the SARS-CoV-2 beta variant (B.1.351) displayed potent cross-neutralizing activity against both the original Wuhan virus and the alpha variant (B.1.117). This is promising for future vaccine strategies based on variant S antigens. Spike subunit vaccines, especially mRNA-based vaccines, can be rapidly redesigned and produced to match variant viruses and can be administered several times, unlike adenovirus-based vaccines that are hampered by anti-vector immune responses.
Induction and durability of vaccine-induced immunity
While one dose of most of the currently approved COVID-19 vaccines is sufficient to provide protection against moderate or severe disease, most SARS-CoV-2 vaccines require two or more doses to achieve durable protection. The higher Ab levels obtained after the second vaccine injection also provide improved cross-neutralizing activity against VoCs. A strategy in situations of vaccine shortage is to vaccinate as many persons in the population as possible with one dose and delay the second dose to provide some level of protection to as many as possible to reduce the number of severe cases and hospitalizations at large. The drawback of this approach is that optimal protection is not achieved in the period between the first and the second dose, resulting in a group of people who may be susceptible to reinfection, especially with VoCs such as delta, and which may contribute to the transmission chain. How the vaccines are administered in the real world is influenced by practical considerations such as availability of vaccines and estimations about what vaccination strategies will most effectively curb high transmission rates in the population.
As for SARS-CoV-2 and other infections, vaccine-induced Abs naturally wane with time; these antibodies drop off quite quickly, with a significant reduction after three months. Ongoing and future studies will reveal how durable the vaccine responses to the SARS-CoV-2 vaccines are. Since the level of Abs (one correlate of protection) required to prevent infection or disease is still not defined, the optimal time point for additional booster vaccination is not yet known and may differ between different age groups. Studies have shown that mRNA vaccine-induced Abs were detected at low levels 6 months after vaccination, and at this time the Ab levels had waned to levels where a significant reduction in the cross-neutralizing capacity to variant strains was observed.
Vaccination after recovering from COVID-19
Protective immunity after SARS-CoV-2 infection is generally good, and the risk to be re-infected is low although not non-existent. The extent to which protective immune responses last depends upon the time that has elapsed since the infection and how robust the peak Ab responses were. Other factors such as health status, age, and whether the re-exposure is with a VoC to which the pre-existing Abs may be less effective also plays a role . Ab responses to vaccination in individuals who were previously infected with SARS-CoV-2 are potent, at the same or higher level than those achieved with two vaccine doses. Some countries have therefore recommended that individuals with a documented prior SARS-CoV-2 infection only need one vaccine dose, and/or should wait an extended period before receiving the second dose. Antibodies induced by vaccination appear to a large extent to resemble those induced by natural infection. Clonal lineages elicited by a prior infection can be expanded and improved upon by subsequent vaccination. Consequently, the neutralizing Ab activity is broader and more cross-reactive against variant viruses in such cases . Preliminary data suggest vaccine-elicited Abs are more focused to the RBD on the S protein than Abs elicited by infection . Further studies aimed at dissecting the Ab response following natural infection or vaccination are needed to determine if there are qualitative differences in the breadth of the neutralizing Ab response between individuals, including against VoCs.
The pandemic has resulted in that new vaccines were successfully developed in record time, capitalizing upon years of scientific advances in molecular technologies and in-depth understanding of immune and infection mechanisms. In the future, it is possible that annual vaccination against SARS-CoV-2, analogous to seasonal influenza vaccines, will be recommended for some age groups, depending on disease susceptibility and the magnitude of community transmission. Furthermore, it will be important to address in large future studies, what Ab titers are required for protection against disease or infection.
Antibodies, immunity and public health
Antibody testing remains our best way to estimate past SARS-CoV-2 infection and a positive vaccine response, although many factors, such as waning responses, need to be considered. In the context of SARS-CoV-2, anti-S Abs are particularly important, as they develop in the majority of infections . As IgM and IgA isotypes generally wane in the peripheral circulation with viral clearance, they are not as useful for monitoring individual and population responses as IgG molecules, although they may help illuminate the clinical picture in a COVID-19 patient. However, not all Ab tests are of equal sensitivity and specificity [201–206], and while high-quality tests are now available, there is a range of tests of varying performance. The considerable inter-individual differences in anti-viral Ab levels and nature [33, 39, 48] call for international guidelines and improved regulatory standards for Ab testing. This would facilitate comparisons between studies monitoring previous infection and vaccination, and positively impact clinical medicine related to COVID-19 at the individual level.
Currently, mass-produced tests for clinical and community use (many of which have low specificity and sensitivity) are based on individual domains of S (e.g., S1, S2, RBD) as these are easier to produce for large distribution. However, as some of these antigens are not produced in a native form, some antigenic specificities may be missed, especially when Ab titers are in the low range, for example, with time from infection/vaccination and if the assay platform has a relatively high limit of detection. For example, lateral flow tests (ideally suited for quick results in the field and for large population surveys) that require a drop of fresh blood to be deposited on a membrane, struggle to detect low titer responses, while anti-SARS-CoV-2 IgG can be detectable at a 1:200,000 serum dilution by ELISA . Therefore, the quality of population seroprevalence studies may vary greatly depending on the configuration of the test that was used.
Even different versions of stabilized S glycoprotein trimers, which aim to mimic the native S conformation in vivo, have different antigenic properties that can impart important differences to detailed molecular studies of Ab specificities, which could be important when analyzing VOCs. The choice of Ag is also important for biological, rather than technical reasons. For example, approximately 10% of PCR-positive individuals do not have detectable anti-nucleocapsid (N)-directed IgG responses [33, 36, 48], although they do have anti-S and -RBD responses at the same time. In the future, platforms with low limits of detection and using novel statistical methods, will improve upon antibody test sensitivity, specificity and error rate , while new technologies for home-based tests will facilitate the logistics of population-wide testing as routine. It seems reasonable that public health authorities provide additional guidelines to public healthcare systems to help them navigate the large number of products on the market, especially as assays for different SARS-CoV-2 variants enter the market.
Despite these technical limitations, thanks to sero-surveillance, before vaccines were widely distributed, we know that no location worldwide had achieved herd immunity after natural SARS-CoV-2 infection, except perhaps isolated populations or clusters. For example, Manaus, Brazil suffered amongst the highest seroprevalence in response to the first wave of SARS-CoV-2, estimated at greater than two-thirds of the population , yet this population was not spared a severe second wave and on-going infection burden. Other locations with a high seroprevalence after the first wave included New York City, USA (20%)  and Lombardy, Italy (23%) . Seroprevalence has been shown to increase alongside on-going viral transmission , and the toll on public health has been severe.
Evaluation of SARS-CoV-2 spike-specific IgG responses at the population level is, therefore, critical for determining public health measures that aim to curtail transmission. Such analyses need to be increasingly applied to different demographic groups, including children, to gain further epidemiological understanding and COVID-19 management strategies. Monitoring individual- and population-level Ab responses after vaccination will also be critical for determining the efficacy of different vaccine platforms, including how long Ab responses last and for issuing ‘vaccine/past infection certificates’, which will be required for several lines of employment (e.g., elderly care home staff), much like the Hepatitis B vaccination is required to practice human and veterinary medicine in most developed economies. Indeed, it could be argued that antibody test results are more useful for demonstrating immunity in those previously vaccinated than the current vaccination certificates, although the specific assays used for this purpose would need additional regulatory oversight.
As viral adaptation to humans continues apace, it is possible that herd immunity to SARS-CoV-2 will not be achieved, even after vaccination, although this remains to be seen. This necessitates the ongoing urgent need for vaccination and the characterization of the molecular response to infection/vaccination over longer timeframes, as well as knowledge about how responses change with regards to different viral variants – to protect those most vulnerable. Indeed, if SARS-CoV-2 is not eradicated, it may turn out to be the case that children born today, unless vaccinated, contract SARS-CoV-2 alongside other respiratory infections of modernity, such as flu, rhinoviruses and endemic CoVs. By the time they reach adulthood, with what we know about SARS-CoV-2 and other infections, it holds that these children will be better equipped immunologically to face re-infection and will accordingly suffer lower morbidity and mortality in response to infection that naïve adults and elderly people do today. Alternatively, new mutations in S could increase re-infection, transmission and disease severity, even in the young, arguing for discussion of vaccination in all age groups, as equitably as possible. Thus, many questions remain about this new human infection. Despite the global challenges posed by SARS-CoV-2, the pandemic provides an unrivalled opportunity to learn about viruses and the human immune system at the population level and improve pandemic preparedness through global cooperation.