Immunity to SARS-CoV-2 induced by infection or vaccination

Introduction

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 [121]) 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 [122]), 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 [123].

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 [127]. 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 [128]. Smaller studies [129] in different contexts (e.g., a fishing vessel outbreak [130] and elderly care homes [131]) 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 [139]. 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 [151], and emerging data suggest that the current SARS-CoV-2 vaccines are no exception [152]. 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 [153], while adoptive transfer of purified IgG from convalescent non-human primates protected naive animals against challenge with SARS-CoV-2 [154].

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 [165], 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 [166]. COVID-19 vaccines given intra-nasally are under development [167], 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 [168].

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.

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 [30]. 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 [33]. 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 [38], 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 [207], 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%) [208] and Lombardy, Italy (23%) [209]. Seroprevalence has been shown to increase alongside on-going viral transmission [210], 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.

Future outlook

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.