One of the biggest challenges for vaccination, especially when it comes to airborne viruses—such as flu viruses, for example—is the emergence of new variants caused by mutations in the virus genome. Mutations occur naturally during the replication of any RNA virus due to the instability of the RNA molecules ^[1]. In the case of COVID-19, even before it was considered a pandemic, data related to the genomic surveillance of SARS-CoV-2 were available as a useful tool for investigating outbreaks and tracking evolution and possible new waves ^[2][3]. As a result, more than 25 billion sequences of SARS-CoV-2 have been performed worldwide, and it is estimated that at least two mutations in the viral genome occur per month ^[3][4]. These additional mutations often result in distinct immune-evasion mechanisms and lead to the appearance of different variants and lineages ^[5]. Currently, there are 21 variants of SARS-CoV-2; among them, variants Alpha a (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529) are considered as variants of concern (VOCs), while Lambda (C.37) and Mu (B.1.621) are considered as variants of interest (VOIs). It is emphasized that, in addition to these two categories, there are also variants under monitoring (VUMs), which are those strains that have genetic mutations that may pose a risk in the future, but for which phenotypic and epidemiological changes are currently unclear ^[6].

Because one of their characteristics is lower susceptibility to vaccines and other therapeutic alternatives, VOCs have been intensively monitored ^[7]. Modifications found in the structure of the S protein of SARS-CoV-2 have been attributed to the greater ability of the virus to escape the action of neutralizing antibodies ^[6][8]. Important examples of mutational mechanisms that lead to increased antigenic properties of protein S are the amino acid substitutions that alter the protein epitope, increase receptor-binding avidity, and lead to changes in glycosylation, deletion or insertion of residues, and allosteric structural effects ^[9]. These factors strongly contribute to the increased mortality and morbidity of SARS-CoV-2 ^[9][10][11], where the transmissibility can be up to 74% higher when compared to the original strain ^[12][13].

Since the SARS-CoV-2 S protein is the main target of COVID-19 vaccines, the mutations in this protein are of great concern, especially those which have the corresponding sequences of reference strain Wuhan-Hu-1—that is, no antigens based on different variants are used ^[14][15]. Thus, the appearance of variants with modifications in the SARS-CoV-2 S protein structure raises questions about the effectiveness of the vaccines available to the population; antibodies derived from the original strain (Wuhan-Hu-1) may have only a partial neutralizing effect against these viruses ^[16]. The vaccines BNT162b2 (brand name Comirnaty), mRNA-1273 (brand name Spikevax), CoronaVac, BBIBP-CorV, AZD-1222 (brand name Vaxzevria or Covishield), and Ad26.COV2-S (brand name Janssen COVID-19 Vaccine) are the most widely used around the world for COVID-19 prophylaxis, since all of them use the S protein as the main activator of the immune system ^[17]. Therefore, different studies have been published or are being conducted to analyze the efficacy or effectiveness of each of these vaccines against SARS-CoV-2 variants of concern.

Analysis of several studies shows that the efficiency or effectiveness of vaccines against SARS-CoV-2 variants depends on many factors, including the sample size, demographic factors, host factors, the type of vaccine, the number of doses, a heterologous or homologous booster vaccination scheme, and the time after primary vaccination is completed ^[7][18][19]. Different authors demonstrated that the application of a booster dose after a certain period is able to increase the humoral immune response against SARS-CoV-2, resulting in increased efficacy or effectiveness of vaccines against the VOC ^{[20][21][22][23][24]}. Bruxvoort et al. ^[25] found data that reinforced the need for booster dose administration, since primary immunization with mRNA-1273 shows limited protection against the Delta, Alpha, Gamma, and Mu variants. Andrews et al. ^[26] reported that administration of the booster dose with BNT162b2 after primary immunization of ChAdOx1, mRNA-1273, or BNT162b2 was able to significantly increase protection against Omicron. Other authors reported that the homologous booster regimen of BNT162b2, mRNA-1273, CoronaVac and BBIBP-CorV vaccines and the heterologous booster with Ad26.COV2.S associated with mRNA-1273 vaccines showed similar performance against Omicron ^[27][28].

Data provided by the Control and Prevention (CDC) show that the number of cases and deaths caused by COVID-19 in the United States is higher among unvaccinated individuals when compared to individuals with a full primary vaccination scheme and/or those who have already received a booster dose, regardless of the vaccine administered (BNT162b2, mRNA-1273, or Ad26.COV2-S) ^[29]. Among those vaccinated, although the three vaccines showed similar efficacy in reducing COVID-19 infection in the period evaluated (April 2021 to February 2022), it was observed that the number of deaths among individuals vaccinated with Ad26.COV2-S was higher when compared to the mRNA vaccines (BNT162b2 and mRNA-1273) ^[29]. In early January 2022, during the wave caused by the Omicron variant, the highest incidence per 100,000 population occurred, where the rates reached 5.44, 2.34, and 1.79 for the Ad26.COV2-S, BNT162b2, and mRNA-1273 vaccines, respectively, after the primary vaccination scheme ^[29]. However, it is important to note that the mortality rate among those who received the Ad26.COV2-S vaccine was lower compared to unvaccinated individuals, where the rate was ~9 times higher. Although it has already been reported that the Ad26.COV2-S vaccine can elicit a stable humoral and cellular response over time, data reported by the CDC suggest that the immune response induced by mRNA vaccines may be more effective in reducing mortality rates ^[30][31]. The greater efficacy observed in mRNA vaccines may be a reflection of their advantages as a technological platform; unlike adenovirus (DNA)-based vaccines, once administered, RNA molecules do not need to cross the nuclear membrane or transcription to start the protein-synthesis process ^[32]. Hence, these data encouraged discussions about the immune protection of the Ad26.COV2-S vaccine, particularly with a view to the possible implementation of the intervals required for the application of new booster doses.

Because of this, since the second half of 2021, health authorities around the world have been recommending booster doses for different vaccines to contain the spread of SARS-CoV-2 and consequently control the pandemic in terms of the number of hospitalizations and deaths ^{[33][34][35][36]}. Andrews et al. ^[37] conducted in England demonstrated that the administration of a booster dose with mRNA vaccines (BNT162b2 or mRNA-1273) compared to the primary immunization showed an efficiency between 94 and 97% in reducing symptomatic cases of the disease, while against hospitalization or death, the value found ranged between 97% and 99%. Studies conducted in Israel have also shown the same trend, which strengthens the importance of this new vaccination strategy ^[38][39][40]. Furthermore, studies involving computer modeling have shown that the administration of the booster dose will be able to decrease the effective reproduction number (R0), while authors have pointed out that the predicted increase in antibody titers induced by the booster dose provides important protection from infection with SARS-CoV-2 variants ^[41][42][43].

Currently, the application of a new booster dose (usually the fourth dose) has been recommended in different countries due to the emergence of the Omicron variant, which has a greater transmission capacity than the other variants and, consequently, has been associated with an increase in the number of reinfection cases ^[44][45][46]. Initially, the administration of this new dose was directed towards priority groups, such as healthcare workers, immunocompromised individuals, and the elderly; however, new groups are expected to be included soon ^[47][48]. A preliminary one released by the Israeli Ministry of Health in adults aged >60 years demonstrated that a fourth dose of the BNT162b2 vaccine was able to increase immune protection up to two-fold against SARS-CoV-2 infection and up to three-fold against severe disease when compared to individuals who received only the third dose ^[49]. The expectation that new VOCs will emerge over time exposes one of the main challenges associated with developing COVID-19 vaccines, that of using products capable of inducing a robust and/or long-lasting immune response against different variants ^[50][51].

In early November, a new COVID-19 sublineage named BA.2 was first reported ^[52] (2 months after variation BA.1, which rapidly became dominant due to immune-escape mechanisms ^[53][54]). In a public statement, WHO defined it as an Omicron sublineage, classifying it as a variant of concern. According to the organization, the amino acids differences in structural proteins have possibly conferred a growth advantage when compared to other Omicron sublineages (BA.1, BA. 1.1.), but not greater severity ^[55]. In later March, the US Centers for Disease Control and Prevention (CDC) reported that BA.2 was responsible for 55% (50.8–59.1%—95% PI) COVID-19 cases ^[56], followed by BA. 1.1 (40.4%, 36.4–44.5%—95% PI). The rapid spread of BA.2 has raised discussions about reinfection and vaccine efficacy. Although BA.2’s ability to evade neutralizing antibodies is unclear, authors have demonstrated evidence that the increasing frequency of BA.2 is probably related to increased transmissibility rather than to enhanced immunologic escape ^[57]. On the other hand, initial data from population-level reinfection studies suggest that infection with BA.1 provides strong protection against reinfection with BA.2 ^[58]. Recent studies have demonstrated that mRNA vaccines (BNT162b2 and mRNA-1273) provide similar protection against BA.1 (46.6% (95% CI: 33.4–57.2%) and BA.2 51.7% (95% CI: 43.2–58.9%) in the first three months, and this declines to about 10% after 4–6 months. These findings show that protection against BA.2 did not seem to wane any faster than protection against BA.1. Furthermore, in both cases, a second dose was able to recuperate immune protection levels ^[59]. Therefore, until now, recent data supported the need for a vaccine targeting the Omicron variant.

Within this context, in January 2022 the companies Pfizer and BioNTech, developers of the BNT162b2 vaccine, started a clinical trial to evaluate the safety, immunogenicity, and tolerability of an Omicron-based vaccine candidate. To this end, it will be conducted with healthy adults between the ages of 18 and 55 who may be allocated into three distinct cohorts with different dose regimens of the vaccine candidate ^[60]. Similarly, the pharmaceutical company Moderna (developer of the mRNA-1273 vaccine) is expected to start a clinical trial for the analysis of a new vaccine candidate against the Omicron variant in the first half of 2022 ^[61]. In addition, different institutes have supported the idea of investing in the development of a pan-coronavirus vaccine capable of protecting against several coronaviruses, including the different strains of SARS-CoV-2 ^[61][62].

Importantly, the development of Omicron-specific vaccines should not completely rule out the use of previously approved vaccines made available to the population, as robust data are still needed to elucidate the induction of the immune response after the first booster dose and its role in controlling infection or disease progression by this variant. Furthermore, one cannot exclude the possible “selective pressure” exerted by vaccines and even by monoclonal antibody therapy in targeting the S protein, since this may have influenced the appearance of new variants with mutations in this region, thus conferring escape mechanisms ^[63]. Therefore, new therapeutic targets must be considered for the development of new vaccines.

Due to the pandemic nature of COVID-19 and the various impacts generated in the global health, social and economic sectors, the vaccines against SARS-CoV-2 infection were made available in record time ^[64]. This was also because many scientists, manufacturers, and research institutions were already developing innovative technology platforms for new vaccines, which were eventually adapted for COVID-19 prevention. However, since no coronavirus vaccine had been licensed and approved for use in humans previously, the rapid development associated with the limited follow-up time post-vaccination and lack of information about long-term side effects of the vaccines aroused great public concern about the safety profile of the available vaccines ^[65]. It is important to note that as mass vaccination progresses, more post-vaccination adverse events are reported ^[66]. This demonstrates that vaccine safety information from ongoing clinical trials and surveillance data is important not only for building public confidence, but also for making evidence-based health-policy decisions ^[67]. The safety of vaccines is evaluated through adverse event monitoring in randomized controlled trials and safety post-licensure surveillance data after immunization campaigns ^[68]. Determining the safety profile of a vaccine is a critical step at the global level and is monitored by the WHO along with manufacturers, health officials, and national regulatory agencies ^[69][70][71], since they are drugs administered in healthy populations. According to the WHO, all available vaccines, including the COVID-19 vaccines, have been rigorously assessed for safety for diverse groups of people, according to age, sex, ethnicity, and medical conditions.

For the mRNA vaccines, the most commonly reported adverse events are local reactions at the injection site, such as pain, redness, and swelling, and systemic reactions, such as headache, myalgia, arthralgia, and chills ^[72]. In clinical studies evaluating the mRNA-1273 and BNT162b2 vaccines, the frequency and severity of these adverse events were higher after the administration of the second dose. When it comes to adenoviral vector vaccines, in the case of the AZD 1222 vaccine, pain, fever, chills, muscle ache, headache, and malaise were the most common adverse reactions. Regarding serious adverse events, seven have been associated with the AZD-122 vaccine, including transverse myelitis ^[73]. Overall, inactivated virus vaccines such as CoronaVac, BBIBP-CorV, and COVXIN have a good safety profile, with few grade 3 adverse reactions. In the elderly population, studies with vaccines of distinct technologies, such as AZD 1222 (modified adenovirus) and NVX-CoV2373 (protein adjuvant), for example, showed a good antibody response and low reactogenicity events after administration, with a higher incidence and severity of adverse events observed in younger subjects ^[74].

Another rare manifestation after vaccination, but which has been reported in different studies, is multisystem inflammatory syndrome (MIS) ^[75]. MIS has still poorly understood pathophysiology, however, it is believed to occur due to an exaggerated immune response against SARS-CoV-2 infection due to persistently high levels of IgG and activation of CD8+ T cells ^[76][77]. Considering the adult population, MIS may result from a delayed and dysregulated immune response and is characterized by the onset of symptoms such as fever, elevated inflammatory markers, as well as multiple-organ involvement (especially of the heart, stomach, and intestines) ^[78][79]. Different case studies have reported the onset of MIS in adults after immunization with the vaccine based on mRNA ^[80], inactivated virus ^[81], and adenovirus ^[82]. However, a crucial question was demonstrated by Belay et al. ^[83], in which the report of MIS after vaccination in adult patients was also associated with prior SARS-CoV-2 infection. These data demonstrate the need for further studies to elucidate the real association between MIS caused purely by vaccination or whether there is a direct relationship with previous viral infection.

It is interesting to highlight that most of the side effects that people experience after COVID-19 vaccination can be attributed to the “nocebo” effect. Nocebo refers to the non-pharmacological adverse effects reported after exposure to a placebo substance, which are usually motivated by the individual’s expectation that, after exposure to a vaccine, drug, or other medical intervention, some disagreeable event will occur ^[84][85]. Haas et al. ^[86] evaluated the frequency of adverse events in the placebo arm in 12 clinical studies of COVID-19 vaccines (mRNA-1273, CoV2 preS dTM, NVX-CoV2373, AZD-1222, BNT162b2, BNT162b1, and SCB-2019) at different phases of clinical development, and the results found demonstrate that while adverse events were mostly reported in the arms receiving the experimental vaccines, subjects receiving the placebo reported a significant frequency of adverse events. These results highlight the importance of critically evaluating the safety of experimental vaccines, especially when some minority groups are known to be resistant to COVID-19 vaccination ^[87][88].

When it comes to serious adverse events, particular concern has emerged related to the safety of COVID-19 during pregnancy due to reported cases of thrombosis and thrombocytopenia syndrome after vaccination with AZD 1222 in early 2021 ^[89]. Despite the devastating consequences of COVID-19 infection in pregnant women and the availability of vaccine safety and efficacy data in different populations, data related to vaccine safety in pregnant women are still limited, since most of the ongoing clinical trials do not include pregnant women ^[90]. However, preclinical and toxicological COVID-19 vaccine studies have found no safety concerns with no adverse effect on female reproduction, fertility, fetal or embryonal, or postnatal development, or miscarriage ^[90][91][92]. For mRNA vaccines, surveillance data demonstrated that vaccine-related adverse events in pregnant women were similar to those in non-pregnant women, with pain in the local area of the injection, fatigue, headache, and myalgia being the most frequent local and systemic reactions after vaccination ^[90]. Regarding the safety of COVID-19 vaccines for the fetus or breastfeeding infant, various expert panels suggest that mRNA-based and adenovirus vector vaccines do not possess any significant risk ^[93][94].

Currently, the main safety concerns for COVID-19 vaccines are related to mRNA vaccines, with the emergence of cases of myocarditis and pericarditis. Myocarditis is the inflammation of the heart muscle, while pericarditis is the inflammation of the outer lining of the heart. In both cases, the immune system causes inflammation in response to an infection or some other factor. Both can occur during infections, including SARS-CoV-2 infection. For inflammation caused by mRNA vaccines, one of the first one involving the evaluation of the incidence of myocarditis after vaccination with Pfizer’s vaccine (BNT162b2 or Comirnaty) was published in October 2021 in the New England Journal of Medicine. It was conducted with patients in a large Israeli healthcare system who had received at least one dose of the vaccine. It was reported an estimated incidence of myocarditis of 2.13 cases per 100,000 people; the highest incidence was among male patients between the ages of 16 and 29. Most of myocarditis were mild or moderate in severity ^[95]. According to the CDC, myocarditis is a rare and serious adverse event that has been associated with mRNA-based COVID-19 vaccines, in this case BNT162b2. The reporting rates of vaccine-associated myocarditis appear to be highest among males aged 12–29 years. As of 31 December 2021, myocarditis among children aged 5–11 years is classified as rare, where 11 Vaccine Adverse Event Reporting System (VAERS)-verified reports were received after the administration of approximately eight million doses of vaccine, and in an active vaccine safety surveillance system, no confirmed reports of myocarditis were observed during the 1–21 days or 1–42 days after 333,000 doses of vaccine were administered to children of the same age. Two deaths following the BNT162b2 vaccine were reported in children with multiple chronic medical conditions, where, in the initial one, no data were found to suggest a causal association between death and vaccination.

It is important to compare the cases among vaccinated and infected ones. The incidence of COVID-19-associated cardiac injury or myocarditis can be 100 times higher than COVID-19 mRNA-vaccine-related myocarditis ^[96][97]. Another relevant observation is that cases of myocarditis and pericarditis have been reported mainly for mRNA vaccines ^[98]; in Brazil, no cases have been reported related to inactivated virus-based vaccines ^[99]. The possible mechanisms underlying heart injury side-effects in specific groups were brightly hypothesized by Heymans and Cooper ^[96], where, according to the authors, mRNA vaccines might trigger immune hyper immunity in a minority population that is genetically susceptible to developing acute myocarditis after viral injury ^[100]. In summary, they indicated three potential mechanisms: hormonal differences (the sex-specific distinction can be explained by hormone-related factors); mRNA immune reactivity (genetic variants in HLA genes); and antibodies to SARS-CoV-2 spike glycoproteins cross-reacting with myocardial contractile proteins (genotypes in desmosomal, cytoskeletal or sarcomeric protein).