Adversomics: a new paradigm for vaccine safety and design

Vaccinomics and adversomics: key elements for a personalized vaccinology

Vaccines are one of the most important and effective tools in the prevention of infectious diseases and research about all the aspects of vaccinology are essential to increase the number of available vaccines more and more safe and effective. Despite the unquestionable value of vaccinations, vaccine hesitancy has spread worldwide compromising the success of vaccinations. Currently, the main purpose of vaccination campaigns is the immunization of whole populations with the same vaccine formulations and schedules for all individuals. A personalized vaccinology approach could improve modern vaccinology counteracting vaccine hesitancy and giving great benefits for human health. This ambitious purpose would be possible by facing and deepening the areas of vaccinomics and adversomics, two innovative areas of study investigating the role of a series of variables able to influence the immune response to vaccinations and the development of serious side effects, respectively. We reviewed the recent scientific knowledge about these innovative sciences focusing on genetic and non-genetic basis involved in the individual response to vaccines in terms of both immune response and side effects.

Assessment of adherence to pre-vaccination precautions and AEFI reporting practices during BCG vaccination in 4 hospitals in Ghana

The BCG vaccine, like all other vaccines, is associated with adverse events following immunization (AEFI). Reducing the incidence of AEFI is crucial in reposing confidence in BCG vaccination and reducing hesitancy associated with the vaccine. This requires safety precautions before and during vaccinations, as well as reporting AEFIs after vaccination. This study assessed the adherence of health-care professionals to pre-vaccination precautions and adverse events following immunization (AEFI) reporting practices during BCG vaccination in four hospitals in Ghana. It is hoped that the findings of the study will serve as a baseline to identify gaps for further studies to generate a stronger evidence for policy formulation aimed at improving BCG vaccine safety in Ghana and other tuberculosis endemic countries. A cross-sectional study design was employed, and Statistical Package for Social Sciences, IBM® SPSS version 25 (SPSS Inc. USA) software was used for analysis. Chi-square and binary logistic regression tests were used to test the association between categorical variables and predictors of adherence to pre-BCG vaccination precautions, respectively, and a p-value of <.05 was considered statistically significant. The AEFIs commonly reported by mothers included abscess, injection site pain, injection site redness, fever, rash, muscle weakness, diarrhea, vomiting, coughing and rhinitis. Ninety-three participants (73.2%) were adherent to pre-BCG vaccination precautions. Ninety-two participants (72.4%) informed mothers to report all AEFIs encountered. Adherence to pre-BCG vaccination precautions and AEFI reporting were generally good; however, there is still room for improvement.

Assessing vaccine safety during a pandemic: Recent experience and lessons learned for the future

During the roll out of vaccines during a pandemic, questions regarding vaccine safety often arise. This was surely true during the SARS-CoV-2 pandemic. Different tools and capabilities exist during the pre-authorization phase and post introduction each with its strengths and limitations. Here we review the various tools and their strengths and limitations and discuss what functioned well in high income settings and the limitations that unequal vaccine safety pharmacovigilance capacity imposed upon middle and low income countries.

Predictors for reactogenicity and humoral immunity to SARS-CoV-2 following infection and mRNA vaccination: A regularized, mixed-effects modelling approach

Introduction

The influence of pre-existing humoral immunity, inter-individual demographic factors, and vaccine-associated reactogenicity on immunogenicity following COVID vaccination remains poorly understood.

Methods

Ten-fold cross-validated least absolute shrinkage and selection operator (LASSO) and linear mixed effects models were used to evaluate symptoms experienced by COVID+ participants during natural infection and following SARS-CoV-2 mRNA vaccination along with demographics as predictors for antibody (AB) responses to recombinant spike protein in a longitudinal cohort study.

Results

In previously infected individuals (n=33), AB were more durable and robust following primary vaccination when compared to natural infection alone. Higher AB were associated with experiencing dyspnea during natural infection, as was the total number of symptoms reported during the COVID-19 disease course. Both local and systemic symptoms following 1st and 2nd dose (n=49 and 48, respectively) of SARS-CoV-2 mRNA vaccines were predictive of higher AB after vaccination. Lastly, there was a significant temporal relationship between AB and days since infection or vaccination, suggesting that vaccination in COVID+ individuals is associated with a more robust immune response.

Discussion

Experiencing systemic and local symptoms post-vaccine was suggestive of higher AB, which may confer greater protection.

Immune Response and Molecular Mechanisms of Cardiovascular Adverse Effects of Spike Proteins from SARS-CoV-2 and mRNA Vaccines

The SARS-CoV-2 (severe acute respiratory syndrome coronavirus responsible for the COVID-19 disease) uses the Spike proteins of its envelope for infecting target cells expressing on the membrane the angiotensin converting enzyme 2 (ACE2) enzyme that acts as a receptor. To control the pandemic, genetically engineered vaccines have been designed for inducing neutralizing antibodies against the Spike proteins. These vaccines do not act like traditional protein-based vaccines, as they deliver the message in the form of mRNA or DNA to host cells that then produce and expose the Spike protein on the membrane (from which it can be shed in soluble form) to alert the immune system. Mass vaccination has brought to light various adverse effects associated with these genetically based vaccines, mainly affecting the circulatory and cardiovascular system. ACE2 is present as membrane-bound on several cell types, including the mucosa of the upper respiratory and of the gastrointestinal tracts, the endothelium, the platelets, and in soluble form in the plasma. The ACE2 enzyme converts the vasoconstrictor angiotensin II into peptides with vasodilator properties. Here we review the pathways for immunization and the molecular mechanisms through which the Spike protein, either from SARS-CoV-2 or encoded by the mRNA-based vaccines, interferes with the Renin-Angiotensin-System governed by ACE2, thus altering the homeostasis of the circulation and of the cardiovascular system. Understanding the molecular interactions of the Spike protein with ACE2 and the consequent impact on cardiovascular system homeostasis will direct the diagnosis and therapy of the vaccine-related adverse effects and provide information for development of a personalized vaccination that considers pathophysiological conditions predisposing to such adverse events.

Will Omics Biotechnologies Save Us from Future Pandemics? Lessons from COVID-19 for Vaccinomics and Adversomics

The COVID-19 pandemic had cross-cutting impacts on planetary health, quotidian life, and society. Mass vaccination with the current gene-based vaccines has helped control the pandemic but unfortunately it has not shown effectiveness in preventing the spread of the virus. In addition, not all individuals respond to these vaccines, while others develop adverse reactions that cannot be neglected. It is also a fact that some individuals are more susceptible to infection while others develop effective immunization post-infection. We note here that the person-to-person and population variations in vaccine efficacy and side effects have been studied in the field of vaccinomics long before the COVID-19 pandemic. Additionally, the field of adversomics examines the mechanisms of individual differences in the side effects of health interventions. In this review, we discuss the potential of a multi-omics approach for comprehensive profiling of the benefit/risk ratios of vaccines. Vaccinomics and adversomics stand to benefit planetary health and contribute to the prevention of future pandemics in the 21st century by offering precision guidance to clinical trials as well as promoting precision use of vaccines in ways that proactively respond to individual and population differences in their efficacy and safety. This vision of pandemic prevention based on personalized instead of mass vaccination also calls for equity in access to precision vaccines and diagnostics that support a vision and practice of vaccinomics and adversomics in planetary health.

2022 AAHA Canine Vaccination Guidelines

These guidelines are an update and extension of previous AAHA peer-reviewed canine vaccination guidelines published in 2017. Vaccination is a cornerstone of canine preventive healthcare and one of the most cost-effective ways of maintaining a dog's health, longevity, and quality of life. Canine vaccination also serves a public health function by forming a barrier against several zoonotic diseases affecting dogs and humans. Canine vaccines are broadly categorized as containing core and noncore immunizing antigens, with administration recommendations based on assessment of individual patient risk factors. The guidelines include a comprehensive table listing canine core and noncore vaccines and a recommended vaccination and revaccination schedule for each vaccine. The guidelines explain the relevance of different vaccine formulations, including those containing modified-live virus, inactivated, and recombinant immunizing agents. Factors that potentially affect vaccine efficacy are addressed, including the patient's prevaccination immune status and vaccine duration of immunity. Because animal shelters are one of the most challenging environments for prevention and control of infectious diseases, the guidelines also provide recommendations for vaccination of dogs presented at or housed in animal shelters, including the appropriate response to an infectious disease outbreak in the shelter setting. The guidelines explain how practitioners can interpret a patient's serological status, including maternally derived antibody titers, as indicators of immune status and suitability for vaccination. Other topics covered include factors associated with postvaccination adverse events, vaccine storage and handling to preserve product efficacy, interpreting product labeling to ensure proper vaccine use, and using client education and healthcare team training to raise awareness of the importance of vaccinations.

Potential Immunologic and Integrative Methods to Enhance Vaccine Safety

Vaccine safety is measured by the disease protection it confers compared to the harm it may cause; both factors and their relative numbers have been the subject of disagreement. Cross-reactive attack of analogous self-antigens modified by dietary and microbiome factors is one of the poorly explored likely causes of harm. Screening for that and other risk factors might point out those most likely to develop severe vaccine reactions. Cooperation from those with opinions for and against vaccination in data gathering and vetting will lead to greater safety. Screening should include an integrative medical perspective regarding diet, microbiome, leaky gut, and other antigen sources. It might include emerging electronic technology or integrative energetic techniques vetted ultimately by cross-reactive lymphocyte testing or genetic evaluation. The knowledge gained from evaluating those with reactions could enhance the screening process and, since similar antigenic stimuli and reactions are involved, help long COVID sufferers. Centers for early identification and rescue from vaccine reactions could lower morbidity and mortality, and increase the percentage of people choosing to be vaccinated. Additional platforms for boosting; using lower dosage; other routes of administration, such as intranasal or intradermal needles; and possibly different antigens could make it easier to vaccinate globally to address the new variants of viruses rapidly arising.

Analyzing the Systems Biology Effects of COVID-19 mRNA Vaccines to Assess Their Safety and Putative Side Effects

COVID-19 vaccines have been instrumental tools in reducing the impact of SARS-CoV-2 infections around the world by preventing 80% to 90% of hospitalizations and deaths from reinfection, in addition to preventing 40% to 65% of symptomatic illnesses. However, the simultaneous large-scale vaccination of the global population will indubitably unveil heterogeneity in immune responses as well as in the propensity to developing post-vaccine adverse events, especially in vulnerable individuals. Herein, we applied a systems biology workflow, integrating vaccine transcriptional signatures with chemogenomics, to study the pharmacological effects of mRNA vaccines. First, we derived transcriptional signatures and predicted their biological effects using pathway enrichment and network approaches. Second, we queried the Connectivity Map (CMap) to prioritize adverse events hypotheses. Finally, we accepted higher-confidence hypotheses that have been predicted by independent approaches. Our results reveal that the mRNA-based BNT162b2 vaccine affects immune response pathways related to interferon and cytokine signaling, which should lead to vaccine success, but may also result in some adverse events. Our results emphasize the effects of BNT162b2 on calcium homeostasis, which could be contributing to some frequently encountered adverse events related to mRNA vaccines. Notably, cardiac side effects were signaled in the CMap query results. In summary, our approach has identified mechanisms underlying both the expected protective effects of vaccination as well as possible post-vaccine adverse effects. Our study illustrates the power of systems biology approaches in improving our understanding of the comprehensive biological response to vaccination against COVID-19.

COVID-19 Pandemic-Revealed Consistencies and Inconsistencies in Healthcare: A Medical and Organizational View

The circumstances of the Coronavirus disease caused by the SARS-CoV-2 virus (COVID-19) pandemic have had a significant impact on global and national developments, affecting the existence of society in all its expressions, as well as the lives of people themselves. In the context of the pandemic, increased attention has been focused on acute measures, but the ending of the pandemic is expected as a resolution of the related healthcare problems. However, there are several indicators that the COVID-19 pandemic might induce long-term consequences for individual and public health. Some of the consequences are inferred and predictable, but there are also areas of medicine that have been indirectly affected by the pandemic, and these consequences have not yet been sufficiently explored. This study is focused on drawing attention to some of the COVID-19 pandemic consistencies and the pandemic-revealed inconsistencies in healthcare. Content analysis and statistical analysis were applied to achieve the aim of the study. The main findings of the study address chronic disease burden (particularly, myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS)), healthcare governance and organizational issues, and the synergy between health policy perspectives and innovative solutions in practice. The study provides insight into the particular healthcare issues affected by the COVID-19 pandemic, such as the increase in mortality in some diagnoses besides COVID-19 and the possible emergence of a new type of resistance—vaccine-resistance—contemporaneously supporting the identification of the tendencies and currently unnoticed indirect consistencies and inconsistencies revealed by the pandemic.

Will Host Genetics Affect the Response to SARS-CoV-2 Vaccines? Historical Precedents

Recent progress in genomics and bioinformatics technologies have allowed for the emergence of immunogenomics field. This intersection of immunology and genetics has broadened our understanding of how the immune system responds to infection and vaccination. While the immunogenetic basis of the huge clinical variability in response to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is currently being extensively studied, the host genetic determinants of SARS-CoV-2 vaccines remain largely unknown. Previous reports evidenced that vaccines may not protect all populations or individuals equally, due to multiple host- and vaccine-specific factors. Several studies on vaccine response to measles, rubella, hepatitis B, smallpox, and influenza highlighted the contribution of genetic mutations or polymorphisms in modulating the innate and adaptive immunity following vaccination. Specifically, genetic variants in genes encoding virus receptors, antigen presentation, cytokine production, or related to immune cells activation and differentiation could influence how an individual responds to vaccination. Although such knowledge could be utilized to generate personalized vaccine strategies to optimize the vaccine response, studies in this filed are still scarce. Here, we briefly summarize the scientific literature related to the immunogenetic determinants of vaccine-induced immunity, highlighting the possible role of host genetics in response to SARS-CoV-2 vaccines as well.

Chronic spontaneous urticaria after BNT162b2 mRNA (Pfizer-BioNTech) vaccination against SARS-CoV-2

Background: The factors that trigger and exacerbate chronic spontaneous urticaria (CSU) are well known, but it is not unclear whether messenger RNA (mRNA) vaccination against severe acute respiratory syndrome coronavirus 2 can trigger new cases of CSU or a relapse of CSU after long-term remission. Objective: To study the clinical cases of patients with new-onset CSU and CSU in remission who relapsed within 3 months after BNT162b2 mRNA vaccination. Methods: All patients with a CSU diagnosis within 12 weeks of BNT162b2 mRNA vaccination were retrospectively identified and included in the new-onset CSU and the relapsed CSU groups. The first control group (CSU control group) retrospectively consisted of patients diagnosed with CSU in complete clinical remission for ≥ 6 months, with no CSU relapse after vaccination. The second control group (healthy control group) consisted of subjects who were fully vaccinated and without CSU, matched 1:2 for age and sex with patients with CSU. Results: Twenty-seven patients were included in the relapsed CSU group, 32 patients in the new-onset CSU group, 179 patients in the CSU control group, and 476 subjects in the healthy control group. The relapsed CSU and new-onset CSU groups had more allergic comorbidities overall (19 [70.4%] and 13 [40.6%], respectively) than the CSU control group and the healthy control group (50 [27.9%] and 110 [23.1%], respectively; p < 0.001). Multiple logistic regression analysis showed that a positive autologous serum skin test result, overall allergic comorbidities, and basopenia were positively associated with the probability of CSU relapse within 3 months after BNT162b2 mRNA vaccination (odds ratio [OR] 5.54 [95% confidence interval {CI}, 2.36-13.02], p < 0.001); OR 6.13 [95% CI, 2.52-14.89], p = 0.001; and OR 2.81 [95% CI, 1.17-6.72, p = 0.020, respectively). Conclusion: It is possible that BNT162b2 mRNA vaccination serves as a provoking and/or relapsing factor of CSU in individuals with allergic diseases and/or predisposed autoimmunity.

Responding to Questions from Parents with Vaccine Concerns

INTRODUCTION

Even with the benefits of vaccinations, some parents refuse vaccinations because of the influence of vaccine opponents. The purpose of this article is to identify common vaccine concerns on public forums and address these concerns with scientific evidence, thereby offering pediatric nurse practitioners (PNPs) information on how to respond.

METHOD

Six electronic databases were searched to identify parental concerns regarding vaccines and provide evidence-based responses to each concern.

RESULTS

Some parents are concerned that health care providers do not obtain written informed consent before vaccinating their children. Another common concern is that pharmaceutical companies are solely motivated by financial profits when manufacturing vaccines. Parents also share concerns about vaccine manufacturers' exemption from liability for those who suffer a vaccine-related injury.

DISCUSSION

PNPs are responsible for addressing parents' concerns regarding vaccines and providing the public with correct information. PNPs are in a prime position to influence parental vaccine decision-making positively.

Adverse events following pediatric immunization in an Indian city

Purpose

Adverse effects are noticeable immediately after vaccination, especially when vaccinated to healthy people at the time of vaccination. The vaccine may cause adverse events which are very rare but adverse event following immunization surveillance becomes correspondingly more important in a less studied population like India. Hence, there is a need for carrying out a study pertaining to vaccine safety in the pediatric population of age 0-12 years and assessing the events occurring post-vaccination.

Materials and Methods

A prospective observational study was conducted in three primary healthcare centers and two tertiary care hospitals for 6 months from April 2016 to September 2016 with a total of 826 children enrolled. Detected adverse events for suspected vaccines were analyzed for causality by the World Health Organization causality assessment instrument. Sex-specific differences in incidences of adverse events were assessed.

Results

The cumulative adverse events were found highest in pentavalent vaccines (510 incidences, 62.04%) followed by the bacillus Calmette-Guérin vaccine (189 incidences, 22.99%). The study didn't reveal any significant association in incidences of adverse events following immunization and sex of the children.

Conclusion

Vaccine safety surveillance studies are need of the hour in developing countries to maintain public trust in vaccines, the ultimate objective being to have vaccines with the most favorable benefit-risk profile. The present study discussed the various adverse events following immunization and suggested the absence of any sex-specific difference in incidences of adverse events in children.

MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses

The recent viral outbreaks and the current pandemic situation urges us to timely address any emerging viral infections by designing therapeutic strategies. Multi-omics and therapeutic data are of great interest to develop early remedial interventions. This work provides a therapeutic data platform (Mammarenavirus (MMV)-db) for pathogenic mammarenaviruses with potential catastrophic effects on human health around the world. The database integrates vaccinomics and RNA-based therapeutics data for seven human pathogenic MMVs associated with severe viral hemorrhagic fever and lethality in humans. Protein-specific cytotoxic T lymphocytes, B lymphocytes, helper T-cell and interferon-inducing epitopes were mapped using a cluster of immune-omics-based algorithms and tools for the seven human pathogenic viral species. Furthermore, the physiochemical and antigenic properties were also explored to guide protein-specific multi-epitope subunit vaccine for each species. Moreover, highly efficacious RNAs (small Interfering RNA (siRNA), microRNA and single guide RNA (sgRNA)) after extensive genome-based analysis with therapeutic relevance were explored. All the therapeutic RNAs were further classified and listed on the basis of predicted higher efficacy. The online platform (http://www.mmvdb.dqweilab-sjtu.com/index.php) contains easily accessible data sets and vaccine designs with potential utility in further computational and experimental work. Conclusively, the current study provides a baseline data platform to secure better future therapeutic interventions against the hemorrhagic fever causing mammarenaviruses. Database URL: http://www.mmvdb.dqweilab-sjtu.com/index.php.

Active Vaccine Safety Surveillance: Global Trends and Challenges in China

Importance. The great success in vaccine-preventable diseases has been accompanied by vaccine safety concerns. This has caused vaccine hesitancy to be the top 10 in threats to global health. The comprehensive understanding of adverse events following immunization should be entirely based on clinical trials and postapproval surveillance. It has increasingly been recognized worldwide that the active surveillance of vaccine safety should be an essential part of immunization programs due to its complementary advantages to passive surveillance and clinical trials.Highlights. In the present study, the framework of vaccine safety surveillance was summarized to illustrate the importance of active surveillance and address vaccine hesitancy or safety concerns. Then, the global progress of active surveillance systems was reviewed, mainly focusing on population-based or hospital-based active surveillance. With these successful paradigms, the practical and reliable ways to create robust and similar systems in China were discussed and presented from the perspective of available databases, methodology challenges, policy supports, and ethical considerations.Conclusion. In the inevitable trend of the global vaccine safety ecosystem, the establishment of an active surveillance system for vaccine safety in China is urgent and feasible. This process can be accelerated with the consensus and cooperation of regulatory departments, research institutions, and data owners.

Ethically utilising COVID-19 host-genomic data

Genetic variants that influence susceptibility to COVID-19 have recently been identified. In this manuscript, we identify and discuss some of the ethical and practical issues raised by these studies. We first outline the ethical case for providing COVID-19 susceptibility testing to healthcare workers, as well as highlighting risks associated with privacy and discrimination. We then argue that the existence of genetically susceptible individuals has implications for the ethical conduct of COVID-19 human challenge trials. Finally, we discuss the ethical issues that could arise from other COVID-19 host–genome interactions, including the prospect of personalized vaccines.

Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development

Vaccination is one of the most important innovations in human history. It has also become a hot research area in a new application - the development of new vaccines against non-infectious diseases such as cancers. However, effective and safe vaccines still do not exist for many diseases, and where vaccines exist, their protective immune mechanisms are often unclear. Although licensed vaccines are generally safe, various adverse events, and sometimes severe adverse events, still exist for a small population. Precision medicine tailors medical intervention to the personal characteristics of individual patients or sub-populations of individuals with similar immunity-related characteristics. Precision vaccinology is a new strategy that applies precision medicine to the development, administration, and post-administration analysis of vaccines. Several conditions contribute to make this the right time to embark on the development of precision vaccinology. First, the increased level of research in vaccinology has generated voluminous "big data" repositories of vaccinology data. Secondly, new technologies such as multi-omics and immunoinformatics bring new methods for investigating vaccines and immunology. Finally, the advent of AI and machine learning software now makes possible the marriage of Big Data to the development of new vaccines in ways not possible before. However, something is missing in this marriage, and that is a common language that facilitates the correlation, analysis, and reporting nomenclature for the field of vaccinology. Solving this bioinformatics problem is the domain of applied biomedical ontology. Ontology in the informatics field is human- and machine-interpretable representation of entities and the relations among entities in a specific domain. The Vaccine Ontology (VO) and Ontology of Vaccine Adverse Events (OVAE) have been developed to support the standard representation of vaccines, vaccine components, vaccinations, host responses, and vaccine adverse events. Many other biomedical ontologies have also been developed and can be applied in vaccine research. Here, we review the current status of precision vaccinology and how ontological development will enhance this field, and propose an ontology-based precision vaccinology strategy to support precision vaccine research and development.

Vaccinomics and Adversomics in the Era of Precision Medicine: A Review Based on HBV, MMR, HPV, and COVID-19 Vaccines

Precision medicine approaches based on pharmacogenomics are now being successfully implemented to enable physicians to predict more efficient treatments and prevention strategies for a given disease based on the genetic background of the patient. This approach has already been proposed for vaccines, but research is lagging behind the needs of society, and precision medicine is far from being implemented here. While vaccinomics concerns the effectiveness of vaccines, adversomics concerns their side effects. This area has great potential to address public concerns about vaccine safety and to promote increased public confidence, higher vaccination rates, and fewer serious adverse events in genetically predisposed individuals. The aim here is to explore the contemporary scientific literature related to the vaccinomic and adversomic aspects of the three most-controversial vaccines: those against hepatitis B, against measles, mumps, and rubella, and against human Papilloma virus. We provide detailed information on the genes that encode human leukocyte antigen, cytokines and their receptors, and transcription factors and regulators associated with the efficacy and safety of the Hepatitis B and Measles, Mumps and Rubella virus vaccines. We also investigate the future prospects of vaccinomics and adversomics of a COVID-19 vaccine, which might represent the fastest development of a vaccine ever.

Human papilloma virus vaccination in males: A pharmacovigilance study on the Vaccine Adverse Event Reporting System

AIMS

Human papilloma virus (HPV) is 1 of the most common sexually transmitted infection responsible for different types of cancer: cervical, penile, vulvar, anal and oropharyngeal. It can affect both males and females. Our aim was to enrich the knowledge on the safety profiles of HPV vaccines in the male population.

METHODS

We reviewed all the reports of adverse events following immunization (AEFI) present in the US Vaccine Adverse Event Reporting System from 1 January 2006 to 30 September 2018. Statistical data mining was performed using the reporting odds ratio with 95% confidence interval in order to detect disproportionality in reporting.

RESULTS

A total of 5493 reports of AEFI were retrieved. The events most reported and that proportionally occurred more frequently with HPV vaccines than with others in males were: syncope (n = 701, reporting odds ratio = 2.85, 95% confidence interval [1.41-5.76p), loss of consciousness (n = 425, 2.79 [1.36-5.72]) and fall (n = 272, 3.54 [2.00-6.26]).

CONCLUSION

Most of the AEFIs were already reported in premarketing clinical trials and acknowledged for the corresponding vaccines. A disproportionate reporting was found for some of these events including syncope. The HPV vaccines are generally well tolerated in males, although limitations own of spontaneous reporting should be considered.

Current Challenges in Vaccinology

The development of vaccines, which prime the immune system to respond to future infections, has led to global declines in morbidity and mortality from dreadful infectious communicable diseases. However, many pathogens of public health importance are highly complex and/or rapidly evolving, posing unique challenges to vaccine development. Several of these challenges include an incomplete understanding of how immunity develops, host and pathogen genetic variability, and an increased societal skepticism regarding vaccine safety. In particular, new high-dimensional omics technologies, aided by bioinformatics, are driving new vaccine development (vaccinomics). Informed by recent insights into pathogen biology, host genetic diversity, and immunology, the increasing use of genomic approaches is leading to new models and understanding of host immune system responses that may provide solutions in the rapid development of novel vaccine candidates.

Causality assessment of adverse events following immunization: the problem of multifactorial pathology

The analysis of Adverse Events Following Immunization (AEFI) is important in a balanced epidemiological evaluation of vaccines and in the issues related to national vaccine injury compensation programs. If manufacturing defects or vaccine storage and delivering errors are excluded, the majority of adverse reactions to vaccines occur as excessive or biased inflammatory and immune responses. These unwanted phenomena, occasionally severe, are associated with many different endogenous and exogenous factors, which often interact in complex ways. The confirmation or denial of the causal link between an AEFI and vaccination is determined pursuant to WHO guidelines, which propose a four-step analysis and algorithmic diagramming. The evaluation process from the onset considers all possible "other causes" that can explain the AEFI and thus exclude the role of the vaccine. Subsequently, even if there was biological plausibility and temporal compatibility for a causal association between the vaccine and the AEFI, the guidelines ask to look for any possible evidence that the vaccine could not have caused that event. Such an algorithmic method presents some concerns that are discussed here, in the light of the multifactorial nature of the inflammatory and immune pathologies induced by vaccines, including emerging knowledge of genetic susceptibility to adverse effects. It is proposed that the causality assessment could exclude a consistent association of the adverse event with the vaccine only when the presumed "other cause" is independent of an interaction with the vaccine. Furthermore, the scientific literature should be viewed not as an exclusion criterion but as a comprehensive analysis of all the evidence for or against the role of the vaccine in causing an adverse reaction. These issues are discussed in relation to the laws that, in some countries, regulate the mandatory vaccinations and the compensation for those who have suffered serious adverse effects.

Causality assessment of adverse events following immunization: the problem of multifactorial pathology

The analysis of Adverse Events Following Immunization (AEFI) is important in a balanced epidemiological evaluation of vaccines and in the issues related to vaccine injury compensation programs. The majority of adverse reactions to vaccines occur as excessive or biased inflammatory and immune responses. These unwanted phenomena, occasionally severe, are associated with many different endogenous and exogenous factors, which often interact in complex ways. The confirmation or denial of the causal link between an AEFI and vaccination is determined pursuant to WHO guidelines, which propose a four-step analysis and algorithmic diagramming. The evaluation process from the onset considers all possible "other causes" that might explain the AEFI and thus exclude the role of the vaccine. Subsequently, even if there was biological plausibility and temporal compatibility for a causal association between the vaccine and the AEFI, the guidelines ask to look for any possible evidence that the vaccine could not have caused that event. Such an algorithmic method presents several concerns that are discussed here, in the light of the multifactorial nature of the inflammatory and immune pathologies induced by vaccines, including emerging knowledge of genetic susceptibility to adverse effects. It is proposed that the causality assessment could exclude a consistent association of the adverse event with the vaccine only when the presumed "other cause" is independent of an interaction with the vaccine. Furthermore, the scientific literature should be viewed not as an exclusion criterion but as a comprehensive analysis of all the evidence for or against the role of the vaccine in causing an adverse reaction. Given these inadequacies in the evaluation of multifactorial diseases, the WHO guidelines need to be reevaluated and revised. These issues are discussed in relation to the laws that, in some countries, regulate the mandatory vaccinations and the compensation for those who have suffered serious adverse effects.

[Distrust of vaccination: Why?]

Vaccines have saved millions of lives and reduced the severity of many infections. A reduction in vaccination coverage is now reflected in the re-emergence of epidemics of mumps, pertussis, measles and chickenpox. Many people do not recognize the effectiveness of vaccination and fear the side effects. The main concern is the safety of vaccines. Lack of information weighs less than lack of trust in health authorities. The greater responsibility of the individual and the respect for his free will, may lead the authorities to a less vigourous promotion of the "vaccination duty" which is also a social duty. The attitude of individuals is guided by their health beliefs which are often supported by an erroneous perception of risk. In addition, insidious anti-vaccine lobbying plays on fears and uses biased reasoning that the media help to amplify. Thus the analysis of the brakes to vaccination both in the general population and among health professionals, the dismantling of the arguments developed by the anti-vaccine leagues and vigilance with regard to "fake news" should allow a concerted communication, transparent, clear and effective, in order to limit the occurrence of preventable deaths.

SleepOMICS: How Big Data Can Revolutionize Sleep Science

Sleep disorders have reached epidemic proportions worldwide, affecting the youth as well as the elderly, crossing the entire lifespan in both developed and developing countries. "Real-life" behavioral (sensor-based), molecular, digital, and epidemiological big data represent a source of an impressive wealth of information that can be exploited in order to advance the field of sleep research. It can be anticipated that big data will have a profound impact, potentially enabling the dissection of differences and oscillations in sleep dynamics and architecture at the individual level ("sleepOMICS"), thus paving the way for a targeted, "one-size-does-not-fit-all" management of sleep disorders ("precision sleep medicine").

Unraveling the enigma: elucidating the relationship between the physicochemical properties of aluminium-based adjuvants and their immunological mechanisms of action

Aluminium salts are by far the most commonly used adjuvants in vaccines. There are only two aluminium salts which are used in clinically-approved vaccines, Alhydrogel® and AdjuPhos®, while the novel aluminium adjuvant used in Gardasil® is a sulphated version of the latter. We have investigated the physicochemical properties of these two aluminium adjuvants and specifically in milieus approximating to both vaccine vehicles and the composition of injection sites. Additionally we have used a monocytic cell line to establish the relationship between their physicochemical properties and their internalisation and cytotoxicity. We emphasise that aluminium adjuvants used in clinically approved vaccines are chemically and biologically dissimilar with concomitantly potentially distinct roles in vaccine-related adverse events.

Adverse Events Following Immunization in Brazil: Age of Child and Vaccine-Associated Risk Analysis Using Logistic Regression

Objective: Vaccines are effective in controlling and eradicating infectious diseases. However, adverse events following immunization (AEFI) can occur in susceptible individuals. The objective of this study was to analyze the Brazilian AEFI database and compare eight vaccines in order to profile risks of AEFIs related to the mandated pediatric schedule of immunization, considering the age and sex of the child, type of vaccine, and reported adverse events. Methods: We analyzed the Brazilian AEFI database integrating reports between 2005 and 2010 for children less than 10-years old immunized with eight mandated vaccines: diphtheria, pertussis, tetanus, Haemophilus influenzae type b (TETRA); diphtheria, tetanus, and pertussis (DTP); Bacillus Calmette–Guerin (BCG); oral poliovirus vaccine (OPV); measles, mumps, and rubella (MMR); oral rotavirus vaccine (ORV); hepatitis B (HB); and yellow fever (YF). We compared the children’s age regarding types of AEFI, evaluated AEFI factors associated with the chance of hospitalization of the child, and estimated the chance of notification of an AEFI as a function of the type of vaccine. In total, 47,105 AEFIs were observed for the mandated vaccines. Results: The highest AEFI rate was for the TETRA vaccine and the lowest was for the OPV vaccine, with 60.1 and 2.3 events per 100,000 inoculations, respectively. The TETRA vaccine showed the highest rate of hypotonic hyporesponsive episode, followed by convulsion and fever. The MMR and YF vaccines were associated with generalized rash. BCG was associated with enlarged lymph glands but showed the largest negative (protective) association with hyporesponsive events and seizures. Compared with children aged 5–9-years old, young children (<1 year) showed significantly higher odds of hospitalization. Conclusions: The Brazilian AEFI registry is useful to compare the magnitude and certain characteristics of adverse events associated with mandated pediatric vaccines.

Vaccines Meet Big Data: State-of-the-Art and Future Prospects. From the Classical 3Is ("Isolate-Inactivate-Inject") Vaccinology 1.0 to Vaccinology 3.0, Vaccinomics, and Beyond: A Historical Overview

Vaccines are public health interventions aimed at preventing infections-related mortality, morbidity, and disability. While vaccines have been successfully designed for those infectious diseases preventable by preexisting neutralizing specific antibodies, for other communicable diseases, additional immunological mechanisms should be elicited to achieve a full protection. “New vaccines” are particularly urgent in the nowadays society, in which economic growth, globalization, and immigration are leading to the emergence/reemergence of old and new infectious agents at the animal–human interface. Conventional vaccinology (the so-called “vaccinology 1.0”) was officially born in 1796 thanks to the contribution of Edward Jenner. Entering the twenty-first century, vaccinology has shifted from a classical discipline in which serendipity and the Pasteurian principle of the three Is (isolate, inactivate, and inject) played a major role to a science, characterized by a rational design and plan (“vaccinology 3.0”). This shift has been possible thanks to Big Data, characterized by different dimensions, such as high volume, velocity, and variety of data. Big Data sources include new cutting-edge, high-throughput technologies, electronic registries, social media, and social networks, among others. The current mini-review aims at exploring the potential roles as well as pitfalls and challenges of Big Data in shaping the future vaccinology, moving toward a tailored and personalized vaccine design and administration.

The use of databases, data mining and immunoinformatics in vaccinology: where are we?

INTRODUCTION

Vaccinology has evolved from a sub-discipline focussed on simplistic vaccine development based on antibody-mediated protection to a separate discipline involving epidemiology, host and pathogen biology, immunology, genomics, proteomics, structure biology, protein engineering, chemical biology, and delivery systems. Data mining in combination with bioinformatics has provided a scaffold linking all these disciplines to the design of vaccines and vaccine adjuvants. Areas covered: This review provides background knowledge on immunological aspects which have been exploited with informatics for the in silico analysis of immune responses and the design of vaccine antigens. Furthermore, the article presents various databases and bioinformatics tools, and discusses B and T cell epitope predictions, antigen design, adjuvant research and systems immunology, highlighting some important examples, and challenges for the future. Expert opinion: Informatics and data mining have not only reduced the time required for experimental immunology, but also contributed to the identification and design of novel vaccine candidates and the determination of biomarkers and pathways of vaccine response. However, more experimental data is required for benchmarking immunoinformatic tools. Nevertheless, developments in immunoinformatics and reverse vaccinology, which are nascent fields, are likely to hasten vaccine discovery, although the path to regulatory approval is likely to remain a necessary impediment.

Early molecular correlates of adverse events following yellow fever vaccination

The innate immune response shapes the development of adaptive immunity following infections and vaccination. However, it can also induce symptoms such as fever and myalgia, leading to the possibility that the molecular basis of immunogenicity and reactogenicity of vaccination are inseparably linked. To test this possibility, we used the yellow fever live-attenuated vaccine (YFLAV) as a model to study the molecular correlates of reactogenicity or adverse events (AEs). We analyzed the outcome of 68 adults who completed a YFLAV clinical trial, of which 43 (63.2%) reported systemic AEs. Through whole-genome profiling of blood collected before and after YFLAV dosing, we observed that activation of innate immune genes at day 1, but not day 3 after vaccination, was directly correlated with AEs. These findings contrast with the gene expression profile at day 3 that we and others have previously shown to be correlated with immunogenicity. We conclude that although the innate immune response is a double-edged sword, its expression that induces AEs is temporally distinct from that which engenders robust immunity. The use of genomic profiling thus provides molecular insights into the biology of AEs that potentially forms a basis for the development of safer vaccines.

Personalized vaccinology: A review

At the current time, the field of vaccinology remains empirical in many respects. Vaccine development, vaccine immunogenicity, and vaccine efficacy have, for the most part, historically been driven by an empiric “isolate-inactivate-inject” paradigm. In turn, a population-level public health paradigm of “the same dose for everyone for every disease” model has been the normative thinking in regard to prevention of vaccine-preventable infectious diseases. In addition, up until recently, no vaccines had been designed specifically to overcome the immunosenescence of aging, consistent with a post-WWII mentality of developing vaccines and vaccine programs for children. It is now recognized that the current lack of knowledge concerning how immune responses to vaccines are generated is a critical barrier to understanding poor vaccine responses in the elderly and in immunoimmaturity, discovery of new correlates of vaccine immunogenicity (vaccine response biomarkers), and a directed approach to new vaccine development.

The new fields of vaccinomics and adversomics provide models that permit global profiling of the innate, humoral, and cellular immune responses integrated at a systems biology level. This has advanced the science beyond that of reductionist scientific approaches by revealing novel interactions between and within the immune system and other biological systems (beyond transcriptional level), which are critical to developing “downstream” adaptive humoral and cellular responses to infectious pathogens and vaccines. Others have applied systems level approaches to the study of antibody responses (a.k.a. “systems serology”), [1] high-dimensional cell subset immunophenotyping through CyTOF, [2,3] and vaccine induced metabolic changes [4]. In turn, this knowledge is being utilized to better understand the following: identifying who is at risk for which infections; the level of risk that exists regarding poor immunogenicity and/or serious adverse events; and the type or dose of vaccine needed to fully protect an individual. In toto, such approaches allow for a personalized approach to the practice of vaccinology, analogous to the substantial inroads that individualized medicine is playing in other fields of human health and medicine. Herein we briefly review the field of vaccinomics, adversomics, and personalized vaccinology.

Assessment of sex-specific differences in adverse events following immunization reporting in Ontario, 2012-15

We assessed sex-specific trends within passive vaccine safety surveillance in Ontario, Canada. AEFIs reported following vaccines administered between 2012 and 2015 were included. There were 2466 AEFI reports; 66.2% were female. Annualized reporting rates were 5.9 and 3.1 per 100,000 population, for females and males respectively. The female:male reporting rate ratio (RRR) was 1.9. Sex-specific differences by age group were greatest in adults 18-64years (RRR 6.3); whereas there were no differences in children <10years. Vaccine-specific RRRs were highest for vaccines recommended for routine use in adults or high risk populations. All event categories were female-predominant. The highest event-specific RRRs were for oculorespiratory syndrome (5.1), anaesthesia/paraesthesia (4.6) and anaphylaxis (3.0). Serious AEFIs (n=113) were more evenly distributed (57.5% female, RRR 1.3) than non-serious (66.6% female, RRR 1.9). AEFI reporting among females was consistently elevated within the passive surveillance system in Ontario. Further study of the relationship between sex/gender and AEFI reporting is needed.

Vaccinology in the third millennium: scientific and social challenges

The epidemiology of deaths due to vaccine-preventable diseases has been significantly and positively altered through the use of vaccines. Despite this, significant challenges remain in vaccine development and use in the third millennium. Both new (Ebola, Chikungunya, Zika, and West Nile) and re-emerging diseases (measles, mumps, and influenza) require the development of new or next-generation vaccines. The global aging of the population, and accumulating numbers of immunocompromised persons, will require new vaccine and adjuvant development to protect large segments of the population. After vaccine development, significant challenges remain globally in the cost and efficient use and acceptance of vaccines by the public. This article raises issues in these two areas and suggests a way forward that will benefit current and future generations.

[Development of new vaccines]

Recent and important advances in the fields of immunology, genomics, functional genomics, immunogenetics, immunogenomics, bioinformatics, microbiology, genetic engineering, systems biology, synthetic biochemistry, proteomics, metabolomics and nanotechnology, among others, have led to new approaches in the development of vaccines. The better identification of ideal epitopes, the strengthening of the immune response due to new adjuvants, and the search of new routes of vaccine administration, are good examples of advances that are already a reality and that will favour the development of more vaccines, their use in indicated population groups, or its production at a lower cost. There are currently more than 130 vaccines are under development against the more wished (malaria or HIV), difficult to get (CMV or RSV), severe re-emerging (Dengue or Ebola), increasing importance (Chagas disease or Leishmania), and nosocomial emerging (Clostridium difficile or Staphylococcus aureus) infectious diseases.