Vaccine design, evaluation, and community-based use for antigenically variable infectious agents

Dynamic immunodominance hierarchy of neutralizing antibody responses to evolving GII.4 noroviruses

A paradigm of RNA viruses is their ability to mutate and escape from herd immunity. Because antibody responses are a major effector for viral immunity, antigenic sites are usually under strong diversifying pressure. Here, we use norovirus as a model to study mechanisms of antigenic diversification of non-enveloped, fast-evolving RNA viruses. We comprehensively characterize all variable antigenic sites involved in virus neutralization and find that single neutralizing monoclonal antibodies (mAbs) map to multiple antigenic sites of GII.4 norovirus. Interactions of multiple epitopes on the viral capsid surface provide a broad mAb-binding repertoire with a remarkable difference in the mAb-binding profiles and immunodominance hierarchy for two distantly related GII.4 variants. Time-ordered mutant viruses confirm a progressive change of antibody immunodominance along with point mutations during the process of norovirus evolution. Thus, in addition to point mutations, switches in immunodominance that redirect immune responses could facilitate immune escape in RNA viruses.

Virulence management: Closing the feedback loop between healthcare interventions and virulence evolution

We study the evolution of virulence of an endemic pathogen in response to healthcare interventions which affect host recovery and pathogen transmission. By anticipating the evolutionary response of the pathogen we may develop effective long-term management strategies for controlling the impact of the endemic on the society. To that end, we use standard Adaptive Dynamics techniques in an SIS model. The recovery rate and the transmission rate, both of which can be affected by healthcare interventions, are used as evolutionary control variables. The effect of interventions may be density-independent (self-help based on healthcare instructions) or density-dependent (when assistance of a healthcare worker is required). We consider the evolutionary response of the pathogen both to abrupt changes and to gradual changes in the level of healthcare intervention. Healthcare intervention is optimised for three alternative objectives: minimisation of virulence, minimisation of the probability that an infected individual dies of the disease, and total eradication of the endemic. We find that the optimal strategy may depend on the objective. High levels of healthcare intervention may eradicate the pathogen, but this option may not be available for budgetary reasons or otherwise. Counterintuitively, to minimise virulence, one should keep healthcare interventions at a minimum, while to minimise the probability for an infected individual to die of the disease, both low and high levels of healthcare intervention suffice. Changes in the level of healthcare intervention should be implemented fast (not gradually) in order to avoid sudden changes in pathogen evolution and the possible emergence of multiple simultaneously coexisting pathogen strains.

Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) Index: a Rapid and Accessible Tool That Exploits Genomic Data in Public Health and Clinical Microbiology Applications

As microbial genomics makes increasingly important contributions to clinical and public health microbiology, the interpretation of whole-genome sequence data by nonspecialists becomes essential. In the absence of capsule-based vaccines, two protein-based vaccines have been used for the prevention of invasive serogroup B meningococcal disease (IMD) since their licensure in 2013 and 2014. These vaccines have different components and different levels of coverage of meningococcal variants. Hence, decisions regarding which vaccine to use in managing serogroup B IMD outbreaks require information about the index case isolate, including (i) the presence of particular vaccine antigen variants, (ii) the expression of vaccine antigens, and (iii) the likely susceptibility of its antigen variants to antibody-dependent bactericidal killing.

As microbial genomics makes increasingly important contributions to clinical and public health microbiology, the interpretation of whole-genome sequence data by nonspecialists becomes essential. In the absence of capsule-based vaccines, two protein-based vaccines have been used for the prevention of invasive serogroup B meningococcal disease (IMD) since their licensure in 2013 and 2014. These vaccines have different components and different levels of coverage of meningococcal variants. Hence, decisions regarding which vaccine to use in managing serogroup B IMD outbreaks require information about the index case isolate, including (i) the presence of particular vaccine antigen variants, (ii) the expression of vaccine antigens, and (iii) the likely susceptibility of its antigen variants to antibody-dependent bactericidal killing. To obtain this information requires a multitude of laboratory assays, impractical in real-time clinical settings, where the information is most urgently needed. To facilitate assessment for public health and clinical purposes, we synthesized genomic and experimental data from published sources to develop and implement the Meningococcal Deduced Vaccine Antigen Reactivity (MenDeVAR) Index, which is publicly available on PubMLST (https://pubmlst.org). Using whole-genome sequences or individual gene sequences obtained from IMD isolates or clinical specimens, the MenDeVAR Index provides rapid evidence-based information on the presence and possible immunological cross-reactivity of different meningococcal vaccine antigen variants. The MenDeVAR Index enables practitioners who are not genomics specialists to assess the likely reactivity of vaccines for individual cases, outbreak management, or the assessment of public health vaccine programs. The MenDeVAR Index has been developed in consultation with, but independently of, both the 4CMenB (Bexsero; GSK) and rLP2086 (Trumenba; Pfizer, Inc.) vaccine manufacturers.

Neisseria gonorrhoeae Population Genomics: Use of the Gonococcal Core Genome to Improve Surveillance of Antimicrobial Resistance

BACKGROUND

Gonorrhea, caused by the bacterium Neisseria gonorrhoeae, is a globally prevalent sexually transmitted infection. The dynamics of gonococcal population biology have been poorly defined due to a lack of resolution in strain typing methods.

METHODS

In this study, we assess how the core genome can be used to improve our understanding of gonococcal population structure compared with current typing schemes.

RESULTS

A total of 1668 loci were identified as core to the gonococcal genome. These were organized into a core genome multilocus sequence typing scheme (N gonorrhoeae cgMLST v1.0). A clustering algorithm using a threshold of 400 allelic differences between isolates resolved gonococci into discrete and stable core genome groups, some of which persisted for multiple decades. These groups were associated with antimicrobial genotypes and non-overlapping NG-STAR and NG-MAST sequence types. The MLST-STs were more widely distributed among core genome groups.

CONCLUSIONS

Clustering with cgMLST identified globally distributed, persistent, gonococcal lineages improving understanding of the population biology of gonococci and revealing its population structure. These findings have implications for the emergence of antimicrobial resistance in gonococci and how this is associated with lineages, some of which are more predisposed to developing antimicrobial resistance than others.

Antigenic variability: Obstacles on the road to vaccines against traditionally difficult targets

Despite the impressive impact of vaccines on public health, the success of vaccines targeting many important pathogens and cancers has to date been limited. The burden of infectious diseases today is mainly caused by antigenically variable pathogens (AVPs), which escape immune responses induced by prior infection or vaccination through changes in molecular structures recognized by antibodies or T cells. Extensive genetic and antigenic variability is the major obstacle for the development of new or improved vaccines against "difficult" targets. Alternative, qualitatively new approaches leading to the generation of disease- and patient-specific vaccine immunogens that incorporate complex permanently changing epitope landscapes of intended targets accompanied by appropriate immunomodulators are urgently needed. In this review, we highlight some of the most critical common issues related to the development of vaccines against many pathogens and cancers that escape protective immune responses owing to antigenic variation, and discuss recent efforts to overcome the obstacles by applying alternative approaches for the rational design of new types of immunogens.

Childhood vaccination in rural southwestern Ethiopia: the nexus with demographic factors and women's autonomy

Introduction

Vaccination can reduce child mortality significantly and is a cost effective way to improve child health.Worldwide, more than 22 million children do not receive the basic recommended vaccinations.Vaccination coverage in Ethiopia remains low. Research on child health has focused on socio-economic factors such as maternal education and access to health care, but little attention has been given to demographic factors and women's autonomy within the household. The purpose of this study was to examine the influences of demographic factors and women's autonomy on the completion of childhood vaccination in rural Ethiopia.

Methods

A cross-sectional community-based study was conducted in a Health and Demographic Survelliance System (HDSS) in southwestern Ethiopia. Data were drawn from a random sample of women with children aged 12-24 months (n = 889). Information on maternal socio-demographic characteristics and household variables were collected using an interviewer-administered structured questionnaire. Vaccination data were obtained from vaccination cards or mother's recall. Multivariate logistic regression was used to assess the association of independent variables with completion of childhood vaccination.

Results

Of 889 children aged 12-24 months, 690 (78%) had received at least one vaccination. Only 37% (95% CI, 33.5-39.9) were fully vaccinated. Women's decision making autonomy, number of under-five children in the household, mother's education, use of antenatal care services and proximity to health facility were the main factors associated with full vaccination status.

Conclusion

Completion of basic vaccination series is very low in the study area. Initiatives that enhance women's autonomy within the household and that promote healthy timing and spacing of pregnancies may help in improving child health through vaccination.

Optimizing reactive responses to outbreaks of immunizing infections: balancing case management and vaccination

For vaccine-preventable infections, immunization generally needs to be supplemented by palliative care of individuals missed by the vaccination. Costs and availability of vaccine doses and palliative care vary by disease and by region. In many situations, resources for delivery of palliative care are independent of resources required for vaccination; however we also need to consider the conservative scenario where there is some trade-off between efforts, which is of potential relevance for resource-poor settings. We formulate an SEIR model that includes those two control strategies – vaccination and palliative care. We consider their relative merit and optimal allocation in the context of a highly efficacious vaccine, and under the assumption that palliative care may reduce transmission. We investigate the utility of a range of mixed or pure strategies that can be implemented after an epidemic has started, and look for rule-of-thumb principles of how best to reduce the burden of disease during an acute outbreak over a spectrum of vaccine-preventable infections. Intuitively, we expect the best strategy to initially focus on vaccination, and enhanced palliative care after the infection has peaked, but a number of plausible realistic constraints for control result in important qualifications on the intervention strategy. The time in the epidemic when one should switch strategy depends sensitively on the relative cost of vaccine to palliative care, the available budget, and . Crucially, outbreak response vaccination may be more effective in managing low- diseases, while high scenarios enhance the importance of routine vaccination and case management.

Demography and Public Health Emergency Preparedness: Making the Connection

The tools and techniques of population sciences are extremely relevant to the discipline of public health emergency preparedness: protecting and securing the population’s health requires information about that population. While related fields such as security studies have successfully integrated demographic tools into their research and literature, the theoretical and practical connection between the methods of demography and the practice of public health emergency preparedness is weak. This article suggests the need to further the interdisciplinary use of demography by examining the need for a systematic use of population science techniques in public health emergency preparedness. Ultimately, we demonstrate how public health emergency preparedness can incorporate demography to develop more effective preparedness plans. Important policy implications emerge: demographers and preparedness experts need to collaborate more formally in order to facilitate community resilience and mitigate the consequences of public health emergencies.

[Benefit-risk assessment of vaccination strategies]

This article summarises the various stages of the risk/benefit assessment of vaccination strategies. Establishing the awaited effectiveness of a vaccination strategy supposes to have an epidemiologic description of the disease to be prevented. The effectiveness of the vaccine strategy will be thus expressed in numbers of cases, hospitalizations or deaths avoided. The effectiveness can be direct, expressed as the reduction of the incidence of the infectious disease in the vaccinated subjects compared to unvaccinated subjects. It can also be indirect, the unvaccinated persons being protected by the suspension in circulation of the pathogenic agent, consecutive to the implementation of the vaccination campaign. The risks of vaccination related to the adverse effects detected during the clinical trials preceding marketing are well quantified, but other risks can occur after marketing: e.g., serious and unexpected adverse effects detected by vaccinovigilance systems, or risk of increase in the age of cases if the vaccination coverage is insufficient. The medico-economic evaluation forms a part of the risks/benefit assessment, by positioning the vaccine strategy comparatively with other interventions for health. Epidemiologic and vaccinovigilance informations must be updated very regularly, which underlines the need for having an operational and reliable real time monitoring system to accompany the vaccination strategies. Lastly, in the context of uncertainty which often accompanies the risks/benefit assessments, it is important that an adapted communication towards the public and the doctors is planned.

A preliminary study of genetic diversity of MSP-1 types in Plasmodium falciparum in southern province of Sistan Baluchistan of Iran

Plasmodiumfalciparum merozoite surface protein-1 (MSP-1) shows extensive antigenic diversity. This is due to the presence of seven variable blocks, five semi-conserved and also five conserved blocks. The variable blocks in the MSP-1 gene are principally dimorphic, displaying either K1 or MAD20 type; except for the block 2 region which is represented by three alleles, an RO33 type in addition to the other two. Allelic diversity is reported to be generated by intra-genic recombination between the variable blocks. A study of allelic variation of MSP-1 gene in Plasmodium falciparum was carried out in the southern province of Sistan Baluchistan in Iran in 2001-2003. Samples were obtained from 30 febrile patients and DNA was extracted and association types between blocks 2 and 6 was identified on each block using specific primers and compared with those from Vietnam, Brazil and Africa. The association types obtained, were similar though less in number than the ones from Vietnam, but more than those from Africa and Brazil.

Plasmodium falciparum: sequence diversity and antibody recognition of the Merozoite surface protein-2 (MSP-2) in Brazilian Amazonia

The merozoite surface protein-2 (MSP-2) of Plasmodium falciparum comprises repeats flanked by dimorphic domains defining the allelic families FC27 and IC1. Here, we examined sequence diversity at the msp-2 locus in Brazil and its impact on MSP-2 antibody recognition by local patients. Only 25 unique partial sequences of msp-2 were found in 61 isolates examined. The finding of identical msp-2 sequences in unrelated parasites, collected 6-13 years apart, suggests that no major directional selection is exerted by variant-specific immunity in this malaria-endemic area. To examine antibody cross-reactivity, recombinant polypeptides derived from locally prevalent and foreign MSP-2 variants were used in ELISA. Foreign IC1-type variants, such as 3D7 (currently tested for human vaccination), were less frequently recognized than FC27-type and local IC1-type variants. Antibodies discriminated between local and foreign IC1-type variants, but cross-recognized structurally different local IC1-type variants. The use of evolutionary models of MSP-2 is suggested to design vaccines that minimize differences between local parasites and vaccine antigens.

Vaccination against infections in chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) is a well-defined mature B-cell neoplasm associated with increased susceptibility to infections. Two major options in prevention of infections in CLL, intravenous gammaglobulin treatment and antimicrobial chemoprophylaxis, have not resulted in satisfactory outcome. A third strategy, antimicrobial vaccination, is the topic of this minireview. We collected articles and their references concerning CLL vaccination from the Medline database starting from 1966 and thirteen relevant studies were found. Plain bacterial polysaccharide vaccines would seem to be ineffective in antibody formation in patients with CLL. However, protein and conjugate vaccines appear to be more immunogenic and their responses may be further enhanced with ranitidine adjuvant treatment. New well-designed investigations are needed to develop appropriate vaccination strategies and evaluate vaccination efficacy in infection morbidity and mortality in CLL.

Herd immunity and herd effect: new insights and definitions

The term herd immunity has been used by various authors to conform to different definitions. Earlier this situation had been identified but not corrected. We propose that it should have precise meaning for which purpose a new definition is offered: "the proportion of subjects with immunity in a given population". This definition dissociates herd immunity from the indirect protection observed in the unimmunised segment of a population in which a large proportion is immunised, for which the term 'herd effect' is proposed. It is defined as: "the reduction of infection or disease in the unimmunised segment as a result of immunising a proportion of the population". Herd immunity can be measured by testing a sample of the population for the presence of the chosen immune parameter. Herd effect can be measured by quantifying the decline in incidence in the unimmunised segment of a population in which an immunisation programme is instituted. Herd immunity applies to immunisation or infection, human to human transmitted or otherwise. On the other hand, herd effect applies to immunisation or other health interventions which reduce the probability of transmission, confined to infections transmitted human to human, directly or via vector. The induced herd immunity of a given vaccine exhibits geographic variation as it depends upon coverage and efficacy of the vaccine, both of which can vary geographically. Herd effect is determined by herd immunity as well as the force of transmission of the corresponding infection. Clear understanding of these phenomena and their relationships will help improve the design of effective and efficient immunisation programmes aimed at control, elimination or eradication of vaccine preventable infectious diseases.

Molecular mimetics of polysaccharide epitopes as vaccine candidates for prevention of Neisseria meningitidis serogroup B disease

Neisseria meningitidis is a major cause of meningitis and sepsis. Despite nearly 25 years of work, there is no promising vaccine candidate for prevention of disease caused by meningococcal B strains. This review summarizes newer approaches for eliciting protective meningococcal B immune responses, including the use of molecular mimetics of group B polysaccharide and conserved membrane proteins as immunogens. The capsular polysaccharide of this organism is conserved and serum antibody to this capsule confers protection against disease. However, the immunogenicity of meningococcal B polysaccharide-based vaccines is poor. Further, a portion of the antibody elicited has autoantibody activity. Recently, our laboratory produced a panel of murine monoclonal antibodies (Mabs) that react specifically with capsular polysaccharide epitopes on meningococcal B that are distinct from host polysialic acid. These Mabs elicit complement-mediated bactericidal activity and confer passive protection in animal models. The anti-capsular Mabs were used to identify molecular mimetics from phage display peptide libraries. The resulting peptides were antigenic mimetics as defined by binding to the Mabs used to select them but, to date, are poor immunogenic mimetics in failing to elicit anti-capsular antibodies.

Allelic diversity and antibody recognition of Plasmodium falciparum merozoite surface protein 1 during hypoendemic malaria transmission in the Brazilian amazon region

The polymorphic merozoite surface protein (MSP-1) of Plasmodium falciparum is a major asexual blood-stage malaria vaccine candidate. The impact of allelic diversity on recognition of MSP-1 during the immune response remains to be investigated in areas of hypoendemicity such as the Brazilian Amazon region. In this study, PCR was used to type variable regions, blocks 2, 4, and 10, of the msp-1 gene and to characterize major gene types (unique combinations of allelic types in variable blocks) in P. falciparum isolates collected across the Amazon basin over a period of 12 years. Twelve of the 24 possible gene types were found among 181 isolates, and 68 (38%) of them had more than one gene type. Temporal, but not spatial, variation was found in the distribution of MSP-1 gene types in the Amazon. Interestingly, some gene types occurred more frequently than expected from random assortment of allelic types in different blocks, as previously found in other areas of endemicity. We also compared the antibody recognition of polymorphic (block 2), dimorphic (block 6), and conserved (block 3) regions of MSP-1 in Amazonian malaria patients and clinically immune Africans, using a panel of recombinant peptides. Results were summarized as follows. (i) All blocks were targeted by naturally acquired cytophilic antibodies of the subclasses IgG1 and IgG3, but the balance between IgG1 and IgG3 depended on the subjects' cumulative exposure to malaria. (ii) The balance between IgG1 and IgG3 subclasses and the duration of antibody responses differed in relation to distinct MSP-1 peptides. (iii) Antibody responses to variable blocks 2 and 6 were predominantly type specific, but variant-specific antibodies that target isolate-specific repetitive motifs within block 2 were more frequent in Amazonian patients than in previously studied African populations.