Exploring the impact of inoculum dose on host immunity and morbidity to inform model-based vaccine design

Symptom propagation in respiratory pathogens of public health concern: a review of the evidence

Symptom propagation occurs when the symptom set an individual experiences is correlated with the symptom set of the individual who infected them. Symptom propagation may dramatically affect epidemiological outcomes, potentially causing clusters of severe disease. Conversely, it could result in chains of mild infection, generating widespread immunity with minimal cost to public health. Despite accumulating evidence that symptom propagation occurs for many respiratory pathogens, the underlying mechanisms are not well understood. Here, we conducted a scoping literature review for 14 respiratory pathogens to ascertain the extent of evidence for symptom propagation by two mechanisms: dose-severity relationships and route-severity relationships. We identify considerable heterogeneity between pathogens in the relative importance of the two mechanisms, highlighting the importance of pathogen-specific investigations. For almost all pathogens, including influenza and SARS-CoV-2, we found support for at least one of the two mechanisms. For some pathogens, including influenza, we found convincing evidence that both mechanisms contribute to symptom propagation. Furthermore, infectious disease models traditionally do not include symptom propagation. We summarize the present state of modelling advancements to address the methodological gap. We then investigate a simplified disease outbreak scenario, finding that under strong symptom propagation, isolating mildly infected individuals can have negative epidemiological implications.

Measles Infection Dose Responses: Insights from Mathematical Modeling

How viral infections develop can change based on the number of viruses initially entering the body. The understanding of the impacts of infection doses remains incomplete, in part due to challenging constraints, and a lack of research. Gaining more insights is crucial regarding the measles virus (MV). The higher the MV infection dose, the earlier the peak of acute viremia, but the magnitude of the peak viremia remains almost constant. Measles is highly contagious, causes immunosuppression such as lymphopenia, and contributes substantially to childhood morbidity and mortality. This work investigated mechanisms underlying the observed wild-type measles infection dose responses in cynomolgus monkeys. We fitted longitudinal data on viremia using maximum likelihood estimation, and used the Akaike Information Criterion (AIC) to evaluate relevant biological hypotheses and their respective model parameterizations. The lowest AIC indicates a linear relationship between the infection dose, the initial viral load, and the initial number of activated MV-specific T cells. Early peak viremia is associated with high initial number of activated MV-specific T cells. Thus, when MV infection dose increases, the initial viremia and associated immune cell stimulation increase, and reduce the time it takes for T cell killing to be sufficient, thereby allowing dose-independent peaks for viremia, MV-specific T cells, and lymphocyte depletion. Together, these results suggest that the development of measles depends on virus-host interactions at the start and the efficiency of viral control by cellular immunity. These relationships are additional motivations for prevention, vaccination, and early treatment for measles.

Effect of Norovirus Inoculum Dose on Virus Kinetics, Shedding, and Symptoms

The effect of norovirus dose on outcomes such as virus shedding and symptoms after initial infection is not well understood. We performed a secondary analysis of a human challenge study by using Bayesian mixed-effects models. As the dose increased from 4.8 to 4,800 reverse transcription PCR units, the total amount of shed virus in feces increased from 4.5 × 1011 to 3.4 × 1012 genomic equivalent copies; in vomit, virus increased from 6.4 × 105 to 3.0 × 107 genomic equivalent copies. Onset time of viral shedding in feces decreased from 1.4 to 0.8 days, and time of peak viral shedding decreased from 2.3 to 1.5 days. Time to symptom onset decreased from 1.5 to 0.8 days. One type of symptom score increased. An increase in norovirus dose was associated with more rapid shedding and symptom onset and possibly increased severity. However, the effect on virus load and shedding was inconclusive.

Utility of Human In Vitro Data in Risk Assessments of Influenza A Virus Using the Ferret Model

As influenza A viruses (IAV) continue to cross species barriers and cause human infection, the establishment of risk assessment rubrics has improved pandemic preparedness efforts. In vivo pathogenicity and transmissibility evaluations in the ferret model represent a critical component of this work. As the relative contribution of in vitro experimentation to these rubrics has not been closely examined, we sought to evaluate to what extent viral titer measurements over the course of in vitro infections are predictive or correlates of nasal wash and tissue measurements for IAV infections in vivo. We compiled data from ferrets inoculated with an extensive panel of over 50 human and zoonotic IAV (inclusive of swine-origin and high- and low-pathogenicity avian influenza viruses associated with human infection) under a consistent protocol, with all viruses concurrently tested in a human bronchial epithelial cell line (Calu-3). Viral titers in ferret nasal wash specimens and nasal turbinate tissue correlated positively with peak titer in Calu-3 cells, whereas additional phenotypic and molecular determinants of influenza virus virulence and transmissibility in ferrets varied in their association with in vitro viral titer measurements. Mathematical modeling was used to estimate more generalizable key replication kinetic parameters from raw in vitro viral titers, revealing commonalities between viral infection progression in vivo and in vitro. Meta-analyses inclusive of IAV that display a diverse range of phenotypes in ferrets, interpreted with mathematical modeling of viral kinetic parameters, can provide critical information supporting a more rigorous and appropriate contextualization of in vitro experiments toward pandemic preparedness. IMPORTANCE Both in vitro and in vivo models are employed for assessing the pandemic potential of novel and emerging influenza A viruses in laboratory settings, but systematic examinations of how well viral titer measurements obtained in vitro align with results from in vivo experimentation are not frequently performed. We show that certain viral titer measurements following infection of a human bronchial epithelial cell line are positively correlated with viral titers in specimens collected from virus-inoculated ferrets and employ mathematical modeling to identify commonalities between viral infection progression between both models. These analyses provide a necessary first step in enhanced interpretation and incorporation of in vitro-derived data in risk assessment activities and highlight the utility of employing mathematical modeling approaches to more closely examine features of virus replication not identifiable by experimental studies alone.

Identifying COVID-19 optimal vaccine dose using mathematical immunostimulation/immunodynamic modelling

INTRODUCTION

Identifying optimal COVID-19 vaccine dose is essential for maximizing their impact. However, COVID-19 vaccine dose-finding has been an empirical process, limited by short development timeframes, and therefore potentially not thoroughly investigated. Mathematical IS/ID modelling is a novel method for predicting optimal vaccine dose which could inform future COVID-19 vaccine dose decision making.

METHODS

Published clinical data on COVID-19 vaccine dose-response was identified and extracted. Mathematical models were calibrated to the dose-response data stratified by subpopulation, where possible to predict optimal dose. Predicted optimal doses were summarised across vaccine type and compared to chosen dose for the primary series of COVID-19 vaccines to identify vaccine doses that may benefit from re-evaluation.

RESULTS

30 clinical dose-response datasets in adults and elderly population were extracted for four vaccine types and optimal doses predicted using the models. Results suggest that, if re-assessed for dose, COVID-19 vaccines Ad26.cov, ChadOx1 n-Cov19, BNT162b2, Coronavac, and NVX-CoV2373 could benefit from increased dose in adults and mRNA-1273 and Coronavac, could benefit from increased and decreased dose for the elderly population, respectively.

DISCUSSION

Future iterations of COVID-19 vaccines could benefit from re-evaluating dose to ensure most effective use of the vaccine and mathematical modelling can support this.

The Correlated Beta Dose Optimisation Approach: Optimal Vaccine Dosing Using Mathematical Modelling and Adaptive Trial Design

Mathematical modelling methods and adaptive trial design are likely to be effective for optimising vaccine dose but are not yet commonly used. This may be due to uncertainty with regard to the correct choice of parametric model for dose-efficacy or dose-toxicity. Non-parametric models have previously been suggested to be potentially useful in this situation. We propose a novel approach for locating optimal vaccine dose based on the non-parametric Continuous Correlated Beta Process model and adaptive trial design. We call this the 'Correlated Beta' or 'CoBe' dose optimisation approach. We evaluated the CoBe dose optimisation approach compared to other vaccine dose optimisation approaches using a simulation study. Despite using simpler assumptions than other modelling-based methods, we found that the CoBe dose optimisation approach was able to effectively locate the maximum efficacy dose for both single and prime/boost administration vaccines. The CoBe dose optimisation approach was also effective in finding a dose that maximises vaccine efficacy and minimises vaccine-related toxicity. Further, we found that these modelling methods can benefit from the inclusion of expert knowledge, which has been difficult for previous parametric modelling methods. This work further shows that using mathematical modelling and adaptive trial design is likely to be beneficial to locating optimal vaccine dose, ensuring maximum vaccine benefit and disease burden reduction, ultimately saving lives.

Mathematical Modelling for Optimal Vaccine Dose Finding: Maximising Efficacy and Minimising Toxicity

Vaccination is a key tool to reduce global disease burden. Vaccine dose can affect vaccine efficacy and toxicity. Given the expense of developing vaccines, optimising vaccine dose is essential. Mathematical modelling has been suggested as an approach for optimising vaccine dose by quantitatively establishing the relationships between dose and efficacy/toxicity. In this work, we performed simulation studies to assess the performance of modelling approaches in determining optimal dose. We found that the ability of modelling approaches to determine optimal dose improved with trial size, particularly for studies with at least 30 trial participants, and that, generally, using a peaking or a weighted model-averaging-based dose–efficacy relationship was most effective in finding optimal dose. Most methods of trial dose selection were similarly effective for the purpose of determining optimal dose; however, including modelling to adapt doses during a trial may lead to more trial participants receiving a more optimal dose. Clinical trial dosing around the predicted optimal dose, rather than only at the predicted optimal dose, may improve final dose selection. This work suggests modelling can be used effectively for vaccine dose finding, prompting potential practical applications of these methods in accelerating effective vaccine development and saving lives.

Estimation of viral kinetics model parameters in young and aged SARS-CoV-2 infected macaques

The SARS-CoV-2 virus disproportionately causes serious illness and death in older individuals. In order to have the greatest impact in decreasing the human toll caused by the virus, antiviral treatment should be targeted to older patients. For this, we need a better understanding of the differences in viral dynamics between SARS-CoV-2 infection in younger and older adults. In this study, we use previously published averaged viral titre measurements from the nose and throat of SARS-CoV-2 infection in young and aged cynomolgus macaques to parametrize a viral kinetics model. We find that all viral kinetics parameters differ between young and aged macaques in the nasal passages, but that there are fewer differences in parameter estimates from the throat. We further use our parametrized model to study the antiviral treatment of young and aged animals, finding that early antiviral treatment is more likely to lead to a lengthening of the infection in aged animals, but not in young animals.

From Bench to Field: A Guide to Formulating and Evaluating Anti-Tick Vaccines Delving beyond Efficacy to Effectiveness

Ticks are ubiquitous blood-sucking ectoparasites capable of transmitting a wide range of pathogens such as bacteria, viruses, protozoa, and fungi to animals and humans. Although the use of chemicals (acaricides) is the predominant method of tick-control, there are increasing incidents of acaricide tick resistance. Furthermore, there are concerns over accumulation of acaricide residues in meat, milk and in the environment. Therefore, alternative methods of tick-control have been proposed, of which anti-tick cattle vaccination is regarded as sustainable and user-friendly. Over the years, tremendous progress has been made in identifying and evaluating novel candidate tick vaccines, yet none of them have reached the global market. Until now, Bm86-based vaccines (Gavac™ in Cuba and TickGARD^PLUS™ Australia-ceased in 2010) are still the only globally commercialized anti-tick vaccines. In contrast to Bm86, often, the novel candidate anti-tick vaccines show a lower protection efficacy. Why is this so? In response, herein, the potential bottlenecks to formulating efficacious anti-tick vaccines are examined. Aside from Bm86, the effectiveness of other anti-tick vaccines is rarely assessed. So, how can the researchers assess anti-tick vaccine effectiveness before field application? The approaches that are currently used to determine anti-tick vaccine efficacy are re-examined in this review. In addition, a model is proposed to aid in assessing anti-tick vaccine effectiveness. Finally, based on the principles for the development of general veterinary vaccines, a pipeline is proposed to guide in the development of anti-tick vaccines.

Effects of N95 Mask Use on Pulmonary Function in Children

OBJECTIVE

To assess whether use of an N95 mask by children is associated with episodes of desaturation or respiratory distress.

STUDY DESIGN

Twenty-two healthy children were assigned at random to 1 of 2 groups: one group wearing N95 masks without an exhalation valve and the other group wearing N95 masks with an exhalation valve. We tracked changes in partial pressure of end-tidal carbon dioxide (P_ETCO2), oxygen saturation, pulse rate, and respiratory rate over 72 minutes of mask use. All subjects were monitored every 15 minutes, the first 30 minutes while not wearing a mask and the next 30 minutes while wearing a mask. They then performed a 12-minute walking test.

RESULTS

The children did not experience a statistically significant change in oxygen saturation or pulse rate during the study. There were significant increases in respiratory rate and P_ETCO2 in the children wearing an N95 mask without an exhalation valve, whereas these increases were seen in the children wearing a mask with an exhalation valve only after the walking test.

CONCLUSIONS

The use of an N95 mask could potentially cause breathing difficulties in children if the mask does not have an exhalation valve, particularly during a physical activity. We believe that wearing a surgical mask may be more appropriate for children.

Whole inactivated dengue virus-loaded trimethyl chitosan nanoparticle-based vaccine: immunogenic properties in ex vivo and in vivo models

Dengue virus (DENV) is a mosquito-borne virus that poses an incomparable public health problem, particularly in tropical and subtropical areas. Vaccination remains the most rational measure for controlling DENV infection. In this study, an ultraviolet irradiation (UV)-inactivated DENV-2 carried by N,N,N-trimethyl chitosan nanoparticles (UV-inactivated DENV2 TMC NPs) was investigated as a potential non-replicating dengue vaccine candidate. Using a human ex vivo model, the human monocyte-derived dendritic cells (MoDCs), we showed that TMC served as both a vaccine vehicle and a potent adjuvant. TMC NPs not only efficiently enhanced UV-inactivated DENV2 internalization into MoDCs but also greatly increased the breadth of UV-inactivated DENV2 immunogenicity to drive the maturation of MoDCs. Moreover, UV-inactivated DENV2 TMC NPs were highly immunogenic in mice, inducing greater levels of antibodies (total IgG, IgG1, IgG2a and neutralizing antibodies) and T cells (activated CD4⁺ and CD8⁺ T cells) against DENV-2 compared to soluble DENV-2 immunogens. Notably, the neutralizing activity of sera from mice immunized with UV-inactivated DENV2 TMC NPs was significantly augmented in the presence of complement activation, leading to the strong elimination of both DENV-2 particles and infected cells. We further showed that the immunogenicity of an inactivated dengue-based vaccine was significantly improved in a concentration-dependent manner. These positive results warrant further investigations of this platform of vaccine delivery for tetravalent vaccines or monovalent vaccines in sequential immunizations.

Host population dynamics in the face of an evolving pathogen

Interactions between hosts and pathogens are dynamic at both ecological and evolutionary levels. In the resultant 'eco-evolutionary dynamics' ecological and evolutionary processes affect each other. For example, the house finch Haemorhous mexicanus and its recently emerged pathogen, the bacterium Mycoplasma gallisepticum, form a system in which evidence suggests that changes in bacterial virulence through time enhance levels of host immunity in ways that drive the evolution of virulence in an arms race. We use data from two associated citizen science projects in order to determine whether this arms race has had any detectable effect at the population level in the north-eastern United States. We used data from two citizen science projects, based on observations of birds at bird feeders, which provide information on the long-term changes in sizes of aggregations of house finches (host population density), and the probabilities that these house finches have observable disease (disease prevalence). The initial emergence of M. gallisepticum caused a rapid halving of house finch densities; this was then followed by house finch populations remaining stable or slowly declining. Disease prevalence also decreased sharply after the initial emergence and has remained low, although with fluctuations through time. Surprisingly, while initially higher local disease prevalence was found at sites with higher local densities of finches, this relationship has reversed over time. The ability of a vertebrate host species, with a generation time of at least 1 year, to maintain stable populations in the face of evolved higher virulence of a bacterium, with generation times measurable in minutes, suggests that genetic changes in the host are insufficient to explain the observed population-level patterns. We suggest that acquired immunity plays an important role in the observed interaction between house finches and M. gallisepticum.

Early events in hepatitis B infection: the role of inoculum dose

The relationship between the inoculum dose and the ability of the pathogen to invade the host is poorly understood. Experimental studies in non-human primates infected with different inoculum doses of hepatitis B virus have shown a non-monotonic relationship between dose magnitude and infection outcome, with high and low doses leading to 100% liver infection and intermediate doses leading to less than 0.1% liver infection, corresponding to CD4 T-cell priming. Since hepatitis B clearance is CD8 T-cell mediated, the question of whether the inoculum dose influences CD8 T-cell dynamics arises. To help answer this question, we developed a mathematical model of virus-host interaction following hepatitis B virus infection. Our model explains the experimental data well, and predicts that the inoculum dose affects both the timing of the CD8 T-cell expansion and the quality of its response, especially the non-cytotoxic function. We find that a low-dose challenge leads to slow CD8 T-cell expansion, weak non-cytotoxic functions, and virus persistence; high- and medium-dose challenges lead to fast CD8 T-cell expansion, strong cytotoxic and non-cytotoxic function, and virus clearance; while a super-low-dose challenge leads to delayed CD8 T-cell expansion, strong cytotoxic and non-cytotoxic function, and virus clearance. These results are useful for designing immune cell-based interventions.

Optimising Vaccine Dose in Inoculation against SARS-CoV-2, a Multi-Factor Optimisation Modelling Study to Maximise Vaccine Safety and Efficacy

Developing a vaccine against the global pandemic SARS-CoV-2 is a critical area of active research. Modelling can be used to identify optimal vaccine dosing; maximising vaccine efficacy and safety and minimising cost. We calibrated statistical models to published dose-dependent seroconversion and adverse event data of a recombinant adenovirus type-5 (Ad5) SARS-CoV-2 vaccine given at doses 5.0 × 10¹⁰, 1.0 × 10¹¹ and 1.5 × 10¹¹ viral particles. We estimated the optimal dose for three objectives, finding: (A) the minimum dose that may induce herd immunity, (B) the dose that maximises immunogenicity and safety and (C) the dose that maximises immunogenicity and safety whilst minimising cost. Results suggest optimal dose [95% confidence interval] in viral particles per person was (A) 1.3 × 10¹¹ [0.8–7.9 × 10¹¹], (B) 1.5 × 10¹¹ [0.3–5.0 × 10¹¹] and (C) 1.1 × 10¹¹ [0.2–1.5 × 10¹¹]. Optimal dose exceeded 5.0 × 10¹⁰ viral particles only if the cost of delivery exceeded £0.65 or cost per 10¹¹ viral particles was less than £6.23. Optimal dose may differ depending on the objectives of developers and policy-makers, but further research is required to improve the accuracy of optimal-dose estimates.

Zika virus dynamics: Effects of inoculum dose, the innate immune response and viral interference

Experimental Zika virus infection in non-human primates results in acute viral load dynamics that can be well-described by mathematical models. The inoculum dose that would be received in a natural infection setting is likely lower than the experimental infections and how this difference affects the viral dynamics and immune response is unclear. Here we study a dataset of experimental infection of non-human primates with a range of doses of Zika virus. We develop new models of infection incorporating both an innate immune response and viral interference with that response. We find that such a model explains the data better than models with no interaction between virus and the immune response. We also find that larger inoculum doses lead to faster dynamics of infection, but approximately the same total amount of viral production.

The relationship between the infecting dose of a pathogen and the subsequent viral dynamics is unclear in many disease settings, and this relationship has implications for both the timing and the required efficacy of antiviral therapy. Since experimental challenge studies often employ higher doses of virus than would generally be present in natural infection assessment of this relationship is particularly important for translation of findings. In this study we used mathematical modelling of viral load data from a multi-dose study of Zika virus infection in a macaque model to describe the impact of varying the dose of Zika virus on model parameters, and developed a novel mathematical model incorporating viral interference with the innate immune response.

Outcomes of COVID-19 Among Hospitalized Health Care Workers in North America

Importance

Although health care workers (HCWs) are at higher risk of acquiring coronavirus disease 2019 (COVID-19), it is unclear whether they are at risk of poorer outcomes.

Objective

To evaluate the association between HCW status and outcomes among patients hospitalized with COVID-19.

Design, Setting, and Participants

This retrospective, observational cohort study included consecutive adult patients hospitalized with a diagnosis of laboratory-confirmed COVID-19 across 36 North American centers from April 15 to June 5, 2020. Data were collected from 1992 patients. Data were analyzed from September 10 to October 1, 2020.

Exposures

Data on patient baseline characteristics, comorbidities, presenting symptoms, treatments, and outcomes were collected, including HCW status.

Main Outcomes and Measures

The primary outcome was a requirement for mechanical ventilation or death. Multivariable logistic regression was performed to yield adjusted odds ratios (AORs) and 95% CIs for the association between HCW status and COVID-19-related outcomes in a 3:1 propensity score-matched cohort, adjusting for residual confounding after matching.

Results

In total, 1790 patients were included, comprising 127 HCWs and 1663 non-HCWs. After 3:1 propensity score matching, 122 HCWs were matched to 366 non-HCWs. Women comprised 71 (58.2%) of matched HCWs and 214 (58.5%) of matched non-HCWs. Matched HCWs had a mean (SD) age of 52 (13) years, whereas matched non-HCWs had a mean (SD) age of 57 (17) years. In the matched cohort, the odds of the primary outcome, mechanical ventilation or death, were not significantly different for HCWs compared with non-HCWs (AOR, 0.60; 95% CI, 0.34-1.04). The HCWs were less likely to require admission to an intensive care unit (AOR, 0.56; 95% CI, 0.34-0.92) and were also less likely to require an admission of 7 days or longer (AOR, 0.53; 95% CI, 0.34-0.83). There were no differences between matched HCWs and non-HCWs in terms of mechanical ventilation (AOR, 0.66; 95% CI, 0.37-1.17), death (AOR, 0.47; 95% CI, 0.18-1.27), or vasopressor requirements (AOR, 0.68; 95% CI, 0.37-1.24).

Conclusions and Relevance

In this propensity score-matched multicenter cohort study, HCW status was not associated with poorer outcomes among hospitalized patients with COVID-19 and, in fact, was associated with a shorter length of hospitalization and decreased likelihood of intensive care unit admission. Further research is needed to elucidate the proportion of HCW infections acquired in the workplace and to assess whether HCW type is associated with outcomes.

Initial Inoculum and the Severity of COVID-19: A Mathematical Modeling Study of the Dose-Response of SARS-CoV-2 Infections

SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) causes a variety of responses in those who contract the virus, ranging from asymptomatic infections to acute respiratory failure and death. While there are likely multiple mechanisms triggering severe disease, one potential cause of severe disease is the size of the initial inoculum. For other respiratory diseases, larger initial doses lead to more severe outcomes. We investigate whether there is a similar link for SARS-CoV-2 infections using the combination of an agent-based model (ABM) and a partial differential equation model (PDM). We use the model to examine the viral time course for different sizes of initial inocula, generating dose-response curves for peak viral load, time of viral peak, viral growth rate, infection duration, and area under the viral titer curve. We find that large initial inocula lead to short infections, but with higher viral titer peaks; and that smaller initial inocula lower the viral titer peak, but make the infection last longer.

Masks Do More Than Protect Others During COVID-19: Reducing the Inoculum of SARS-CoV-2 to Protect the Wearer

Although the benefit of population-level public facial masking to protect others during the COVID-19 pandemic has received a great deal of attention, we discuss for one of the first times the hypothesis that universal masking reduces the "inoculum" or dose of the virus for the mask-wearer, leading to more mild and asymptomatic infection manifestations. Masks, depending on type, filter out the majority of viral particles, but not all. We first discuss the near-century-old literature around the viral inoculum and severity of disease (conceptualized as the LD50 or lethal dose of the virus). We include examples of rising rates of asymptomatic infection with population-level masking, including in closed settings (e.g., cruise ships) with and without universal masking. Asymptomatic infections may be harmful for spread but could actually be beneficial if they lead to higher rates of exposure. Exposing society to SARS-CoV-2 without the unacceptable consequences of severe illness with public masking could lead to greater community-level immunity and slower spread as we await a vaccine. This theory of viral inoculum and mild or asymptomatic disease with SARS-CoV-2 in light of population-level masking has received little attention so this is one of the first perspectives to discuss the evidence supporting this theory.

Uncovering drivers of dose-dependence and individual variation in malaria infection outcomes

To understand why some hosts get sicker than others from the same type of infection, it is essential to explain how key processes, such as host responses to infection and parasite growth, are influenced by various biotic and abiotic factors. In many disease systems, the initial infection dose impacts host morbidity and mortality. To explore drivers of dose-dependence and individual variation in infection outcomes, we devised a mathematical model of malaria infection that allowed host and parasite traits to be linear functions (reaction norms) of the initial dose. We fitted the model, using a hierarchical Bayesian approach, to experimental time-series data of acute Plasmodium chabaudi infection across doses spanning seven orders of magnitude. We found evidence for both dose-dependent facilitation and debilitation of host responses. Most importantly, increasing dose reduced the strength of activation of indiscriminate host clearance of red blood cells while increasing the half-life of that response, leading to the maximal response at an intermediate dose. We also explored the causes of diverse infection outcomes across replicate mice receiving the same dose. Besides random noise in the injected dose, we found variation in peak parasite load was due to unobserved individual variation in host responses to clear infected cells. Individual variation in anaemia was likely driven by random variation in parasite burst size, which is linked to the rate of host cells lost to malaria infection. General host vigour in the absence of infection was also correlated with host health during malaria infection. Our work demonstrates that the reaction norm approach provides a useful quantitative framework for examining the impact of a continuous external factor on within-host infection processes.

An approximate solution of the interferon-dependent viral kinetics model of influenza

The analysis of viral kinetics models is mostly achieved by numerical methods. We present an approach via a Magnus expansion that allows us to give an approximate solution to the interferon-dependent viral infection model of influenza which is compared with numerical results. The time of peak viral load is calculated from the approximation and stays within 10% in the studied range of interferon (IFN) efficacy ϵ ∈ [0, 1000]. We utilize our solution to interpret the effect of varying IFN efficacy, suggesting a competition between virions and interferon that can cause an additional peak in the usually exponential increase in the viral load.

Ferreting Out Influenza Virus Pathogenicity and Transmissibility: Past and Future Risk Assessments in the Ferret Model

As influenza A viruses continue to jump species barriers, data generated in the ferret model to assess influenza virus pathogenicity, transmissibility, and tropism of these novel strains continues to inform an increasing scope of public health-based applications. This review presents the suitability of ferrets as a small mammalian model for influenza viruses and describes the breadth of pathogenicity and transmissibility profiles possible in this species following inoculation with a diverse range of viruses. Adaptation of aerobiology-based techniques and analyses have furthered our understanding of data obtained from this model and provide insight into the capacity of novel and emerging influenza viruses to cause human infection and disease.

Response Type and Host Species may be Sufficient to Predict Dose-Response Curve Shape for Adenoviral Vector Vaccines

Vaccine dose-response curves can follow both saturating and peaking shapes. Dose-response curves for adenoviral vector vaccines have not been systematically described. In this paper, we explore the dose-response shape of published adenoviral animal and human studies. Where data were informative, dose-response was approximately five times more likely to be peaking than saturating. There was evidence that host species and response type may be sufficient for prediction of dose-response curve shape. Dose-response curve shape prediction could decrease clinical trial costs, accelerating the development of life-saving vaccines.

Immunologic Dose-Response to Adenovirus-Vectored Vaccines in Animals and Humans: A Systematic Review of Dose-Response Studies of Replication Incompetent Adenoviral Vaccine Vectors when Given via an Intramuscular or Subcutaneous Route

Optimal vaccine dosing is important to ensure the greatest protection and safety. Analysis of dose-response data, from previous studies, may inform future studies to determine the optimal dose. Implementing more quantitative modelling approaches in vaccine dose finding have been recently suggested to accelerate vaccine development. Adenoviral vectored vaccines are in advanced stage of development for a variety of prophylactic and therapeutic indications, however dose-response has not yet been systematically determined. To further inform adenoviral vectored vaccines dose identification, historical dose-response data should be systematically reviewed. A systematic literature review was conducted to collate and describe the available dose-response studies for adenovirus vectored vaccines. Of 2787 papers identified by Medline search strategy, 35 were found to conform to pre-defined criteria. The majority of studies were in mice or humans and studied adenovirus serotype 5. Dose-response data were available for 12 different immunological responses. The majority of papers evaluated three dose levels, only two evaluated more than five dose levels. The most common dosing range was 107-1010 viral particles in mouse studies and 108-1011 viral particles in human studies. Data were available on adenovirus vaccine dose-response, primarily on adenovirus serotype 5 backbones and in mice and humans. These data could be used for quantitative adenoviral vectored vaccine dose optimisation analysis.

Characterising antibody kinetics from multiple influenza infection and vaccination events in ferrets

The strength and breadth of an individual's antibody repertoire is an important predictor of their response to influenza infection or vaccination. Although progress has been made in understanding qualitatively how repeated exposures shape the antibody mediated immune response, quantitative understanding remains limited. We developed a set of mathematical models describing short-term antibody kinetics following influenza infection or vaccination and fit them to haemagglutination inhibition (HI) titres from 5 groups of ferrets which were exposed to different combinations of trivalent inactivated influenza vaccine (TIV with or without adjuvant), A/H3N2 priming inoculation and post-vaccination A/H1N1 inoculation. We fit models with various immunological mechanisms that have been empirically observed but have not previously been included in mathematical models of antibody landscapes, including: titre ceiling effects, antigenic seniority and exposure-type specific cross reactivity. Based on the parameter estimates of the best supported models, we describe a number of key immunological features. We found quantifiable differences in the degree of homologous and cross-reactive antibody boosting elicited by different exposure types. Infection and adjuvanted vaccination generally resulted in strong, broadly reactive responses whereas unadjuvanted vaccination resulted in a weak, narrow response. We found that the order of exposure mattered: priming with A/H3N2 improved subsequent vaccine response, and the second dose of adjuvanted vaccination resulted in substantially greater antibody boosting than the first. Either antigenic seniority or a titre ceiling effect were included in the two best fitting models, suggesting a role for a mechanism describing diminishing antibody boosting with repeated exposures. Although there was considerable uncertainty in our estimates of antibody waning parameters, our results suggest that both short and long term waning were present and would be identifiable with a larger set of experiments. These results highlight the potential use of repeat exposure animal models in revealing short-term, strain-specific immune dynamics of influenza.

Role of the Microbiota in the Modulation of Vaccine Immune Responses

The human immune system and the microbiota co-evolve, and their balanced relationship is based on crosstalk between the two systems through the course of life. This tight association and the overall composition and richness of the microbiota play an important role in the modulation of host immunity and may impact the immune response to vaccination. The availability of innovative technologies, such as next-generation sequencing (NGS) and correlated bioinformatics tools, allows a deeper investigation of the crosstalk between the microbiota and human immune responses. This review discusses the current knowledge on the influence of the microbiota on the immune response to vaccination and novel tools to deeply analyze the impact of the microbiome on vaccine responses.

The rate of viral transfer between upper and lower respiratory tracts determines RSV illness duration

Respiratory syncytial virus can lead to serious lower respiratory infection (LRI), particularly in children and the elderly. LRI can cause longer infections, lingering respiratory problems, and higher incidence of hospitalization. In this paper, we use a simplified ordinary differential equation model of viral dynamics to study the role of transport mechanisms in the occurrence of LRI. Our model uses two compartments to simulate the upper respiratory tract and the lower respiratory tract (LRT) and assumes two distinct types of viral transfer between the two compartments: diffusion and advection. We find that a range of diffusion and advection values lead to long-lasting infections in the LRT, elucidating a possible mechanism for the severe LRI infections observed in humans.

Uncovering critical properties of the human respiratory syncytial virus by combining in vitro assays and in silico analyses

Many aspects of the respiratory syncytial virus (RSV) are still poorly understood. Yet these knowledge gaps have had and could continue to have adverse, unintended consequences for the efficacy and safety of antivirals and vaccines developed against RSV. Mathematical modelling was used to test and evaluate hypotheses about the rate of loss of RSV infectivity and the mechanisms and kinetics of RSV infection spread in SIAT cells in vitro. While the rate of loss of RSV integrity, as measured via qRT-PCR, is well-described by an exponential decay, the latter mechanism failed to describe the rate at which RSV A Long loses infectivity over time in vitro based on the data presented herein. This is unusual given that other viruses (HIV, HCV, influenza) have been shown to lose their infectivity exponentially in vitro, and indeed an exponential rate of loss of infectivity is always assumed in mathematical modelling and experimental analyses. The infectivity profile of RSV in HEp-2 and SIAT cells remained consistent over the course of an RSV infection, over time and a large range of infectivity. However, SIAT cells were found to be ∼ 100× less sensitive to RSV infection than HEp-2 cells. In particular, we found that RSV spreads inefficiently in SIAT cells, in a manner we show is consistent with the establishment of infection resistance in uninfected cells. SIAT cells are a good in vitro model in which to study RSV in vivo dissemination, yielding similar infection timescales. However, the higher sensitivity of HEp-2 cells to RSV together with its RSV infectivity profile being similar to that of SIAT cells, makes HEp-2 cells more suitable for quantifying RSV infectivity over the course of in vitro RSV infections in SIAT cells. Our findings highlight the importance and urgency of resolving the mechanisms at play in the dissemination of RSV infections in vitro, and the processes by which this infectivity is lost.