scholarly journals High-Resolution Epidemic Simulation Using Within-Host Infection and Contact Data

2017 ◽  
Author(s):  
Van Kinh Nguyen ◽  
Rafael Mikolajczyk ◽  
Esteban A. Hernandez-Vargas
Keyword(s):  
Experimental Data ◽  
Infectious Diseases ◽  
Case Fatality ◽  
Population Data ◽  
Contact Network ◽  
Infection Model ◽  
Transmission Potential ◽  
Infection Dynamics ◽  
Specific Contact ◽  
Host Infection

AbstractBackgroundTransmission in epidemics of infectious diseases is characterized by a high level of subject-specific elements. These include heterogeneous infection conditions, time-dependent transmission potential, and age-dependent contact structure. These insights are often lost in epidemic models using population data. Here we submit an approach that can capture these details, paving the way for studying epidemics in a more mechanistic and realistic way.MethodsUsing experimental data, we formulated mathematical models of a pathogen infection dynamics from which we can simulate its transmission potential mechanistically. The models were then embedded in our implement of an age-specific contact network structure that allows to express all elements relevant to the transmission process. This approach is illustrated here with an example of Ebola virus (EBOV).ResultsThe results showed that within-host infection dynamics can capture EBOV’s transmission parameters as good as approaches using population data. Population age-structure, contact distribution and patterns can also be captured with our network generating algorithm. This framework opens vast opportunities for the investigations of each element involved in the epidemic process. Here, estimating EBOV’s reproduction number revealed a heterogeneous pattern among age-groups, prompting questions on current estimates which are not adjusted for this factor. Assessments of mass vaccination strategies showed that a time window from five months before to one week after the start of an epidemic appeared to be effective. Noticeably, compared to a non-intervention scenario, a low vaccination coverage of 33% could reduce number of cases by ten to hundred times as well as lessen the case-fatality rate.ConclusionsThis is the first effort coupling directly within-host infection model into an age-structured epidemic network model, adding more realistic elements in simulating epidemic processes. Experimental data at the within-host infection are shown able to capture upfront key parameters of a pathogen; the applications of this approach will give us more time to prepare for potential epidemics. Population of interest in epidemic assessments could be modeled with an age-specific contact network without exhaustive amount of data. Further assessments and adaptations for different pathogens and scenarios are underway to explore multilevel aspects in infectious diseases epidemics.

scholarly journals Diphtheria is declining but continues to kill many children: analysis of data from a sentinel centre in Delhi, 1997

1999 ◽  
Vol 123 (2) ◽  
pp. 209-215 ◽  
Author(s):  
J. SINGH ◽  
A. K. HARIT ◽  
D. C. JAIN ◽  
R. C. PANDA ◽  
K. N. TEWARI ◽  
...  
Keyword(s):  
Early Diagnosis ◽  
Infectious Diseases ◽  
Vaccine Coverage ◽  
Case Fatality ◽  
The Third

Although diphtheria is declining in Delhi, case fatality rates (CFRs) are rising. In 1997, of 143 clinically suspected cases admitted to the Infectious Diseases Hospital 45 (32%) died. We examined their records to understand the epidemiology and reasons for high CFRs. About 53% of cases were from Delhi; they were not limited to any particular area. All the deaths and 92% (131/143) of cases occurred in children below 10 years of age. Only 12% of cases had received one or more doses of DPT. Muslims contributed significantly more cases than Hindus. CFRs were significantly higher in young (P=0·03) and unvaccinated (P=0·01) children and in those who received antitoxin on the third day of illness or later (P=0·03). The study highlights the importance of improved vaccine coverage and early diagnosis and prompt administration of antitoxin in reducing CFRs for diphtheria in Delhi.

scholarly journals 2716. Persistence of 13-Valent Pneumococcal Conjugate Vaccine (PCV13) Serotypes in Invasive Pneumococcal Disease in Adults in Southern Ontario Canada Despite Routine Pediatric Vaccination

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S955-S956
Author(s):  
Allison McGeer ◽  
Agron Plevneshi ◽  
Karen Green ◽  
Brenda Coleman ◽  
Sarah Nayani ◽  
...  
Keyword(s):  
Invasive Pneumococcal Disease ◽  
Pneumococcal Disease ◽  
Medical Information ◽  
Herd Immunity ◽  
Case Fatality ◽  
Population Data ◽  
Vaccination Programs ◽  
Significant Difference ◽  
Statistics Canada ◽  
Pediatric Vaccination

Abstract Background In Ontario, Canada, PCV13 is covered for immunocompromised (IC) adults over 50y. PCV13 programs are thought not to be cost-effective in other adults because it is assumed that herd immunity from pediatric vaccination programs (PCV7 since 2005; PCV13 since 2010) will reduce PCV13 disease burden dramatically in adults. We analyzed data from the Toronto Invasive Bacterial Diseases Network (TIBDN) to ask whether PCV13-type invasive pneumococcal disease (IPD) in adults persists in our population. Methods TIBDN performs population-based surveillance for IPD in Toronto+Peel Region, Ontario (pop4.1M). All microbiology laboratories receiving specimens from residents report cases of IPD and submit isolates to a central study lab for serotyping; annual audits are conducted. Demographic, medical and vaccination information are obtained from patients, families and physicians. Population data are from Statistics Canada. Results Since 1995, 10,365 episodes of IPD have been identified; detailed medical information was available for 9,801 (95%) and serotyping for 9411 (91%). Among 8658 adult cases, 4,273 (49%) were in those aged 15–64 years, and 4,285 (51%) in those aged >645 years. The most common diagnoses were pneumonia (5,978/8,025, 74%) and bacteremia without focus (1,030, 13%); 470 (4.6%) cases had meningitis; the case fatality rate (CFR) was 21%. The incidence of disease due to STs in PCV13 in adults declined from 7.0/100,000/year 2001 to 2.9/100,000/year in 2015–2018 and was stable from 2015–2018 (Figure 1). The incidence was > 5/100,000/year in non-IC patients over 65 years, and younger patients with cancer and kidney disease (Figure 2). In IPD from 2015 to 2018, adult patients with PCV13 ST disease were younger (median age 64 years vs. 67 years, P = .03) than other patients; there was no significant difference in the proportion with at least one underlying chronic condition (253, 69% PCV13ST, vs. 541,74% other ST, P = 0.08), or in CFR (59, 16% PCV13 vs. 145, 20% other, P = 0.13). The ST distribution of cases due to PCV13 STs is shown in Figure 3. Conclusion A significant burden of IPD due to PCV13 serotypes persists in adults in our population despite 8 years of routine pediatric PCV13 vaccination. This burden needs to be considered in assessing the value and cost-effectiveness of PCV programs for adults. Disclosures All authors: No reported disclosures.

Rodent malaria parasites suffer from the presence of conspecific clones in three-clonePlasmodium chabaudiinfections

Parasitology ◽  
2003 ◽  
Vol 127 (5) ◽  
pp. 411-418 ◽  
Author(s):  
J. C. DE ROODE ◽  
A. F. READ ◽  
B. H. K. CHAN ◽  
M. J. MACKINNON
Keyword(s):  
Growth Rate ◽  
Acute Phase ◽  
Chronic Phase ◽  
The Other ◽  
Host Immune System ◽  
Plasmodium Chabaudi ◽  
Rodent Malaria ◽  
Transmission Potential ◽  
Infection Dynamics ◽  
Single Clone

We studied infection dynamics ofPlasmodium chabaudiin mice infected with 3 genetically distinct clones – 1 less virulent than the other 2 – either on their own or in mixtures. During the acute phase of infection, total numbers of asexual parasites in mixed-clone infections were equal to those produced by the 3 clones alone, suggesting strong in-host competition among clones. During the chronic phase of the infection, mixed-clone infections produced more asexual parasites than single-clone infections, suggesting lower levels of competition than during the acute phase, and indicating that a genetically diverse infection is harder to control by the host immune system. Transmission potential over the whole course of infection was lower from mixed-clone infections than from the average of the 3 single-clone infections. These results suggest that in-host competition reduces both growth rate and probability of transmission for individual parasite clones.

scholarly journals Socio-economic status, iron deficiency anemia and COVID-19 disease burden – an appraisal

2021 ◽  
Vol 19 (1) ◽  
pp. 52-58
Author(s):  
Kusum Ghosh ◽  
◽  
Diptendu Chatterjee ◽  
Abhisikta Ghosh Roy ◽  
Arup Ratan Bandyopadhyay ◽  
...  
Keyword(s):  
Iron Deficiency ◽  
Infectious Diseases ◽  
Iron Deficiency Anemia ◽  
Economic Status ◽  
Case Fatality ◽  
Therapeutic Interventions ◽  
Deficiency Anemia ◽  
Iron Stores ◽  
Socio Economic Status ◽  
Mild Anemia

Introduction. Severe Acute Respiratory Syndrome-2, possesses varying degrees of susceptibility and lethality worldwide and WHO declared this as a pandemic of this century. Aim. In this background, the aim of this present narrative is to provide a complementary overview of how low iron stores and mild anemia offers protection from infectious diseases like COVID-19 by restricting the viral replication and also to suggest some potential adjuvant therapeutic interventions. Material and methods. Therefore, we performed a literature search reviewing pertinent articles and documents. PubMed, Google Scholar, Chemrxiv, MedRxiv, BioRxiv, Preprints and ResearchGate were investigated. Analysis of the literature. Recent studies reported drastic systemic events taking place that contribute to the severe clinical outcomes such as decreased hemoglobin indicating anemia, hypoxia, altered iron metabolism, hypercoagulability, oxidative stress, cytokine storm, hyper-ferritinemia and thus Multi Organ Failure, reportedly hailed as the hallmark of the COVID-19 hyper- inflammatory state. Interestingly it is globally observed that, countries with higher Socio-economic status (SES) have considerably lower prevalence of Iron Deficiency Anemia (IDA) but higher Case Fatality Rate (CFR) rate due to COVID-19 while, low SES countries characterized by the higher prevalence of IDA, are less affected to COVID-19 infection and found to have less CFR, which is almost half to that of the higher SES counterpart. Conclusion. Present review presumed that,low iron stores and mild anemia may play a beneficial role in some cases by offering protection from infectious diseases as low iron restricts the viral replication.Thus, suggested iron chelation or iron sequestration as an alternative beneficial adjuvant in treating COVID-19 infection.

scholarly journals Prioritizing high-contact occupations raises effectiveness of vaccination campaigns

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Hendrik Nunner ◽  
Arnout van de Rijt ◽  
Vincent Buskens
Keyword(s):  
Practical Problem ◽  
Network Science ◽  
Personal Characteristic ◽  
Contact Network ◽  
Occupational Groups ◽  
Occupational Category ◽  
Disease Propagation ◽  
Specific Contact ◽  
Concrete Operational ◽  
Vaccination Campaigns

AbstractA twenty-year-old idea from network science is that vaccination campaigns would be more effective if high-contact individuals were preferentially targeted. Implementation is impeded by the ethical and practical problem of differentiating vaccine access based on a personal characteristic that is hard-to-measure and private. Here, we propose the use of occupational category as a proxy for connectedness in a contact network. Using survey data on occupation-specific contact frequencies, we calibrate a model of disease propagation in populations undergoing varying vaccination campaigns. We find that vaccination campaigns that prioritize high-contact occupational groups achieve similar infection levels with half the number of vaccines, while also reducing and delaying peaks. The paper thus identifies a concrete, operational strategy for dramatically improving vaccination efficiency in ongoing pandemics.

scholarly journals Reconstructing contact network structure and cross-immunity patterns from multiple infection histories

2021 ◽  
Vol 17 (9) ◽  
pp. e1009375
Author(s):  
Christian Selinger ◽  
Samuel Alizon
Keyword(s):  
Infectious Diseases ◽  
Multiple Infection ◽  
Contact Network ◽  
Multiple Infections ◽  
Similarity Metrics ◽  
Summary Statistics ◽  
Transmission Networks ◽  
Contact Patterns ◽  
Network Properties ◽  
Cross Immunity

Interactions within a population shape the spread of infectious diseases but contact patterns between individuals are difficult to access. We hypothesised that key properties of these patterns can be inferred from multiple infection data in longitudinal follow-ups. We developed a simulator for epidemics with multiple infections on networks and analysed the resulting individual infection time series by introducing similarity metrics between hosts based on their multiple infection histories. We find that, depending on infection multiplicity and network sampling, multiple infection summary statistics can recover network properties such as degree distribution. Furthermore, we show that by mining simulation outputs for multiple infection patterns, one can detect immunological interference between pathogens (i.e. the fact that past infections in a host condition future probability of infection). The combination of individual-based simulations and analysis of multiple infection histories opens promising perspectives to infer and validate transmission networks and immunological interference for infectious diseases from longitudinal cohort data.

scholarly journals Modelling infectious diseases with herd immunity in a randomly mixed population

2021 ◽  
Author(s):  
Kian Boon Law ◽  
Kalaiarasu M. Peariasamy ◽  
Hishamshah Mohd. Ibrahim ◽  
Noor Hisham Abdullah
Keyword(s):  
Infectious Disease ◽  
Infectious Diseases ◽  
Transmission Rate ◽  
Herd Immunity ◽  
Sir Model ◽  
Mixed Population ◽  
Transmission Dynamics ◽  
Transmission Model ◽  
Infection Model ◽  
Vaccination Rates

Abstract Background The conventional susceptible-infectious-recovered (SIR) model tends to overestimate the transmission dynamics of infectious diseases and ends up with total infections and total immunized population exceeding the threshold required for control and eradication of infectious diseases. The study aims to overcome the limitation by allowing the transmission rate of infectious disease to decline along with the reducing risk of contact infection. Methods Two new SIR models were developed to mimic the declining transmission rate of infectious diseases at different stages of transmission. Model A mimicked the declining transmission rate along with the reducing risk of transmission following infection, while Model B mimicked the declining transmission rate following recovery. Then, the conventional SIR model, Model A and Model B were used to simulate an infectious disease with a basic reproduction number (r0) of 3.0 and a herd immunity threshold (HIT) of 0.667 with and without vaccination. The infectious disease was expected to be controlled or eradicated when the total immunized population either through infection or vaccination reached the level predicted by the HIT. Outcomes of simulations were assessed at the time when the total immunized population reached the level predicted by the HIT, and at the end of simulations. Findings All three models performed likewise at the beginning of the transmission when sizes of infectious and recovered were relatively small as compared with the population size. The infectious disease modelled using the conventional SIR model appeared completely out of control even when the HIT was achieved in all scenarios with and without vaccination. The infectious disease modelled using Model A appeared to be controlled at the level predicted by the HIT in all scenarios with and without vaccination. Model B projected the infectious disease to be controlled at the level predicted by the HIT only at high vaccination rates. At lower vaccination rates or without vaccination, the level at which the infectious disease was controlled cannot be accurately predicted by the HIT. Conclusion Transmission dynamics of infectious diseases with herd immunity can accurately be modelled by allowing the transmission rate of infectious disease to decline along with the combined risk of contact infection. Model B provides a more credible framework for modelling infectious diseases with herd immunity in a randomly mixed population.

scholarly journals Comparing antiviral strategies against COVID-19 via multiscale within-host modelling

2021 ◽  
Vol 8 (8) ◽  
pp. 210082
Author(s):  
F. Fatehi ◽  
R. J. Bingham ◽  
E. C. Dykeman ◽  
P. G. Stockley ◽  
R. Twarock
Keyword(s):  
Disease Progression ◽  
Synergistic Effects ◽  
Treatment Options ◽  
Model Parameters ◽  
Clinical Environment ◽  
Plasma Therapy ◽  
Delayed Treatment ◽  
Infection Dynamics ◽  
Duration Of Infection ◽  
Host Infection

Within-host models of COVID-19 infection dynamics enable the merits of different forms of antiviral therapy to be assessed in individual patients. A stochastic agent-based model of COVID-19 intracellular dynamics is introduced here, that incorporates essential steps of the viral life cycle targeted by treatment options. Integration of model predictions with an intercellular ODE model of within-host infection dynamics, fitted to patient data, generates a generic profile of disease progression in patients that have recovered in the absence of treatment. This is contrasted with the profiles obtained after variation of model parameters pertinent to the immune response, such as effector cell and antibody proliferation rates, mimicking disease progression in immunocompromised patients. These profiles are then compared with disease progression in the presence of antiviral and convalescent plasma therapy against COVID-19 infections. The model reveals that using both therapies in combination can be very effective in reducing the length of infection, but these synergistic effects decline with a delayed treatment start. Conversely, early treatment with either therapy alone can actually increase the duration of infection, with infectious virions still present after the decline of other markers of infection. This suggests that usage of these treatments should remain carefully controlled in a clinical environment.

scholarly journals Predicting the effects of COVID-19 related interventions in urban settings by combining activity-based modelling, agent-based simulation, and mobile phone data

2021 ◽  
Author(s):  
Sebastian A. Müller ◽  
Michael Balmer ◽  
William Charlton ◽  
Ricardo Ewert ◽  
Andreas Neumann ◽  
...  
Keyword(s):  
Human Mobility ◽  
Leisure Activities ◽  
Contact Tracing ◽  
Mobile Phone Data ◽  
Infection Model ◽  
Mobility Data ◽  
Progression Model ◽  
Infection Dynamics ◽  
Political Decisions ◽  
Over Time

Epidemiological simulations as a method are used to better understand and predict the spreading of infectious diseases, for example of COVID-19. This paper presents an approach that combines a well-established approach from transportation modelling that uses person-centric data-driven human mobility modelling with a mechanistic infection model and a person-centric disease progression model. The model includes the consequences of different room sizes, air exchange rates, disease import, changed activity participation rates over time (coming from mobility data), masks, indoors vs. outdoors leisure activities, and of contact tracing. The model is validated against the infection dynamics in Berlin (Germany). The model can be used to understand the contributions of different activity types to the infection dynamics over time. The model predicts the effects of contact reductions, school closures/vacations, masks, or the effect of moving leisure activities from outdoors to indoors in fall, and is thus able to quantitatively predict the consequences of interventions. It is shown that these effects are best given as additive changes of the reinfection rate R. The model also explains why contact reductions have decreasing marginal returns, i.e. the first 50% of contact reductions have considerably more effect than the second 50%. Our work shows that is is possible to build detailed epidemiological simulations from microscopic mobility models relatively quickly. They can be used to investigate mechanical aspects of the dynamics, such as the transmission from political decisions via human behavior to infections, consequences of different lockdown measures, or consequences of wearing masks in certain situations. The results can be used to inform political decisions.

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