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Article ; Online: Models and analyses to understand threats to polio eradication.

Koopman, James S

BMC medicine

2017 Volume 15, Issue 1, Page(s) 221

Abstract: To achieve complete polio eradication, the live oral poliovirus vaccine (OPV) currently used must be phased out after the end of wild poliovirus transmission. However, poorly understood threats may arise when OPV use is stopped. To counter these threats, ...

Abstract	To achieve complete polio eradication, the live oral poliovirus vaccine (OPV) currently used must be phased out after the end of wild poliovirus transmission. However, poorly understood threats may arise when OPV use is stopped. To counter these threats, better models than those currently available are needed. Two articles recently published in BMC Medicine address these issues. Mercer et al. (BMC Med 15:180, 2017) developed a statistical model analysis of polio case data and characteristics of cases occurring in several districts in Pakistan to inform resource allocation decisions. Nevertheless, despite having the potential to accelerate the elimination of polio cases, their analyses are unlikely to advance our understanding OPV cessation threats. McCarthy et al. (BMC Med 15:175, 2017) explored one such threat, namely the emergence and transmission of serotype 2 circulating vaccine derived poliovirus (cVDPV2) after OPV2 cessation, and found that the risk of persistent spread of cVDPV2 to new areas increases rapidly 1-5 years after OPV2 cessation. Thus, recently developed models and analysis methods have the potential to guide the required steps to surpass these threats. 'Big data' scientists could help with this; however, datasets covering all eradication efforts should be made readily available.Please see related articles: https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-017-0937-y and https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-017-0941-2 .
MeSH term(s)	Disease Eradication ; Disease Outbreaks/prevention & control ; Humans ; Pakistan ; Poliomyelitis/epidemiology ; Poliovirus/immunology ; Poliovirus Vaccine, Oral/immunology
Chemical Substances	Poliovirus Vaccine, Oral
Language	English
Publishing date	2017--22
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Comment
ISSN	1741-7015
ISSN (online)	1741-7015
DOI	10.1186/s12916-017-0991-5
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Effect of Population Partitioning on the Probability of Silent Circulation of Poliovirus.

Vallejo, Celeste / Pearson, Carl A B / Koopman, James S / Hladish, Thomas J

Bulletin of mathematical biology

2022 Volume 84, Issue 6, Page(s) 62

Abstract: Polio can circulate unobserved in regions that are challenging to monitor. To assess the probability of silent circulation, simulation models can be used to understand transmission dynamics when detection is unreliable. Model assumptions, however, impact ...

Abstract	Polio can circulate unobserved in regions that are challenging to monitor. To assess the probability of silent circulation, simulation models can be used to understand transmission dynamics when detection is unreliable. Model assumptions, however, impact the estimated probability of silent circulation. Here, we examine the impact of having distinct populations, rather than a single well-mixed population, with a discrete-individual model including environmental surveillance. We show that partitioning a well-mixed population into networks of distinct communities may result in a higher probability of silent circulation as a result of the time it takes for the detection of a circulation event. Population structure should be considered when assessing polio control in a region with many loosely interacting communities.
MeSH term(s)	Humans ; Mathematical Concepts ; Models, Biological ; Poliomyelitis/diagnosis ; Poliomyelitis/epidemiology ; Poliomyelitis/prevention & control ; Poliovirus ; Probability
Language	English
Publishing date	2022-05-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	184905-0
ISSN	1522-9602 ; 0007-4985 ; 0092-8240
ISSN (online)	1522-9602
ISSN	0007-4985 ; 0092-8240
DOI	10.1007/s11538-022-01014-6
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Article ; Online: Modeling the population effects of escape mutations in SARS-CoV-2 to guide vaccination strategies.

Koopman, James S / Simon, Carl P / Getz, Wayne M / Salter, Richard

Epidemics

2021 Volume 36, Page(s) 100484

Abstract: SARS-Cov-2 escape mutations (EM) have been detected and are spreading. Vaccines may need adjustment to respond to these or future mutations. We designed a population level model integrating both waning immunity and EM. We also designed a set of criteria ... ...

Abstract	SARS-Cov-2 escape mutations (EM) have been detected and are spreading. Vaccines may need adjustment to respond to these or future mutations. We designed a population level model integrating both waning immunity and EM. We also designed a set of criteria for elaborating and fitting this model to cross-neutralization and other data with a goal of minimizing vaccine decision errors. We formulated four related models. These differ regarding which strains can drift to escape immunity in the host when that immunity was elicited by different strains. Across changing waning and escape mutation parameter values, these model variations led to patterns where: 1) EM are rare in the first epidemic, 2) rebound outbreaks after the first outbreak are accelerated by increasing waning and by increasing drifting, 3) the long term endemic level of infection is determined mostly by waning rates with small effects of the drifting parameter, 4) EM caused loss of vaccine effectiveness, and under some conditions: vaccines induced EM that caused higher levels of infection with vaccines than without them. The differences and similarities across the four models suggest paths for developing models specifying the epitopes where EM act. This model provides a base on which to construct epitope specific evolutionary models using new high-throughput assay data from population samples to guide vaccine decisions.
MeSH term(s)	COVID-19 ; Humans ; Mutation/genetics ; SARS-CoV-2 ; Vaccination
Language	English
Publishing date	2021-07-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2467993-8
ISSN	1878-0067 ; 1755-4365
ISSN (online)	1878-0067
ISSN	1755-4365
DOI	10.1016/j.epidem.2021.100484
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Article ; Online: Modeling the dynamics of SARS-CoV-2 immunity waning, antigenic drifting, and population serology patterns

Koopman, James S / Simon, Carl P

medRxiv

Abstract: Reinfection with SARS-CoV-2 can result from either waning immunity, a drift in the virus that escapes previously stimulated immunity, or both. The nature of such reinfection risks will affect the choice of control tactics and vaccines. We constructed an ... ...

Abstract	Reinfection with SARS-CoV-2 can result from either waning immunity, a drift in the virus that escapes previously stimulated immunity, or both. The nature of such reinfection risks will affect the choice of control tactics and vaccines. We constructed an SIR transmission model of waning and drifting that can be fitted to cross-neutralization serological data. In this model, waning occurs in individuals who have recovered from previous infections while drifting occurs during transmission to a previously infected individual. Interactions at the population level generate complex dynamics that cause drifting to occur in unanticipated but explainable ways across waning and drifting parameter sets. In particular, raising the fraction of transmissions where drifting occurs slows the rise of drifted strains to high levels and changes the equilibrium distribution of strains from ∪ shaped (extreme strains dominate) to ∩ shaped (central strains dominate). In ∪ shaped parameter regimes, endemic infection levels can rise after many years to above the original epidemic peak. The model simulates results from cross-neutralization assays given sera from previously infected individuals when multiple drifted strains are used in the assays. Fitting the model to such assay data can estimate waning and drifting parameters. Given the parameters, the model predicts infection patterns. We propose a process for using fits of our model to serological and other data called Decision Robustness and Identifiability Analysis (DRIA). This can inform decisions about vaccine options such as whether to prepare for changes in vaccine composition because the virus is changing to escape immunity.
Keywords	covid19
Language	English
Publishing date	2020-09-11
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2020.09.10.20192153
Database	COVID19

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Book ; Article ; Online: Eliminación de aguas negras, suministro de agua y diarréa endémica en un barrio urbano pobre de Cali, Colombia

Koopman, James S

2015

Keywords	Diarreia ; Diarreia Infantil ; Eliminação de Resíduos ; Abastecimento de Água ; Colômbia
Publishing date	2015-12-08T03:09:16Z
Document type	Book ; Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A runtime alterable epidemic model with genetic drift, waning immunity and vaccinations.

Getz, Wayne M / Salter, Richard / Luisa Vissat, Ludovica / Koopman, James S / Simon, Carl P

Journal of the Royal Society, Interface

2021 Volume 18, Issue 184, Page(s) 20210648

Abstract: We present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes ... ...

Abstract	We present methods for building a Java Runtime-Alterable-Model Platform (RAMP) of complex dynamical systems. We illustrate our methods by building a multivariant SEIR (epidemic) RAMP. Underlying our RAMP is an individual-based model that includes adaptive contact rates, pathogen genetic drift, waning and cross-immunity. Besides allowing parameter values, process descriptions and scriptable runtime drivers to be easily modified during simulations, our RAMP can used within R-Studio and other computational platforms. Process descriptions that can be runtime altered within our SEIR RAMP include pathogen variant-dependent host shedding, environmental persistence, host transmission and within-host pathogen mutation and replication. They also include adaptive social distancing and adaptive application of vaccination rates and variant-valency of vaccines. We present simulation results using parameter values and process descriptions relevant to the current COVID-19 pandemic. Our results suggest that if waning immunity outpaces vaccination rates, then vaccination rollouts may fail to contain the most transmissible variants, particularly if vaccine valencies are not adapted to deal with escape mutations. Our SEIR RAMP is designed for easy use by others. More generally, our RAMP concept facilitates construction of highly flexible complex systems models of all types, which can then be easily shared as stand-alone application programs.
MeSH term(s)	COVID-19 ; Genetic Drift ; Humans ; Pandemics ; SARS-CoV-2 ; Vaccination
Language	English
Publishing date	2021-11-24
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2156283-0
ISSN	1742-5662 ; 1742-5689
ISSN (online)	1742-5662
ISSN	1742-5689
DOI	10.1098/rsif.2021.0648
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Article ; Online: Strong influence of behavioral dynamics on the ability of testing and treating HIV to stop transmission.

Henry, Christopher J / Koopman, James S

Scientific reports

2015 Volume 5, Page(s) 9467

Abstract: Choosing between strategies to control HIV transmission with antivirals requires understanding both the dynamics affecting those strategies' effectiveness and what causes those dynamics. Alternating episodes of high and low contact rates (episodic risk) ... ...

Abstract	Choosing between strategies to control HIV transmission with antivirals requires understanding both the dynamics affecting those strategies' effectiveness and what causes those dynamics. Alternating episodes of high and low contact rates (episodic risk) interact with increased transmission probabilities during early infection to strongly influence HIV transmission dynamics. To elucidate the mechanics of this interaction and how these alter the effectiveness of universal test and treat (UT8T) strategies, we formulated a model of UT8T effects. Analysis of this model shows how and why changing the dynamics of episodic risk changes the fraction of early transmissions (FET) and the basic reproduction number (R0) and consequently causes UT8T to vary from easily eliminating transmission to having little effect. As the length of risk episodes varies from days to lifetimes, FET first increases, then falls. Endemic prevalence varies similarly. R0, in contrast, increases monotonically and is the major determinant of UT8T effects. At some levels of episodic risk, FET can be high, but eradication is easy because R0 is low. At others FET is lower, but a high R0 makes eradication impossible and control ineffective. Thus changes in individual risk over time must be measured and analyzed to plan effective control strategies with antivirals.
MeSH term(s)	Anti-HIV Agents/therapeutic use ; HIV Infections/diagnosis ; HIV Infections/drug therapy ; HIV Infections/transmission ; Humans ; Models, Theoretical ; Risk ; Sexual Behavior/psychology
Chemical Substances	Anti-HIV Agents
Language	English
Publishing date	2015-04-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/srep09467
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Article ; Online: Modeling the population effects of epitope specific escape mutations in SARS-CoV-2 to guide vaccination strategies

Koopman, James S / Simon, Carl P / Getz, Wayne M / Salter, Richard

medRxiv

Abstract: Escape mutations (EM) to SARS-Cov-2 have been detected and are spreading. Vaccines may need adjustment to respond to these or future mutations. We designed a population level model integrating both waning immunity and EM. We also designed a set of ... ...

Abstract	Escape mutations (EM) to SARS-Cov-2 have been detected and are spreading. Vaccines may need adjustment to respond to these or future mutations. We designed a population level model integrating both waning immunity and EM. We also designed a set of criteria for elaborating and fitting this model to cross-neutralization and other data in a manner that minimizes vaccine decision errors. We formulated four model variations. These define criteria for which prior infections provide immunity that can be escaped. They also specify different sequences where one EM follows another. At all reasonable parameter values, these model variations led to patterns where: 1) EM were rare in the first epidemic, 2) rebound epidemics after the first epidemic were accelerated more by increasing drifting than by increasing waning (with some exceptions), 3) the long term endemic level of infection was determined mostly by waning rates with small effects of the drifting parameter, 4) EM caused loss of vaccine effectiveness and under some conditions, vaccines induced EM that caused higher levels of infection with vaccines than without them. The differences and similarities across the four models suggest paths for developing models specifying the epitopes where EM act. This model is a base on which to construct epitope specific evolutionary models using new high-throughput assay data from population samples to guide vaccine decisions.
Keywords	covid19
Language	English
Publishing date	2021-01-20
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.01.19.21250114
Database	COVID19

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Article ; Online: Adaptive vaccination may be needed to extirpate COVID-19: Results from a runtime-alterable strain-drift and waning-immunity model

Getz, Wayne M / Salter, Richard / Vissat, Ludovica Luisa / Koopman, James S / Simon, Carl P

medRxiv

Abstract: We developed an elaborated susceptible-infected-recovered (SIR) individual-based model (IBM) with pathogen strain drift, waning and cross immunity, implemented as a novel Java Runtime-Alterable-Model Platform (J-RAMP). This platform allows parameter ... ...

Abstract	We developed an elaborated susceptible-infected-recovered (SIR) individual-based model (IBM) with pathogen strain drift, waning and cross immunity, implemented as a novel Java Runtime-Alterable-Model Platform (J-RAMP). This platform allows parameter values, process formulations, and scriptable runtime drivers to be easily added at the start of simulation. It includes facility for integration into the R statistical and other data analysis platforms. We selected a set of parameter values and process descriptions relevant to the current COVID-19 pandemic. These include pathogen-specific shedding, environmental persistence, host transmission and mortality, within-host pathogen mutation and replication, adaptive social distancing, and time dependent vaccine rate and strain valency specifications. Our simulations illustrate that if waning immunity outpaces vaccination rates, then vaccination rollouts may fail to contain the most transmissible strains. Our study highlights the need for adaptive vaccination rollouts, which depend on reliable real-time monitoring and surveillance of strain proliferation and reinfection data needed to ensure that vaccines target emerging strains and constrain escape mutations. Together with such data, our platform has the potential to inform the design of vaccination programs that extirpate rather than exacerbate local outbreaks. Finally, our RAMP concept promotes the development of highly flexible models that can be easily shared among researchers and policymakers not only addressing healthcare crises, but other types of environmental crises as well.
Keywords	covid19
Language	English
Publishing date	2021-06-11
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.06.07.21258504
Database	COVID19

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Article ; Online: HIV transmissions by stage in dynamic sexual partnerships.

Kim, Jong-Hoon / Koopman, James S

Journal of theoretical biology

2012 Volume 298, Page(s) 147–153

Abstract: Most models assessing relative transmissions during different progressive stages of human immunodeficiency virus (HIV) infection assume that infections are transmitted through instantaneous sexual contacts. In reality, however, HIV will often be ... ...

Abstract	Most models assessing relative transmissions during different progressive stages of human immunodeficiency virus (HIV) infection assume that infections are transmitted through instantaneous sexual contacts. In reality, however, HIV will often be transmitted through repeated sex acts during partnerships that form and dissolve at varying rates. We sought to understand how dynamic sexual partnerships would influence transmissions during different progression stages of HIV infection: primary HIV infection (PHI) and chronic stage. Using a system of ordinary differential equations with a pair approximation technique, we constructed a model of HIV transmission in a homogeneous population in which sexual partnerships form and dissolve. We derived analytical expressions for useful epidemiological quantities such as basic reproduction number and also did simulation runs of the model. Partnership dynamics strongly influence transmissions during progressive stages of HIV infection. The fraction of transmissions during PHI has a U-shaped relationship with respect to the rate of partnership change, where the minimum and maximum occur given partnerships of about 100 days and fixed partnerships, respectively. Models that assume instantaneous contacts may overestimate transmissions during PHI for real, dynamic sexual partnerships with varying (non-zero) durations.
MeSH term(s)	Basic Reproduction Number ; Disease Progression ; HIV Infections/psychology ; HIV Infections/transmission ; Humans ; Models, Biological ; Sexual Behavior ; Sexual Partners ; Time Factors
Language	English
Publishing date	2012-01-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2972-5
ISSN	1095-8541 ; 0022-5193
ISSN (online)	1095-8541
ISSN	0022-5193
DOI	10.1016/j.jtbi.2011.12.021
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