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  1. Article ; Online: Is epidemiology ready for Big Software?

    Kerr, Cliff C

    Pathogens and disease

    2019  Volume 77, Issue 1

    Abstract: Large-scale, open-source software projects like EMOD offer a new approach to epidemiological modeling. Built by a team of professional software developers, EMOD offers significant advantages over 'single-use' models designed by individual research teams, ...

    Abstract Large-scale, open-source software projects like EMOD offer a new approach to epidemiological modeling. Built by a team of professional software developers, EMOD offers significant advantages over 'single-use' models designed by individual research teams, including comprehensive documentation, automated testing and extensive support. In addition, as an individual-based model, it allows much greater complexity and flexibility than the compartmental models that are most commonly used in epidemiology. Adopting modern software development practices, as embodied by EMOD, is essential for ensuring that the best models are available to the greatest number of people.
    MeSH term(s) Epidemiologic Methods ; Humans ; Models, Theoretical ; Software
    Language English
    Publishing date 2019-01-14
    Publishing country United States
    Document type Letter
    ISSN 2049-632X
    ISSN (online) 2049-632X
    DOI 10.1093/femspd/ftz006
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Is epidemiology ready for Big Software?

    Kerr, Cliff C

    Pathogens and disease. 2019 Jan. 30, v. 77, no. 1

    2019  

    Abstract: Large-scale, open-source software projects like EMOD offer a new approach to epidemiological modeling. Built by a team of professional software developers, EMOD offers significant advantages over ‘single-use’ models designed by individual research teams, ...

    Abstract Large-scale, open-source software projects like EMOD offer a new approach to epidemiological modeling. Built by a team of professional software developers, EMOD offers significant advantages over ‘single-use’ models designed by individual research teams, including comprehensive documentation, automated testing and extensive support. In addition, as an individual-based model, it allows much greater complexity and flexibility than the compartmental models that are most commonly used in epidemiology. Adopting modern software development practices, as embodied by EMOD, is essential for ensuring that the best models are available to the greatest number of people.
    Keywords automation ; computer software ; epidemiology ; models ; researchers
    Language English
    Dates of publication 2019-0130
    Publishing place Oxford University Press
    Document type Article
    ISSN 2049-632X
    DOI 10.1093/femspd/ftz006
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: The changing health impact of vaccines in the COVID-19 pandemic: A modeling study.

    Cohen, Jamie A / Stuart, Robyn M / Panovska-Griffiths, Jasmina / Mudimu, Edinah / Abeysuriya, Romesh G / Kerr, Cliff C / Famulare, Michael / Klein, Daniel J

    Cell reports

    2023  Volume 42, Issue 4, Page(s) 112308

    Abstract: Much of the world's population had already been infected with COVID-19 by the time the Omicron variant emerged at the end of 2021, but the scale of the Omicron wave was larger than any that had come before or has happened since, and it left a global ... ...

    Abstract Much of the world's population had already been infected with COVID-19 by the time the Omicron variant emerged at the end of 2021, but the scale of the Omicron wave was larger than any that had come before or has happened since, and it left a global imprinting of immunity that changed the COVID-19 landscape. In this study, we simulate a South African population and demonstrate how population-level vaccine effectiveness and efficiency changed over the course of the first 2 years of the pandemic. We then introduce three hypothetical variants and evaluate the impact of vaccines with different properties. We find that variant-chasing vaccines have a narrow window of dominating pre-existing vaccines but that a variant-chasing vaccine strategy may have global utility, depending on the rate of spread from setting to setting. Next-generation vaccines might be able to overcome uncertainty in pace and degree of viral evolution.
    MeSH term(s) Humans ; COVID-19/prevention & control ; Pandemics/prevention & control ; SARS-CoV-2 ; Vaccines
    Chemical Substances Vaccines
    Language English
    Publishing date 2023-03-15
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2023.112308
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Can we know in advance whether models will get it right?

    Wilson, David P / Kerr, Cliff C

    The Lancet. Global health

    2015  Volume 3, Issue 10, Page(s) e577–8

    MeSH term(s) Female ; HIV Infections/epidemiology ; Humans ; Male ; Models, Theoretical
    Language English
    Publishing date 2015-10
    Publishing country England
    Document type Comment ; Journal Article
    ZDB-ID 2723488-5
    ISSN 2214-109X ; 2214-109X
    ISSN (online) 2214-109X
    ISSN 2214-109X
    DOI 10.1016/S2214-109X(15)00160-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Modeling COVID-19 vaccination strategies in LMICs considering uncertainty in viral evolution and immunity

    Klein, Daniel J / Yang, Luojun / Kerr, Cliff C / Fowler, Greer / Cohen, Jamie A

    medRxiv

    Abstract: Vaccines against the SARS-CoV-2 virus were developed in record time, but their distribution has been highly unequal. With demand saturating in high-income countries, many low- and middle-income countries (LMIC) finally have an opportunity to acquire ... ...

    Abstract Vaccines against the SARS-CoV-2 virus were developed in record time, but their distribution has been highly unequal. With demand saturating in high-income countries, many low- and middle-income countries (LMIC) finally have an opportunity to acquire COVID-19 vaccines. But the pandemic has taken its toll, and a majority of LMIC populations have partial immunity to COVID-19 disease due primarily to viral infection. This existing immunity, combined with resource limitations, raises the question of how LMICs should prioritize COVID-19 vaccines relative to other competing health priorities. We modify an established computational model, Covasim, to address these questions in four diverse country-like settings under a variety of viral evolution, vaccine delivery, and novel immunity scenarios. Under continued Omicron-like viral evolution and mid-level immunity assumptions, results show that COVID-19 vaccines could avert up to 2 deaths per 1,000 doses if administered to high-risk (60+) populations as prime+boost or annual boosting campaigns. Similar immunization efforts reaching healthy children and adults would avert less than 0.1 deaths per 1,000 doses. Together, these modeling results can help to support normative guidelines and programmatic decision making towards objectively maximizing population health.
    Keywords covid19
    Language English
    Publishing date 2023-03-15
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2023.03.15.23287285
    Database COVID19

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  6. Article ; Online: The influence of constraints on the efficient allocation of resources for HIV prevention.

    Stuart, Robyn M / Kelly, Sherrie L / Kerr, Cliff C / Martin-Hughes, Rowan / Wilson, David P

    AIDS (London, England)

    2019  Volume 33, Issue 12, Page(s) 1949–1950

    MeSH term(s) Acquired Immunodeficiency Syndrome ; HIV Infections ; Health Resources ; Humans ; Resource Allocation
    Language English
    Publishing date 2019-09-06
    Publishing country England
    Document type Letter ; Comment
    ZDB-ID 639076-6
    ISSN 1473-5571 ; 0269-9370 ; 1350-2840
    ISSN (online) 1473-5571
    ISSN 0269-9370 ; 1350-2840
    DOI 10.1097/QAD.0000000000002267
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    In stock of ZB MED Cologne/Königswinter

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  7. Article ; Online: How to do (or not to do)… health resource allocations using constrained mathematical optimization.

    Stuart, Robyn M / Fraser-Hurt, Nicole / Shubber, Zara / Vu, Lung / Cheik, Nejma / Kerr, Cliff C / Wilson, David P

    Health policy and planning

    2022  

    Abstract: Despite the push towards evidence-based health policy, decisions about how to allocate health resources are all too often made on the basis of political forces or a continuation of the status quo. This results in wastage in health systems and loss of ... ...

    Abstract Despite the push towards evidence-based health policy, decisions about how to allocate health resources are all too often made on the basis of political forces or a continuation of the status quo. This results in wastage in health systems and loss of potential population health. However, if health systems are to serve people best, then they must operate efficiently and equitably, and appropriate valuation methods are needed to determine how to do this. With the advances in computing power over the past few decades, advanced mathematical optimization algorithms can now be run on personal computers, and can be used to provide comprehensive, evidence-based recommendations for policy makers on how to prioritize health spending considering policy objectives, interactions of interventions, real-world system constraints, and budget envelopes. Such methods provide an invaluable complement to traditional or extended cost-effectiveness analyses (CEA or ECEA) or league tables. In this paper, we describe how such methods work, how policy makers and program managers can access them and implement their recommendations, and how they have changed health spending in the world to date.
    Language English
    Publishing date 2022-11-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 632896-9
    ISSN 1460-2237 ; 0268-1080
    ISSN (online) 1460-2237
    ISSN 0268-1080
    DOI 10.1093/heapol/czac096
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  8. Article ; Online: The changing health impact of vaccines in the COVID-19 pandemic

    Jamie A. Cohen / Robyn M. Stuart / Jasmina Panovska-Griffiths / Edinah Mudimu / Romesh G. Abeysuriya / Cliff C. Kerr / Michael Famulare / Daniel J. Klein

    Cell Reports, Vol 42, Iss 4, Pp 112308- (2023)

    A modeling study

    2023  

    Abstract: Summary: Much of the world’s population had already been infected with COVID-19 by the time the Omicron variant emerged at the end of 2021, but the scale of the Omicron wave was larger than any that had come before or has happened since, and it left a ... ...

    Abstract Summary: Much of the world’s population had already been infected with COVID-19 by the time the Omicron variant emerged at the end of 2021, but the scale of the Omicron wave was larger than any that had come before or has happened since, and it left a global imprinting of immunity that changed the COVID-19 landscape. In this study, we simulate a South African population and demonstrate how population-level vaccine effectiveness and efficiency changed over the course of the first 2 years of the pandemic. We then introduce three hypothetical variants and evaluate the impact of vaccines with different properties. We find that variant-chasing vaccines have a narrow window of dominating pre-existing vaccines but that a variant-chasing vaccine strategy may have global utility, depending on the rate of spread from setting to setting. Next-generation vaccines might be able to overcome uncertainty in pace and degree of viral evolution.
    Keywords CP: Immunology ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-04-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Frequent and unpredictable changes in COVID-19 policies and restrictions reduce the accuracy of model forecasts.

    Houdroge, Farah / Palmer, Anna / Delport, Dominic / Walsh, Tom / Kelly, Sherrie L / Hainsworth, Samuel W / Abeysuriya, Romesh / Stuart, Robyn M / Kerr, Cliff C / Coplan, Paul / Wilson, David P / Scott, Nick

    Scientific reports

    2023  Volume 13, Issue 1, Page(s) 1398

    Abstract: Between June and August 2020, an agent-based model was used to project rates of COVID-19 infection incidence and cases diagnosed as positive from 15 September to 31 October 2020 for 72 geographic settings. Five scenarios were modelled: a baseline ... ...

    Abstract Between June and August 2020, an agent-based model was used to project rates of COVID-19 infection incidence and cases diagnosed as positive from 15 September to 31 October 2020 for 72 geographic settings. Five scenarios were modelled: a baseline scenario where no future changes were made to existing restrictions, and four scenarios representing small or moderate changes in restrictions at two intervals. Post hoc, upper and lower bounds for number of diagnosed Covid-19 cases were compared with actual data collected during the prediction window. A regression analysis with 17 covariates was performed to determine correlates of accurate projections. It was found that the actual data fell within the lower and upper bounds in 27 settings and out of bounds in 45 settings. The only statistically significant predictor of actual data within the predicted bounds was correct assumptions about future policy changes (OR 15.04; 95% CI 2.20-208.70; p = 0.016). Frequent changes in restrictions implemented by governments, which the modelling team was not always able to predict, in part explains why the majority of model projections were inaccurate compared with actual outcomes and supports revision of projections when policies are changed as well as the importance of modelling teams collaborating with policy experts.
    MeSH term(s) Humans ; COVID-19/epidemiology ; Policy ; Forecasting ; Regression Analysis
    Language English
    Publishing date 2023-01-25
    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/s41598-023-27711-3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Local responses to local epidemics for national impact need advanced spatially explicit tools.

    Grantham, Kelsey L / Kerr, Cliff C / Wilson, David P

    AIDS (London, England)

    2016  Volume 30, Issue 9, Page(s) 1481–1482

    MeSH term(s) Epidemics ; HIV Infections ; Humans ; Models, Biological
    Language English
    Publishing date 2016--01
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 639076-6
    ISSN 1473-5571 ; 0269-9370 ; 1350-2840
    ISSN (online) 1473-5571
    ISSN 0269-9370 ; 1350-2840
    DOI 10.1097/QAD.0000000000001106
    Database MEDical Literature Analysis and Retrieval System OnLINE

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