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Iwu-Jaja C, Ndlovu NL, Rachida S, Yousif M, Taukobong S, Macheke M, Mhlanga L, van Schalkwyk C, Pulliam JRC, Moultrie T, le Roux W, Schaefer L, Pocock G, Coetzee LZ, Mans J, Bux F, Pillay L, de Villiers D, du Toit AP, Jambo D, Gomba A, Groenink S, Madgewick N, van der Walt M, Mutshembele A, Berkowitz N, Suchard M, McCarthy K. The role of wastewater-based epidemiology for SARS-CoV-2 in developing countries: Cumulative evidence from South Africa supports sentinel site surveillance to guide public health decision-making. Sci Total Environ 2023; 903:165817. [PMID: 37506905 DOI: 10.1016/j.scitotenv.2023.165817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 07/30/2023]
Abstract
The uptake of wastewater-based epidemiology (WBE) for SARS-CoV-2 as a complementary tool for monitoring population-level epidemiological features of the COVID-19 pandemic in low-and-middle-income countries (LMICs) is low. We report on the findings from the South African SARS-CoV-2 WBE surveillance network and make recommendations regarding the implementation of WBE in LMICs. Eight laboratories quantified influent wastewater collected from 87 wastewater treatment plants in all nine South African provinces from 01 June 2021 to 31 May 2022 inclusive, during the 3rd and 4th waves of COVID-19. Correlation and regression analyses between wastewater levels of SARS-CoV-2 and district laboratory-confirmed caseloads were conducted. The sensitivity and specificity of novel 'rules' based on WBE data to predict an epidemic wave were determined. Amongst 2158 wastewater samples, 543/648 (85 %) samples taken during a wave tested positive for SARS-CoV-2 compared with 842 positive tests from 1512 (55 %) samples taken during the interwave period. Overall, the regression-co-efficient was 0,66 (95 % confidence interval = 0,6-0,72, R2 = 0.59), ranging from 0.14 to 0.87 by testing laboratory. Early warning of the 4th wave of SARS-CoV-2 in Gauteng Province in November-December 2021 was demonstrated. A 50 % increase in log copies of SARS-CoV-2 compared with a rolling mean over the previous five weeks was the most sensitive predictive rule (58 %) to predict a new wave. Our findings support investment in WBE for SARS-CoV-2 surveillance in LMICs as an early warning tool. Standardising test methodology is necessary due to varying correlation strengths across laboratories and redundancy across testing plants. A sentinel site model can be used for surveillance networks without affecting WBE finding for decision-making. Further research is needed to identify optimal test frequency and the need for normalisation to population size to identify predictive and interpretive rules to support early warning and public health action.
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Affiliation(s)
- Chinwe Iwu-Jaja
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, South Africa.
| | - Nkosenhle Lindo Ndlovu
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, South Africa.
| | - Said Rachida
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, South Africa
| | - Mukhlid Yousif
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, South Africa; School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Setshaba Taukobong
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, South Africa
| | - Mokgaetji Macheke
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, South Africa
| | - Laurette Mhlanga
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Cari van Schalkwyk
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Tom Moultrie
- Centre for Actuarial Research, University of Cape Town, South Africa
| | - Wouter le Roux
- Water Centre, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Lisa Schaefer
- Water Centre, Council for Scientific and Industrial Research, Pretoria, South Africa
| | | | | | - Janet Mans
- Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | - Leanne Pillay
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, South Africa
| | | | - A P du Toit
- Lumegen Laboratories (Pty) Ltd, Potchefstroom, South Africa
| | - Don Jambo
- National Institute for Occupational Health, South Africa
| | | | | | | | | | | | | | - Melinda Suchard
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, South Africa; School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Kerrigan McCarthy
- Centre for Vaccines and Immunology, National Institute for Communicable Diseases, South Africa; School of Pathology, University of the Witwatersrand, Johannesburg, South Africa; School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
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Azam JM, Pang X, Are EB, Pulliam JRC, Ferrari MJ. Modelling outbreak response impact in human vaccine-preventable diseases: A systematic review of differences in practices between collaboration types before COVID-19. Epidemics 2023; 45:100720. [PMID: 37944405 DOI: 10.1016/j.epidem.2023.100720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 07/01/2023] [Accepted: 10/02/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Outbreak response modelling often involves collaboration among academics, and experts from governmental and non-governmental organizations. We conducted a systematic review of modelling studies on human vaccine-preventable disease (VPD) outbreaks to identify patterns in modelling practices between two collaboration types. We complemented this with a mini comparison of foot-and-mouth disease (FMD), a veterinary disease that is controllable by vaccination. METHODS We searched three databases for modelling studies that assessed the impact of an outbreak response. We extracted data on author affiliation type (academic institution, governmental, and non-governmental organizations), location studied, and whether at least one author was affiliated to the studied location. We also extracted the outcomes and interventions studied, and model characteristics. Included studies were grouped into two collaboration types: purely academic (papers with only academic affiliations), and mixed (all other combinations) to help investigate differences in modelling patterns between collaboration types in the human disease literature and overall differences with FMD collaboration practices. RESULTS Human VPDs formed 227 of 252 included studies. Purely academic collaborations dominated the human disease studies (56%). Notably, mixed collaborations increased in the last seven years (2013-2019). Most studies had an author affiliated to an institution in the country studied (75.2%) but this was more likely among the mixed collaborations. Contrasted to the human VPDs, mixed collaborations dominated the FMD literature (56%). Furthermore, FMD studies more often had an author with an affiliation to the country studied (92%) and used complex model design, including stochasticity, and model parametrization and validation. CONCLUSION The increase in mixed collaboration studies over the past seven years could suggest an increase in the uptake of modelling for outbreak response decision-making. We encourage more mixed collaborations between academic and non-academic institutions and the involvement of locally affiliated authors to help ensure that the studies suit local contexts.
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Affiliation(s)
- James M Azam
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom; DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch 7600, South Africa.
| | - Xiaoxi Pang
- Department of Mathematics, The University of Manchester, Manchester, United Kingdom
| | - Elisha B Are
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch 7600, South Africa; Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Juliet R C Pulliam
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch 7600, South Africa
| | - Matthew J Ferrari
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA, USA
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Silal SP, Pulliam JRC, Meyer-Rath G, Jamieson L, Nichols BE, Norman J, Hounsell R, Mayet S, Kagoro F, Moultrie H. The National COVID-19 Epi Model (NCEM): Estimating cases, admissions and deaths for the first wave of COVID-19 in South Africa. PLOS Glob Public Health 2023; 3:e0001070. [PMID: 37093784 PMCID: PMC10124849 DOI: 10.1371/journal.pgph.0001070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 03/27/2023] [Indexed: 04/25/2023]
Abstract
In March 2020 the South African COVID-19 Modelling Consortium was formed to support government planning for COVID-19 cases and related healthcare. Models were developed jointly by local disease modelling groups to estimate cases, resource needs and deaths due to COVID-19. The National COVID-19 Epi Model (NCEM) while initially developed as a deterministic compartmental model of SARS-Cov-2 transmission in the nine provinces of South Africa, was adapted several times over the course of the first wave of infection in response to emerging local data and changing needs of government. By the end of the first wave, the NCEM had developed into a stochastic, spatially-explicit compartmental transmission model to estimate the total and reported incidence of COVID-19 across the 52 districts of South Africa. The model adopted a generalised Susceptible-Exposed-Infectious-Removed structure that accounted for the clinical profile of SARS-COV-2 (asymptomatic, mild, severe and critical cases) and avenues of treatment access (outpatient, and hospitalisation in non-ICU and ICU wards). Between end-March and early September 2020, the model was updated 11 times with four key releases to generate new sets of projections and scenario analyses to be shared with planners in the national and provincial Departments of Health, the National Treasury and other partners. Updates to model structure included finer spatial granularity, limited access to treatment, and the inclusion of behavioural heterogeneity in relation to the adoption of Public Health and Social Measures. These updates were made in response to local data and knowledge and the changing needs of the planners. The NCEM attempted to incorporate a high level of local data to contextualise the model appropriately to address South Africa's population and health system characteristics that played a vital role in producing and updating estimates of resource needs, demonstrating the importance of harnessing and developing local modelling capacity.
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Affiliation(s)
- Sheetal Prakash Silal
- Department of Statistical Sciences, Modelling and Simulation Hub, Africa (MASHA), University of Cape Town, Cape Town, South Africa
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Juliet R. C. Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Gesine Meyer-Rath
- Department of Internal Medicine, Health Economics and Epidemiology Research Office, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Global Health, School of Public Health, Boston University, Boston, MA, United States of America
| | - Lise Jamieson
- Department of Internal Medicine, Health Economics and Epidemiology Research Office, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Brooke E. Nichols
- Department of Internal Medicine, Health Economics and Epidemiology Research Office, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Global Health, School of Public Health, Boston University, Boston, MA, United States of America
- Department of Medical Microbiology, Amsterdam University Medical Center, Amsterdam, the Netherlands
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - Jared Norman
- Department of Statistical Sciences, Modelling and Simulation Hub, Africa (MASHA), University of Cape Town, Cape Town, South Africa
| | - Rachel Hounsell
- Department of Statistical Sciences, Modelling and Simulation Hub, Africa (MASHA), University of Cape Town, Cape Town, South Africa
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Saadiyah Mayet
- Department of Statistical Sciences, Modelling and Simulation Hub, Africa (MASHA), University of Cape Town, Cape Town, South Africa
| | - Frank Kagoro
- Division of Clinical Pharmacology, Department of Medicine, Collaborating Centre for Optimising Antimalarial Therapy, University of Cape Town, Cape Town, South Africa
| | - Harry Moultrie
- National Institute for Communicable Diseases (NICD), a Division of the National Health Laboratory Service, Johannesburg, South Africa
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Shanta IS, Luby SP, Hossain K, Heffelfinger JD, Kilpatrick AM, Haider N, Rahman T, Chakma S, Ahmed SSU, Sharker Y, Pulliam JRC, Kennedy ED, Gurley ES. Human Exposure to Bats, Rodents and Monkeys in Bangladesh. Ecohealth 2023; 20:53-64. [PMID: 37099204 PMCID: PMC10131556 DOI: 10.1007/s10393-023-01628-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/28/2023] [Accepted: 04/05/2023] [Indexed: 06/11/2023]
Abstract
Bats, rodents and monkeys are reservoirs for emerging zoonotic infections. We sought to describe the frequency of human exposure to these animals and the seasonal and geographic variation of these exposures in Bangladesh. During 2013-2016, we conducted a cross-sectional survey in a nationally representative sample of 10,002 households from 1001 randomly selected communities. We interviewed household members about exposures to bats, rodents and monkeys, including a key human-bat interface-raw date palm sap consumption. Respondents reported observing rodents (90%), bats (52%) and monkeys (2%) in or around their households, although fewer reported direct contact. The presence of monkeys around the household was reported more often in Sylhet division (7%) compared to other divisions. Households in Khulna (17%) and Rajshahi (13%) were more likely to report drinking date palm sap than in other divisions (1.5-5.6%). Date palm sap was mostly consumed during winter with higher frequencies in January (16%) and February (12%) than in other months (0-5.6%). There was a decreasing trend in drinking sap over the three years. Overall, we observed substantial geographic and seasonal patterns in human exposure to animals that could be sources of zoonotic disease. These findings could facilitate targeting emerging zoonoses surveillance, research and prevention efforts to areas and seasons with the highest levels of exposure.
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Affiliation(s)
- Ireen Sultana Shanta
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh.
| | | | - Kamal Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | | | | | - Najmul Haider
- The Royal Veterinary College, University of London, London, UK
| | - Taifur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Shovon Chakma
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Syed Sayeem Uddin Ahmed
- Department of Epidemiology and Public Health, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Yushuf Sharker
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
- University of Florida, Gainesville, USA
| | - Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Erin D Kennedy
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Emily S Gurley
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
- Johns Hopkins Bloomberg School of Public Health, Baltimore, USA
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Perofsky AC, Tempia S, Bingham J, Maslo C, Toubkin M, Laubscher A, Walaza S, Pulliam JRC, Viboud C, Cohen C. Direct and Indirect Effects of the Coronavirus Disease 2019 Pandemic on Private Healthcare Utilization in South Africa, March 2020-September 2021. Clin Infect Dis 2022; 75:e1000-e1010. [PMID: 35084450 PMCID: PMC8807275 DOI: 10.1093/cid/ciac055] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The coronavirus disease 2019 (COVID-19) pandemic caused severe disruptions to healthcare in many areas of the world, but data remain scarce for sub-Saharan Africa. METHODS We evaluated trends in hospital admissions and outpatient emergency department (ED) and general practitioner (GP) visits to South Africa's largest private healthcare system during 2016-2021. We fit time series models to historical data and, for March 2020-September 2021, quantified changes in encounters relative to baseline. RESULTS The nationwide lockdown on 27 March 2020 led to sharp reductions in care-seeking behavior that persisted for 18 months after initial declines. For example, total admissions dropped 59.6% (95% confidence interval [CI], 52.4-66.8) during home confinement and were 33.2% (95% CI, 29-37.4) below baseline in September 2021. We identified 3 waves of all-cause respiratory encounters consistent with COVID-19 activity. Intestinal infections and non-COVID-19 respiratory illnesses experienced the most pronounced declines, with some diagnoses reduced 80%, even as nonpharmaceutical interventions (NPIs) relaxed. Non-respiratory hospitalizations, including injuries and acute illnesses, were 20%-60% below baseline throughout the pandemic and exhibited strong temporal associations with NPIs and mobility. ED attendances exhibited trends similar to those for hospitalizations, while GP visits were less impacted and have returned to pre-pandemic levels. CONCLUSIONS We found substantially reduced use of health services during the pandemic for a range of conditions unrelated to COVID-19. Persistent declines in hospitalizations and ED visits indicate that high-risk patients are still delaying seeking care, which could lead to morbidity or mortality increases in the future.
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Affiliation(s)
- Amanda C Perofsky
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jeremy Bingham
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
| | - Caroline Maslo
- Clinical Division, Netcare Limited, Johannesburg, South Africa
| | - Mande Toubkin
- Emergency and Trauma Department, Netcare Limited, Johannesburg, South Africa
| | | | - Sibongile Walaza
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Bingham J, Tempia S, Moultrie H, Viboud C, Jassat W, Cohen C, Pulliam JRC. Estimating the time-varying reproduction number for COVID-19 in South Africa during the first four waves using multiple measures of incidence for public and private sectors across four waves. medRxiv 2022:2022.07.22.22277932. [PMID: 35982666 PMCID: PMC9387150 DOI: 10.1101/2022.07.22.22277932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Objectives We aimed to quantify transmission trends in South Africa during the first four waves of the COVID-19 pandemic using estimates of the time-varying reproduction number (R) and to compare the robustness of R estimates based on three different data sources and using data from public and private sector service providers. Methods We estimated R from March 2020 through April 2022, nationally and by province, based on time series of rt-PCR-confirmed cases, hospitalizations, and hospital-associated deaths, using a method which models daily incidence as a weighted sum of past incidence. We also estimated R separately using public and private sector data. Results Nationally, the maximum case-based R following the introduction of lockdown measures was 1.55 (CI: 1.43-1.66), 1.56 (CI: 1.47-1.64), 1.46 (CI: 1.38-1.53) and 3.33 (CI: 2.84-3.97) during the first (Wuhan-Hu), second (Beta), third (Delta), and fourth (Omicron) waves respectively. Estimates based on the three data sources (cases, hospitalisations, deaths) were generally similar during the first three waves but case-based estimates were higher during the fourth wave. Public and private sector R estimates were generally similar except during the initial lockdowns and in case-based estimates during the fourth wave. Discussion Agreement between R estimates using different data sources during the first three waves suggests that data from any of these sources could be used in the early stages of a future pandemic. High R estimates for Omicron relative to earlier waves is interesting given a high level of exposure pre-Omicron. The agreement between public and private sector R estimates highlights the fact that clients of the public and private sectors did not experience two separate epidemics, except perhaps to a limited extent during the strictest lockdowns in the first wave.
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Affiliation(s)
- Jeremy Bingham
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Harry Moultrie
- Centre for Tuberculosis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cecile Viboud
- Fogarty International Center, NIH, Bethesda, MD, USA
| | - Waasila Jassat
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Right to Care, Pretoria, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
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Pulliam JRC, van Schalkwyk C, Govender N, von Gottberg A, Cohen C, Groome MJ, Dushoff J, Mlisana K, Moultrie H. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. Science 2022. [PMID: 35289632 DOI: 10.1101/2021.11.11.21266068] [Citation(s) in RCA: 169] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
We provide two methods for monitoring reinfection trends in routine surveillance data to identify signatures of changes in reinfection risk and apply these approaches to data from South Africa's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic to date. Although we found no evidence of increased reinfection risk associated with circulation of the Beta (B.1.351) or Delta (B.1.617.2) variants, we did find clear, population-level evidence to suggest immune evasion by the Omicron (B.1.1.529) variant in previously infected individuals in South Africa. Reinfections occurring between 1 November 2021 and 31 January 2022 were detected in individuals infected in all three previous waves, and there has been an increase in the risk of having a third infection since mid-November 2021.
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Affiliation(s)
- Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Cari van Schalkwyk
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michelle J Groome
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jonathan Dushoff
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
- McMaster University, Hamilton, Ontario, Canada
| | - Koleka Mlisana
- National Health Laboratory Service, Johannesburg, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Harry Moultrie
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Pulliam JRC, van Schalkwyk C, Govender N, von Gottberg A, Cohen C, Groome MJ, Dushoff J, Mlisana K, Moultrie H. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. Science 2022. [PMID: 35289632 DOI: 10.5281/zenodo.6108448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We provide two methods for monitoring reinfection trends in routine surveillance data to identify signatures of changes in reinfection risk and apply these approaches to data from South Africa's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic to date. Although we found no evidence of increased reinfection risk associated with circulation of the Beta (B.1.351) or Delta (B.1.617.2) variants, we did find clear, population-level evidence to suggest immune evasion by the Omicron (B.1.1.529) variant in previously infected individuals in South Africa. Reinfections occurring between 1 November 2021 and 31 January 2022 were detected in individuals infected in all three previous waves, and there has been an increase in the risk of having a third infection since mid-November 2021.
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Affiliation(s)
- Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Cari van Schalkwyk
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michelle J Groome
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jonathan Dushoff
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
- McMaster University, Hamilton, Ontario, Canada
| | - Koleka Mlisana
- National Health Laboratory Service, Johannesburg, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Harry Moultrie
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Pulliam JRC, van Schalkwyk C, Govender N, von Gottberg A, Cohen C, Groome MJ, Dushoff J, Mlisana K, Moultrie H. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. Science 2022; 376:eabn4947. [PMID: 35289632 PMCID: PMC8995029 DOI: 10.1126/science.abn4947] [Citation(s) in RCA: 441] [Impact Index Per Article: 220.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/09/2022] [Indexed: 12/12/2022]
Abstract
We provide two methods for monitoring reinfection trends in routine surveillance data to identify signatures of changes in reinfection risk and apply these approaches to data from South Africa's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic to date. Although we found no evidence of increased reinfection risk associated with circulation of the Beta (B.1.351) or Delta (B.1.617.2) variants, we did find clear, population-level evidence to suggest immune evasion by the Omicron (B.1.1.529) variant in previously infected individuals in South Africa. Reinfections occurring between 1 November 2021 and 31 January 2022 were detected in individuals infected in all three previous waves, and there has been an increase in the risk of having a third infection since mid-November 2021.
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Affiliation(s)
- Juliet R. C. Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Cari van Schalkwyk
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michelle J. Groome
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jonathan Dushoff
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
- McMaster University, Hamilton, Ontario, Canada
| | - Koleka Mlisana
- National Health Laboratory Service, Johannesburg, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Harry Moultrie
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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10
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Pulliam JRC, van Schalkwyk C, Govender N, von Gottberg A, Cohen C, Groome MJ, Dushoff J, Mlisana K, Moultrie H. Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa. Science 2022. [PMID: 35289632 DOI: 10.5281/zenodo.5807591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We provide two methods for monitoring reinfection trends in routine surveillance data to identify signatures of changes in reinfection risk and apply these approaches to data from South Africa's severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic to date. Although we found no evidence of increased reinfection risk associated with circulation of the Beta (B.1.351) or Delta (B.1.617.2) variants, we did find clear, population-level evidence to suggest immune evasion by the Omicron (B.1.1.529) variant in previously infected individuals in South Africa. Reinfections occurring between 1 November 2021 and 31 January 2022 were detected in individuals infected in all three previous waves, and there has been an increase in the risk of having a third infection since mid-November 2021.
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Affiliation(s)
- Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Cari van Schalkwyk
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Nevashan Govender
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michelle J Groome
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jonathan Dushoff
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
- McMaster University, Hamilton, Ontario, Canada
| | - Koleka Mlisana
- National Health Laboratory Service, Johannesburg, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Harry Moultrie
- National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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11
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Azam JM, Saitta B, Bonner K, Ferrari MJ, Pulliam JRC. Modelling the relative benefits of using the measles vaccine outside cold chain for outbreak response. Vaccine 2021; 39:5845-5853. [PMID: 34481696 DOI: 10.1016/j.vaccine.2021.08.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/30/2021] [Accepted: 08/13/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Rapid outbreak response vaccination is a strategy for measles control and elimination. Measles vaccines must be stored and transported within a specified temperature range, but this can present significant challenges when targeting remote populations. Measles vaccine licensure for delivery outside cold chain (OCC) could provide more vaccine transport/storage space without ice packs, and a solution to shorten response times. However, due to vaccine safety and wastage considerations, the OCC strategy will require other operational changes, potentially including the use of 1-dose (monodose) instead of 10-dose vials, requiring larger transport/storage equipment currently achieved with 10-dose vials. These trade-offs require quantitative comparisons of vaccine delivery options to evaluate their relative benefits. METHODS We developed a modelling framework combining elements of the vaccine supply chain - cold chain, vial, team, and transport equipment types - with a measles transmission dynamics model to compare vaccine delivery options. We compared 10 strategies resulting from combinations of the vaccine supply elements and grouped into three main classes: OCC, partial cold chain (PCC), and full cold chain (FCC). For each strategy, we explored a campaign with 20 teams sequentially targeting 5 locations with 100,000 individuals each. We characterised the time needed to freeze ice packs and complete the campaign (campaign duration), vaccination coverage, and cases averted, assuming a fixed pre-deployment delay before campaign commencement. We performed sensitivity analyses of the pre-deployment delay, population sizes, and two team allocation schemes. RESULTS The OCC, PCC, and FCC strategies achieve campaign durations of 50, 51, and 52 days, respectively. Nine of the ten strategies can achieve a vaccination coverage of 80%, and OCC averts the most cases. DISCUSSION The OCC strategy, therefore, presents improved operational and epidemiological outcomes relative to current practice and the other options considered.
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Affiliation(s)
- James M Azam
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa.
| | - Barbara Saitta
- Access Campaign, Médecins Sans Frontières, New York, United States
| | - Kimberly Bonner
- University of Minnesota, Twin Cities, Minneapolis, United States
| | - Matthew J Ferrari
- The Center for Infectious Disease Dynamics, The Pennsylvania State University, PA, United States
| | - Juliet R C Pulliam
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
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12
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Nichols JD, Bogich TL, Howerton E, Bjørnstad ON, Borchering RK, Ferrari M, Haran M, Jewell C, Pepin KM, Probert WJM, Pulliam JRC, Runge MC, Tildesley M, Viboud C, Shea K. Strategic testing approaches for targeted disease monitoring can be used to inform pandemic decision-making. PLoS Biol 2021; 19:e3001307. [PMID: 34138840 PMCID: PMC8241114 DOI: 10.1371/journal.pbio.3001307] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 06/29/2021] [Indexed: 12/20/2022] Open
Abstract
More than 1.6 million Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) tests were administered daily in the United States at the peak of the epidemic, with a significant focus on individual treatment. Here, we show that objective-driven, strategic sampling designs and analyses can maximize information gain at the population level, which is necessary to increase situational awareness and predict, prepare for, and respond to a pandemic, while also continuing to inform individual treatment. By focusing on specific objectives such as individual treatment or disease prediction and control (e.g., via the collection of population-level statistics to inform lockdown measures or vaccine rollout) and drawing from the literature on capture-recapture methods to deal with nonrandom sampling and testing errors, we illustrate how public health objectives can be achieved even with limited test availability when testing programs are designed a priori to meet those objectives.
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Affiliation(s)
- James D. Nichols
- U.S. Geological Survey, Eastern Ecological Science Center at the Patuxent Research Refuge, Laurel, Maryland, United States of America
| | - Tiffany L. Bogich
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Emily Howerton
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Ottar N. Bjørnstad
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Department of Entomology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Rebecca K. Borchering
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Matthew Ferrari
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Murali Haran
- Department of Statistics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Christopher Jewell
- Lancaster Medical School, Lancaster University, Lancaster, United Kingdom
| | - Kim M. Pepin
- National Wildlife Research Center, United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Fort Collins, Colorado, United States of America
| | - William J. M. Probert
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Juliet R. C. Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Michael C. Runge
- U.S. Geological Survey, Eastern Ecological Science Center at the Patuxent Research Refuge, Laurel, Maryland, United States of America
| | - Michael Tildesley
- Zeeman Institute: Systems Biology and Infectious Disease Epidemiology Research (SBIDER), Mathematics Institute and School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Katriona Shea
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- The Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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13
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Abstract
Recent evidence indicates that a single dose of mRNA-based vaccines produce similar immune responses in people with evidence of past infection compared with two doses in immunologically naive individuals. For COVID-19 vaccines with two dose regimens, point-of-care antibody testing for prior infection when administering the first dose could enable expanded vaccine access in a cost-effective manner. Generally, antibody tests with sensitivity and specificity well below that typically accepted for product licensure would still enable expanded vaccine coverage, though to be cost-beneficial total test cost (i.e. procurement and administration) needs to be less than roughly a third of total vaccine dose cost. For highly sensitive (90%) and specific (99%) tests, coverage could be expanded by more than 33%. Tests with the appropriate performance characteristics are plausible, though likely need setting specific tailoring.
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14
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Nichols BE, Jamieson L, Zhang SRC, Rao GA, Silal S, Pulliam JRC, Sanne I, Meyer-Rath G. The Role of Remdesivir in South Africa: Preventing COVID-19 Deaths Through Increasing Intensive Care Unit Capacity. Clin Infect Dis 2021; 72:1642-1644. [PMID: 32628744 PMCID: PMC7454458 DOI: 10.1093/cid/ciaa937] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 07/02/2020] [Indexed: 11/14/2022] Open
Abstract
Countries such as South Africa have limited intensive care unit (ICU) capacity to handle the expected number of patients with COVID-19 requiring ICU care. Remdesivir can prevent deaths in countries such as South Africa by decreasing the number of days people spend in ICU, therefore freeing up ICU bed capacity.
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Affiliation(s)
- Brooke E Nichols
- Department of Global Health, School of Public Health, Boston University, Boston, Massachusetts, USA.,Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lise Jamieson
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Sabrina R C Zhang
- Massachusetts College of Pharmacy and Health Sciences, Boston, Massachusetts, USA
| | - Gabriella A Rao
- Department of Global Health, School of Public Health, Boston University, Boston, Massachusetts, USA
| | - Sheetal Silal
- Modelling and Simulation Hub, Africa, Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Juliet R C Pulliam
- South African Department of Science and Innovation-National Research Foundation Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Ian Sanne
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gesine Meyer-Rath
- Department of Global Health, School of Public Health, Boston University, Boston, Massachusetts, USA.,Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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15
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Adetokunboh OO, Mthombothi ZE, Dominic EM, Djomba-Njankou S, Pulliam JRC. African based researchers' output on models for the transmission dynamics of infectious diseases and public health interventions: A scoping review. PLoS One 2021; 16:e0250086. [PMID: 33956823 PMCID: PMC8101744 DOI: 10.1371/journal.pone.0250086] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/30/2021] [Indexed: 11/24/2022] Open
Abstract
Background Applied epidemiological models are used in predicting future trends of diseases, for the basic understanding of disease and health dynamics, and to improve the measurement of health indicators. Mapping the research outputs of epidemiological modelling studies concerned with transmission dynamics of infectious diseases and public health interventions in Africa will help to identify the areas with substantial levels of research activities, areas with gaps, and research output trends. Methods A scoping review of applied epidemiological models of infectious disease studies that involved first or last authors affiliated to African institutions was conducted. Eligible studies were those concerned with the transmission dynamics of infectious diseases and public health interventions. The review was consistent with the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) extension for scoping reviews. Four electronic databases were searched for peer-reviewed publications up to the end of April 2020. Results Of the 5927 publications identified, 181 met the inclusion criteria. The review identified 143 publications with first authors having an African institutional affiliation (AIA), while 81 had both first and last authors with an AIA. The publication authors were found to be predominantly affiliated with institutions based in South Africa and Kenya. Furthermore, human immunodeficiency virus, malaria, tuberculosis, and Ebola virus disease were found to be the most researched infectious diseases. There has been a gradual increase in research productivity across Africa especially in the last ten years, with several collaborative efforts spread both within and beyond Africa. Conclusions Research productivity in applied epidemiological modelling studies of infectious diseases may have increased, but there remains an under-representation of African researchers as leading authors. The study findings indicate a need for the development of research capacity through supporting existing institutions in Africa and promoting research funding that will address local health priorities.
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Affiliation(s)
- Olatunji O. Adetokunboh
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
- Division of Epidemiology and Biostatistics, Department of Global Health, Stellenbosch University, Cape Town, South Africa
- * E-mail:
| | - Zinhle E. Mthombothi
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Emanuel M. Dominic
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Sylvie Djomba-Njankou
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Juliet R. C. Pulliam
- DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
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16
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Jo Y, Jamieson L, Edoka I, Long L, Silal S, Pulliam JRC, Moultrie H, Sanne I, Meyer-Rath G, Nichols BE. Cost-effectiveness of Remdesivir and Dexamethasone for COVID-19 Treatment in South Africa. Open Forum Infect Dis 2021; 8:ofab040. [PMID: 33732750 PMCID: PMC7928624 DOI: 10.1093/ofid/ofab040] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/24/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Dexamethasone and remdesivir have the potential to reduce coronavirus disease 2019 (COVID)-related mortality or recovery time, but their cost-effectiveness in countries with limited intensive care resources is unknown. METHODS We projected intensive care unit (ICU) needs and capacity from August 2020 to January 2021 using the South African National COVID-19 Epi Model. We assessed the cost-effectiveness of (1) administration of dexamethasone to ventilated patients and remdesivir to nonventilated patients, (2) dexamethasone alone to both nonventilated and ventilated patients, (3) remdesivir to nonventilated patients only, and (4) dexamethasone to ventilated patients only, all relative to a scenario of standard care. We estimated costs from the health care system perspective in 2020 US dollars, deaths averted, and the incremental cost-effectiveness ratios of each scenario. RESULTS Remdesivir for nonventilated patients and dexamethasone for ventilated patients was estimated to result in 408 (uncertainty range, 229-1891) deaths averted (assuming no efficacy [uncertainty range, 0%-70%] of remdesivir) compared with standard care and to save $15 million. This result was driven by the efficacy of dexamethasone and the reduction of ICU-time required for patients treated with remdesivir. The scenario of dexamethasone alone for nonventilated and ventilated patients requires an additional $159 000 and averts 689 [uncertainty range, 330-1118] deaths, resulting in $231 per death averted, relative to standard care. CONCLUSIONS The use of remdesivir for nonventilated patients and dexamethasone for ventilated patients is likely to be cost-saving compared with standard care by reducing ICU days. Further efforts to improve recovery time with remdesivir and dexamethasone in ICUs could save lives and costs in South Africa.
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Affiliation(s)
- Youngji Jo
- Section of Infectious Disease, Department of Medicine, Boston Medical Center, Boston, Massachusetts, USA
| | - Lise Jamieson
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ijeoma Edoka
- SAMRC Centre for Health Economics and Decision Science-PRICELESS SA, School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Lawrence Long
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Global Health, School of Public Health, Boston University, Boston, Massachusetts, USA
| | - Sheetal Silal
- Modelling and Simulation Hub, Africa, Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | - Harry Moultrie
- Division of the National Health Laboratory Service, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa
| | - Ian Sanne
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gesine Meyer-Rath
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Global Health, School of Public Health, Boston University, Boston, Massachusetts, USA
| | - Brooke E Nichols
- Health Economics and Epidemiology Research Office, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Global Health, School of Public Health, Boston University, Boston, Massachusetts, USA
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17
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Lee KH, Nikolay B, Sazzad HMS, Hossain MJ, Khan AKMD, Rahman M, Satter SM, Nichol ST, Klena JD, Pulliam JRC, Kilpatrick AM, Sultana S, Afroj S, Daszak P, Luby S, Cauchemez S, Salje H, Gurley ES. Changing Contact Patterns Over Disease Progression: Nipah Virus as a Case Study. J Infect Dis 2021; 222:438-442. [PMID: 32115627 DOI: 10.1093/infdis/jiaa091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/27/2020] [Indexed: 01/30/2023] Open
Abstract
Contact patterns play a key role in disease transmission, and variation in contacts during the course of illness can influence transmission, particularly when accompanied by changes in host infectiousness. We used surveys among 1642 contacts of 94 Nipah virus case patients in Bangladesh to determine how contact patterns (physical and with bodily fluids) changed as disease progressed in severity. The number of contacts increased with severity and, for case patients who died, peaked on the day of death. Given transmission has only been observed among fatal cases of Nipah virus infection, our findings suggest that changes in contact patterns during illness contribute to risk of infection.
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Affiliation(s)
- Kyu Han Lee
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Birgit Nikolay
- Mathematical Modelling of Infectious Diseases Unit Institut Pasteur, Paris, France
| | - Hossain M S Sazzad
- Infectious Disease Division, icddr,b, Dhaka, Bangladesh.,Kirby Institute, University of New South Wales, Sydney, Australia
| | - M Jahangir Hossain
- Infectious Disease Division, icddr,b, Dhaka, Bangladesh.,Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | - Mahmudur Rahman
- Infectious Disease Division, icddr,b, Dhaka, Bangladesh.,Institute of Epidemiology Disease Control and Research, Dhaka, Bangladesh
| | | | - Stuart T Nichol
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John D Klena
- Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - A Marm Kilpatrick
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Sharmin Sultana
- Institute of Epidemiology Disease Control and Research, Dhaka, Bangladesh
| | - Sayma Afroj
- Infectious Disease Division, icddr,b, Dhaka, Bangladesh
| | | | - Stephen Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Simon Cauchemez
- Mathematical Modelling of Infectious Diseases Unit Institut Pasteur, Paris, France
| | - Henrik Salje
- Mathematical Modelling of Infectious Diseases Unit Institut Pasteur, Paris, France
| | - Emily S Gurley
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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18
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Azam JM, Are EB, Pang X, Ferrari MJ, Pulliam JRC. Outbreak response intervention models of vaccine-preventable diseases in humans and foot-and-mouth disease in livestock: a protocol for a systematic review. BMJ Open 2020; 10:e036172. [PMID: 33020081 PMCID: PMC7537453 DOI: 10.1136/bmjopen-2019-036172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
INTRODUCTION Outbreaks of vaccine-preventable diseases continue to threaten public health, despite the proven effectiveness of vaccines. Interventions such as vaccination, social distancing and palliative care are usually implemented, either individually or in combination, to control these outbreaks. Mathematical models are often used to assess the impact of these interventions and for supporting outbreak response decision making. The objectives of this systematic review, which covers all human vaccine-preventable diseases, are to determine the relative impact of vaccination compared with other outbreak interventions, and to ascertain the temporal trends in the use of modelling in outbreak response decision making. We will also identify gaps and opportunities for future research through a comparison with the foot-and-mouth disease outbreak response modelling literature, which has good examples of the use of modelling to inform outbreak response intervention decision making. METHODS AND ANALYSIS We searched on PubMed, Scopus, Web of Science, Google Scholar and some preprint servers from the start of indexing to 15 January 2020. Inclusion: modelling studies, published in English, that use a mechanistic approach to evaluate the impact of an outbreak intervention. Exclusion: reviews, and studies that do not describe or use mechanistic models or do not describe an outbreak. We will extract data from the included studies such as their objectives, model types and composition, and conclusions on the impact of the intervention. We will ascertain the impact of models on outbreak response decision making through visualisation of time trends in the use of the models. We will also present our results in narrative style. ETHICS AND DISSEMINATION This systematic review will not require any ethics approval since it only involves scientific articles. The review will be disseminated in a peer-reviewed journal and at various conferences fitting its scope. PROSPERO REGISTRATION NUMBER CRD42020160803.
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Affiliation(s)
- James M Azam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Elisha B Are
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Cape Town, Western Cape, South Africa
| | - Xiaoxi Pang
- Department of Mathematics, The University of Manchester, Manchester, UK
| | - Matthew J Ferrari
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Juliet R C Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Cape Town, Western Cape, South Africa
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19
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Jo Y, Jamieson L, Edoka I, Long L, Silal S, Pulliam JRC, Moultrie H, Sanne I, Meyer-Rath G, Nichols BE. Cost-effectiveness of remdesivir and dexamethasone for COVID-19 treatment in South Africa. medRxiv 2020. [PMID: 32995824 DOI: 10.1101/2020.09.24.20200196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background South Africa recently experienced a first peak in COVID-19 cases and mortality. Dexamethasone and remdesivir both have the potential to reduce COVID-related mortality, but their cost-effectiveness in a resource-limited setting with scant intensive care resources is unknown. Methods We projected intensive care unit (ICU) needs and capacity from August 2020 to January 2021 using the South African National COVID-19 Epi Model. We assessed cost-effectiveness of 1) administration of dexamethasone to ventilated patients and remdesivir to non-ventilated patients, 2) dexamethasone alone to both non-ventilated and ventilated patients, 3) remdesivir to non-ventilated patients only, and 4) dexamethasone to ventilated patients only; all relative to a scenario of standard care. We estimated costs from the healthcare system perspective in 2020 USD, deaths averted, and the incremental cost effectiveness ratios of each scenario. Results Remdesivir for non-ventilated patients and dexamethasone for ventilated patients was estimated to result in 1,111 deaths averted (assuming a 0-30% efficacy of remdesivir) compared to standard care, and save $11.5 million. The result was driven by the efficacy of the drugs, and the reduction of ICU-time required for patients treated with remdesivir. The scenario of dexamethasone alone to ventilated and non-ventilated patients requires additional $159,000 and averts 1,146 deaths, resulting in $139 per death averted, relative to standard care. Conclusions The use of dexamethasone for ventilated and remdesivir for non-ventilated patients is likely to be cost-saving compared to standard care. Given the economic and health benefits of both drugs, efforts to ensure access to these medications is paramount.
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20
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Thompson RN, Hollingsworth TD, Isham V, Arribas-Bel D, Ashby B, Britton T, Challenor P, Chappell LHK, Clapham H, Cunniffe NJ, Dawid AP, Donnelly CA, Eggo RM, Funk S, Gilbert N, Glendinning P, Gog JR, Hart WS, Heesterbeek H, House T, Keeling M, Kiss IZ, Kretzschmar ME, Lloyd AL, McBryde ES, McCaw JM, McKinley TJ, Miller JC, Morris M, O'Neill PD, Parag KV, Pearson CAB, Pellis L, Pulliam JRC, Ross JV, Tomba GS, Silverman BW, Struchiner CJ, Tildesley MJ, Trapman P, Webb CR, Mollison D, Restif O. Key questions for modelling COVID-19 exit strategies. Proc Biol Sci 2020; 287:20201405. [PMID: 32781946 PMCID: PMC7575516 DOI: 10.1098/rspb.2020.1405] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 07/21/2020] [Indexed: 12/15/2022] Open
Abstract
Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute 'Models for an exit strategy' workshop (11-15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.
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Affiliation(s)
- Robin N. Thompson
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK
- Christ Church, University of Oxford, St Aldates, Oxford OX1 1DP, UK
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | | | - Valerie Isham
- Department of Statistical Science, University College London, Gower Street, London WC1E 6BT, UK
| | - Daniel Arribas-Bel
- School of Environmental Sciences, University of Liverpool, Brownlow Street, Liverpool L3 5DA, UK
- The Alan Turing Institute, British Library, 96 Euston Road, London NW1 2DB, UK
| | - Ben Ashby
- Department of Mathematical Sciences, University of Bath, North Road, Bath BA2 7AY, UK
| | - Tom Britton
- Department of Mathematics, Stockholm University, Kräftriket, 106 91 Stockholm, Sweden
| | - Peter Challenor
- College of Engineering, Mathematical and Physical Sciences, University of Exeter, Exeter EX4 4QE, UK
| | - Lauren H. K. Chappell
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK
| | - Hannah Clapham
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive, Singapore117549, Singapore
| | - Nik J. Cunniffe
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - A. Philip Dawid
- Statistical Laboratory, University of Cambridge, Wilberforce Road, Cambridge CB3 0WB, UK
| | - Christl A. Donnelly
- Department of Statistics, University of Oxford, St Giles', Oxford OX1 3LB, UK
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial CollegeLondon, Norfolk Place, London W2 1PG, UK
| | - Rosalind M. Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Sebastian Funk
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Nigel Gilbert
- Department of Sociology, University of Surrey, Stag Hill, Guildford GU2 7XH, UK
| | - Paul Glendinning
- Department of Mathematics, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Julia R. Gog
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - William S. Hart
- Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK
| | - Hans Heesterbeek
- Department of Population Health Sciences, Utrecht University, Yalelaan, 3584 CL Utrecht, The Netherlands
| | - Thomas House
- IBM Research, The Hartree Centre, Daresbury, Warrington WA4 4AD, UK
- Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Matt Keeling
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - István Z. Kiss
- School of Mathematical and Physical Sciences, University of Sussex, Falmer, Brighton BN1 9QH, UK
| | - Mirjam E. Kretzschmar
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Heidelberglaan 100, 3584CX Utrecht, The Netherlands
| | - Alun L. Lloyd
- Biomathematics Graduate Program and Department of Mathematics, North Carolina State University, Raleigh, NC 27695, USA
| | - Emma S. McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland 4811, Australia
| | - James M. McCaw
- School of Mathematics and Statistics, University of Melbourne, Carlton, Victoria 3010, Australia
| | - Trevelyan J. McKinley
- College of Medicine and Health, University of Exeter, Barrack Road, Exeter EX2 5DW, UK
| | - Joel C. Miller
- Department of Mathematics and Statistics, La Trobe University, Bundoora, Victoria 3086, Australia
| | - Martina Morris
- Department of Sociology, University of Washington, Savery Hall, Seattle, WA 98195, USA
| | - Philip D. O'Neill
- School of Mathematical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Kris V. Parag
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial CollegeLondon, Norfolk Place, London W2 1PG, UK
| | - Carl A. B. Pearson
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Jonkershoek Road, Stellenbosch 7600, South Africa
| | - Lorenzo Pellis
- Centre for Mathematical Sciences, University of Cambridge, Wilberforce Road, Cambridge CB3 0WA, UK
| | - Juliet R. C. Pulliam
- South African DSI-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Jonkershoek Road, Stellenbosch 7600, South Africa
| | - Joshua V. Ross
- School of Mathematical Sciences, University of Adelaide, South Australia 5005, Australia
| | | | - Bernard W. Silverman
- Department of Statistics, University of Oxford, St Giles', Oxford OX1 3LB, UK
- Rights Lab, University of Nottingham, Highfield House, Nottingham NG7 2RD, UK
| | - Claudio J. Struchiner
- Escola de Matemática Aplicada, Fundação Getúlio Vargas, Praia de Botafogo, 190 Rio de Janeiro, Brazil
| | - Michael J. Tildesley
- Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research, School of Life Sciences and Mathematics Institute, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Pieter Trapman
- Department of Mathematics, Stockholm University, Kräftriket, 106 91 Stockholm, Sweden
| | - Cerian R. Webb
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Denis Mollison
- Department of Actuarial Mathematics and Statistics, Heriot-Watt University, Edinburgh EH14 4AS, UK
| | - Olivier Restif
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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21
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Becker DJ, Washburne AD, Faust CL, Pulliam JRC, Mordecai EA, Lloyd-Smith JO, Plowright RK. Dynamic and integrative approaches to understanding pathogen spillover. Philos Trans R Soc Lond B Biol Sci 2019; 374:20190014. [PMID: 31401959 PMCID: PMC6711302 DOI: 10.1098/rstb.2019.0014] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2019] [Indexed: 12/23/2022] Open
Affiliation(s)
- Daniel J. Becker
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Alex D. Washburne
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Christina L. Faust
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Juliet R. C. Pulliam
- South African Centre for Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa
| | | | - James O. Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Raina K. Plowright
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
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22
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Sokolow SH, Nova N, Pepin KM, Peel AJ, Pulliam JRC, Manlove K, Cross PC, Becker DJ, Plowright RK, McCallum H, De Leo GA. Ecological interventions to prevent and manage zoonotic pathogen spillover. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180342. [PMID: 31401951 PMCID: PMC6711299 DOI: 10.1098/rstb.2018.0342] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Spillover of a pathogen from a wildlife reservoir into a human or livestock host requires the pathogen to overcome a hierarchical series of barriers. Interventions aimed at one or more of these barriers may be able to prevent the occurrence of spillover. Here, we demonstrate how interventions that target the ecological context in which spillover occurs (i.e. ecological interventions) can complement conventional approaches like vaccination, treatment, disinfection and chemical control. Accelerating spillover owing to environmental change requires effective, affordable, durable and scalable solutions that fully harness the complex processes involved in cross-species pathogen spillover. This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
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Affiliation(s)
- Susanne H Sokolow
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA.,Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA.,Marine Science Institute, University of California, Santa Barbara, CA 93106, USA
| | - Nicole Nova
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Kim M Pepin
- National Wildlife Research Center, USDA-APHIS, Fort Collins, CO 80521, USA
| | - Alison J Peel
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Juliet R C Pulliam
- South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch 7600, South Africa
| | - Kezia Manlove
- Department of Wildland Resources and Ecology Center, Utah State University, Logan, UT 84321, USA
| | - Paul C Cross
- US Geological Survey, Northern Rocky Mountain Science Center, Bozeman, MT 59715, USA
| | - Daniel J Becker
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA.,Department of Biology, Indiana University, Bloomington, IN 47403, USA
| | - Raina K Plowright
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
| | - Giulio A De Leo
- Hopkins Marine Station, Stanford University, Pacific Grove, CA 93950, USA.,Woods Institute for the Environment, Stanford University, Stanford, CA 94305, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA
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23
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Nikolay B, Salje H, Hossain MJ, Khan AKMD, Sazzad HMS, Rahman M, Daszak P, Ströher U, Pulliam JRC, Kilpatrick AM, Nichol ST, Klena JD, Sultana S, Afroj S, Luby SP, Cauchemez S, Gurley ES. Transmission of Nipah Virus - 14 Years of Investigations in Bangladesh. N Engl J Med 2019; 380:1804-1814. [PMID: 31067370 PMCID: PMC6547369 DOI: 10.1056/nejmoa1805376] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND Nipah virus is a highly virulent zoonotic pathogen that can be transmitted between humans. Understanding the dynamics of person-to-person transmission is key to designing effective interventions. METHODS We used data from all Nipah virus cases identified during outbreak investigations in Bangladesh from April 2001 through April 2014 to investigate case-patient characteristics associated with onward transmission and factors associated with the risk of infection among patient contacts. RESULTS Of 248 Nipah virus cases identified, 82 were caused by person-to-person transmission, corresponding to a reproduction number (i.e., the average number of secondary cases per case patient) of 0.33 (95% confidence interval [CI], 0.19 to 0.59). The predicted reproduction number increased with the case patient's age and was highest among patients 45 years of age or older who had difficulty breathing (1.1; 95% CI, 0.4 to 3.2). Case patients who did not have difficulty breathing infected 0.05 times as many contacts (95% CI, 0.01 to 0.3) as other case patients did. Serologic testing of 1863 asymptomatic contacts revealed no infections. Spouses of case patients were more often infected (8 of 56 [14%]) than other close family members (7 of 547 [1.3%]) or other contacts (18 of 1996 [0.9%]). The risk of infection increased with increased duration of exposure of the contacts (adjusted odds ratio for exposure of >48 hours vs. ≤1 hour, 13; 95% CI, 2.6 to 62) and with exposure to body fluids (adjusted odds ratio, 4.3; 95% CI, 1.6 to 11). CONCLUSIONS Increasing age and respiratory symptoms were indicators of infectivity of Nipah virus. Interventions to control person-to-person transmission should aim to reduce exposure to body fluids. (Funded by the National Institutes of Health and others.).
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Affiliation(s)
- Birgit Nikolay
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Henrik Salje
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - M Jahangir Hossain
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - A K M Dawlat Khan
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Hossain M S Sazzad
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Mahmudur Rahman
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Peter Daszak
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Ute Ströher
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Juliet R C Pulliam
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - A Marm Kilpatrick
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Stuart T Nichol
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - John D Klena
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Sharmin Sultana
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Sayma Afroj
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Stephen P Luby
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Simon Cauchemez
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
| | - Emily S Gurley
- From the Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, Centre National de la Recherche Scientifique, Paris (B.N., H.S., S.C.); the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine, Banjul, The Gambia (M.J.H.); the Infectious Diseases Division, icddr,b, (M.J.H., A.K.M.D.K., H.M.S.S., S.A., E.S.G.), and the Institute of Epidemiology Disease Control and Research (M.R., S.S.) - both in Dhaka, Bangladesh; the Kirby Institute, University of New South Wales, Sydney (H.M.S.S.); the EcoHealth Alliance, New York (P.D.); the Viral Special Pathogens Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta (U.S., S.T.N., J.D.K.); the South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, Stellenbosch, South Africa (J.R.C.P.); the Department of Ecology and Evolutionary Biology, University of California, Santa Cruz (A.M.K.), and the Infectious Diseases and Geographic Medicine Division, Stanford University, Stanford (S.P.L.) - both in California; Auburn University, Auburn, AL (S.A.); and the Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore (E.S.G.)
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24
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Ogden NH, Wilson JRU, Richardson DM, Hui C, Davies SJ, Kumschick S, Le Roux JJ, Measey J, Saul WC, Pulliam JRC. Emerging infectious diseases and biological invasions: a call for a One Health collaboration in science and management. R Soc Open Sci 2019; 6:181577. [PMID: 31032015 PMCID: PMC6458372 DOI: 10.1098/rsos.181577] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/18/2019] [Indexed: 05/11/2023]
Abstract
The study and management of emerging infectious diseases (EIDs) and of biological invasions both address the ecology of human-associated biological phenomena in a rapidly changing world. However, the two fields work mostly in parallel rather than in concert. This review explores how the general phenomenon of an organism rapidly increasing in range or abundance is caused, highlights the similarities and differences between research on EIDs and invasions, and discusses shared management insights and approaches. EIDs can arise by: (i) crossing geographical barriers due to human-mediated dispersal, (ii) crossing compatibility barriers due to evolution, and (iii) lifting of environmental barriers due to environmental change. All these processes can be implicated in biological invasions, but only the first defines them. Research on EIDs is embedded within the One Health concept-the notion that human, animal and ecosystem health are interrelated and that holistic approaches encompassing all three components are needed to respond to threats to human well-being. We argue that for sustainable development, biological invasions should be explicitly considered within One Health. Management goals for the fields are the same, and direct collaborations between invasion scientists, disease ecologists and epidemiologists on modelling, risk assessment, monitoring and management would be mutually beneficial.
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Affiliation(s)
- Nick H. Ogden
- National Microbiology Laboratory, Public Health Agency of Canada, Canada
- South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, South Africa
| | - John R. U. Wilson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, Cape Town, South Africa
| | - David M. Richardson
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
| | - Cang Hui
- Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, Matieland 7602, South Africa
- Mathematical and Physical Biosciences, African Institute for Mathematical Sciences (AIMS), Muizenberg 7945, South Africa
| | - Sarah J. Davies
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
| | - Sabrina Kumschick
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- South African National Biodiversity Institute, Kirstenbosch Research Centre, Claremont, Cape Town, South Africa
| | - Johannes J. Le Roux
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
| | - John Measey
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
| | - Wolf-Christian Saul
- Centre for Invasion Biology, Department of Botany and Zoology, Stellenbosch University, South Africa
- Centre for Invasion Biology, Department of Mathematical Sciences, Stellenbosch University, Matieland 7602, South Africa
| | - Juliet R. C. Pulliam
- South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch University, South Africa
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25
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Abstract
The epidemiological curve (epicurve) is one of the simplest yet most useful tools used by field epidemiologists, modellers, and decision makers for assessing the dynamics of infectious disease epidemics. Here, we present the free, open-source package incidence for the R programming language, which allows users to easily compute, handle, and visualise epicurves from unaggregated linelist data. This package was built in accordance with the development guidelines of the R Epidemics Consortium (RECON), which aim to ensure robustness and reliability through extensive automated testing, documentation, and good coding practices. As such, it fills an important gap in the toolbox for outbreak analytics using the R software, and provides a solid building block for further developments in infectious disease modelling. incidence is available from https://www.repidemicsconsortium.org/incidence.
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Affiliation(s)
- Zhian N Kamvar
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology , School of Public Health, Imperial College London, London, UK
| | - Jun Cai
- Ministry of Education Key Laboratory for Earth System Modelling, Department of Earth System Science, Tsinghua University, Beijing, 100084, China
| | - Juliet R C Pulliam
- South African DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA),, Stellenbosch University, Stellenbosch, South Africa
| | | | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology , School of Public Health, Imperial College London, London, UK.,Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
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26
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Blohm GM, Lednicky JA, Márquez M, White SK, Loeb JC, Pacheco CA, Nolan DJ, Paisie T, Salemi M, Rodríguez-Morales AJ, Glenn Morris J, Pulliam JRC, Paniz-Mondolfi AE. Evidence for Mother-to-Child Transmission of Zika Virus Through Breast Milk. Clin Infect Dis 2018; 66:1120-1121. [PMID: 29300859 PMCID: PMC6019007 DOI: 10.1093/cid/cix968] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/30/2017] [Indexed: 11/13/2022] Open
Abstract
Zikavirus (ZIKV) is an emerging viral pathogen that continues to spread throughout different regions of the world. Herein we report a case that provides further evidence that ZIKV transmission can occur through breastfeeding by providing a detailed clinical, genomic, and virological case-based description.
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Affiliation(s)
- Gabriela M Blohm
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
- Emerging Pathogens Institute, University of Florida, Gainesville
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Universidad Centroccidental Lisandro Alvarado, Lara, Venezuela
| | - John A Lednicky
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
- Emerging Pathogens Institute, University of Florida, Gainesville
| | - Marilianna Márquez
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Universidad Centroccidental Lisandro Alvarado, Lara, Venezuela
- Health Sciences Department, College of Medicine, Universidad Centroccidental Lisandro Alvarado, Lara, Venezuela
| | - Sarah K White
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
- Emerging Pathogens Institute, University of Florida, Gainesville
| | - Julia C Loeb
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville
- Emerging Pathogens Institute, University of Florida, Gainesville
| | | | - David J Nolan
- Emerging Pathogens Institute, University of Florida, Gainesville
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville
- Bioinfoexperts LLC, Thibodaux, Louisiana
| | - Taylor Paisie
- Emerging Pathogens Institute, University of Florida, Gainesville
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville
| | - Alfonso J Rodríguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Colombia
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville
- Department of Internal Medicine, Division of Infectious Diseases and Global Medicine, Department of Medicine, College of Medicine, University of Florida, Gainesville
| | - Juliet R C Pulliam
- Emerging Pathogens Institute, University of Florida, Gainesville
- DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), Stellenbosch, South Africa
| | - Alberto E Paniz-Mondolfi
- Infectious Diseases Research Incubator and the Zoonosis and Emerging Pathogens Regional Collaborative Network, Universidad Centroccidental Lisandro Alvarado, Lara, Venezuela
- Department of Infectious Diseases and Tropical Medicine, Instituto Diagnóstico Barquisimeto, IDB Biomedical Research Institute, Lara, Barquisimeto, Venezuela
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27
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Borchering RK, Bellan SE, Flynn JM, Pulliam JRC, McKinley SA. Resource-driven encounters among consumers and implications for the spread of infectious disease. J R Soc Interface 2017; 14:20170555. [PMID: 29021163 PMCID: PMC5665835 DOI: 10.1098/rsif.2017.0555] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/18/2017] [Indexed: 11/12/2022] Open
Abstract
Animals share a variety of common resources, which can be a major driver of conspecific encounter rates. In this work, we implement a spatially explicit mathematical model for resource visitation behaviour in order to examine how changes in resource availability can influence the rate of encounters among consumers. Using simulations and asymptotic analysis, we demonstrate that, under a reasonable set of assumptions, the relationship between resource availability and consumer conspecific encounters is not monotonic. We characterize how the maximum encounter rate and associated critical resource density depend on system parameters like consumer density and the maximum distance from which consumers can detect and respond to resources. The assumptions underlying our theoretical model and analysis are motivated by observations of large aggregations of black-backed jackals at carcasses generated by seasonal outbreaks of anthrax among herbivores in Etosha National Park, Namibia. As non-obligate scavengers, black-backed jackals use carcasses as a supplemental food resource when they are available. While jackals do not appear to acquire disease from ingesting anthrax carcasses, changes in their movement patterns in response to changes in carcass abundance do alter jackals' conspecific encounter rate in ways that may affect the transmission dynamics of other diseases, such as rabies. Our theoretical results provide a method to quantify and analyse the hypothesis that the outbreak of a fatal disease among herbivores can potentially facilitate outbreaks of an entirely different disease among jackals. By analysing carcass visitation data, we find support for our model's prediction that the number of conspecific encounters at resource sites decreases with additional increases in resource availability. Whether or not this site-dependent effect translates to an overall decrease in encounters depends, unexpectedly, on the relationship between the maximum distance of detection and the resource density.
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Affiliation(s)
| | - Steve E Bellan
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA, USA
- Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Jason M Flynn
- Department of Mathematics, Tulane University, New Orleans, LA, USA
| | - Juliet R C Pulliam
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
- South African Centre for Epidemiological Modelling and Analysis, Stellenbosch University, Stellenbosch, South Africa
| | - Scott A McKinley
- Department of Mathematics, Tulane University, 6823 St Charles Avenue, New Orleans, LA 70118, USA
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28
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Norris SA, Daar A, Balasubramanian D, Byass P, Kimani-Murage E, Macnab A, Pauw C, Singhal A, Yajnik C, Akazili J, Levitt N, Maatoug J, Mkhwanazi N, Moore SE, Nyirenda M, Pulliam JRC, Rochat T, Said-Mohamed R, Seedat S, Sobngwi E, Tomlinson M, Toska E, van Schalkwyk C. Understanding and acting on the developmental origins of health and disease in Africa would improve health across generations. Glob Health Action 2017; 10:1334985. [PMID: 28715931 PMCID: PMC5533158 DOI: 10.1080/16549716.2017.1334985] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/10/2017] [Indexed: 01/09/2023] Open
Abstract
Data from many high- and low- or middle-income countries have linked exposures during key developmental periods (in particular pregnancy and infancy) to later health and disease. Africa faces substantial challenges with persisting infectious disease and now burgeoning non-communicable disease.This paper opens the debate to the value of strengthening the developmental origins of health and disease (DOHaD) research focus in Africa to tackle critical public health challenges across the life-course. We argue that the application of DOHaD science in Africa to advance life-course prevention programmes can aid the achievement of the Sustainable Development Goals, and assist in improving health across generations. To increase DOHaD research and its application in Africa, we need to mobilise multisectoral partners, utilise existing data and expertise on the continent, and foster a new generation of young African scientists engrossed in DOHaD.
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Affiliation(s)
- Shane A. Norris
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Abdallah Daar
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
- Dalla Lana School of Public Health and Department of Surgery, University of Toronto, Toronto, Canada
| | - Dorairajan Balasubramanian
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
- L V Prasad Eye Institute, Hyderabad, India
| | - Peter Byass
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
- Department of Public Health and Clinical Medicine, Umeå University, Umea, Sweden
| | - Elizabeth Kimani-Murage
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
- African Population and Health Research Center, Kenya
| | - Andrew Macnab
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | - Christoff Pauw
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Atul Singhal
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
- Institute of Child Health, University College London, London, UK
| | - Chittaranjan Yajnik
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
- King Edward Memorial Hospital Research Centre, Pune, India
| | | | - Naomi Levitt
- Department of Diabetic Medicine and Endocrinology, University of Cape Town, Cape Town, South Africa
| | - Jihene Maatoug
- Department of Epidemiology, Hospital Farhat Hached, Sousse, Tunisia
| | - Nolwazi Mkhwanazi
- Department of Anthropology, University of the Witwatersrand, Johannesburg, South Africa
| | - Sophie E. Moore
- Division of Women’s Health, King’s College London, London, UK
| | | | - Juliet R. C. Pulliam
- DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), University of Stellenbosch, Stellenbosch, South Africa
| | - Tamsen Rochat
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Human and Social Development Research Programme, Human Sciences Research Council, Durban, South Africa
| | - Rihlat Said-Mohamed
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Soraya Seedat
- Department of Psychiatry, Stellenbosch University, Stellenbosch, South Africa
| | - Eugene Sobngwi
- Department of Applied Epidemiology, University of Yaoundé, Yaounde, Cameroon
| | - Mark Tomlinson
- Department of Psychology, Stellenbosch University, Stellenbosch, South Africa
| | - Elona Toska
- Department of Social Policy and Intervention, University of Oxford, Oxford, UK
| | - Cari van Schalkwyk
- DST-NRF Centre of Excellence in Epidemiological Modelling and Analysis (SACEMA), University of Stellenbosch, Stellenbosch, South Africa
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Hladish TJ, Pearson CAB, Chao DL, Rojas DP, Recchia GL, Gómez-Dantés H, Halloran ME, Pulliam JRC, Longini IM. Projected Impact of Dengue Vaccination in Yucatán, Mexico. PLoS Negl Trop Dis 2016; 10:e0004661. [PMID: 27227883 PMCID: PMC4882069 DOI: 10.1371/journal.pntd.0004661] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/02/2016] [Indexed: 01/17/2023] Open
Abstract
Dengue vaccines will soon provide a new tool for reducing dengue disease, but the effectiveness of widespread vaccination campaigns has not yet been determined. We developed an agent-based dengue model representing movement of and transmission dynamics among people and mosquitoes in Yucatán, Mexico, and simulated various vaccine scenarios to evaluate effectiveness under those conditions. This model includes detailed spatial representation of the Yucatán population, including the location and movement of 1.8 million people between 375,000 households and 100,000 workplaces and schools. Where possible, we designed the model to use data sources with international coverage, to simplify re-parameterization for other regions. The simulation and analysis integrate 35 years of mild and severe case data (including dengue serotype when available), results of a seroprevalence survey, satellite imagery, and climatological, census, and economic data. To fit model parameters that are not directly informed by available data, such as disease reporting rates and dengue transmission parameters, we developed a parameter estimation toolkit called AbcSmc, which we have made publicly available. After fitting the simulation model to dengue case data, we forecasted transmission and assessed the relative effectiveness of several vaccination strategies over a 20 year period. Vaccine efficacy is based on phase III trial results for the Sanofi-Pasteur vaccine, Dengvaxia. We consider routine vaccination of 2, 9, or 16 year-olds, with and without a one-time catch-up campaign to age 30. Because the durability of Dengvaxia is not yet established, we consider hypothetical vaccines that confer either durable or waning immunity, and we evaluate the use of booster doses to counter waning. We find that plausible vaccination scenarios with a durable vaccine reduce annual dengue incidence by as much as 80% within five years. However, if vaccine efficacy wanes after administration, we find that there can be years with larger epidemics than would occur without any vaccination, and that vaccine booster doses are necessary to prevent this outcome. Dengue is a mosquito-transmitted viral disease that is common throughout the tropics. Despite a long history in humans and extensive efforts to control dengue transmission in many countries, the number, severity, and geographic range of reported cases is increasing. Most control efforts have focused on controlling mosquito populations, but the main vector, Aedes aegypti, flourishes in human-disturbed and indoor environments. Because the mosquitoes prefer to bite during the day when people are active and potentially moving around high-risk locations, fixed barriers like bed nets are not effective. Several dengue vaccines are being actively developed and may become valuable tools in dengue control. Using historical dengue data from Yucatán, Mexico, we fit a detailed simulation of human and mosquito populations to project future transmission, then used efficacy data from vaccine trials to evaluate the benefit of potential vaccination deployment strategies in the region. For a durable vaccine, we find that population-level, annual vaccine effectiveness approaches 65% by the end of the 20-year forecast period. For waning vaccines, however, effectiveness is greatly reduced–and sometimes negative–unless booster vaccinations are used.
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Affiliation(s)
- Thomas J. Hladish
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Carl A. B. Pearson
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Dennis L. Chao
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Diana Patricia Rojas
- Department of Epidemiology, University of Florida, Gainesville, Florida, United States of America
| | - Gabriel L. Recchia
- Institute for Intelligent Systems, University of Memphis, Memphis, Tennessee, United States of America
| | - Héctor Gómez-Dantés
- Health Systems Research Center, National Institute of Public Health, Cuernavaca, Morelos, Mexico
| | - M. Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Center for Inference and Dynamics of Infectious Diseases, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Juliet R. C. Pulliam
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Ira M. Longini
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Biostatistics, University of Florida, Gainesville, Florida, United States of America
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Lord JS, Al-Amin HM, Chakma S, Alam MS, Gurley ES, Pulliam JRC. Sampling Design Influences the Observed Dominance of Culex tritaeniorhynchus: Considerations for Future Studies of Japanese Encephalitis Virus Transmission. PLoS Negl Trop Dis 2016; 10:e0004249. [PMID: 26726881 PMCID: PMC4699645 DOI: 10.1371/journal.pntd.0004249] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
Mosquito sampling during Japanese encephalitis virus (JEV)-associated studies, particularly in India, has usually been conducted via aspirators or light traps to catch mosquitoes around cattle, which are dead-end hosts for JEV. High numbers of Culex tritaeniorhynchus, relative to other species, have often been caught during these studies. Less frequently, studies have involved sampling outdoor resting mosquitoes. We aimed to compare the relative abundance of mosquito species between these two previously used mosquito sampling methods. From September to December 2013 entomological surveys were undertaken in eight villages in a Japanese encephalitis (JE) endemic area of Bangladesh. Light traps were used to collect active mosquitoes in households, and resting boxes and a Bina Pani Das hop cage were used near oviposition sites to collect resting mosquitoes. Numbers of humans and domestic animals present in households where light traps were set were recorded. In five villages Cx. tritaeniorhynchus was more likely to be selected from light trap samples near hosts than resting collection samples near oviposition sites, according to log odds ratio tests. The opposite was true for Cx. pseudovishnui and Armigeres subalbatus, which can also transmit JEV. Culex tritaeniorhynchus constituted 59% of the mosquitoes sampled from households with cattle, 28% from households without cattle and 17% in resting collections. In contrast Cx. pseudovishnui constituted 5.4% of the sample from households with cattle, 16% from households with no cattle and 27% from resting collections, while Ar. subalbatus constituted 0.15%, 0.38%, and 8.4% of these samples respectively. These observations may be due to differences in timing of biting activity, host preference and host-seeking strategy rather than differences in population density. We suggest that future studies aiming to implicate vector species in transmission of JEV should consider focusing catches around hosts able to transmit JEV. The relative numbers of individuals of each mosquito species in an area are important to estimate when identifying species that contribute the most to vector-borne pathogen transmission. However, methods to sample mosquitoes and enumerate the number of individuals collected often vary in their catch efficacy between species. For example, species that take a bloodmeal during daylight hours are less likely to be caught using a light trap than a species that feeds predominantly at night. Similarly, sampling near a mammalian host will more likely collect mosquitoes with a preference for mammals than those with a preference for birds. In this study we compare sampling methods for assessing the relative abundance of mosquito species that may be involved in Japanese encephalitis virus (JEV) transmission. Collections near cattle- a species unable to transmit JEV- have been influential in implicating Cx. tritaeniorhynchus as the primary vector of JEV in South Asia, due to the high number of individuals of this species caught relative to other species. Indeed, this mosquito constituted the majority of the mosquitoes collected by light traps in households with cattle in this study. However, other species were more common when sampling households without cattle or resting mosquitoes near oviposition sites. We propose that methods used to sample mosquitoes in studies aiming to implicate species in JEV transmission in South Asia be reconsidered given that there are other mosquito species that are able to transmit JEV, and these species may be underrepresented when sampling using light traps near cattle.
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Affiliation(s)
- Jennifer S. Lord
- Vector Group, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | | | - Sumit Chakma
- Centre for Communicable Diseases, icddr,b, Mohakhali, Dhaka, Bangladesh
| | | | - Emily S. Gurley
- Centre for Communicable Diseases, icddr,b, Mohakhali, Dhaka, Bangladesh
| | - Juliet R. C. Pulliam
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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Hayman DTS, Pulliam JRC, Marshall JC, Cryan PM, Webb CT. Environment, host, and fungal traits predict continental-scale white-nose syndrome in bats. Sci Adv 2016; 2:e1500831. [PMID: 27152322 PMCID: PMC4846429 DOI: 10.1126/sciadv.1500831] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
White-nose syndrome is a fungal disease killing bats in eastern North America, but disease is not seen in European bats and is less severe in some North American species. We show that how bats use energy during hibernation and fungal growth rates under different environmental conditions can explain how some bats are able to survive winter with infection and others are not. Our study shows how simple but nonlinear interactions between fungal growth and bat energetics result in decreased survival times at more humid hibernation sites; however, differences between species such as body size and metabolic rates determine the impact of fungal infection on bat survival, allowing European bat species to survive, whereas North American species can experience dramatic decline.
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Affiliation(s)
- David T. S. Hayman
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Private Bag, 11 222, Palmerston North 4442, New Zealand
| | - Juliet R. C. Pulliam
- Department of Biology, University of Florida, Gainesville, FL 32611, USA
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jonathan C. Marshall
- Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, Massey University, Private Bag, 11 222, Palmerston North 4442, New Zealand
- Institute of Fundamental Sciences, Massey University, Private Bag, 11 222, Palmerston North 4442, New Zealand
| | - Paul M. Cryan
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO 80526, USA
| | - Colleen T. Webb
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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Affiliation(s)
- Jennifer S. Lord
- Vector Group, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
| | - Emily S. Gurley
- Centre for Communicable Diseases, icddr,b, Mohakhali, Dhaka, Bangladesh
| | - Juliet R. C. Pulliam
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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Pulliam JRC, Bellan SE, Gambhir M, Meyers LA, Dushoff J. Evaluating Ebola vaccine trials: insights from simulation. Lancet Infect Dis 2015; 15:1134. [PMID: 26461945 DOI: 10.1016/s1473-3099(15)00303-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 08/24/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Juliet R C Pulliam
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA.
| | - Steve E Bellan
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA
| | - Manoj Gambhir
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia; Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA; The Santa Fe Institute, Santa Fe, NM, USA
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Bellan SE, Pulliam JRC, Pearson CAB, Champredon D, Fox SJ, Skrip L, Galvani AP, Gambhir M, Lopman BA, Porco TC, Meyers LA, Dushoff J. Statistical power and validity of Ebola vaccine trials in Sierra Leone: a simulation study of trial design and analysis. Lancet Infect Dis 2015; 15:703-10. [PMID: 25886798 DOI: 10.1016/s1473-3099(15)70139-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Safe and effective vaccines could help to end the ongoing Ebola virus disease epidemic in parts of west Africa, and mitigate future outbreaks of the virus. We assess the statistical validity and power of randomised controlled trial (RCT) and stepped-wedge cluster trial (SWCT) designs in Sierra Leone, where the incidence of Ebola virus disease is spatiotemporally heterogeneous, and is decreasing rapidly. METHODS We projected district-level Ebola virus disease incidence for the next 6 months, using a stochastic model fitted to data from Sierra Leone. We then simulated RCT and SWCT designs in trial populations comprising geographically distinct clusters at high risk, taking into account realistic logistical constraints, and both individual-level and cluster-level variations in risk. We assessed false-positive rates and power for parametric and non-parametric analyses of simulated trial data, across a range of vaccine efficacies and trial start dates. FINDINGS For an SWCT, regional variation in Ebola virus disease incidence trends produced increased false-positive rates (up to 0·15 at α=0·05) under standard statistical models, but not when analysed by a permutation test, whereas analyses of RCTs remained statistically valid under all models. With the assumption of a 6-month trial starting on Feb 18, 2015, we estimate the power to detect a 90% effective vaccine to be between 49% and 89% for an RCT, and between 6% and 26% for an SWCT, depending on the Ebola virus disease incidence within the trial population. We estimate that a 1-month delay in trial initiation will reduce the power of the RCT by 20% and that of the SWCT by 49%. INTERPRETATION Spatiotemporal variation in infection risk undermines the statistical power of the SWCT. This variation also undercuts the SWCT's expected ethical advantages over the RCT, because an RCT, but not an SWCT, can prioritise vaccination of high-risk clusters. FUNDING US National Institutes of Health, US National Science Foundation, and Canadian Institutes of Health Research.
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Affiliation(s)
- Steven E Bellan
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX, USA.
| | - Juliet R C Pulliam
- Department of Biology, University of Florida, Gainesville, FL, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Carl A B Pearson
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - David Champredon
- School of Computational Science and Engineering, McMaster University, Hamilton, ON, Canada
| | - Spencer J Fox
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Laura Skrip
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Alison P Galvani
- Center for Infectious Disease Modeling and Analysis, Yale School of Public Health, Yale University, New Haven, CT, USA; Department of Ecology and Evolution, Yale University, New Haven, CT, USA
| | - Manoj Gambhir
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Australia; Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; IHRC Inc, Atlanta, GA, USA
| | - Ben A Lopman
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA; Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Travis C Porco
- Francis I Proctor Foundation, University of California, San Francisco, CA, USA; Department of Ophthalmology, University of California, San Francisco, CA, USA; Department of Epidemiology & Biostatistics, University of California, San Francisco, CA, USA
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA; The Santa Fe Institute, Santa Fe, NM, USA
| | - Jonathan Dushoff
- Department of Biology, McMaster University, Hamilton, ON, Canada
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Heesterbeek H, Anderson RM, Andreasen V, Bansal S, De Angelis D, Dye C, Eames KTD, Edmunds WJ, Frost SDW, Funk S, Hollingsworth TD, House T, Isham V, Klepac P, Lessler J, Lloyd-Smith JO, Metcalf CJE, Mollison D, Pellis L, Pulliam JRC, Roberts MG, Viboud C. Modeling infectious disease dynamics in the complex landscape of global health. Science 2015; 347:aaa4339. [PMID: 25766240 PMCID: PMC4445966 DOI: 10.1126/science.aaa4339] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Despite some notable successes in the control of infectious diseases, transmissible pathogens still pose an enormous threat to human and animal health. The ecological and evolutionary dynamics of infections play out on a wide range of interconnected temporal, organizational, and spatial scales, which span hours to months, cells to ecosystems, and local to global spread. Moreover, some pathogens are directly transmitted between individuals of a single species, whereas others circulate among multiple hosts, need arthropod vectors, or can survive in environmental reservoirs. Many factors, including increasing antimicrobial resistance, increased human connectivity and changeable human behavior, elevate prevention and control from matters of national policy to international challenge. In the face of this complexity, mathematical models offer valuable tools for synthesizing information to understand epidemiological patterns, and for developing quantitative evidence for decision-making in global health.
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Affiliation(s)
- Hans Heesterbeek
- Faculty of Veterinary Medicine, University of Utrecht, Utrecht, Netherlands.
| | | | | | | | | | | | - Ken T D Eames
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene Tropical Medicine, London, UK
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene Tropical Medicine, London, UK
| | | | | | - T Deirdre Hollingsworth
- School of Life Sciences, University of Warwick, UK. School of Tropical Medicine, University of Liverpool, UK
| | - Thomas House
- Warwick Mathematics Institute, University of Warwick, Coventry, UK
| | - Valerie Isham
- Department of Statistical Science, University College London, London, UK
| | | | - Justin Lessler
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - James O Lloyd-Smith
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - C Jessica E Metcalf
- Department of Zoology, University of Oxford, Oxford, UK, and Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | | | - Lorenzo Pellis
- Warwick Mathematics Institute, University of Warwick, Coventry, UK
| | - Juliet R C Pulliam
- Department of Biology-Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA. Division of International Epidemiology and Population Studies, Fogarty International Center, NIH, Bethesda, MD, USA
| | - Mick G Roberts
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Cecile Viboud
- Division of International Epidemiology and Population Studies, Fogarty International Center, NIH, Bethesda, MD, USA
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Peel AJ, Pulliam JRC, Luis AD, Plowright RK, O'Shea TJ, Hayman DTS, Wood JLN, Webb CT, Restif O. The effect of seasonal birth pulses on pathogen persistence in wild mammal populations. Proc Biol Sci 2015; 281:rspb.2013.2962. [PMID: 24827436 PMCID: PMC4046395 DOI: 10.1098/rspb.2013.2962] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The notion of a critical community size (CCS), or population size that is likely to result in long-term persistence of a communicable disease, has been developed based on the empirical observations of acute immunizing infections in human populations, and extended for use in wildlife populations. Seasonal birth pulses are frequently observed in wildlife and are expected to impact infection dynamics, yet their effect on pathogen persistence and CCS have not been considered. To investigate this issue theoretically, we use stochastic epidemiological models to ask how host life-history traits and infection parameters interact to determine pathogen persistence within a closed population. We fit seasonal birth pulse models to data from diverse mammalian species in order to identify realistic parameter ranges. When varying the synchrony of the birth pulse with all other parameters being constant, our model predicted that the CCS can vary by more than two orders of magnitude. Tighter birth pulses tended to drive pathogen extinction by creating large amplitude oscillations in prevalence, especially with high demographic turnover and short infectious periods. Parameters affecting the relative timing of the epidemic and birth pulse peaks determined the intensity and direction of the effect of pre-existing immunity in the population on the pathogen's ability to persist beyond the initial epidemic following its introduction.
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Affiliation(s)
- A J Peel
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK Environmental Futures Research Institute, Griffith University, Brisbane, 4111, Australia
| | - J R C Pulliam
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA Department of Biology, University of Florida, Gainesville, FL 32611, USA Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA
| | - A D Luis
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - R K Plowright
- Center for Infectious Disease Dynamics, The Pennsylvania State University, University Park, PA 16802, USA
| | - T J O'Shea
- US Geological Survey (retired), PO Box 65, Glen Haven, CO 80532, USA
| | - D T S Hayman
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - J L N Wood
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - C T Webb
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - O Restif
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
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Affiliation(s)
- Steve E Bellan
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA
| | - Juliet R C Pulliam
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA
| | - Jonathan Dushoff
- Department of Biology and Institute of Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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Tran CH, Sugimoto JD, Pulliam JRC, Ryan KA, Myers PD, Castleman JB, Doty R, Johnson J, Stringfellow J, Kovacevich N, Brew J, Cheung LL, Caron B, Lipori G, Harle CA, Alexander C, Yang Y, Longini IM, Halloran ME, Morris JG, Small PA. School-located influenza vaccination reduces community risk for influenza and influenza-like illness emergency care visits. PLoS One 2014; 9:e114479. [PMID: 25489850 PMCID: PMC4260868 DOI: 10.1371/journal.pone.0114479] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 11/07/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND School-located influenza vaccination (SLIV) programs can substantially enhance the sub-optimal coverage achieved under existing delivery strategies. Randomized SLIV trials have shown these programs reduce laboratory-confirmed influenza among both vaccinated and unvaccinated children. This work explores the effectiveness of a SLIV program in reducing the community risk of influenza and influenza-like illness (ILI) associated emergency care visits. METHODS For the 2011/12 and 2012/13 influenza seasons, we estimated age-group specific attack rates (AR) for ILI from routine surveillance and census data. Age-group specific SLIV program effectiveness was estimated as one minus the AR ratio for Alachua County versus two comparison regions: the 12 county region surrounding Alachua County, and all non-Alachua counties in Florida. RESULTS Vaccination of ∼50% of 5-17 year-olds in Alachua reduced their risk of ILI-associated visits, compared to the rest of Florida, by 79% (95% confidence interval: 70, 85) in 2011/12 and 71% (63, 77) in 2012/13. The greatest indirect effectiveness was observed among 0-4 year-olds, reducing AR by 89% (84, 93) in 2011/12 and 84% (79, 88) in 2012/13. Among all non-school age residents, the estimated indirect effectiveness was 60% (54, 65) and 36% (31, 41) for 2011/12 and 2012/13. The overall effectiveness among all age-groups was 65% (61, 70) and 46% (42, 50) for 2011/12 and 2012/13. CONCLUSION Wider implementation of SLIV programs can significantly reduce the influenza-associated public health burden in communities.
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Affiliation(s)
- Cuc H. Tran
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Clinical Translational Science Institute, University of Florida, Gainesville, Florida, United States of America
| | - Jonathan D. Sugimoto
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Department of Epidemiology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Juliet R. C. Pulliam
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, Florida, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kathleen A. Ryan
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Paul D. Myers
- Florida Department of Health in Alachua County, Gainesville, Florida, United States of America
| | - Joan B. Castleman
- College of Nursing, University of Florida, Gainesville, Florida, United States of America
| | - Randell Doty
- College of Pharmacy, University of Florida, Gainesville, Florida, United States of America
| | - Jackie Johnson
- Alachua County Public Schools, Gainesville, Florida, United States of America
| | - Jim Stringfellow
- Partnership for Strong Families, Gainesville, Florida, United States of America
| | - Nadia Kovacevich
- Florida Department of Health in Alachua County, Gainesville, Florida, United States of America
| | - Joe Brew
- Department of Epidemiology, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Department of Epidemiology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
- Florida Department of Health in Alachua County, Gainesville, Florida, United States of America
| | - Lai Ling Cheung
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
| | - Brad Caron
- Florida Department of Health in Alachua County, Gainesville, Florida, United States of America
| | - Gloria Lipori
- University of Florida Health Integrated Data Repository, UF Health, Gainesville, Florida, United States of America
| | - Christopher A. Harle
- Clinical Translational Science Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Health Services Research, Management and Policy, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
| | - Charles Alexander
- Florida Department of Health, Tallahassee, Florida, United States of America
| | - Yang Yang
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Department of Biostatistics, Colleges of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Ira M. Longini
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Biostatistics, College of Public Health and Health Professions, University of Florida, Gainesville, Florida, United States of America
- Department of Biostatistics, Colleges of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - M. Elizabeth Halloran
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - J. Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida, United States of America
| | - Parker A. Small
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
- Department of Pediatrics, College of Medicine, University of Florida, Gainesville, Florida, United States of America
- Department of Pathology, College of Medicine, University of Florida, Gainesville, Florida, United States of America
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39
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Affiliation(s)
- Steve E Bellan
- Center for Computational Biology and Bioinformatics, The University of Texas at Austin, Austin, TX 78712, USA.
| | - Juliet R C Pulliam
- Department of Biology and Emerging Pathogens Institute, University of Florida, Gainesville, FL, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan Dushoff
- Department of Biology and Institute of Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Lauren Ancel Meyers
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA; Santa Fe Institute, Santa Fe, NM, USA
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Blumberg S, Funk S, Pulliam JRC. Detecting differential transmissibilities that affect the size of self-limited outbreaks. PLoS Pathog 2014; 10:e1004452. [PMID: 25356657 PMCID: PMC4214794 DOI: 10.1371/journal.ppat.1004452] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 09/04/2014] [Indexed: 12/19/2022] Open
Abstract
Our ability to respond appropriately to infectious diseases is enhanced by identifying differences in the potential for transmitting infection between individuals. Here, we identify epidemiological traits of self-limited infections (i.e. infections with an effective reproduction number satisfying [0 < R eff < 1) that correlate with transmissibility. Our analysis is based on a branching process model that permits statistical comparison of both the strength and heterogeneity of transmission for two distinct types of cases. Our approach provides insight into a variety of scenarios, including the transmission of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) in the Arabian peninsula, measles in North America, pre-eradication smallpox in Europe, and human monkeypox in the Democratic Republic of the Congo. When applied to chain size data for MERS-CoV transmission before 2014, our method indicates that despite an apparent trend towards improved control, there is not enough statistical evidence to indicate that R eff has declined with time. Meanwhile, chain size data for measles in the United States and Canada reveal statistically significant geographic variation in R eff, suggesting that the timing and coverage of national vaccination programs, as well as contact tracing procedures, may shape the size distribution of observed infection clusters. Infection source data for smallpox suggests that primary cases transmitted more than secondary cases, and provides a quantitative assessment of the effectiveness of control interventions. Human monkeypox, on the other hand, does not show evidence of differential transmission between animals in contact with humans, primary cases, or secondary cases, which assuages the concern that social mixing can amplify transmission by secondary cases. Lastly, we evaluate surveillance requirements for detecting a change in the human-to-human transmission of monkeypox since the cessation of cross-protective smallpox vaccination. Our studies lay the foundation for future investigations regarding how infection source, vaccination status or other putative transmissibility traits may affect self-limited transmission.
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Affiliation(s)
- Seth Blumberg
- Francis I. Proctor Foundation, University of California San Francisco, San Francisco, California, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sebastian Funk
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Juliet R. C. Pulliam
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Biology, University of Florida, Gainesville, Florida, United States of America
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America
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41
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Hollingsworth TD, Pulliam JRC, Funk S, Truscott JE, Isham V, Lloyd AL. Seven challenges for modelling indirect transmission: vector-borne diseases, macroparasites and neglected tropical diseases. Epidemics 2014; 10:16-20. [PMID: 25843376 PMCID: PMC4383804 DOI: 10.1016/j.epidem.2014.08.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 08/22/2014] [Accepted: 08/23/2014] [Indexed: 12/04/2022] Open
Abstract
Many of the challenges which face modellers of directly transmitted pathogens also arise when modelling the epidemiology of pathogens with indirect transmission – whether through environmental stages, vectors, intermediate hosts or multiple hosts. In particular, understanding the roles of different hosts, how to measure contact and infection patterns, heterogeneities in contact rates, and the dynamics close to elimination are all relevant challenges, regardless of the mode of transmission. However, there remain a number of challenges that are specific and unique to modelling vector-borne diseases and macroparasites. Moreover, many of the neglected tropical diseases which are currently targeted for control and elimination are vector-borne, macroparasitic, or both, and so this article includes challenges which will assist in accelerating the control of these high-burden diseases. Here, we discuss the challenges of indirect measures of infection in humans, whether through vectors or transmission life stages and in estimating the contribution of different host groups to transmission. We also discuss the issues of “evolution-proof” interventions against vector-borne disease.
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Affiliation(s)
- T Déirdre Hollingsworth
- Mathematics Institute, University of Warwick, Coventry CV4 7AL, UK; School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK.
| | - Juliet R C Pulliam
- Department of Biology, University of Florida, Gainesville, FL 32611, USA; Emerging Pathogens Institute, University of Florida, Gainesville, FL 32610, USA; Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sebastian Funk
- Centre for the Mathematical Modelling of Infectious Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | - James E Truscott
- London Centre for Neglected Tropical Disease Research, Department of Infectious Disease Epidemiology, School of Public Health, Faculty of Medicine, Imperial College London, W2 1PG London, UK
| | - Valerie Isham
- Department of Statistical Science, University College London, WC1E 6BT, UK
| | - Alun L Lloyd
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA; Department of Mathematics and Biomathematics Graduate Program, North Carolina State University, NC 27695, USA
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42
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Smith DL, Perkins TA, Reiner RC, Barker CM, Niu T, Chaves LF, Ellis AM, George DB, Le Menach A, Pulliam JRC, Bisanzio D, Buckee C, Chiyaka C, Cummings DAT, Garcia AJ, Gatton ML, Gething PW, Hartley DM, Johnston G, Klein EY, Michael E, Lloyd AL, Pigott DM, Reisen WK, Ruktanonchai N, Singh BK, Stoller J, Tatem AJ, Kitron U, Godfray HCJ, Cohen JM, Hay SI, Scott TW. Recasting the theory of mosquito-borne pathogen transmission dynamics and control. Trans R Soc Trop Med Hyg 2014; 108:185-97. [PMID: 24591453 PMCID: PMC3952634 DOI: 10.1093/trstmh/tru026] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Mosquito-borne diseases pose some of the greatest challenges in public health, especially
in tropical and sub-tropical regions of the world. Efforts to control these diseases have
been underpinned by a theoretical framework developed for malaria by Ross and Macdonald,
including models, metrics for measuring transmission, and theory of control that
identifies key vulnerabilities in the transmission cycle. That framework, especially
Macdonald's formula for R0 and its entomological derivative,
vectorial capacity, are now used to study dynamics and design interventions for many
mosquito-borne diseases. A systematic review of 388 models published between 1970 and 2010
found that the vast majority adopted the Ross–Macdonald assumption of homogeneous
transmission in a well-mixed population. Studies comparing models and data question these
assumptions and point to the capacity to model heterogeneous, focal transmission as the
most important but relatively unexplored component in current theory. Fine-scale
heterogeneity causes transmission dynamics to be nonlinear, and poses problems for
modeling, epidemiology and measurement. Novel mathematical approaches show how
heterogeneity arises from the biology and the landscape on which the processes of mosquito
biting and pathogen transmission unfold. Emerging theory focuses attention on the
ecological and social context for mosquito blood feeding, the movement of both hosts and
mosquitoes, and the relevant spatial scales for measuring transmission and for modeling
dynamics and control.
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Affiliation(s)
- David L Smith
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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43
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Affiliation(s)
- Juliet R C Pulliam
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL 32611
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44
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Luis AD, Hayman DTS, O'Shea TJ, Cryan PM, Gilbert AT, Pulliam JRC, Mills JN, Timonin ME, Willis CKR, Cunningham AA, Fooks AR, Rupprecht CE, Wood JLN, Webb CT. A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special? Proc Biol Sci 2013; 280:20122753. [PMID: 23378666 DOI: 10.1098/rspb.2012.2753rspb.2012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023] Open
Abstract
Bats are the natural reservoirs of a number of high-impact viral zoonoses. We present a quantitative analysis to address the hypothesis that bats are unique in their propensity to host zoonotic viruses based on a comparison with rodents, another important host order. We found that bats indeed host more zoonotic viruses per species than rodents, and we identified life-history and ecological factors that promote zoonotic viral richness. More zoonotic viruses are hosted by species whose distributions overlap with a greater number of other species in the same taxonomic order (sympatry). Specifically in bats, there was evidence for increased zoonotic viral richness in species with smaller litters (one young), greater longevity and more litters per year. Furthermore, our results point to a new hypothesis to explain in part why bats host more zoonotic viruses per species: the stronger effect of sympatry in bats and more viruses shared between bat species suggests that interspecific transmission is more prevalent among bats than among rodents. Although bats host more zoonotic viruses per species, the total number of zoonotic viruses identified in bats (61) was lower than in rodents (68), a result of there being approximately twice the number of rodent species as bat species. Therefore, rodents should still be a serious concern as reservoirs of emerging viruses. These findings shed light on disease emergence and perpetuation mechanisms and may help lead to a predictive framework for identifying future emerging infectious virus reservoirs.
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Affiliation(s)
- Angela D Luis
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
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45
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Reiner RC, Perkins TA, Barker CM, Niu T, Chaves LF, Ellis AM, George DB, Le Menach A, Pulliam JRC, Bisanzio D, Buckee C, Chiyaka C, Cummings DAT, Garcia AJ, Gatton ML, Gething PW, Hartley DM, Johnston G, Klein EY, Michael E, Lindsay SW, Lloyd AL, Pigott DM, Reisen WK, Ruktanonchai N, Singh BK, Tatem AJ, Kitron U, Hay SI, Scott TW, Smith DL. A systematic review of mathematical models of mosquito-borne pathogen transmission: 1970-2010. J R Soc Interface 2013; 10:20120921. [PMID: 23407571 PMCID: PMC3627099 DOI: 10.1098/rsif.2012.0921] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Mathematical models of mosquito-borne pathogen transmission originated in the early twentieth century to provide insights into how to most effectively combat malaria. The foundations of the Ross–Macdonald theory were established by 1970. Since then, there has been a growing interest in reducing the public health burden of mosquito-borne pathogens and an expanding use of models to guide their control. To assess how theory has changed to confront evolving public health challenges, we compiled a bibliography of 325 publications from 1970 through 2010 that included at least one mathematical model of mosquito-borne pathogen transmission and then used a 79-part questionnaire to classify each of 388 associated models according to its biological assumptions. As a composite measure to interpret the multidimensional results of our survey, we assigned a numerical value to each model that measured its similarity to 15 core assumptions of the Ross–Macdonald model. Although the analysis illustrated a growing acknowledgement of geographical, ecological and epidemiological complexities in modelling transmission, most models during the past 40 years closely resemble the Ross–Macdonald model. Modern theory would benefit from an expansion around the concepts of heterogeneous mosquito biting, poorly mixed mosquito-host encounters, spatial heterogeneity and temporal variation in the transmission process.
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Affiliation(s)
- Robert C Reiner
- Fogarty International Center, National Institutes of Health, Bethesda, MD, USA.
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46
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Luis AD, Hayman DTS, O'Shea TJ, Cryan PM, Gilbert AT, Pulliam JRC, Mills JN, Timonin ME, Willis CKR, Cunningham AA, Fooks AR, Rupprecht CE, Wood JLN, Webb CT. A comparison of bats and rodents as reservoirs of zoonotic viruses: are bats special? Proc Biol Sci 2013; 280:20122753. [PMID: 23378666 DOI: 10.1098/rspb.2012.2753] [Citation(s) in RCA: 404] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Bats are the natural reservoirs of a number of high-impact viral zoonoses. We present a quantitative analysis to address the hypothesis that bats are unique in their propensity to host zoonotic viruses based on a comparison with rodents, another important host order. We found that bats indeed host more zoonotic viruses per species than rodents, and we identified life-history and ecological factors that promote zoonotic viral richness. More zoonotic viruses are hosted by species whose distributions overlap with a greater number of other species in the same taxonomic order (sympatry). Specifically in bats, there was evidence for increased zoonotic viral richness in species with smaller litters (one young), greater longevity and more litters per year. Furthermore, our results point to a new hypothesis to explain in part why bats host more zoonotic viruses per species: the stronger effect of sympatry in bats and more viruses shared between bat species suggests that interspecific transmission is more prevalent among bats than among rodents. Although bats host more zoonotic viruses per species, the total number of zoonotic viruses identified in bats (61) was lower than in rodents (68), a result of there being approximately twice the number of rodent species as bat species. Therefore, rodents should still be a serious concern as reservoirs of emerging viruses. These findings shed light on disease emergence and perpetuation mechanisms and may help lead to a predictive framework for identifying future emerging infectious virus reservoirs.
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Affiliation(s)
- Angela D Luis
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA.
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47
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Restif O, Hayman DTS, Pulliam JRC, Plowright RK, George DB, Luis AD, Cunningham AA, Bowen RA, Fooks AR, O'Shea TJ, Wood JLN, Webb CT. Model-guided fieldwork: practical guidelines for multidisciplinary research on wildlife ecological and epidemiological dynamics. Ecol Lett 2012; 15:1083-94. [PMID: 22809422 PMCID: PMC3466409 DOI: 10.1111/j.1461-0248.2012.01836.x] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Revised: 02/02/2012] [Accepted: 06/20/2012] [Indexed: 12/25/2022]
Abstract
Infectious disease ecology has recently raised its public profile beyond the scientific community due to the major threats that wildlife infections pose to biological conservation, animal welfare, human health and food security. As we start unravelling the full extent of emerging infectious diseases, there is an urgent need to facilitate multidisciplinary research in this area. Even though research in ecology has always had a strong theoretical component, cultural and technical hurdles often hamper direct collaboration between theoreticians and empiricists. Building upon our collective experience of multidisciplinary research and teaching in this area, we propose practical guidelines to help with effective integration among mathematical modelling, fieldwork and laboratory work. Modelling tools can be used at all steps of a field-based research programme, from the formulation of working hypotheses to field study design and data analysis. We illustrate our model-guided fieldwork framework with two case studies we have been conducting on wildlife infectious diseases: plague transmission in prairie dogs and lyssavirus dynamics in American and African bats. These demonstrate that mechanistic models, if properly integrated in research programmes, can provide a framework for holistic approaches to complex biological systems.
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Affiliation(s)
- Olivier Restif
- Disease Dynamics Unit, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
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48
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Abstract
Henipaviruses cause fatal infection in humans and domestic animals. Transmission from fruit bats, the wildlife reservoirs of henipaviruses, is putatively driven (at least in part) by anthropogenic changes that alter host ecology. Human and domestic animal fatalities occur regularly in Asia and Australia, but recent findings suggest henipaviruses are present in bats across the Old World tropics. We review the application of the One Health approach to henipavirus research in three locations: Australia, Malaysia and Bangladesh. We propose that by recognising and addressing the complex interaction among human, domestic animal and wildlife systems, research within the One Health paradigm will be more successful in mitigating future human and domestic animal deaths from henipavirus infection than alternative single-discipline approaches.
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Affiliation(s)
- David T S Hayman
- Department of Biology, Colorado State University, Fort Collins, CO, 80523, USA,
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49
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Hayman DTS, Gurley ES, Pulliam JRC, Field HE. The Application of One Health Approaches to Henipavirus Research. Curr Top Microbiol Immunol 2012. [DOI: 10.1007/978-3-662-45792-4_276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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50
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Pulliam JRC, Epstein JH, Dushoff J, Rahman SA, Bunning M, Jamaluddin AA, Hyatt AD, Field HE, Dobson AP, Daszak P. Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis. J R Soc Interface 2011; 9:89-101. [PMID: 21632614 PMCID: PMC3223631 DOI: 10.1098/rsif.2011.0223] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Emerging zoonoses threaten global health, yet the processes by which they emerge are complex and poorly understood. Nipah virus (NiV) is an important threat owing to its broad host and geographical range, high case fatality, potential for human-to-human transmission and lack of effective prevention or therapies. Here, we investigate the origin of the first identified outbreak of NiV encephalitis in Malaysia and Singapore. We analyse data on livestock production from the index site (a commercial pig farm in Malaysia) prior to and during the outbreak, on Malaysian agricultural production, and from surveys of NiV's wildlife reservoir (flying foxes). Our analyses suggest that repeated introduction of NiV from wildlife changed infection dynamics in pigs. Initial viral introduction produced an explosive epizootic that drove itself to extinction but primed the population for enzootic persistence upon reintroduction of the virus. The resultant within-farm persistence permitted regional spread and increased the number of human infections. This study refutes an earlier hypothesis that anomalous El Niño Southern Oscillation-related climatic conditions drove emergence and suggests that priming for persistence drove the emergence of a novel zoonotic pathogen. Thus, we provide empirical evidence for a causative mechanism previously proposed as a precursor to widespread infection with H5N1 avian influenza and other emerging pathogens.
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Affiliation(s)
- Juliet R C Pulliam
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
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