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VITAL SIGNS VITAL Health Security in South Africa Security Health SIGNS Health security in South Africa Edited by Wilmot James Edited by Wilmot James by Wilmot Edited FOUNDATION BRENTHURST THE VITALSIGNS Health Security in South Africa First published in January 2020 by The Brenthurst Foundation (Pty) Limited St. Andrew’s House 6 St Andrew’s Road Parktown Johannesburg South Africa www.thebrenthurstfoundation.org ISBN 978-0-620-86603-3 e-ISBN 978-0-620-86604-0 © 2020 Wilmot James for assembling and editing © 2020 individual authors and contributors for their chapters. All rights reserved. No part of this publication may be reproduced, stored or introduced into a retrieval system, or transmitted in any form or by any means (electronic, mechanical, photocopying, recording or otherwise), without the prior written permission of the publisher. Any person who does any unauthorised act in relation to this publication may be liable to criminal prosecution and civil claims for damages. Design and layout by Sheaf Publishing cc, Benoni Printed by Law Print (Pty) Ltd, Midrand Contents List of tables iv List of figures iv Abbreviations and acronyms v List of authors x Executive overview xiii Introduction xxii Wilmot James 1 – Nuclear and radiological: changing risks from apartheid to democracy 1 Michael Kahn and Terence McNamee 2 – Reaction and action: chemical and environmental security 18 Michael Kahn and Brett Cohen 3 – Biological and infectious disease risks 34 Lizeka Tandwa and Janusz T. Paweska 4 – Climate, drought, food security and health 49 Robbie Parks, Megan McLaren, Ulrike Rivett and Madeleine Thomson 5 – The CBRN threat environment in South Africa 61 Jaco-Louis du Plessis, Greg Mills and Wilmot James 6 – Investing in health security preparedness 76 Jonatan Davén, Wilmot James and Michael Kahn 7 – Conclusion 94 Wilmot James and Gregory Hooks A – The JEE Mission Reports 100 Hannah Bender B – Health Security Symposium report back 127 Maria A. Papathanasopoulos and Martin Veller Endnotes 142 Index 163 List of tables Table 1.1: Nuclear security publications, by science category 13 Table 2.1: Industrial chemicals share of total manufacturing sales 20 Table 2.2: Fatality and injury rates per million hours, by commodity, 2005 and 2015. 23 Table 3.1: Examples of endemic and exotic pathogens for South Africa 39 List of figures Figure 2.1: Research publications on mining and chemical risk, 1993–2017 31 Figure 6.1: Expenditure (past and projected) of key research institutions, 2009/10–2021/22 (nominal prices) 79 Figure 6.2: SANAS expenditure and budget, 2015/16– 2021/22 81 Figure 6.3: Expenditure and budget for Environmental and Port Health Services, 2015/16–2021/22 82 Figure 6.4: Expenditure on Support for the People in R million and as a percentage of total DoD expenditure, 2015/16–2021/22 83 Figure A.1: Map re-drawn from Epidemiology of Rabies in Lesotho: The Importance of Routine Surveillance and Virus Characterization 125 Abbreviations and acronyms AEB Atomic Energy Board AFRA Africa Regional Cooperative Agreement AFRA-NEST AFRA Network for Education in Nuclear Science and Technology Africa CDC Africa Center for Disease Control and Prevention AIRT Animal and Products Identification, Recording and Traceability AMCU Association of Mineworkers and Construction Union AMD Acid Mine Drainage AMR Antimicrobial resistance AMS Antimicrobial stewardship ANC African National Congress APHF Africa Public Health Foundation API application programming interface ARC Agricultural Research Council ARPA Advanced Research Projects Agency ART anti-retroviral therapy ASSAF Academy of Science of South Africa bOPV bivalent oral poliovirus vaccine BRICS Brazil, Russia, India, China and South Africa BSLn Biosafety level n BTWC Biological and Toxin Weapons Convention CAIA Chemical and Allied Industries Association CAT computer assisted tomography CBRN chemical, biological, radiological and nuclear CBW chemical and biological warfare CDC Centers for Disease Control and Prevention CDW Central Data Warehouse CEPI Coalition for Epidemic Preparedness Innovations CEPPWAWU Chemical, Energy, Paper, Printing, Wood and Allied Workers’ Union CMJAH Charlotte Maxeke Johannesburg Academic Hospital CoCT City of Cape Town CW Chemical warfare CWC Chemical Weapons Convention DAFF Department of Agriculture, Forestry and Fisheries DMA Disaster Management Authority Abbreviations and acronyms v DRC Democratic Republic of the Congo DURC dual use research of concern EAC East African Community EDL Essential drug list EFF Economic Freedom Fighters EID Emerging infectious diseases EIU Economist Intelligence Unit ENSO El Niño–Southern Oscillation EOC Emergency Operation Centre EPI Expanded Program for Immunization EQA External Quality Assurance EVD Ebola Virus Disease FETP Field Epidemiology Training Program GARP-SA Global Antibiotic Resistance Partnership in South Africa GAVI Global Alliance for Vaccines and Immunization GHI Global Hunger Index GHS Index Global Health Security Index GHSA Global Health Security Agenda GLASS Global Antimicrobial Resistance Surveillance System GNI Gross National Income HCAI healthcare associated infection HE2RO Health Economics and Epidemiology Research Office HEU Highly-enriched uranium HIV Human Immunodeficiency Virus HRD Human Resource Development IAEA International Atomic Energy Agency ICT information and communication technology IDSR Integrated Disease Surveillance and Response IHR International Health Regulations (2005) IoT Internet of Things IPC Infection Prevention and Control IPCC Intergovernmental Panel on Climate Change IPV Inactivated poliovirus vaccine IRI International Research Institute for Climate and Society ISS Institute of Security Studies JEE Joint External Evaluation KNPS Koeberg Nuclear Power Station LEU Low-enriched uranium LM Listeria monocytogenes MCM Medical countermeasures vi Vital Signs MECs Members of Executive Councils MERS Middle East respiratory syndrome MNORT Multi-Sectoral National Outbreak Response Team MoU Memoranda of understanding MPRDA Mineral and Petroleum Resources Development Act (No. 28 of 2002) MRL Mineral Research Laboratory NAJOINTS National Joint Operational and Intelligence Structure NAP National Action Plan NAPHISA National Public Health Institute of South Africa NAPHS National Action Plan Health Security NATHOC National Health Operations Centre NATJOC National Joint Operational Centre NCACC National Conventional Arms Control Committee NCID National Institute for Communicable Diseases NCS National Core Standards NDMC National Disaster Management Centre NDOH National Department of Health NDP National Development Plan NDR National Dose Register NECSA Nuclear Energy Corporation of South Africa NEM National Environmental Management NEM: AQA Air Quality Act NEM: WA Waste Act NFP National Focal Points NHI National Health Insurance NHLS National Health Laboratory Services NICD National Institute for Communicable Diseases NIOH National Institute for Occupational Health NMC Notifiable Medical Conditions NNDMP National Nuclear Disaster Management Plan NNR National Nuclear Regulator NNSA National Nuclear Security Administration NPT Treaty on the Non-Proliferation of Nuclear Weapons NUM National Union of Mineworkers OMT Oppenheimer Memorial Trust PBMR pebble-bed modular reactor PER Performance and expenditure reviews PFMA Public Financial Management Act PHEIC Public Health Emergency of International Concern PHEOC Public Health Emergency Operations Centre PIH Partners in Health Abbreviations and acronyms vii PIP Pandemic Influenza Preparedness PNEs Peaceful Nuclear Explosives POPs Persistent Organic Pollutants PPE personal protective equipment PoVS Performance of Veterinarian Services PVS Pig Veterinary Society R&D Research and development RCC Regional Collaborating Center RED Reaching Every District RRL Roodeplaat Research Laboratory RVF Rift Valley Fever SA-RCC Southern Africa Regional Collaborating Center SAAHA South African Animal Health Association SAASP South African Antibiotic Stewardship Program SACIDS Southern African Centre for Infectious Disease Surveillance SACOMD South African Committee of Medical Deans SADC Southern African Development Community SAFELTP South African Field Epidemiology and Laboratory Training Program SAGE WHO Strategic Advisory Group of Experts on Immunization SAICM Strategic Approach to International Chemicals Management SAIPS Systems for Improved Access to Pharmaceuticals and Services SAMRC South African Medical Research Council SAMS South African Military Medical Service SANAS South African National Accreditation System SARS Severe acute respiratory syndrome Sasol South African Steamcoal and Oil company SDGs Sustainable Development Goals SOEs State-Owned Enterprises STG Standard treatment guidelines TB tuberculosis TFCA Transfrontier Conservation Areas TRC Truth and Reconciliation Commission UHC Universal Health Coverage UN United Nations UNICEF United Nations Children’s Fund UNSCR United Nations Security Council Resolution WEF World Economic Forum viii Vital Signs WHO World Health Organization WHO AFRO World Health Organisation Regional Office for Africa WHO framework WHO biorisk spectrum WMD Weapons of mass destruction XDR-TB Extensively drug-resistant tuberculosis ZNPHI Zambia National Public Health Institute Abbreviations and acronyms ix List of authors Hannah Bender is a medical student at Harvard University. She holds a BA in Biology from Columbia University and was research assistant in the Department of Pediatrics on projects to enhance pandemic preparedness and map pediatric