labmetcalf/SSA-SARS-CoV-2

Repository for Metcalf Lab et al Project on SARS-CoV-2 in sub-Saharan Africa # Variation expected in the pace and burden of SARS-CoV-2 outbreaks across sub-Saharan Africa ## This repository contains data and code associated with a manuscript and Shiny-based online tool ### A pre-print of the manuscript is available on medRxiv **Link to manuscript** ### The SSA-SARS-CoV-2 online companion tool is now live **Link to Shiny Tool** - Shiny led by Marjolein Bruijning, Malavika Rajeev, Ian Miller #### Authors Benjamin L. Rice 1,2 , Akshaya Annapragada 3 , Rachel E. Baker 1,4 , Marjolein Bruijning 1 , Winfred Dotse-Gborgbortsi 5 , Keitly Mensah 6 , Ian F. Miller 1 , Nkengafac Villyen Motaze 7,8 , Antso Raherinandrasana 9,10 , Malavika Rajeev 1 , Julio Rakotonirina 9,10 , Tanjona Ramiadantsoa 11,12,13 , Fidisoa Rasambainarivo 1,14 , Weiyu Yu 15 , Bryan T. Grenfell 1,16 , Andrew J. Tatem 5 , C. Jessica E. Metcalf 1,16 1. Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA 2. Madagascar Health and Environmental Research (MAHERY), Maroantsetra, Madagascar 3. Johns Hopkins University School of Medicine, Baltimore, MD, USA 4. Princeton Environmental Institute, Princeton University, Princeton, NJ, USA. 5. WorldPop, School of Geography and Environmental Science, University of Southampton, Southampton, UK 6. Centre population et Développement CEPED (Université de Paris), Institut Recherche et Développement, Paris, France 7. Centre for Vaccines and Immunology (CVI), National Institute for Communicable Diseases (NICD) a division of the National Health Laboratory Service (NHLS), South Africa 8. Department of Global Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa 9. Faculty of Medicine, University of Antananarivo, Madagascar 10. Institute of Public Health Analakely, Antananarivo, Madagascar 11. Department of Life Science, University of Fianarantsoa, Madagascar 12. Department of Mathematics, University of Fianarantsoa, Madagascar 13. Department of Int …