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

The SSA-SARS-CoV-2 online companion tool is now live

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 Integrative Biology, University of Wisconsin-Madison, WI, USA
14. Mahaliana Labs SARL, Antananarivo, Madagascar
15. School of Geography and Environmental Science, University of Southampton, Southampton, UK
16. Princeton School of Public and International Affairs, Princeton University, NJ, USA}

For a related project focusing on Madagascar, see the dashboard led by Fidisoa Rasambainarivo

Link to Madagascar dashboard

(twitter: @fidydvm)

Questions and suggestions welcome!

Please contact Benny Rice (b.rice@princeton.edu) (twitter: @bennyvary) or any of the co-authors