A Spatial SEIR Model for COVID-19 in South Africa

Inger Fabris-Rotelli; Jenny Holloway; Zaid Kimmie; Sally Archibald; Pravesh Debba; Raeesa Manjoo-Docrat; Alize le Roux; Nontembeko Dudeni-Tlhone; Charl Janse van Rensburg; Renate Thiede; Nada Abdelatif; Sibusisiwe Makhanya; Arminn Potgieter

doi:10.52933/jdssv.v2i7.46

A Spatial SEIR Model for COVID-19 in South Africa

Authors

Inger Fabris-Rotelli Department of Statistics, University of Pretoria https://orcid.org/0000-0002-2192-4873
Jenny Holloway Council for Scientific Research South Africa
Zaid Kimmie Foundation for Human Rights, South Africa
Sally Archibald School of Animal, Plant and Environmental Sciences, University of Witwatersrand
Pravesh Debba Council for Scientific Research South Africa https://orcid.org/0000-0003-4870-988X
Raeesa Manjoo-Docrat Department of Statistics and Actuarial Science, University of Witwatersrand https://orcid.org/0000-0003-2039-0440
Alize le Roux Council for Scientific Research, South Africa https://orcid.org/0000-0002-9214-5076
Nontembeko Dudeni-Tlhone Council for Scientific Research, South Africa https://orcid.org/0000-0002-8853-3121
Charl Janse van Rensburg Biostatistics Research Unit, South African Medical Research Council
Renate Thiede Department of Statistics, University of Pretoria https://orcid.org/0000-0003-0934-5374
Nada Abdelatif Biostatistics Research Unit, South African Medical Research Council
Sibusisiwe Makhanya IBM, South Africa
Arminn Potgieter Department of Statistics, University of Pretoria https://orcid.org/0000-0001-6649-9690

DOI:

https://doi.org/10.52933/jdssv.v2i7.46

Keywords:

COVID-19, SEIR model, spatial, excess deaths, South Africa, hospitilisations

Abstract

The virus SARS-CoV-2 has resulted in numerous modelling approaches arising rapidly to understand the spread of the disease COVID-19 and to plan for future interventions. Herein, we present an SEIR model with a spatial spread component as well as four infectious compartments to account for the variety of symptom levels and transmission rate. The model takes into account the pattern of spatial vulnerability in South Africa through a vulnerability index that is based on socioeconomic and health susceptibility characteristics. Another spatially relevant factor in this context is level of mobility throughout. The thesis of this study is that without the contextual spatial spread modelling, the heterogeneity in COVID-19 prevalence in the South African setting would not be captured. The model is illustrated on South African COVID-19 case counts and hospitalisations.

Author Biographies

Inger Fabris-Rotelli, Department of Statistics, University of Pretoria

Inger Fabris-Rotelli is currently an associate professor in the Department of Statistics, University of Pretoria. She holds a PhD Mathematical Sciences, an MSc Applied Mathematics, a double BSc(Hons) in Mathematical Statistics and Applied Mathematics and a BSc Applied Mathematics. Her research interests are in spatial statistics and image processing. She has an National Research Foundation rating.

Jenny Holloway, Council for Scientific Research South Africa

Jenny Holloway is a senior statistician at the Council for Scientific and Industrial Research (CSIR) since 1993. She holds a BSc Mathematics and Statistics, a BSc(Hons) Statistics, and an MSc Mathematical Statistics. Her research includes application of statistical techniques or other quantitative methods to complex problems, particularly in the area of time series modelling and forecasting, as well as the design and implementation of simulation models. She is a chartered member of the Institute of Certified and Chartered Statisticians of South Africa in the field of Econometrics, and a member of the South African Statistical Association.

Zaid Kimmie, Foundation for Human Rights, South Africa

Zaid Kimmie is Programmes Manager at the Foundation for Human Rights, where he oversees a number of human rights interventions. He has previously worked at the CSIR as a statistician and as the Head of Planning, and at the Community Agency for Social Enquiry as a researcher. Zaid has a PhD in Mathematics from the University of Cape Town and a Masters in Public Health from Harvard University.

Sally Archibald, School of Animal, Plant and Environmental Sciences, University of Witwatersrand

Sally Archibald is a professor in the School of Animal Plant and Environmental Sciences at the University of the Witwatersrand, Johannesburg. She studied at University of Cape Town, Princeton University, and graduated with a PhD from Wits University in 2010. Before her academic position she spent 10 years at the CSIR doing applied research. Her work integrates field ecological data, remote sensing, modelling and biogeochemistry to ask questions around the dynamics of savanna ecosystems in the context of global change. She is a member of the Association for Tropical Biology and has received the Mercer Award for the best paper by a young scientist.

Pravesh Debba, Council for Scientific Research South Africa

Pravesh Debba is currently the manager for Inclusive Smart Settlements and Regions within Smart Places at the Council for Scientific and Industrial Research (CSIR). He completed an MSc in Biostatistics at Universiteit Hasselt in Belgium and a PhD in Spatial Statistics in 2006 from the International Institute for Geo-Information Science and Earth Observation (ITC) and Wageningen University in the Netherlands. Professor Debba has been the president of the South African Statistical Association (SASA) and Chairperson of the Institute for Certificated and Chartered Statisticians of South Africa (ICCSSA). He is currently the chair of the Body of Trustees of ICCSSA. He has supervised MSc and PhD students. His research achievements include, about 50 national or international presentations at conferences or workshops, two popular articles, and over 30 peer-reviewed publications published at ISI rated journals or conference proceedings.

Raeesa Manjoo-Docrat, Department of Statistics and Actuarial Science, University of Witwatersrand

Raeesa Manjoo-Docrat is a lecturer in the School of Statistics and Actuarial Sciences at the University of the Witwatersrand. She holds a BSc Mathematics, a post-graduate diploma in Science - Actuarial Science, a double honours in Mathematics and Statistics, and an MSc in Statistics. She is currently working towards her PhD in Statistics. Her current research interests include stochastic processes, spatial statistics and infectious disease modelling. She is a member of the South African Statistical Association and RLadies. She was awarded the Liberty medal, given to the best mathematical statistics honours student.

Alize le Roux, Council for Scientific Research, South Africa

Alize le Roux is a principal researcher at the Council for Scientific and Industrial Research (CSIR). She holds a BSc Geoinformatics, BSc(Hons) Geoinformatics and an MSc in Geographical Sciences. Her research is on planning and decision support, multi-hazard risk analyses, disaster risk reduction, land use change modelling, and intra-settlement growth modelling.

Nontembeko Dudeni-Tlhone, Council for Scientific Research, South Africa

Nontembeko Dudeni-Tlhone is a researcher at the Council for Scientific and Industrial Research (CSIR). She holds a BSc in Statistics ad Chemistry, a BSc(Hons) Statistics and an MSc Statistics. Her research focuses on statistical modelling and data analysis in various sector initiatives and applications involving spatial planning, transport, health, natural environment and energy. Current research interests involve modelling and analysis of high-dimensional sensor data within the remote sensing research domain. She is a member of the South African Statistical Association.

Charl Janse van Rensburg, Biostatistics Research Unit, South African Medical Research Council

Charl Janse van Rensburg is a statistician at the Biostatistics Research Unit, South African Medical Research Council. He holds a BSc Actuarial and Financial Mathematics, a BSc(Hons) Mathematical Statistics and an MSc Mathematical Statistics. He is interested in machine learning in medical research and subgroup analysis in precision medicine. He is a member of the South African Statistical Association.

Renate Thiede, Department of Statistics, University of Pretoria

Renate Thiede is a PhD student and part-time lecturer at the University of Pretoria. She holds a BSc Mathematical Statistics, BSc(Hons) Mathematical Statistics and an MSc Mathematical Statistics. Her research involves remote sensing, image analysis, uncertainty quantification and spatial statistics. She is a member of the South African Statistical Association.

Nada Abdelatif, Biostatistics Research Unit, South African Medical Research Council

Nada Abdelatif is a senior statistician at the Biostatistics Research Unit, South African Medical Research Council. She holds a BCom Statistics, BCom(Hons) Statistics and an MSc Statistics. She is interested in spatial modeling and how it relates to disease distribution, especially in the context of changing climate. She is a member of the International Biometrics Society, the International Society for Clinical Biostatistics and the South African Statistical Association.

Sibusisiwe Makhanya, IBM, South Africa

Sibusisiwe Makhanya is a Research Scientist based at the South African laboratory of IBM Research. Her technical background is in Statistics and she remains keenly interested in spatial data science and in general using statistical learning to contribute to solutions targeting sustainable development challenges. She previously worked for over 10 years as a Researcher at the Council for Scientific and Industrial Research in South Africa. She holds a PhD in Spatial Statistics from the University of Twente in the Netherlands, an MSc in Mathematical Statistics from the Witwatersrand University and undergraduate Bachelor of Science degrees from the University of KwaZulu Natal in South Africa.

Arminn Potgieter, Department of Statistics, University of Pretoria

Arminn Potgieter completed his undergraduate BSc and BSc(Hons) Mathematical Statistics at the University of Pretoria, and is currently busy with his MSc Advanced Data Analytics at the University of Pretoria.

A Spatial SEIR Model for COVID-19 in South Africa

Authors

DOI:

Keywords:

Abstract

Author Biographies

Inger Fabris-Rotelli, Department of Statistics, University of Pretoria

Jenny Holloway, Council for Scientific Research South Africa

Zaid Kimmie, Foundation for Human Rights, South Africa

Sally Archibald, School of Animal, Plant and Environmental Sciences, University of Witwatersrand

Pravesh Debba, Council for Scientific Research South Africa

Raeesa Manjoo-Docrat, Department of Statistics and Actuarial Science, University of Witwatersrand

Alize le Roux, Council for Scientific Research, South Africa

Nontembeko Dudeni-Tlhone, Council for Scientific Research, South Africa

Charl Janse van Rensburg, Biostatistics Research Unit, South African Medical Research Council

Renate Thiede, Department of Statistics, University of Pretoria

Nada Abdelatif, Biostatistics Research Unit, South African Medical Research Council

Sibusisiwe Makhanya, IBM, South Africa

Arminn Potgieter, Department of Statistics, University of Pretoria

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