SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic
Wael H. Roshdy,
Mohamed K. Khalifa,
James Emmanuel San,
Houriiyah Tegally,
Eduan Wilkinson,
Shymaa Showky,
Darren Patrick Martin,
Monika Moir,
Amel Naguib,
Nancy Elguindy,
Mokhtar R. Gomaa,
Manal Fahim,
Hanaa Abu Elsood,
Amira Mohsen,
Ramy Galal,
Mohamed Hassany,
Richard J. Lessells,
Ahmed A. Al-Karmalawy,
Rabeh EL-Shesheny,
Ahmed M. Kandeil,
Mohamed A. Ali,
Tulio de Oliveira
Affiliations
Wael H. Roshdy
Central Public Health Laboratory, Ministry of Health and Population, Cairo 11613, Egypt
Mohamed K. Khalifa
Omicsense, Cairo 11799, Egypt
James Emmanuel San
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
Houriiyah Tegally
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
Eduan Wilkinson
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
Shymaa Showky
Central Public Health Laboratory, Ministry of Health and Population, Cairo 11613, Egypt
Darren Patrick Martin
Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7700, South Africa
Monika Moir
Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
Amel Naguib
Central Public Health Laboratory, Ministry of Health and Population, Cairo 11613, Egypt
Nancy Elguindy
Central Public Health Laboratory, Ministry of Health and Population, Cairo 11613, Egypt
Mokhtar R. Gomaa
Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza 12622, Egypt
Manal Fahim
Department of Surveillance and Epidemiology, Ministry of Health and Population, Cairo 12622, Egypt
Hanaa Abu Elsood
Department of Surveillance and Epidemiology, Ministry of Health and Population, Cairo 12622, Egypt
Amira Mohsen
World Health Organization, Egypt Country Office, Cairo 12622, Egypt
Ramy Galal
Public Health Initiative, Cairo 11613, Egypt
Mohamed Hassany
National Hepatology and Tropical Medicine Research Institute, Ministry of Health and Population, Cairo 11613, Egypt
Richard J. Lessells
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
Ahmed A. Al-Karmalawy
Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt
Rabeh EL-Shesheny
Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza 12622, Egypt
Ahmed M. Kandeil
Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza 12622, Egypt
Mohamed A. Ali
Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza 12622, Egypt
Tulio de Oliveira
KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
COVID-19 was first diagnosed in Egypt on 14 February 2020. By the end of November 2021, over 333,840 cases and 18,832 deaths had been reported. As part of the national genomic surveillance, 1027 SARS-CoV-2 near whole-genomes were generated and published by the end of July 2021. Here we describe the genomic epidemiology of SARS-CoV-2 in Egypt over this period using a subset of 976 high-quality Egyptian genomes analyzed together with a representative set of global sequences within a phylogenetic framework. A single lineage, C.36, introduced early in the pandemic was responsible for most of the cases in Egypt. Furthermore, to remain dominant in the face of mounting immunity from previous infections and vaccinations, this lineage acquired several mutations known to confer an adaptive advantage. These results highlight the value of continuous genomic surveillance in regions where VOCs are not predominant and the need for enforcement of public health measures to prevent expansion of the existing lineages.
