{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T04:30:00Z","timestamp":1772253000750,"version":"3.50.1"},"reference-count":42,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2022,8,25]],"date-time":"2022-08-25T00:00:00Z","timestamp":1661385600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Research Centre","award":["JAF #2020\/049"],"award-info":[{"award-number":["JAF #2020\/049"]}]},{"name":"Ministry of Higher Education and Scientific Research","award":["JAF #2020\/049"],"award-info":[{"award-number":["JAF #2020\/049"]}]},{"name":"Ministry of Health and Population","award":["JAF #2020\/049"],"award-info":[{"award-number":["JAF #2020\/049"]}]},{"name":"South African Department of Science and Innovation (DSI)","award":["JAF #2020\/049"],"award-info":[{"award-number":["JAF #2020\/049"]}]},{"name":"South African Medical Research Council (SAMRC) under the BRICS","award":["JAF #2020\/049"],"award-info":[{"award-number":["JAF #2020\/049"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>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.<\/jats:p>","DOI":"10.3390\/v14091878","type":"journal-article","created":{"date-parts":[[2022,8,31]],"date-time":"2022-08-31T02:09:36Z","timestamp":1661911776000},"page":"1878","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8412-3128","authenticated-orcid":false,"given":"Wael H.","family":"Roshdy","sequence":"first","affiliation":[{"name":"Central Public Health Laboratory, Ministry of Health and Population, Cairo 11613, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohamed K.","family":"Khalifa","sequence":"additional","affiliation":[{"name":"Omicsense, Cairo 11799, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5736-664X","authenticated-orcid":false,"given":"James Emmanuel","family":"San","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7102-8540","authenticated-orcid":false,"given":"Houriiyah","family":"Tegally","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"},{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2503-9441","authenticated-orcid":false,"given":"Eduan","family":"Wilkinson","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"},{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shymaa","family":"Showky","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratory, Ministry of Health and Population, Cairo 11613, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Darren Patrick","family":"Martin","sequence":"additional","affiliation":[{"name":"Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, Cape Town 7700, South Africa"},{"name":"Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), University of Cape Town, Observatory, Cape Town 7700, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1095-1910","authenticated-orcid":false,"given":"Monika","family":"Moir","sequence":"additional","affiliation":[{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amel","family":"Naguib","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratory, Ministry of Health and Population, Cairo 11613, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5876-237X","authenticated-orcid":false,"given":"Nancy","family":"Elguindy","sequence":"additional","affiliation":[{"name":"Central Public Health Laboratory, Ministry of Health and Population, Cairo 11613, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7947-3609","authenticated-orcid":false,"given":"Mokhtar R.","family":"Gomaa","sequence":"additional","affiliation":[{"name":"Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza 12622, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7206-4818","authenticated-orcid":false,"given":"Manal","family":"Fahim","sequence":"additional","affiliation":[{"name":"Department of Surveillance and Epidemiology, Ministry of Health and Population, Cairo 12622, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hanaa","family":"Abu Elsood","sequence":"additional","affiliation":[{"name":"Department of Surveillance and Epidemiology, Ministry of Health and Population, Cairo 12622, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amira","family":"Mohsen","sequence":"additional","affiliation":[{"name":"World Health Organization, Egypt Country Office, Cairo 12622, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ramy","family":"Galal","sequence":"additional","affiliation":[{"name":"Public Health Initiative, Cairo 11613, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6001-8793","authenticated-orcid":false,"given":"Mohamed","family":"Hassany","sequence":"additional","affiliation":[{"name":"National Hepatology and Tropical Medicine Research Institute, Ministry of Health and Population, Cairo 11613, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Richard J.","family":"Lessells","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8173-6073","authenticated-orcid":false,"given":"Ahmed A.","family":"Al-Karmalawy","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8798-2240","authenticated-orcid":false,"given":"Rabeh","family":"EL-Shesheny","sequence":"additional","affiliation":[{"name":"Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza 12622, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3253-6961","authenticated-orcid":false,"given":"Ahmed M.","family":"Kandeil","sequence":"additional","affiliation":[{"name":"Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza 12622, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5615-3212","authenticated-orcid":false,"given":"Mohamed A.","family":"Ali","sequence":"additional","affiliation":[{"name":"Centre of Scientific Excellence for Influenza Viruses, National Research Centre, Dokki, Giza 12622, Egypt"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tulio","family":"de Oliveira","sequence":"additional","affiliation":[{"name":"KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa"},{"name":"Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa"},{"name":"Department of Global Health, University of Washington, Seattle, WA 98195, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2022,8,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1038\/s41576-021-00408-x","article-title":"The biological and clinical significance of emerging SARS-CoV-2 variants","volume":"22","author":"Tao","year":"2021","journal-title":"Nat. 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