SARS-CoV-2 Genetic Diversity and Lineage Dynamics in Egypt during the First 18 Months of the Pandemic

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...

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Published inViruses Vol. 14; no. 9; p. 1878
Main Authors Roshdy, Wael H., Khalifa, Mohamed K., San, James Emmanuel, Tegally, Houriiyah, Wilkinson, Eduan, Showky, Shymaa, Martin, Darren Patrick, Moir, Monika, Naguib, Amel, Elguindy, Nancy, Gomaa, Mokhtar R., Fahim, Manal, Abu Elsood, Hanaa, Mohsen, Amira, Galal, Ramy, Hassany, Mohamed, Lessells, Richard J., Al-Karmalawy, Ahmed A., EL-Shesheny, Rabeh, Kandeil, Ahmed M., Ali, Mohamed A., de Oliveira, Tulio
Format Journal Article
LanguageEnglish
Published Switzerland MDPI AG 25.08.2022
MDPI
Subjects
COVID-19
COVID-19 - epidemiology
COVID-19 infection
Egypt
Egypt - epidemiology
Epidemics
Epidemiology
Genetic aspects
Genetic diversity
genetic variation
genome
genomic epidemiology
Genomics
Humans
immunity
Laboratories
monitoring
Mutation
pandemic
Pandemics
Phylogeny
Public health
SARS-CoV-2
SARS-CoV-2 - genetics
Severe acute respiratory syndrome coronavirus 2
Virus research
Egypt
United States > US
Spain
genomic epidemiology
SARS-CoV-2
Egypt
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Summary: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.
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These authors contributed equally to this work.
ISSN:1999-4915
1999-4915
DOI:10.3390/v14091878