SARS-CoV-2 genetic diversity and lineage dynamics in Egypt during the first 18 months of the pandemic

SARS-CoV-2 genetic diversity and lineage dynamics in Egypt during the first 18 months of the pandemic. Roshdy, W. H, Khalifa, M. K, San, J. E., Tegally, H., Wilkinson, E., Showky, S., Martin, D. P., Moir, M., Naguib, A., Elguindy, N., Gomaa, M. R, Fahim, M., Elsood, H. A., Mohsen, A., Galal, R., Hassany, M., Lessells, R. J, Al-Karmalawy, A. A, El-Shesheny, R., Kandeil, A. M, Ali, M. A, & De Oliveira, T. Viruses, 14(9):1878, Multidisciplinary Digital Publishing Institute, aug, 2022.

Paper doi abstract bibtex

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.

@article{Roshdy2022a,
abstract = {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.},
author = {Roshdy, Wael H and Khalifa, Mohamed K and San, James Emmanuel and Tegally, Houriiyah and Wilkinson, Eduan and Showky, Shymaa and Martin, Darren Patrick and Moir, Monika and Naguib, Amel and Elguindy, Nancy and Gomaa, Mokhtar R and Fahim, Manal and Elsood, Hanaa Abu and Mohsen, Amira and Galal, Ramy and Hassany, Mohamed and Lessells, Richard J and Al-Karmalawy, Ahmed A and El-Shesheny, Rabeh and Kandeil, Ahmed M and Ali, Mohamed A and {De Oliveira}, Tulio},
doi = {10.3390/V14091878},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Roshdy et al. - 2022 - SARS-CoV-2 genetic diversity and lineage dynamics in Egypt during the first 18 months of the pandemic.pdf:pdf},
issn = {1999-4915},
journal = {Viruses},
keywords = {2,CoV,Egypt,OA,OA{\_}PMC,SARS,fund{\_}not{\_}ack,genomic epidemiology,original},
mendeley-tags = {OA,OA{\_}PMC,fund{\_}not{\_}ack,original},
month = {aug},
number = {9},
pages = {1878},
pmid = {36146685},
publisher = {Multidisciplinary Digital Publishing Institute},
title = {{SARS-CoV-2 genetic diversity and lineage dynamics in Egypt during the first 18 months of the pandemic}},
url = {https://www.mdpi.com/1999-4915/14/9/1878/htm https://www.mdpi.com/1999-4915/14/9/1878},
volume = {14},
year = {2022}
}

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