SARS-CoV-2 genetic diversity and lineage dynamics of in Egypt

SARS-CoV-2 genetic diversity and lineage dynamics of in Egypt. 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. medRxiv, Cold Spring Harbor Laboratory Press, jan, 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 national genomic surveillance, 1,027 SARS-CoV-2 near whole-genomes had been generated and published by the end of May 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 analysed together with a representative set of global sequences within a phylogenetic framework. We show that a single lineage, C.36, introduced early in the pandemic was responsible for most cases in Egypt. Furthermore, we show that to remain dominant in the face of mounting immunity from previous infection and vaccination, this lineage evolved into various sub-lineages acquiring several mutations known to confer adaptive advantage and pathogenic properties. These results highlight the value of continuous genomic surveillance in regions where VOCs are not predominant and enforcement of public health measures to prevent expansion of existing lineages. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The research reported in this publication/article was supported by an internal grant from the National Research Centre, Ministry of Higher Education and Scientific Research, and Ministry of Health and Population in Egypt. The team from CERI/KRISP was supported by funding from the South African Department of Science and Innovation (DSI) and the South African Medical Research Council (SAMRC) under the BRICS JAF #2020/049. The content and findings reported/illustrated herein are the sole deduction, view and responsibility of the researcher/s and do not reflect the official position and sentiments of the funders. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethical approval was obtained from the Ethics Committee of the National Research Centre, Giza, Egypt protocol number 14155, on 22 March 2020. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced are available online on GISAID \textlesshttp://www.gisaid.org\textgreater

@article{Roshdy2022,
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 national genomic surveillance, 1,027 SARS-CoV-2 near whole-genomes had been generated and published by the end of May 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 analysed together with a representative set of global sequences within a phylogenetic framework. We show that a single lineage, C.36, introduced early in the pandemic was responsible for most cases in Egypt. Furthermore, we show that to remain dominant in the face of mounting immunity from previous infection and vaccination, this lineage evolved into various sub-lineages acquiring several mutations known to confer adaptive advantage and pathogenic properties. These results highlight the value of continuous genomic surveillance in regions where VOCs are not predominant and enforcement of public health measures to prevent expansion of existing lineages. {\#}{\#}{\#} Competing Interest Statement The authors have declared no competing interest. {\#}{\#}{\#} Funding Statement The research reported in this publication/article was supported by an internal grant from the National Research Centre, Ministry of Higher Education and Scientific Research, and Ministry of Health and Population in Egypt. The team from CERI/KRISP was supported by funding from the South African Department of Science and Innovation (DSI) and the South African Medical Research Council (SAMRC) under the BRICS JAF {\#}2020/049. The content and findings reported/illustrated herein are the sole deduction, view and responsibility of the researcher/s and do not reflect the official position and sentiments of the funders. {\#}{\#}{\#} Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethical approval was obtained from the Ethics Committee of the National Research Centre, Giza, Egypt protocol number 14155, on 22 March 2020. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All data produced are available online on GISAID {\textless}http://www.gisaid.org{\textgreater}},
author = {Roshdy, Wael H and Khalifa, Mohamed K and San, James Emmanuel and Tegally, Houriiyah and Wilkinson, Eduan and Showky, Shymaa and Martin, Daren 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 = {10.1101/2022.01.05.22268646},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Roshdy et al. - 2022 - SARS-CoV-2 genetic diversity and lineage dynamics of in Egypt.pdf:pdf},
journal = {medRxiv},
keywords = {OA,fund{\_}not{\_}ack,original},
mendeley-tags = {OA,fund{\_}not{\_}ack,original},
month = {jan},
pages = {2022.01.05.22268646},
publisher = {Cold Spring Harbor Laboratory Press},
title = {{SARS-CoV-2 genetic diversity and lineage dynamics of in Egypt}},
url = {https://www.medrxiv.org/content/10.1101/2022.01.05.22268646v1 https://www.medrxiv.org/content/10.1101/2022.01.05.22268646v1.abstract},
year = {2022}
}

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Here we describe the genomic epidemiology of SARS-CoV-2 in Egypt over this period using a subset of 976 high-quality Egyptian genomes analysed together with a representative set of global sequences within a phylogenetic framework. We show that a single lineage, C.36, introduced early in the pandemic was responsible for most cases in Egypt. Furthermore, we show that to remain dominant in the face of mounting immunity from previous infection and vaccination, this lineage evolved into various sub-lineages acquiring several mutations known to confer adaptive advantage and pathogenic properties. These results highlight the value of continuous genomic surveillance in regions where VOCs are not predominant and enforcement of public health measures to prevent expansion of existing lineages. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement The research reported in this publication/article was supported by an internal grant from the National Research Centre, Ministry of Higher Education and Scientific Research, and Ministry of Health and Population in Egypt. The team from CERI/KRISP was supported by funding from the South African Department of Science and Innovation (DSI) and the South African Medical Research Council (SAMRC) under the BRICS JAF #2020/049. 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Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. 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