Dataset Information

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

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.

SUBMITTER: Roshdy WH

PROVIDER: S-EPMC9502207 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature

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Publications

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

Roshdy Wael H WH Khalifa Mohamed K MK San James Emmanuel JE Tegally Houriiyah H Wilkinson Eduan E Showky Shymaa S Martin Darren Patrick DP Moir Monika M Naguib Amel A Elguindy Nancy N Gomaa Mokhtar R MR Fahim Manal M Abu Elsood Hanaa H Mohsen Amira A Galal Ramy R Hassany Mohamed M Lessells Richard J RJ Al-Karmalawy Ahmed A AA El-Shesheny Rabeh R Kandeil Ahmed M AM Ali Mohamed A MA de Oliveira Tulio T

Viruses 20220825 9

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 f ...[more]

PMID: 36146685

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Project description:BackgroundThe uncertainties surrounding the COVID-19 pandemic have been associated with increased parental concern. The aim of this study is to explore if this increased level of concern is associated with certain individual/household characteristics or if parents adapted to the ever-changing realities of the COVID-19 pandemic over time.MethodsThis prospective study explored COVID-19 concern trajectories and associated family characteristics of 765 UK parents caring for an immunosuppressed child during the first 18 months of the pandemic using growth mixture modelling. Qualitative analysis was performed to examine in more detail the source of concern.ResultsFour different trajectories of parental COVID-19 concern were identified. Ongoing very high concern was associated with caring for children with nephrotic or respiratory disease; having a child on an organ transplant waiting list; residency in the North of England; or parental vocational inactivity. Explicit concerns voiced by the parents generally followed national trends, but vulnerable status specific concerns were also reported.ConclusionDiagnosis and prescribed medication of the immunosuppressed child, geographical location, household composition, and employment status of parent were associated with the different concern trajectories. This information can be helpful in targeting psychological family care where it is most needed.ImpactMany British parents caring for a clinically vulnerable child during the first 18 months of the COVID-19 pandemic showed high levels of concern with little sign of psychological adaptation. Consistent with findings from non-vulnerable populations, parents mentioned the impact of shielding and repeated isolation on their child's education, social life, and mental health. Unique to the clinically vulnerable population, parents were worried about child's health status, impact of delayed healthcare, and were confused by the contradictory information received from government, doctors, and media. Psychological family care can be targeted to those parents at greater risk for high levels of concern.

Dataset Information

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

Publications

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

Similar Datasets

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