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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. [ABSTRACT FROM AUTHOR]

Monkeypox virus has recently been detected in multiple countries. Two cases of monkeypox virus were reported in Egypt as part of an ongoing international outbreak. We report the whole-genome sequence of a monkeypox virus that was retrieved from the first confirmed case in Egypt. The virus was fully sequenced on the Illumina platform, and phylogenetic analysis demonstrated that the current monkeypox strain is closely related to clade IIb, which caused recent multicountry outbreaks., Competing Interests: The authors declare no conflict of interest.

The inappropriate use of antibiotics in the community is one of the major causes of antimicrobial resistance. This study aimed to explore the physician prescribing pattern of antibiotics for acute respiratory infections (ARIs) and to explore the knowledge, attitudes, and practices of patients regarding antibiotic use for ARIs. The study was conducted in Upper Egypt and used quantitative and qualitative research techniques. Eligible patients exiting outpatient clinics with ARIs were invited to participate in the study. A qualitative study was conducted through 20 focus group discussions. Out of 350 encounters for patients with various ARIs, 292 (83%) had been prescribed at least one antibiotic. Factors significantly associated with antibiotic prescribing for adults included patient preference that an antibiotic be prescribed. For children younger than 18, presentation with fever, cough, loss of appetite, and sore throat, along with the caregiver's antibiotic preference, were associated with an antibiotic prescription. Several misconceptions regarding antibiotic use among community members were stated, such as the strong belief of the curing and prophylactic power of antibiotics for the common cold. Interventions to promote proper antibiotic use for ARIs need to be piloted, targeting both physicians and the public. Educational programs for physicians and campaigns to raise public awareness regarding proper antibiotic use for ARIs need to be developed.