SARS-CoV-2 genome variations and evolution patterns in Egypt: a multi-center study.

A serious global public health emergency emerged late November 2019 in Wuhan City, China, by a new highly pathogenic virus, SARS-CoV-2. The virus evolution spread has been tracked by three developing databases: GISAID, Nextstrain and PANGO to understand its circulating variants. In this study, 110 diagnosed positive COVID-19 patient's samples, were collected from Kasr Al-Aini Hospital and the Children Cancer Hospital Egypt 57357 between May 2020 and January 2021, with clinical severity ranging from mild to severe. The viral genomes were sequenced by next generation sequencing, and phylogenetic analysis was performed to understand viral transmission dynamics. According to Nextstrain clades, most of our sequenced samples belonged to clades 20A and 20D, which in addition to clade 20B were present from the beginning of sample collection in May 2020. Clades 19A and 19B, on the other hand, appeared in the mid and late 2020 respectively, followed by the disappearance of clade 20B at the end of 2020. We identified a relatively high prevalence of the D614G spike protein variant and novel patterns of mutations associated together and with different clades. We also identified four mutations, spike H49Y, ORF3a H78Y, ORF8 E64stop and nucleocapsid E378V, associated with higher disease severity. Altogether, our study contributes genetic, phylogenetic, and clinical correlation data about the spread of the SARS-CoV-2 pandemic in Egypt.

The Role of Infection Control Measures in Ophthalmology: Do They Prevent COVID-19 Infection Among Ophthalmologists in Egypt? A Survey-Based Study.

INTRODUCTION: Ophthalmologists are at a high risk of coronavirus disease 2019 (COVID-19) infection owing to their working environments and proximity to patients during examinations. Compliance with infection control measures in examination offices can lessen the risk of infection to this group. In Egypt, several deaths from COVID-19 have been reported among ophthalmologists; therefore, we studied the prevalence of COVID-19 infections in this group and assessed ophthalmologists' commitments to recommended infection control measures. AIM: To evaluate the rate of COVID-19 infections among ophthalmologists, identify risk factors for infections, and evaluate ophthalmologists' commitments to infection control measures in their medical facilities. METHODS: An online questionnaire was designed and distributed to ophthalmologists in the Cairo Governorate from May 1, 2021 to mid-June 2021. RESULTS: Out of 161 responders, the percentage of COVID-19 infections was 52.8% (85 responders). This was significantly higher among younger ophthalmologists (P-value = 0.019) and those with fewer years of experience (P-value = 0.010). Adopting full precautions while examining patients with or without respiratory illness were significantly associated with a lower infection rate (P-value = 0.019 and 0.046, respectively). A significantly higher infection rate was reported for ophthalmologists who examined known COVID-19 patients at outpatient clinics, even when taking precautions (P-value = 0.032). A lower rate of COVID-19 infection was significantly associated with adopting full precautions while operating on suspected or nonsuspected COVID-19 patients (P-value = 0.007 and 0.003, respectively). CONCLUSION: Both young age and limited experience were significant infection risk factors in our study. The most important infection control measures that significantly decreased infection risks were adherence to full protective measures while working in outpatient clinics and operating rooms.