Comparison of SARS-Cov-2 omicron variant with the previously identified SARS-Cov-2 variants in Egypt, 2020-2022: insight into SARS-Cov-2 genome evolution and its impact on epidemiology, clinical picture, disease severity, and mortality.

BACKGROUND: The o severe acute respiratory coronavirus 2 (SARS-CoV-2) pandemic has killed millions of people and caused widespread concern around the world. Multiple genetic variants of SARS-CoV-2 have been identified as the pandemic continues. Concerns have been raised about high transmissibility and lower vaccine efficacy against omicron. There is an urgent need to better describe how omicron will impact clinical presentation and vaccine efficacy. This study aims at comparing the epidemiologic, clinical, and genomic characteristics of the omicron variant prevalent during the fifth wave with those of other VOCs between May 2020 and April 2022. METHODS: Epidemiological data were obtained from the National Electronic Diseases Surveillance System. Secondary data analysis was performed on all confirmed COVID-19 patients. Descriptive data analysis was performed for demographics and patient outcome and the incidence of COVID-19 was calculated as the proportion of SARS-CoV-2 confirmed patients out of the total population of Egypt. Incidence and characteristics of the omicron cohort from January- April 2022, were compared to those confirmed from May 2020-December 2021. We performed the whole-genome sequencing of SARS-CoV-2 on 1590 specimens using Illumina sequencing to describe the circulation of the virus lineages in Egypt. RESULTS: A total of 502,629 patients enrolled, including 60,665 (12.1%) reported in the fifth wave. The incidence rate of omicron was significantly lower than the mean of incidences in the previous subperiod (60.1 vs. 86.3/100,000 population, p < 0.001). Symptoms were reported less often in the omicron cohort than in patients with other variants, with omicron having a lower hospitalization rate and overall case fatality rate as well. The omicron cohort tended to stay fewer days at the hospital than did those with other variants. We analyzed sequences of 2433 (1590 in this study and 843 were obtained from GISAID platform) Egyptian SARS-CoV-2 full genomes. The first wave that occurred before the emergence of global variants of concern belonged to the B.1 clade. The second and third waves were associated with C.36. Waves 4 and 5 included B.1.617.2 and BA.1 clades, respectively. CONCLUSIONS: The study indicated that Omicron-infected patients had milder symptoms and were less likely to be hospitalized; however, patients hospitalized with omicron had a more severe course and higher fatality rates than those hospitalized with other variants. Our findings demonstrate the importance of combining epidemiological data and genomic analysis to generate actionable information for public health decision-making.

Epidemiological characterization of viral etiological agents of the central nervous system infections among hospitalized patients in Egypt between 2016 and 2019.

Viral infections of the central nervous system (CNS) are common worldwide and result in considerable morbidity and mortality associated with neurologic illness. Until now, there have been no epidemiologic data regarding viruses causing aseptic meningitis, encephalitis, and CNS infections in Egypt. We investigated 1735 archived cerebrospinal fluid samples collected from Egyptian patients between 2016 and 2019 and performed molecular characterization for infection for12 different viruses: herpes simplex viruses 1 and 2 (HSV-1 and HSV-2), varicella-zoster virus (VZV), Epstein-Barr virus (EBV), cytomegalovirus (CMV), human herpesviruses 6 and 7 (HHV-6 and HHV-7), human enteroviruses (HEVs), human parechovirus (HPeV), parvovirus B19 (B19V), adenovirus (AdV), and mumps virus (MuV). All included samples were negative for bacterial infection. Our results indicated a relatively high prevalence of viral infection, with HEVs being the most prevalent viruses, followed by HSV-1, EBV, and then HSV-2. The highest prevalence was among male patients, peaking during the summer. Data obtained from this study will contribute to improving the clinical management of viral infections of the CNS in Egypt.

Whole-Genome Sequence of a Human Monkeypox Virus Strain Detected in Egypt.

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.

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

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.

Patient Attitudes and Beliefs and Provider Practices Regarding Antibiotic Use for Acute Respiratory Tract Infections in Minya, Egypt.

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.

Incidence and pathogen distribution of healthcare-associated infections in pilot hospitals in Egypt.

OBJECTIVE: To report type and rates of healthcare-associated infections (HAIs) as well as pathogen distribution and antimicrobial resistance patterns from a pilot HAI surveillance system in Egypt. METHODS: Prospective surveillance was conducted from April 2011 through March 2012 in 46 intensive care units (ICUs) in Egypt. Definitions were adapted from the Centers for Disease Control and Prevention's National Healthcare Safety Network. Trained healthcare workers identified HAIs and recorded data on clinical symptoms and up to 4 pathogens. A convenience sample of clinical isolates was tested for antimicrobial resistance at a central reference laboratory. Multidrug resistance was defined by international consensus criteria. RESULTS: ICUs from 11 hospitals collected 90,515 patient-days of surveillance data. Of 472 HAIs identified, 47% were pneumonia, 22% were bloodstream infections, and 15% were urinary tract infections; case fatality among HAI case patients was 43%. The highest rate of device-associated infections was reported for ventilator-associated pneumonia (pooled mean rate, 7.47 cases per 1,000 ventilator-days). The most common pathogens reported were Acinetobacter species (21.8%) and Klebsiella species (18.4%). All Acinetobacter isolates tested (31/31) were multidrug resistant, and 71% (17/24) of Klebsiella pneumoniae isolates were extended-spectrum ß-lactamase producers. CONCLUSIONS: Infection control priorities in Egypt should include preventing pneumonia and preventing infections due to antimicrobial-resistant pathogens.