COVID-19 vaccination coverage in Egypt: a large-scale national survey - to help achieving vaccination target, March-May, 2022.

BACKGROUND: Only 57 countries have vaccinated 70% of their population against COVID-19, most of them in high-income countries, whereas almost one billion people in low-income countries remained unvaccinated. In March-May 2022, Egypt's Ministry of Health and Population (MoHP) conducted a nationwide community-based survey to determine COVID-19 vaccine coverage and people's perceptions of vaccination in order to improve COVID-19 vaccination uptake and confidence among Egyptians, as well as to prioritize interventions. METHODS: A cross-sectional population-based household survey among Egyptians ≥ 18 years of age was implemented in two phases using a multistage random sampling technique in all of Egypt's 27 governorates. A sample of 18,000 subjects divided into 450 clusters of 20 households each was calculated in proportion to each governorate and the main occupation of the population. Participants were interviewed using a semistructured questionnaire that included demographics, vaccination information from the vaccination card, history of COVID-19 infection, reasons for vaccine refusal among the unvaccinated, and vaccination experience among vaccinated subjects. Vaccination coverage rates were calculated by dividing numbers by the total number of participants. Bivariate and multivariate analyses were performed by comparing the vaccinated and unvaccinated to identify the risk factors for low vaccine uptake. RESULTS: Overall 18,107 were interviewed, their mean age was 42 ± 16 years and 58.8% were females. Of them, 8,742 (48.3%) had COVID-19 vaccine and 8,020 (44.3%) were fully vaccinated. Factors associated with low vaccination uptake by multivariate analysis included: age groups (18-29 and 30-39) (ORs 2.0 (95% C.I. 1.8-2.2) and 1.3 (95% C.I.1.2-1.4), respectively), residences in urban or frontier governorates (ORs 1.6 (95% C.I. 1.5-1.8) and 1.2 (95% C.I. 1.1-1.4), respectively), housewives and self-employed people (ORs 1.3 (95% C.I. 1.2-1.4) and 1.2 (95% C.I. 1.1-1.4), respectively), married people (ORs 1.3 (95% C.I. 1.2-1.4), and primary and secondary educated (ORs 1.1 (95% C.I. 1.01-1.2) and 1.1(1.04-1.2) respectively). Vaccine hesitancy was due to fear of adverse events (17.5%), mistrust of vaccine (10.2%), concern over safety during pregnancy and lactation (6.9%), and chronic diseases (5.0%). CONCLUSIONS: Survey identified lower vaccination coverage in Egypt compared to the WHO 70% target. Communication programs targeting the groups with low vaccine uptake are needed to eliminate barriers related to vaccination convenience, side effects, and safety to effectively promote vaccine uptake. Findings from the survey could contribute significantly to vaccination promotion by guiding decision-making efforts on the risky groups and preventing vaccine hesitancy.

Adapting an integrated acute respiratory infections sentinel surveillance to the COVID-19 pandemic requirements, Egypt, 2020-2022.

Objectives: In Egypt, an integrated surveillance for acute respiratory infections (ARIs) was established in 2016 to identify the causes of ARIs. The surveillance system includes 19 governmental hospitals. In response to the coronavirus disease 2019 (COVID-19) pandemic, the World Health Organisation (WHO) requested surveillance adaptation to address the emerging challenges. This study aims to describe the experience in Egypt of adapting ARI surveillance to the COVID-19 pandemic. Methods: WHO case definitions were used to identify patients with ARIs. Nasopharyngeal/oropharyngeal swabs were collected for SARS-CoV-2 and influenza testing. Demographic and clinical information were obtained by interviewing patients at the hospitals. During the COVID-19 pandemic, the first two outpatients daily and every fifth admitted patient were enrolled in the study. To determine the status of ARIs in Egypt during the pandemic, patient demographic, clinical and laboratory data from 2020 to 2022 were obtained and descriptive analyses were performed. Results: Overall, 18,160 patients were enrolled in the study, including 7923 (43.6%) seen at outpatient clinics and 10,237 (56.4%) inpatients. Of the study participants, 6453 (35.5%) tested positive for ARIs, including 5620 (87.1%) for SARS-CoV-2, 781 (12.1%) for influenza and 52 (0.8%) for SARS-CoV-2/influenza coinfection. SARS-CoV-2 was the cause for 95.3% of admitted patients and 65.4% of outpatients. Influenza subtypes included A/H3 (55.7%), Influenza-B (29.1%) and H1/pdm09 (14.2%). Compared with influenza, SARS-CoV-2 tended to infect the elderly, in warm weather and in urban governorates, and resulted in more hospitalisations, longer hospital stays and higher case fatalities (16.3% vs 6.6%, p < 0.001). Conclusions: ARI surveillance in Egypt was successfully adapted to the COVID-19 pandemic and effectively described the clinical characteristics and severity of circulating viruses. Surveillance reported the re-emergence of influenza with a severe course and high fatality. Surveillance is essential for monitoring the activity of respiratory viruses with the aim of guiding clinical management, including preventative and control measures.

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.

Insight into Genetic Characteristics of Identified SARS-CoV-2 Variants in Egypt from March 2020 to May 2021.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first detected in Egypt in February 2020. Data about the prevalence rates of the SARS-CoV-2 lineages are relatively scarce. To understand the genetic characteristics of SARS-CoV-2 in Egypt during several waves of the pandemic, we analyzed sequences of 1256 Egyptian SARS-CoV-2 full genomes from March 2020 to May 2021. From one wave to the next, dominant strains have been observed to be replaced by other dominant strains. We detected an emerging lineage of SARS-CoV-2 in Egypt that shares mutations with the variant of concern (VOC). The neutralizing capacity of sera collected from cases infected with C.36.3 against dominant strains detected in Egypt showed a higher cross reactivity of sera with C.36.3 compared to other strains. Using in silico tools, mutations in the spike of SARS-CoV-2 induced a difference in binding affinity to the viral receptor. The C.36 lineage is the most dominant SARS-CoV-2 lineage in Egypt, and the heterotrophic antigenicity of SARS-CoV-2 variants is asymmetric. These results highlight the value of genetic and antigenic analyses of circulating strains in regions where published sequences are limited.

Epidemiology and outcome of influenza-associated infections among hospitalized patients with acute respiratory infections, Egypt national surveillance system, 2016-2019.

INTRODUCTION: Egypt has established different types of surveillance systems to monitor influenza activities, early detect outbreaks, and tailor efficient prevention and control strategies. This is the first study to describe epidemiology and outcome of influenza-associated infections among hospitalized patients using the National Electronic Disease Surveillance System (NEDSS) data, 2016-2019. METHODS: Data reported from 284 hospitals all over Egypt were extracted from the NEDSS. Data of hospitalized patients with Acute Respiratory Infections (ARI), 2016-2019, were included in the analysis. Laboratory testing for influenza by RT-PCR according to US CDC testing protocol was used to confirm influenza type and subtype. RESULTS: Overall 46 417 patients hospitalized with ARI were identified, their mean age was 30.9 ± 26 and 52.9% were males. Among 41 512 (89.4%) laboratory-tested patients, 7167 (17.3%) were positive for one or more types of influenza viruses. Influenza viruses circulated in all ages and throughout the year, with higher rates in winter, late childhood, and middle ages. Mortality from influenza was significantly higher than other causes of ARIs (5.0% vs 3.8%, P < .001), and it was associated with older ages, December-May, delay in hospital admission, residence in urban and frontier governorates and infection with A/H1N1 virus. The distribution of influenza subtype by time shows alternate pattern between A/H1N1 and H3N2, each subtype peaks every other year with a high peak of A/H1N1 in 2016. CONCLUSIONS: The national Egyptian surveillance succeeded to describe the epidemiology of hospitalized patients with ARIs and influenza in Egypt over time. Surveillance with strain-specific laboratory testing and annual assessment of associated severity might be useful to guide influenza prevention and control strategies including vaccination and case management.

Comparison of common acute respiratory infection case definitions for identification of hospitalized influenza cases at a population-based surveillance site in Egypt.

BACKGROUND: Multiple case definitions are used to identify hospitalized patients with community-acquired acute respiratory infections (ARI). We evaluated several commonly used hospitalized ARI case definitions to identify influenza cases. METHODS: The study included all patients from a population-based surveillance site in Damanhour, Egypt hospitalized for a broad set of criteria consistent with community acquired ARIs. Naso- and oropharyngeal (NP/OP) swabs were tested for influenza using RT-PCR. Sensitivity, specificity and PPV for influenza identification was compared between the 2014 WHO Severe Acute Respiratory Infection (SARI) definition (fever ≥38°C and cough with onset within 10 days), the 2011 WHO SARI definition (fever ≥38°C and cough with onset within 7 days), the 2006 PAHO SARI definition, the International Emerging Infections Program (IEIP) pneumonia case definition, and the International Management of Childhood Illness (IMCI) case definitions for moderate and severe pneumonia. RESULTS: From June 2009-December 2012, 5768 NP/OP swabs were obtained from 6113 hospitalized ARI patients; 799 (13.9%) were influenza positive. The 2014 WHO SARI case definition captured the greatest number of ARI patients, influenza positive patients and ARI deaths compared to the other case definitions examined. Sensitivity for influenza detection was highest for the 2014 WHO SARI definition with 88.6%, compared to the 2011 WHO SARI (78.2%) the 2006 PAHO SARI (15.8%) the IEIP pneumonia (61.0%) and the IMCI moderate and severe pneumonia (33.8% and 38.9%) case definitions (IMCI applies to <5 only). CONCLUSIONS: Our results support use of the 2014 WHO SARI definition for identifying influenza positive hospitalized SARI cases as it captures the highest proportion of ARI deaths and influenza positive cases. Routine use of this case definition for hospital-based surveillance will provide a solid, globally comparable foundation on which to build needed response efforts for novel pandemic viruses.

Evaluating tools to define influenza baseline and threshold values using surveillance data, Egypt, season 2016/17.

BACKGROUND: Establishing influenza thresholds and transmission intensity can help evaluate seasonal changes in influenza severity and potential pandemics. We aimed to evaluate the moving epidemic method (MEM) for calculating influenza thresholds for season 2016/17 in Egypt using four parameters, to identify the most useful parameter. Also to measure the agreement between both the country-specific statistical empirical method and World Health Organization method to MEM for determining the length and intensity level of activity of the influenza season. METHODS: Routinely epidemiological and laboratory data from sentinel surveillance sites for Severe Acute Respiratory Infection (SARI) and influenza-like illness (ILI) were used for calculating thresholds for seasons between 2010/11 and 2015/16 to test 2016/17 season. The parameters calculated were: screened ILI consultation rate × 1000, screened ILI composite parameter, influenza positivity percentage among sampled SARI cases, and influenza positivity percentage among sampled ILI and SARI cases. These parameters assess seasonality and intensity of influenza activity using the three proposed methods (mentioned above). Agreement between the three methods was done using several approaches. RESULTS: The intensity of influenza activity by MEM was lower than the other two methods. Agreement between MEM and each of the other two techniques varied appreciably from good to very good for seasonal duration, and poor to fair for intensity level. In addition, parameters including laboratory data showed a pattern of bi-wave activity; the first wave occurred in winter mostly between epidemiological weeks 39 and 52 and the second occurred in spring mostly between weeks 12 and 17. CONCLUSION: Parameters including laboratory data were more useful in defining seasonality of influenza. Further exploration of the MEM model in future seasons may help to provide a more comprehensive understanding of its use and application.

Evidence of sustained reductions in the relative risk of acute hepatitis B and C virus infections, and the increasing burden of hepatitis a virus infection in Egypt: comparison of sentinel acute viral hepatitis surveillance results, 2001-17.

BACKGROUND: Egypt ranks fifth for the burden of viral hepatitis worldwide. As part of Egypt's renewed national strategy for the elimination of viral hepatitis, surveillance for acute viral hepatitis (AVH) was re-established during 2014-2017 to describe the current epidemiology and associated risk factors, and changes from surveillance conducted during 2001-2004. METHODS: Patients with suspected AVH were enrolled, completed a questionnaire, and provided blood for testing for hepatitis viruses A (HAV), B (HBV), C (HCV), D, and E (HEV) infections by enzyme-linked immunosorbent assay. Odds ratios and Chi2 were used to detect differences between hepatitis types by patient characteristics and exposures. Newcombe-Wilson method was used to compare results between surveillance periods 2001-2004 and 2014-2017. RESULTS: Between 2014 and 2017, among 9321 patients enrolled, 8362 (89.7%) had one or more markers of AVH including 7806 (93.4%) HAV, 252 (3.0%) HCV, 238 (2.8%) HBV, and 31 (0.4%) HEV infection. HAV infection occurred most commonly among children < 16 years age, while HBV infection occurred among ages 16-35 years and HCV infection in ages greater than 45 years. Healthcare-associated exposures were significantly associated with HBV and HCV infections compared to HAV infection including receiving therapeutic injections, surgery, wound suture, or urinary catheter and IV line insertions, while significant lifestyle exposures included exposure to blood outside the healthcare system, IV drug use, or incarceration. Exposures significantly associated with HAV infection were attending nursery or pre-school, contact with person attending nursery or pre-school, having meals outside the home, or contact with HAV case. Compared with AVH surveillance during 2001-2004, there was a significant increase in the proportion of HAV infections from 40.2 to 89.7% (RR = 2.3) with corresponding reductions in the proportions of HBV and HCV infections from 30.0 to 2.8% (RR = 0.1) and 29.8 to 3.0% (RR = 0.1), respectively. CONCLUSIONS: Healthcare-associated exposures were significantly association with and remain the greatest risk for HBV and HCV infections in Egypt. Additional studies to evaluate factors associated with the reductions in HBV and HCV infections, and cost effectiveness of routine HAV immunization might help Egypt guide and evaluate control measures.