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

Abstract 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

Adapting an integrated acute respiratory infections sentinel surveillance to the COVD-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

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

BackgroundMultiple 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.MethodsThe 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.ResultsFrom 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 ConclusionsOur 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

Increased Number of Human Cases of Influenza Virus A(H5N1) Infection, Egypt, 2014–15

During November 2014–April 2015, a total of 165 case-patients with influenza virus A(H5N1) infection, including 6 clusters and 51 deaths, were identified in Egypt. Among infected persons, 99% reported poultry exposure: 19% to ill poultry and 35% to dead poultry. Only 1 person reported wearing personal protective equipment while working with poultry

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

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