Incidence of influenza virus-associated Severe Acute Respiratory Infections in three districts in 2018 at Gharbia governorate, Egypt.

AIMS: Influenza remains a contributor to substantial global morbidity and mortality. There is very limited data on disease burden in Egypt. The purpose of this study was to estimate the incidence of influenza-associated Severe Acute Respiratory Illness (SARI) in three districts in Gharbia governorate in 2018. METHODS: This study Followed the World Health Organization (WHO) manual for estimating disease burden associated with seasonal influenza. The hospital admission database was screened for SARI patients in three districts at Gharbia governorate in 2018. A hospital admission survey (HAS) was used to define the catchment population. The incidence rate estimation was computed as the number of influenza-positive SARI cases per 100,000 population. RESULTS: A total of 180 SARI cases were identified in the catchment area. The median age was 23 years [IQR: 2-53], and 45% were males. Out of the total SARI cases, 33.3% influenza was confirmed by the laboratory test of RP-PCR. Influenza A(H3N2) virus predominated representing 55.0% of patients, thanA(H1N1) 26.7% and Flu-B virus 18.3%. Influenza prevailed in winter and spring; no deaths from influenza were reported. The annual incidence of influenza-associated SARIs found higher in <2 years (282 /100,000) and ≥65 years patients (215/100,000) at significant level p<0.001. CONCLUSION: The WHO Manual for estimating disease burden associated with seasonal influenza was successfully operationalized in the three districts of Gharbia governorate. It can be used in other districts. A considerable burden was associated with influenza viruses requiring hospitalization, especially among the older adult group.

Evidence for the elimination of viral hepatitis B and C in Egypt: Results of a nationwide survey in 2022.

INTRODUCTION: Viral hepatitis C (HCV) and B (HBV) were at the top of Egypt's most significant public health challenges, with an estimated 14.7% of its population having antibodies to HCV in 2008. Egypt issued an ambitious action plan in 2014 to eliminate viral hepatitis through strengthening infection control and improving patient care. In 2018, an extensive HCV mass screening campaign was conducted for the entire country's population with treating more than 4 million patients with antivirals. This study aimed to evaluate the current prevalence of viral hepatitis in Egypt after all these efforts. METHODS: A cross-sectional household cluster survey was conducted in all 27 Egyptian governorates to obtain a representative sample of Egypt's population. Subjects aged 1-70 years were interviewed using a standardised questionnaire that included demographics, viral hepatitis knowledge, previous infection and risk factors data. Laboratory testing was performed for all subjects for anti-HCV and HBsAg using chemiluminescence. Subjects positive for anti-HCV were further tested for HCV-RNA by RT-PCR. Prevalence rates were calculated by demographic groups and compared to the demographic health survey 2015 results. RESULTS: Of 20 881 subjects interviewed, 48.8% were males, 20.2% were children <15 years of age, and 53.7% were residents of rural areas. Of all subjects, 92 (0.4%) were HCV-infected, 1577 (7.6%) were anti-HCV positive and 177 (0.8%) were HBV-chronically infected, including one patient who had mixed HBV and HCV current infection. The prevalence of HCV-current and HBV chronic infections decreased by 93% and 20%, respectively, compared to 2015. CONCLUSIONS: Egypt achieved the elimination of the viral hepatitis goal. To maintain low rates of viral hepatitis, community health education, in addition to maintaining infection control and blood safety programs, is essential.

Comparative analysis of COVID-19 and influenza prevalence among Egyptian pilgrims returning from Hajj and Umrah in 2022: epidemiology, clinical characteristics, and genomic sequencing.

PURPOSE: To describe the changes that occurred in the SARS-CoV-2 and influenza Prevalence, epidemiology, clinical picture, and prevalent genotypes among the Egyptian pilgrims returning from Hajj and Umrah 2022 seasons. METHODS: Pilgrims were contacted at the airport and invited to participate in the survey. Pilgrims who consented were interviewed using a standardized line list that included participant demographics, respiratory symptoms if any, previous COVID-19 infection, influenza vaccination whereas COVID-19 vaccination information were collected from vaccination cards. Participants were asked to provide throat and nasopharyngeal swabs for SARS-CoV-2 and influenza testing using RT-PCR and a subset of isolates were sequenced. Descriptive data analysis was performed to describe the epidemiology and clinical symptoms of SARS-CoV-2 and influenza. Prevalence rates of SARS-CoV-2 and influenza during Hajj were calculated and compared to Umrah surveys using chi2 and t-test with a significance level < 0.05. RESULTS: Overall, 3,862 Egyptian pilgrims enrolled, their mean age was 50.5 ± 47 years, half of them were > 50 years of age and 58.2% were males. Of them, 384 (9.9%) tested positive for SARS-CoV-2 and 51 (1.3%) for influenza viruses. Prevalence of SARS-CoV-2 infections (vaccine breakthrough) increased significantly between the Umrah and Hajj surveys (6.7% vs. 9.9%, p < 0.001), and variants of the virus varied considerably. Whereas no significant difference was found in influenza prevalence, vaccine coverage and vaccine breakthrough infection rates (11.7 vs. 9.2%, 26.9 vs. 26.8%, and 1.4 vs. 1.1% respectively). CONCLUSIONS: SARS-CoV-2 prevalence among Egyptian pilgrims returning from Hajj in July increased with reduced vaccine effectiveness compared to Umrah in March 2022 suggesting a possible wave of SARS-CoV-2 in the upcoming winter.

Multicenter study to describe viral etiologies, clinical profiles, and outcomes of hospitalized children with severe acute respiratory infections, Egypt 2022.

In late 2022, severe acute respiratory infections (SARI) surveillance reported an abrupt increase in non-COVID-19 infections among children after three years of drastic reductions. Signals of increased absenteeism due to respiratory symptoms among primary and preparatory school children were detected by Event-Based Surveillance. We conducted a hospital-based survey of children who were admitted with SARI to identify the causative pathogen(s) and estimate the burden of infection. A survey was conducted among children < 16 years in 21 referral hospitals in the three governorates with the highest SARI rates. Patients' demographics, clinical symptoms, and severity were collected from medical records using a line list. Patients were swabbed and tested for a panel of 33 respiratory pathogens by RT-PCR at the Central Laboratory in Cairo. Descriptive data analysis was performed for demographic data. Patients' characteristics were compared by causative agents' clinical picture and severity using Chi2 with a p < 0.05 significance. Overall, 317 patients were enrolled, 58.3% were ≤ 1 year of age, 61.5% were males. Of 229 (72.7%) of positively tested patients, viruses caused 92.1% including RSV 63.8%, Rhinovirus 10.0%, Influenza 9.2%, Adenovirus 5.2%, and 1.3% co-infected with two viruses. Bacteria caused 3.5% of cases and 4.4% had mixed viral-bacterial infections. Rhinovirus was the most common cause of death among children with SARI, followed by RSV (8.7% and 1.4%), whereas influenza and Adenovirus did not result in any deaths. Patients with viral-bacterial infections are more likely to be admitted to ICU and die at the hospital than bacterial or viral infections (60% and 20% vs. 31.8% and 1.9% vs. 12.5% and 12.5%, p < 0.001). Viruses particularly RSV are the leading cause of SARI causing significant health problem among children < 16 years in Egypt. Bacterial on top of viral infection can worsen disease courses and outcomes. Studies are required to estimate the SARI burden accurately among Egyptian children and a comprehensive approach tailored to Egypt is necessary to reduce its burden.

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.

Resurgence of influenza and respiratory syncytial virus in Egypt following two years of decline during the COVID-19 pandemic: outpatient clinic survey of infants and children, October 2022.

INTRODUCTION: Two years after unprecedented low rates of circulation of most common respiratory viruses (SARS-CoV-2), the Egyptian ARI surveillance system detected an increase in acute respiratory infections (ARIs) with a reduced circulation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), especially among school children. A national survey was conducted to estimate the burden and identify the viral causes of ARIs among children < 16 years of age. METHODS: A one-day survey was carried out in 98 governmental outpatient clinics distributed all over Egypt 26 governorates. The four largest referral hospitals in each governorate where most influenza-like illness (ILI) patients seek care were selected. Using the WHO case definition, the first five patients < 16 years of age with ILI symptoms visiting the selected outpatient clinics on the survey day were enrolled. Basic demographic and clinical data of patients were collected using a linelist. Patients were swabbed and tested for SARS-CoV-2, influenza, and Respiratory Syncytial virus (RSV) by RT-PCR at the Central Laboratory in Cairo. RESULTS: Overall, 530 patients enrolled, their mean age was 5.8 ± 4.2, 57.1% were males, and 70.2% reside in rural or semi-rural areas. Of all patients, 134 (25.3%) had influenza, 111 (20.9%) RSV, and 14 (2.8%) coinfections. Influenza-positive children were older compared to RSV, (7.2 ± 4.1, 4.3 ± 4.1, p < 0.001), with more than half of them (53.0%) being school students. Dyspnea was reported in RSV more than in influenza (62.2% vs. 49.3%, p < 0.05). Among RSV patients, children < 2 years had a higher rate of dyspnea than others (86.7% vs. 53.1%, < 0.001). CONCLUSIONS: A resurgence of influenza and RSV was detected in Egypt in the 2022-2023 winter season. Influenza caused a higher rate of infection than RSV, while RSV caused more severe symptoms than influenza. Monitoring a broader range of respiratory pathogens is recommended to estimate the ARI burden and risky groups for severe disease in Egypt.

Clinical features and severe outcome predictors of COVID-19 vaccine breakthrough infection among hospitalized patients: results from Egypt severe acute respiratory infections sentinel surveillance, 2021-2022.

BACKGROUND: COVID-19 vaccines are effective against infections and outcomes; however, breakthrough infections (VBT) are increasingly reported, possibly due to waning of vaccine-induced immunity or emerging variants. Most studies have focused on determining VBT rate based on antibody levels. This study aims at describing clinical features, risks, time trends, and outcomes of COVID-19 VBT among hospitalized patients in Egypt. METHODS: Data of SARS-CoV-2 confirmed patients hospitalized in 16 hospitals was obtained from the severe acute respiratory infections surveillance database, September 2021-April 2022. Data includes patients' demographics, clinical picture, and outcomes. Descriptive analysis was performed and patients with VBT were compared to not fully vaccinated (UPV). Bivariate and multivariate analyses were performed using Epi Info7 with a significance level < 0.05 to identify VBT risk factors. RESULTS: Overall, 1,297 patients enrolled, their mean age 56.7 ± 17.0 years, 41.5% were males, 64.7% received inactivated, 25.% viral vector, and 7.7% mRNA vaccine. VBT was identified in 156(12.0%) patients with an increasing trend over time. VBT significantly was higher in (16-35 years) age, males, in those who received inactivated vaccine compared to corresponding groups of UPV (14.1 vs. 9.0%, p < 0.05 and 57.1 vs. 39.4%, p < 0.001 and 64.7 vs. 45.1, p < 0.01 respectively). Whereas receiving mRNA vaccine was significantly protective against VBT (7.7 vs. 21.6%, p < 001). VBT patients tend to have shorter hospital stays and lower case fatality (mean hospital days = 6.6 ± 5.5 vs. 7.9 ± 5.9, p < 0.01 and CFR = 28.2 vs. 33.1, p < 0.01 respectively). MVA identified younger ages, male gender, and inactivated vaccines as risks for VBT. CONCLUSION: The study indicated that COVID-19 vaccines significantly reduce hospital days and fatality. VBT trend is on the rise and males, young ages, and inactivated vaccine receivers are at higher risk. Caution regarding relaxation of personal preventive measures in areas with higher or increasing incidences of COVID-19, particularly for the at-risk group even if they are vaccinated. The vaccination strategy should be revised to reduce VBT rate and increase vaccine effectiveness.

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.

Epidemiology, Disease Severity and Outcome of Severe Acute Respiratory Syndrome Coronavirus 2 and Influenza Viruses Coinfection Seen at Egypt Integrated Acute Respiratory Infections Surveillance, 2020-2022.

Background: Cocirculation of influenza (Flu) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (SARS-CoV-2/Flu) represent a public health concern as it may worsen the severity and increase fatality from coronavirus disease 2019. An increase in the number of patients with coinfection was recently reported. We studied epidemiology, severity, and outcome of patients with SARS-CoV-2/Flu coinfection seen at Egypt's integrated acute respiratory infections surveillance to better describe disease impact and guide effective preventive measures. Methods: The first two outpatients were seen daily, and every fifth patient admitted to 19 sentinel hospitals with respiratory symptoms was enrolled. Patients were interviewed using a standardized questionnaire and provided nasopharyngeal swabs to be tested for SARS-CoV-2 and influenza by real-time polymerase chain reaction at the central laboratory. Data from all patients with coinfection were obtained, and descriptive data analysis was performed for patients' demographics, clinical course, and outcome. Results: The total number of patients enrolled between January 2020 and April 2022 was 18,160 and 6,453 (35.5%) tested positive for viruses, including 52 (0.8%) coinfection. Of them, 36 (69.2%) were coinfected with Flu A/H3, 9 (17.3%) Flu-B, and 7 (13.5%) Flu A/H1. Patients' mean age was 33.2 ± 21, 55.8% were males, and 20 (38.5%) were hospitalized, with mean hospital days 6.7 ± 6. At the hospital, 14 (70.0%) developed pneumonia, 6 (30.0%) ICU admitted, and 4 (20.0%) died. The hospitalization rate among patients coinfected with Flu-B and Flu A/H3 was 55.6 and 41.7%, with mean hospital days (8.0 ± 6 and 6.4 ± 6), pneumonia infection (40.0 and 80.0%), ICU admission (40.0 and 26.7%), and death (20.0% for both), while no patients hospitalized with A/H1. Conclusions: The recent increase in the number of SARS-CoV-2/Flu coinfections was identified in Egypt. The disease could have a severe course and high fatality, especially in those coinfected with Flu-B and Flu A/H3. Monitoring disease severity and impact is required to guide preventive strategy.

Incidence, risk factors, and whole-genome sequence of SARs-CoV-2 and influenza virus among the Egyptian pilgrims returning from Umrah mass gathering in Saudi Arabia, April-May 2022.

BACKGROUND: Ramadan Umrah is the second largest Islamic pilgrimage with 2.75 million pilgrims allowed in 2022. This report presents the results of a survey among Egyptian pilgrims returning from Ramadan Umrah to monitor SARS-CoV-2 and influenza activity and identify prevalent SARS-CoV-2 variants after this mass gathering. METHODS: Cross-sectional survey conducted at Cairo airport from 30th April 2022-5 th May 2022. Pilgrims were invited to participate voluntarily. After consenting, participants interviewed using questionnaire including demographics, health status, and vaccination information and asked to provide NP/OP swabs for SARS-CoV-2 and influenza testing by RT-PCR. Whole-genome sequencing performed for 29 SARS-CoV-2 isolates. Incidence calculated, descriptive data analysis performed, and SARS-CoV-2 patients were compared to negatively tested participants using chi2 and p value< 0.05. RESULTS: Overall, 1003 subjects participated, their mean age 50.9 ± 13 years, 594 (59.2%) were males. Of them, 76(7.6%) tested positive including 67(6.7%) SARS-CoV-2, 7(0.7%) influenza and 2(0.2%) SARS-CoV-2/influenza coinfection. Omicron sublineage BA.2 was the prevalent variant with no difference in severity identified between BA.1 and BA.2. No difference was identified between COVID-19 incidence among receivers of different vaccine types or between fully vaccinated and booster dose receivers. CONCLUSIONS: Survey indicated a low incidence of SARs-CoV-2 and influenza among Egyptian pilgrims returning from Ramadan Umrah. Patients had mild or no symptoms with no hospitalization or deaths reported. Full vaccination and booster doses of COVID-19 vaccines proved equally effective. Enhancing COVID-19 and influenza vaccination before mass gatherings and close monitoring of respiratory viruses among pilgrims returning from Hajj and Umrah are crucial for outbreak early detection and mitigation.

The value of contact tracing and isolation in mitigation of COVID-19 epidemic: findings from outbreak investigation of COVID-19 onboard Nile Cruise Ship, Egypt, March 2020.

WHO informed Egypt health authorities of individuals of different nationalities who proved positive for COVID-19 after returning from Egypt. Patients were among touristic group who visited Cairo and spent 1-week onboard Nile cruise ship. Investigation performed to confirm outbreak, detect source, and implement containment measures. Active case finding and contact tracing performed among contacts of the index cases and their contacts. Contacts defined as anyone within 6 feet from confirmed or suspected COVID-19 case for ≥15 min. Overall, 331 contacts, including 201 ship boarders and 130 hotel guests, were listed and interviewed using semistructured questionnaire and tested for COVID-19 by PCR. Among them, 136 (41.1%) were close contacts of index cases and 195 (58.9%) contacted secondary cases. Their mean age was 34.6±11.5 years, 251 (75.8%) were males and 126 (38.1%) non-Egyptians. Of them, 67 (20.2%) tested positive for COVID-19, including 57 (28.4%) ship boarders and 10 (7.7%) hotel guests. Per cent positive was significantly higher in: contacts of index cases, Egyptians, ship boarders and in males than corresponding categories (35.3% vs 9.7%, 22.9% vs 15.9%, 27.4% vs 7.7%, 24.7% vs 6.3%), respectively. Of all positive cases, 40 (59.7%) were asymptomatic where ship boarders, non-Egyptians, >50 years old and females were more likely to be asymptomatic than corresponding categories (85.0 vs 48.9%, 72.7 vs 54.5%, 100.0 vs 56.5%), respectively. COVID-19 patients among group of tourists triggered an outbreak onboard Nile ship and hotel in Egypt. Outbreak quickly contained through lab testing, case isolation, strict infection control measures and contact tracing which proved effective in reducing COVID-19 transmission early in pandemic.

Risk Factors of COVID-19 Critical Outcomes in the Eastern Mediterranean Region: Multicountry Retrospective Study.

BACKGROUND: The establishment of empirical evidence in the Eastern Mediterranean Region necessitates the implementation of wide-scale studies to describe the demographic, clinical features, and severity profile of patients with COVID-19. OBJECTIVE: This study aims to assess the patterns of COVID-19 severity and mortality in seven countries, and to determine the risk factors of COVID-19 severity and mortality. METHODS: This multicountry study was based on a retrospective review of medical records of hospitalized patients confirmed to have COVID-19. This study includes data from Iraq, Pakistan, Sudan, Somalia, Morocco, Egypt, and Yemen. All demographic and clinical data were extracted from hospital records (paper files) by trained data collectors. RESULTS: A total of 4141 patients were included in this study from seven countries. Comorbidities were reported by nearly half of the patients, with hypertension (n=1021, 24.7%) and diabetes (n=939, 22.7%) being the most common. Older age, diabetes mellitus, hypertension, and heart diseases were significantly associated with COVID-19 severity and mortality. Ever smoking and renal diseases were significantly associated with severity but not mortality, while male gender, respiratory diseases, and malignancy were significantly associated with mortality but not severity. CONCLUSIONS: The study confirms the role of comorbidities and demographic features on the severity and mortality of COVID-19. Understanding the contributing factors ensures attentive care and informs clinical management of patients with poorer prognoses in the early stages of diseases.

COVID-19 outcomes among pregnant and nonpregnant women at reproductive age in Egypt.

BACKGROUND: To describe demographic, clinical and epidemiological characteristics of pregnant and nonpregnant women with confirmed COVID-19 at reproductive age and determine risk factors of COVID-19 severe outcomes during pregnancy. METHODS: A retrospective study for females aged 18-49 with confirmed COVID-19 by RT-PCR in Egypt, February-July 2020. Data were obtained from Egypt National Surveillance, bivariate and multivariate analysis for demographic and clinical characteristics and outcomes of COVID-19 between pregnant and nonpregnant women including ICU admission, need for ventilator and death was performed. RESULTS: A total of 23 095 females were identified, with mean (SD) age of 35.1 (8.1) year. Of those, 408 (1.8%) were pregnant, with mean (SD) age of 29.3 (8.1) years. Compared to nonpregnant, pregnant patients were more likely to be admitted to hospital (OR = 1.7 CI = 1.4-2.1), ICU (OR = 2.4, CI = 1.3-4.3), need ventilator (OR = 3.9, CI = 2.1-7.4) and have severe outcome (OR = 3.0, CI = 1.9-4.7). Factors associated with severe outcome included: pregnancy, age > 30 years, underlying medical conditions, and living in rural areas. CONCLUSION: Pregnant women with COVID-19 are at higher risk of severe symptoms and outcome including ICU admission, requiring ventilator and death. To reduce risk of severe outcome, counseling about for seeking medical care and health education about COVID-19 preventive measures should be performed.

Mental health impacts of COVID-19 on healthcare workers in the Eastern Mediterranean Region: a multi-country study.

BACKGROUND: Healthcare workers (HCWs) fighting against the COVID-19 pandemic are under incredible pressure, which puts them at risk of developing mental health problems. This study aimed to determine the prevalence of depression, anxiety, and stress among HCWs responding to COVID-19 and its associated factors. METHODS: A multi-country cross-sectional study was conducted during July-August 2020 among HCWs responding to COVID-19 in nine Eastern Mediterranean Region (EMR) countries. Data were collected using an online questionnaire administered using KoBo Toolbox. Mental problems were assessed using the Depression, Anxiety, and Stress Scale (DASS-21). RESULTS: A total of 1448 HCWs from nine EMR countries participated in this study. About 51.2% were male and 52.7% aged ≤ 30 years. Of all HCWs, 57.5% had depression, 42.0% had stress, and 59.1% had anxiety. Considering the severity, 19.2%, 16.1%, 26.6% of patients had severe to extremely severe depression, stress, and anxiety, respectively. Depression, stress, anxiety, and distress scores were significantly associated with participants' residency, having children, preexisting psychiatric illness, and being isolated for COVID-19. Furthermore, females, those working in a teaching hospital, and specialists had significantly higher depression and stress scores. Married status, current smoking, diabetes mellitus, having a friend who died with COVID-19, and high COVID-19 worry scores were significantly associated with higher distress scores. CONCLUSIONS: Mental problems were prevalent among HCWs responding to COVID-19 in EMR. Therefore, special interventions to promote mental well-being among HCWs responding to COVID-19 need to be immediately implemented.

Public health workers' knowledge, attitude and practice regarding COVID-19: the impact of Field Epidemiology Training Program in the Eastern Mediterranean Region.

BACKGROUND: This study aimed to compare knowledge, attitude and practice (KAP) regarding COVID-19 between public health workers (PHWs) attended field epidemiology training program (FETP-trained) and those who did not attend FETP (non-FETP trained). METHODS: Multi-country cross-sectional survey was conducted among PHWs who participated in COVID-19 pandemic in 10 countries at EMR. Online questionnaire that included demographic information, KAP regarding COVID-19 pandemic was distributed among HCWs. Scoring system was used to quantify the answers, bivariate and Multivariate analysis performed to compare FETP-trained with non-FETP trained PHWs. RESULTS: Overall, 1337 PHWs participated, with 835 (62.4%) < 40 years of age, and 851 (63.6%) males. Of them, 423 (31.6%) had FETP, including that 189 (44.7%) had advanced level, 155 (36.6%) intermediate and 79 (18.7%) basic level training. Compared with non-FETP trained, FETP trained were older, having higher KAP scores. FETP participation was low in infection control, and PH laboratories. KAP mean scores for intermediate level attendees are comparable to advanced level. CONCLUSIONS: FETP-trained are having better KAP than non-FETP PHWs. Expanding the intermediate level, maintain the Rapid Response training and introduce the laboratory component are recommended to maximize the benefit from FETP. Infection control, antimicrobial resistance and coordination are areas where training should include.

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.

The Impact of Implementing the Egypt Pandemic Preparedness Plan for Acute Respiratory Infections in Combating the Early Stage of the COVID-19 Pandemic, February-July 2020: Viewpoint.

This article briefly describes Egypt's acute respiratory infection (ARI) epidemic preparedness and containment plan and illustrates the impact of implementation of the plan on combating the early stage of the COVID-19 epidemic in Egypt. Pillars of the plan include crisis management, enhancing surveillance systems and contact tracing, case and hospital management, raising community awareness, and quarantine and entry points. To identify the impact of the implementation of the plan on epidemic mitigation, a literature review was performed of studies published from Egypt in the early stage of the pandemic. In addition, data for patients with COVID-19 from February to July 2020 were obtained from the National Egyptian Surveillance system and studied to describe the situation in the early stage of the epidemic in Egypt. The lessons learned indicated that the single most important key to success in early-stage epidemic containment is the commitment of all partners to a predeveloped and agreed-upon preparedness plan. This information could be useful for other countries in the region and worldwide in mitigating future anticipated ARI epidemics and pandemics. Postepidemic evaluation is needed to better assess Egypt's national response to the COVID-19 epidemic.

Coinfection With SARS-CoV-2 and Influenza A(H1N1) in a Patient Seen at an Influenza-like Illness Surveillance Site in Egypt: Case Report.

BACKGROUND: Sentinel surveillance of influenza-like illness (ILI) in Egypt started in 2000 at 8 sentinel sites geographically distributed all over the country. In response to the COVID-19 pandemic, SARS-CoV-2 was added to the panel of viral testing by polymerase chain reaction for the first 2 patients with ILI seen at one of the sentinel sites. We report the first SARS-CoV-2 and influenza A(H1N1) virus co-infection with mild symptoms detected through routine ILI surveillance in Egypt. OBJECTIVE: This report aims to describe how the case was identified and the demographic and clinical characteristics and outcomes of the patient. METHODS: The case was identified by Central Public Health Laboratory staff, who contacted the ILI sentinel surveillance officer at the Ministry of Health. The case patient was contacted through a telephone call. Detailed information about the patient's clinical picture, course of disease, and outcome was obtained. The contacts of the patient were investigated for acute respiratory symptoms, disease confirmation, and outcomes. RESULTS: Among 510 specimens collected from patients with ILI symptoms from October 2019 to August 2020, 61 (12.0%) were COVID-19-positive and 29 (5.7%) tested positive for influenza, including 15 (51.7%) A(H1N1), 11 (38.0%) A(H3N2), and 3 (10.3%) influenza B specimens. A 21-year-old woman was confirmed to have SARS-CoV-2 and influenza A(H1N1) virus coinfection. She had a high fever of 40.2 °C and mild respiratory symptoms that resolved within 2 days with symptomatic treatment. All five of her family contacts had mild respiratory symptoms 2-3 days after exposure to the confirmed case, and their symptoms resolved without treatment or investigation. CONCLUSIONS: This case highlights the possible occurrence of SARS-CoV-2/influenza A(H1N1) coinfection in younger and healthy people, who may resolve the infection rapidly. We emphasize the usefulness of the surveillance system for detection of viral causative agents of ILI and recommend broadening of the testing panel, especially if it can guide case management.