Introduction: An integrated surveillance for acute respiratory infections (ARIs) was established 2016 at network of 19 governmental hospitals to identify causes of ARIs in Egypt. In response to COVID-19 pandemic, WHO requested surveillance adaptation to address the emerging challenges. This report aims at describing Egypt experience in adapting ARI surveillance to COVID-19 pandemic. Surveillance methods: WHO case definitions are used to identify ARI patients. NP/OP swabs collected for influenza testing by RT-PCR at central laboratories. Data collected by interviewing patients for demographic and clinical information and entered at sites. During COVID-19 pandemic, the first two outpatients daily and every fifth admitted patient were enrolled. Patients COVID-19 clinical data and testing for SARS-CoV-2 by RT-PCR were added. Results: Between January 2020-April 2022, 18,160 patients were enrolled including 7,923(43.6%) outpatients and 10,237(56.4%) admitted. Of them 6,453(35.5%) tested positive including 5,620(87.1%) SARS-CoV-2, 781(12.1%) influenza and 52(0.8%) SARS-CoV-2/influenza coinfection. SARS CoV-2 caused 95.3% of admitted cases and 65.4% of outpatients. Influenza subtypes included A/H3 (55.7%), Flu-B (29.1%), H1/pdm09 (14.2%). Compared to influenza, SARS-CoV-2 infections prevail in elderly, warm weather, and urban governorates. SARS-CoV-2 caused more hospitalization, longer hospital stay, more severe course and higher case fatality than influenza (16.3 vs 6.6%, p<0.001). Conclusion: Egypt ARI surveillance was successfully adapted to COVID-19 pandemic and effectively describe clinical characteristics and severity of circulating viruses. Surveillance reported re-emergence of influenza viruses with severe course and high fatality. Maintaining ARI surveillance is essential to monitor respiratory viruses activity for guiding clinical management and preventive and control measures.

Background: Co-circulation of influenza and SARS-CoV-2 (SARS-CoV-2/Flu) represent public health concern as it may worsen the severity and increase fatality from COVID-19. An increase in number of patients with coinfection was recently reported. We studied epidemiology, severity, and outcome of SARS-CoV-2/Flu coinfections seen at Egypt acute respiratory (ARI) surveillance eight hospitals to better describe disease impact and guide effective preventive measures. Methods: Every fifth patient admitted and first two outpatients seen daily with ARI are enrolled. Standardized questionnaire is used to interview patients who provide nasopharyngeal swabs to be tested weekly at the central laboratory for SARS-CoV-2 and influenza by RT-PCR. Data of all patients with coinfection extracted from surveillance database and descriptive analysis performed for demographics, clinical course, and outcome. Results: Of 18,160 patients enrolled January 2020-April 2022, 6,453(35.5%) were positive for viruses including 52(0.8%) coinfection. Of them 36(69.2%) coinfected with FluA/H3, 9(17.3%) Flu-B and 7(13.5%) FluA/H1. Patients’ mean age was 33.2±21, and 55.8% were males, 20(38.5%) hospitalized, mean hospital days (6.7±6). At hospital 14(70.0%) developed pneumonia, 6(30.0%) ICU admitted, and 4(20.0%) died. Hospitalization rate among coinfection with Flu-B and FluA/H3 was (55.6 and 41.7%), mean hospital days (8.0±6 and 6.4±6), pneumonia (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: An increasing number of SARS-CoV-2/Flu coinfection identified in Egypt with severe course and high fatality. Patients coinfected with Flu-B and FluA/H3 had severe disease than A/H1. Monitoring disease severity and impact is required to guide preventive strategy.