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