Molecular and Seroepidemiology of SARS-CoV-2 among Influenza-Like Illness and Severe Acute Respiratory Illness Cases in Selected Health Facilities in Ethiopia

Adamu Tayachew^1,2*Dawit Arimide^3*Wolde Shure¹Dejenie Shiferaw Teklu¹Ayele Gebeyehu¹Tsegaye Berkesa¹Gizaw Teka¹Mandefro Kebede¹Mesfin Wossen¹Melkamu Abte¹Mesay Hailu Dangisso¹Zelalem Mekuria⁴Nega Berhe²Patrik Medstrand^5,6,7Nigatu Kebede²

• ¹Ethiopian Public Health Institute, Addis Ababa, Ethiopia
• ²Addis Ababa University, Aklilu Lemma Institute of Pathobiology, Addis Ababa, Ethiopia
• ³Translational Medicine, Clinical Virology, Lund University, Malmö, Sweden, Malmö, Sweden
• ⁴Department of Veterinary Preventive Medicine, Ohio State University College of Veterinary Medicine, 1920 Coffey Road, Columbus, United States
• ⁵Translational Medicine, Clinical Virology, Lund University, Malmö, Sweden
• ⁶Science for Life Laboratory, Lund University, Lund, Sweden
• ⁷Clinical Microbiology, Infection Control and Prevention, Laboratory Medicine, Lund, Sweden

Background: SARS-CoV-2 remains globally circulating, yet post-pandemic molecular and serological data from low-resource settings like Ethiopia are scarce. We investigated SARS-CoV-2 epidemiology among influenza-like illness (ILI) and severe acute respiratory infection (SARI) cases from May 2023-April 2024 at 21 influenza sentinel surveillance sites. Methods: Respiratory swabs from 8,881 ILI/SARI patients were tested for SARS-CoV-2 by real-time polymerase chain reaction (RT-PCR) and underwent whole-genome sequencing on selected positive samples using Oxford Nanopore Technology; blood samples from participants ≥12 years were also tested by enzyme-linked immunosorbent assay (ELISA). Results: Among 8,881 participants, the overall SARS-CoV-2 detection rate was 3.3%. Compared to children <2 years, older age groups showed increased odds: 15-49 years (AOR: 1.6, 95% CI: 1.16-2.21), 50-64 years (AOR: 2.15, 95% CI: 1.31-3.54), and ≥65 years (AOR: 2.37, 95% CI: 1.42-3.95). ILI cases had higher positivity rate than SARI cases (AOR: 2.26, 95% CI: 1.75-2.91). SARS-CoV-2 was detected across all seasons, with positivity rates ranging from 1.9% in spring to 6.0% in summer. Whole genome sequencing (n=80) identified 19 Omicron sub-lineages, predominantly JN.1.18 (31.3%), JN.1(8.8%), XBB.1.28 (8.8%), BA.2.86 (7.5%) and XBB.1.34.1 (6.3%). Serologic analysis showed positivity rate of 96.8% among 690 individuals. Conclusions: These findings confirm ongoing SARS-CoV-2 circulation in Ethiopia, predominantly among adult ILI cases, with seasonal peaks in summer. Omicron was the exclusive variant detected and JN.1 and its descendants have dominated since late 2023 and coincided with the COVID-19 surge reported in the period. Sustained genomic and syndromic surveillance remains essential to track the viral evolution and support effective public health intervention.