# Molecular and seroepidemiology of SARS-CoV-2 among influenza-like illness and severe Acute respiratory illness cases in selected health facilities in Ethiopia

## TL;DR

This study tracks SARS-CoV-2 in Ethiopia using molecular and serological methods, finding ongoing Omicron variant circulation and high adult infection rates.

## Contribution

The study provides comprehensive molecular and seroepidemiological data on SARS-CoV-2 in Ethiopia, a low-resource setting, highlighting Omicron sub-lineage dominance and seasonal trends.

## Key findings

- SARS-CoV-2 detection rate was 3.3% among ILI/SARI cases, with higher rates in older age groups.
- Omicron sub-lineages JN.1.18 and JN.1 were predominant in Ethiopia during late 2023.
- Seropositivity was 96.8%, with no significant demographic variation.

## Abstract

SARS-CoV-2 remains globally circulating, yet post-pandemic comprehensive molecular, serological, and population-level immunity data from low-resource settings such as Ethiopia are limited. This study employed genomic surveillance with seroepidemiological assessment to characterize the epidemiology of SARS-CoV-2 among individuals presenting with influenza-like illness (ILI) and severe acute respiratory infection (SARI) between May 2023 and April 2024 across 21 influenza sentinel surveillance sites representing diverse regions of Ethiopia.

Respiratory swabs from 8,881 ILI/SARI patients were tested for SARS-CoV-2 by real-time polymerase chain reaction (RT-PCR). Whole-genome sequencing was performed on samples with cycle threshold (Ct) values ≤ 30 using Oxford Nanopore Technology, and serological testing was performed on blood samples collected from participants aged ≥12 years using the WANTAI enzyme-linked immunosorbent assay (ELISA) targeting the spike receptor-binding domain (RBD).

Among 8,881 participants, the overall SARS-CoV-2 detection rate was 3.3 (95% CI: 2.9–3.6). Compared to children under 2 years, older age groups had significantly higher odds of infection: 15–49 years (AOR: 1.60; 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 demonstrated higher positivity 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 of (n = 80) revealed exclusive circulation of Omicron lineages, identifying 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%). Serological analysis of 690 samples demonstrated 96.8% (95% CI: 95.2–98.0%) seropositivity, with no significant demographic variation.

This study demonstrates the continued circulation of SARS-CoV-2 in Ethiopia, primarily among adults with influenza-like illness, with distinct seasonal peaks during the summer. The Omicron variant remained dominant, with JN.1 and its descendants prevailing since late 2023 in parallel with a national rise in COVID-19 cases. These findings reinforce that ongoing genomic and syndromic surveillance utilizing established ILI/SARI platforms remain vital for monitoring viral evolution and guiding targeted public health interventions in low-resource settings.