Genomic Surveillance of SARS-CoV-2 in Tunisia during the Omicron Era: Insights from the National Influenza & Other Respiratory Viruses Laboratory

Abstract

Background Omicron sublineages have dominated global SARS-CoV-2 circulation since late 2021, but there are limited multi-year datasets describing lineage dynamics and genomic surveillance performance in North Africa. Tunisia’s National Influenza and Other Respiratory Viruses Laboratory has implemented integrated SARS-CoV-2 genomic surveillance through the national sentinel network. Methods Between 1 November 2021 and 30 September 2025, 8,635 nasopharyngeal swabs from the sentinel network were tested for SARS-CoV-2 by real-time RT-PCR, of which 1,020 (11.8%) were positive. A total of 669 (65.6%) positives were sequenced with an Illumina respiratory virus panel. Pango lineages and GISAID clades were assigned with standard tools, and sequencing coverage, geographic representativeness, temporal trends, lineage diversity, mutational profiles and phylogenetic placement were summarized descriptively. Results The SARS-CoV-2 positivity rate was 9.8%. Median sequencing coverage among RT-PCR–positive samples was 60%, and the share of sequences closely matched the share of positives (r=0.99). Testing volumes showed recurrent winter increases, while SARS-CoV-2–positive NPS displayed distinct epidemic waves, including large mid-2022 and mid-2023 peaks and subsequent winter waves, each linked to the emergence or replacement of dominant Omicron lineages. XBB*, BA.4/BA.5*, JN.1* and BA.2* predominated, and almost all genomes fell within Omicron-associated GISAID clades GK and GRA. Conclusions Rapid Omicron sublineage turnover and frequent co-circulation of other respiratory viruses were captured by genomic monitoring embedded within Tunisia’s influenza-based sentinel network, which achieved high and geographically consistent sequencing coverage. This integrated, multi-pathogen platform provides a scalable model for sustained genomic surveillance and future respiratory pandemic preparedness in the region.