Genomic surveillance of SARS-CoV-2 in Tunisia during the omicron era: insights from the national influenza & other respiratory viruses laboratory

Abstract

Omicron sublineages have dominated global SARS-CoV-2 circulation since late 2021, but there aren’t enough multi-year datasets that detail lineage dynamics and genomic surveillance performance in North Africa. The National Influenza and Other Respiratory Viruses Laboratory in Tunisia has been conducting integrated SARS-CoV-2 genomic surveillance for four years. Between 1 November 2021 and 30 September 2025, 8,635 nasopharyngeal swabs (NPS) received through the national 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%) positive samples were successfully sequenced using Illumina RNA Prep with Enrichment and a respiratory virus panel. Pango lineages and GISAID clades were assigned with standard tools, and sequencing coverage, geographic representativeness, turnaround times, temporal trends, lineage diversity, mutational profiles, and phylogenetic placement were summarized descriptively. The overall SARS-CoV-2 positivity rate was 11.8%. Median governorate-level sequencing coverage among RT-PCR–positive samples was 60.0% (IQR 28.6–88.9), and the share of sequences closely matched the share of positives (r = 0.992), indicating near-proportional sampling.While SARS-CoV-2-positive NPS displayed several waves, including substantial peaks in mid-2022 and mid-2023 and subsequent winter peaks, each linked to the establishment or replacement of dominant Omicron lineages, testing volumes indicated recurrent winter rises. Among the 669 sequenced SARS-CoV-2-positive samples, 92 (13.8%) showed co-detection with at least one other respiratory virus, including 16 (2.4%) involving influenza viruses.XBB* lineages accounted for 25.0% of genomes, followed by BA.4/BA.5* (22.1%), JN.1* and descendants (13.6%), BA.2* (12.6%), and BA.1* (9.0%), while Delta represented 8.7% of genomes; the remaining 9.1% belonged to other lineages, including pre-Omicron variants and non-XBB recombinants. Almost all genomes belonged to Omicron-associated GISAID clades GK and GRA. Overall, sequencing quality was high (mapped reads typically ≥0.9), while Tunisian SARS-CoV-2 genomes showed a progressive increase in amino acid changes—from ~30–50 substitutions in early Delta/BA.1/BA.2 to >70–80 in later XBB and JN.1* sublineages, with some recombinants approaching 100 substitutions. Phylogenetic analyses showed that Tunisian genomes clustered within globally circulating Delta and Omicron clades. Rapid Omicron sublineage turnover and co-detections with other respiratory viruses, including influenza, were captured by genomic monitoring integrated into Tunisia’s influenza-based sentinel network, which achieved broad sequencing coverage and overall near-proportional sampling despite subnational heterogeneity.This integrated, multi-pathogen approach provides a scalable model for sustained genomic surveillance and future respiratory pandemic preparedness in the region.