What question did this study set out to answer?

To evaluate multi-year SARS-CoV-2 lineage dynamics, genomic diversity, and surveillance network performance during the Omicron era using an integrated respiratory disease monitoring system.

September 17, 2026Virology JournalOpen Access

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

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Authors

ZHZaineb Hamzaoui SFSana Ferjani TBTakoua Bouchouicha

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Overview

Sentinel surveillance reveals rapid Omicron sublineage turnover and viral co-infections in respiratory samples, indicating the feasibility of integrated multi-pathogen pandemic monitoring.

Key Points

To evaluate multi-year SARS-CoV-2 lineage dynamics, genomic diversity, and surveillance network performance during the Omicron era using an integrated respiratory disease monitoring system.
Tested 8,635 nasopharyngeal swabs collected via a national sentinel network between November 1, 2021, and September 30, 2025, using real-time RT-PCR.
Sequenced 669 of 1,020 RT-PCR–positive samples (65.6%) using Illumina RNA Prep with Enrichment and a targeted respiratory virus panel.
Assigned Pango lineages and GISAID clades while evaluating geographic representativeness, sequencing quality, mutational accumulation, and phylogenetic placement.
Sequenced genomes comprised XBB* (25.0%), BA.4/BA.5* (22.1%), JN.1* (13.6%), BA.2* (12.6%), BA.1* (9.0%), and Delta (8.7%), displaying an increase from ~30–50 amino acid substitutions in early strains to >70–80 in later sublineages.
Achieved a median governorate-level sequencing coverage of 60.0% (IQR 28.6–88.9) among positive samples, with sequence volume correlating strongly with positive cases (r = 0.992).
Identified co-detection of at least one other respiratory virus in 92 of 669 sequenced SARS-CoV-2 samples (13.8%), including 16 samples (2.4%) co-infected with influenza viruses.

Cite This Study

Hamzaoui et al. (2026) studied this question.

synapsesocial.com/papers/6aabb75d5f706d05830e65d3 https://doi.org/10.1186/s12985-026-03262-7

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September 17, 2026Virology JournalOpen Access

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

View Full Paper

Ask AI

Bookmark

Authors

ZHZaineb Hamzaoui SFSana Ferjani TBTakoua Bouchouicha

Discussion

Member takes

Overview

Sentinel surveillance reveals rapid Omicron sublineage turnover and viral co-infections in respiratory samples, indicating the feasibility of integrated multi-pathogen pandemic monitoring.

Key Points

To evaluate multi-year SARS-CoV-2 lineage dynamics, genomic diversity, and surveillance network performance during the Omicron era using an integrated respiratory disease monitoring system.
Tested 8,635 nasopharyngeal swabs collected via a national sentinel network between November 1, 2021, and September 30, 2025, using real-time RT-PCR.
Sequenced 669 of 1,020 RT-PCR–positive samples (65.6%) using Illumina RNA Prep with Enrichment and a targeted respiratory virus panel.
Assigned Pango lineages and GISAID clades while evaluating geographic representativeness, sequencing quality, mutational accumulation, and phylogenetic placement.
Sequenced genomes comprised XBB* (25.0%), BA.4/BA.5* (22.1%), JN.1* (13.6%), BA.2* (12.6%), BA.1* (9.0%), and Delta (8.7%), displaying an increase from ~30–50 amino acid substitutions in early strains to >70–80 in later sublineages.
Achieved a median governorate-level sequencing coverage of 60.0% (IQR 28.6–88.9) among positive samples, with sequence volume correlating strongly with positive cases (r = 0.992).
Identified co-detection of at least one other respiratory virus in 92 of 669 sequenced SARS-CoV-2 samples (13.8%), including 16 samples (2.4%) co-infected with influenza viruses.

Cite This Study

Hamzaoui et al. (2026) studied this question.

synapsesocial.com/papers/6aabb75d5f706d05830e65d3 https://doi.org/10.1186/s12985-026-03262-7

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