Evidence map›Paper›PMID 41011493›Full record

ArticleMicroorganisms2025

The Omicron Wave in Tunisia: Dynamic, Diversity, and Phylogenetic Analyses.

Yasmine Chaari, Sondes Haddad-Boubaker, Haifa Khemiri, Wasfi Fares, Anissa Chouikha, Cesare Camma, Alessio Lorusso, Hanen Smaoui, Khaoula Meftah, Ouafa Kallala and 12 more

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Article in Microorganisms, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

22 authors.

Yasmine ChaariFaculty of Pharmacy of Monastir, University of Monastir, Monastir 5000, Tunisia.
Sondes Haddad-BoubakerLaboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belvédère, Tunis 1002, Tunisia.ORCID 0000-0001-9705-4387
Haifa KhemiriLaboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belvédère, Tunis 1002, Tunisia.
Wasfi FaresLaboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belvédère, Tunis 1002, Tunisia.
Anissa ChouikhaLaboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belvédère, Tunis 1002, Tunisia.ORCID 0000-0001-5616-0204
Cesare CammaDepartment of Virology, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy.ORCID 0000-0002-7547-1195
Alessio LorussoDepartment of Virology, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, 64100 Teramo, Italy.ORCID 0000-0001-6156-8212
Hanen SmaouiDepartment of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia.ORCID 0000-0002-4026-0259
Khaoula MeftahDepartment of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia.ORCID 0000-0003-3312-8265
Ouafa KallalaLaboratory of Microbiology, Sahloul Hospital of Sousse, Sousse 4054, Tunisia.ORCID 0000-0002-3240-3045
Abdelhalim TrabelsiLaboratory of Microbiology, Sahloul Hospital of Sousse, Sousse 4054, Tunisia.
Amel ChtourouLaboratory of Microbiology, Habib Bourguiba University Hospital, Rue El Ferdaous, Sfax 3003, Tunisia.
Awatef TaktakLaboratory of Microbiology, Habib Bourguiba University Hospital, Rue El Ferdaous, Sfax 3003, Tunisia.
Olfa BahriDepartment of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia.ORCID 0000-0002-0610-2708
Manel HamdounDepartment of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia.ORCID 0000-0001-8175-1743
Yassine ChaabouniLaboratory of Medical Biology, Ibn El Jazzar Hospital, Kairouan 3100, Tunisia.
Henda TouziLaboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belvédère, Tunis 1002, Tunisia.
Amel SadraouiLaboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belvédère, Tunis 1002, Tunisia.
Zina MeddebLaboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belvédère, Tunis 1002, Tunisia.
Nissaf Ben AlayaDepartment of Microbiology, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis 1007, Tunisia.ORCID 0000-0002-3326-9861
Mariem GdouraLaboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belvédère, Tunis 1002, Tunisia.ORCID 0000-0002-2031-6534
Henda TrikiLaboratory of Clinical Virology, WHO Regional Reference Laboratory for Poliomyelitis and Measles for in the Eastern Mediterranean Region, Institut Pasteur de Tunis, University of Tunis El Manar, 13 10 place Pasteur, BP74 1002 le Belvédère, Tunis 1002, Tunisia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The SARS-CoV-2 Omicron variant has exhibited a rapid progression around the world, but its molecular insights in North Africa remain understudied. This study characterizes the genetic diversity, dynamics, and evolutionary trends of the Omicron variant in Tunisia over a 33-month period (December 2021-August 2024). In total, 928 high-quality whole-genome sequences were considered in this study, of which 559 were retrieved from the GISAID database and 369 were generated in our laboratory. Phylogenetic analysis of the dominant subvariants (BA.1, BA.2, and BA.5) was performed using IQ-TREE. BA.2 was the predominant subvariant (38%), followed by BA.1 (24.0%), Omicron recombinants (19%), and BA.5 (18%). BA.2 diversified into JN, KP, and BN sub-lineages. Recombinants were dominated by XBB (98.8%), primarily including EG.4, XBB.1.5, and XBB.2.3.11, with rare detection of XDK and XDQ. Phylogenetic analysis revealed local clusters in BA.1, BA.2, and BA.5 alongside imported strains. Tunisia's Omicron wave was mainly driven by BA.2 and its recombinants, with evidence of localized viral evolution and sporadic introductions. The detection of rare recombinants underlines the importance of integrating regional genomic surveillance with epidemiological data in order to help guide future public health strategies.

Indexed as

North Africaomicron variantphylogenetic analysisrecombinants (XBBSARS-CoV-2XDKXDQ)

Identifiers

PMID41011493
PMCPMC12473128

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.