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Hamzaoui Z, Ferjani S, Medini I, Charaa L, Landolsi I, Ben Ali R, Khaled W, Chammam S, Abid S, Kanzari L, Ferjani A, Fakhfakh A, Kebaier D, Bouslah Z, Ben Sassi M, Trabelsi S, Boutiba-Ben Boubaker I. Genomic surveillance of SARS-CoV-2 in North Africa: 4 years of GISAID data sharing. IJID Reg 2024; 11:100356. [PMID: 38655560 PMCID: PMC11035039 DOI: 10.1016/j.ijregi.2024.100356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/26/2024]
Abstract
Objectives This study aimed to construct geographically, temporally, and epidemiologically representative data sets for SARS-CoV-2 in North Africa, focusing on Variants of Concern (VOCs), Variants of Interest (VOIs), and Variants Under Monitoring (VUMs). Methods SARS-CoV-2 genomic sequences and metadata from the EpiCoV database via the Global Initiative on Sharing All Influenza Data platform were analyzed. Data analysis included cases, deaths, demographics, patient status, sequencing technologies, and variant analysis. Results A comprehensive analysis of 10,783 viral genomic sequences from six North African countries revealed notable insights. SARS-CoV-2 sampling methods lack standardization, with a majority of countries lacking clear strategies. Over 59% of analyzed genomes lack essential clinical and demographic metadata, including patient age, sex, underlying health conditions, and clinical outcomes, which are essential for comprehensive genomic analysis and epidemiological studies, as submitted to the Global Initiative on Sharing All Influenza Data. Morocco reported the highest number of confirmed COVID-19 cases (1,272,490), whereas Tunisia leads in reported deaths (29,341), emphasizing regional variations in the pandemic's impact. The GRA clade emerged as predominant in North African countries. The lineage analysis showcased a diversity of 190 lineages in Egypt, 26 in Libya, 121 in Tunisia, 90 in Algeria, 146 in Morocco, and 10 in Mauritania. The temporal dynamics of SARS-CoV-2 variants revealed distinct waves driven by different variants. Conclusions This study contributes valuable insights into the genomic landscape of SARS-CoV-2 in North Africa, highlighting the importance of genomic surveillance in understanding viral dynamics and informing public health strategies.
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Affiliation(s)
- Zaineb Hamzaoui
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Sana Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ines Medini
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Latifa Charaa
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ichrak Landolsi
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Roua Ben Ali
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Wissal Khaled
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Sarra Chammam
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
| | - Salma Abid
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Lamia Kanzari
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Asma Ferjani
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Ahmed Fakhfakh
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Dhouha Kebaier
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Zoubeir Bouslah
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
| | - Mouna Ben Sassi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Tunis Tunisia
| | - Sameh Trabelsi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Tunis Tunisia
| | - Ilhem Boutiba-Ben Boubaker
- Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Microbiology, Charles Nicolle Hospital, Tunis, Tunisia
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Abid S, Ferjani S, El Moussi A, Ferjani A, Nasr M, Landolsi I, Saidi K, Gharbi H, Letaief H, Hechaichi A, Safer M, Ben Alaya NBE, Boubaker IBB. Assessment of sample pooling for SARS-CoV-2 molecular testing for screening of asymptomatic persons in Tunisia. Diagn Microbiol Infect Dis 2020; 98:115125. [PMID: 32768876 PMCID: PMC7335417 DOI: 10.1016/j.diagmicrobio.2020.115125] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/03/2022]
Abstract
The aim of this study is to test a pooling approach for the RT-PCR test to detect low viral loads of SARS-CoV-2. We found that a single positive specimen can still be detected in pools of up to 10. Each laboratory should conduct its own evaluation and validation of pooling protocols according to its specific context.
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Affiliation(s)
- Salma Abid
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Sana Ferjani
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia.
| | - Awatef El Moussi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Asma Ferjani
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
| | - Mejda Nasr
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Ichrak Landolsi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Karima Saidi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Hanène Gharbi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Hajer Letaief
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | - Aicha Hechaichi
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | - Mouna Safer
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006, Tunis, Tunisia
| | | | - Ilhem Boutiba-Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES09, 1007, Tunis, Tunisia
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