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Sassi MB, Ferjani S, Mkada I, Arbi M, Safer M, Elmoussi A, Abid S, Souiai O, Gharbi A, Tejouri A, Gaies E, Eljabri H, Ayed S, Hechaichi A, Daghfous R, Gouider R, Khelil JB, Kharrat M, Kacem I, Alya NB, Benkahla A, Trabelsi S, Boubaker IBB. Phylogenetic and amino acid signature analysis of the SARS-CoV-2s lineages circulating in Tunisia. Infection, Genetics and Evolution 2022; 102:105300. [PMID: 35552003 PMCID: PMC9085353 DOI: 10.1016/j.meegid.2022.105300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 05/01/2022] [Accepted: 05/05/2022] [Indexed: 11/19/2022]
Abstract
Since the beginning of the Coronavirus disease-2019 pandemic, there has been a growing interest in exploring SARS-CoV-2 genetic variation to understand the origin and spread of the pandemic, improve diagnostic methods and develop the appropriate vaccines. The objective of this study was to identify the SARS-CoV-2s lineages circulating in Tunisia and to explore their amino acid signature in order to follow their genome dynamics. Whole genome sequencing and genetic analyses of fifty-eight SARS-CoV-2 samples collected during one-year between March 2020 and March 2021 from the National Influenza Center were performed using three sampling strategies.. Multiple lineage introductions were noted during the initial phase of the pandemic, including B.4, B.1.1, B.1.428.2, B.1.540 and B.1.1.189. Subsequently, lineages B1.160 (24.2%) and B1.177 (22.4%) were dominant throughout the year. The Alpha variant (B.1.1.7 lineage) was identified in February 2021 and firstly observed in the center of our country. In addition, A clear diversity of lineages was observed in the North of the country. A total of 335 mutations including 10 deletions were found. The SARS-CoV-2 proteins ORF1ab, Spike, ORF3a, and Nucleocapsid were observed as mutation hotspots with a mutation frequency exceeding 20%. The 2 most frequent mutations, D614G in S protein and P314L in Nsp12 appeared simultaneously and are often associated with increased viral infectivity. Interestingly, deletions in coding regions causing consequent deletions of amino acids and frame shifts were identified in NSP3, NSP6, S, E, ORF7a, ORF8 and N proteins. These findings contribute to define the COVID-19 outbreak in Tunisia. Despite the country's limited resources, surveillance of SARS-CoV-2 genomic variation should be continued to control the occurrence of new variants.
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Affiliation(s)
- Mouna Ben Sassi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Sana 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.
| | - Imen Mkada
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia
| | - Marwa Arbi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Mouna Safer
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006 Tunis, Tunisia
| | - Awatef Elmoussi
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Salma Abid
- Charles Nicolle Hospital, Laboratory of Microbiology, Virology unit, National Influenza and other Respiratory Viruses Center-Tunisia, Boulevard 9 Avril, Tunis 1006, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Alya Gharbi
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia; Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia
| | - Asma Tejouri
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Emna Gaies
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Hanene Eljabri
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia
| | - Samia Ayed
- Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia; Abderrahmen Mami Hospital, Department of Medical Intensive Care, 2080 Ariana, Tunisia
| | - Aicha Hechaichi
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006 Tunis, Tunisia
| | - Riadh Daghfous
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 Tunis, Tunisia
| | - Riadh Gouider
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia; Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia
| | - Jalila Ben Khelil
- Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia; Abderrahmen Mami Hospital, Department of Medical Intensive Care, 2080 Ariana, Tunisia
| | - Maher Kharrat
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Imen Kacem
- Department of Neurology, LR18SP03, Razi Universitary Hospital, 1 rue des orangers Manouba, 2010 Tunis, Tunisia; Clinical Investigation Centre (CIC) "Neurosciences and Mental Health", Razi Universitary Hospital, 1 rue des orangers Manouba, 2010, Tunis, Tunisia; Faculty of Medicine of Tunis, University of Tunis El Manar, 15, Rue DjebelAkhdhar - La Rabta - 1007, Tunis, Tunisia
| | - Nissaf Ben Alya
- Ministry of Health, National Observatory of New and Emerging Diseases, 1006 Tunis, Tunisia
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics-LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar (UTM), Tunis, Tunisia
| | - Sameh Trabelsi
- National Center Chalbibelkahia of Pharmacovigilance of Tunis, Laboratory of Clinical Pharmacology, Boulevard 9 Dr Zouhier Essafi, Tunis 1006, Tunisia; University of Tunis El Manar, Faculty of Medicine of Tunis, LR16SP02, 1007 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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