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. 2024 Mar 19:11:100356.
doi: 10.1016/j.ijregi.2024.100356. eCollection 2024 Jun.

Genomic surveillance of SARS-CoV-2 in North Africa: 4 years of GISAID data sharing

Zaineb Hamzaoui  1 , Sana Ferjani  1 , Ines Medini  2 , Latifa Charaa  3 , Ichrak Landolsi  3 , Roua Ben Ali  2 , Wissal Khaled  3 , Sarra Chammam  2 , Salma Abid  1   3 , Lamia Kanzari  1   3 , Asma Ferjani  1   3 , Ahmed Fakhfakh  1   3 , Dhouha Kebaier  1   3 , Zoubeir Bouslah  1   3 , Mouna Ben Sassi  2   4 , Sameh Trabelsi  2   4 , Ilhem Boutiba-Ben Boubaker  1   3
Affiliations

Genomic surveillance of SARS-CoV-2 in North Africa: 4 years of GISAID data sharing

Zaineb Hamzaoui et al. IJID Reg. .

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.

Keywords: Epidemiological dynamics; Genomic sequences; Lineages; North Africa; SARS-CoV-2; Variants.

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Conflict of interest statement

The authors have no competing interests to declare.

Figures

Figure 1
Figure 1
Regional variation in SARS-CoV-2 clade distribution across North African countries (based on data downloaded from Global Initiative on Sharing All Influenza Data per 15 September 2023).
Figure 2
Figure 2
Relative distribution of SARS-CoV-2 lineages in North African countries (February 2020 to September 2023) Based on whole genome sequencing (based on data downloaded from Global Initiative on Sharing All Influenza Data per 15 September 2023). The diagram illustrates the relative distribution (%) of SARS-CoV-2 lineages in North African countries. Different lineages are color-coded, and those with higher proportions are marked in black font for easy identification. (a) Represents the distribution over 5044 sequences obtained in Egypt. (b) Illustrates the distribution over 178 sequences in Libya. (c) Shows the distribution over 2455 sequences in Tunisia. (d) Depicts the distribution over 880 sequences in Algeria. (e) Displays the distribution over 2168 sequences in Morocco. (f) Represents the distribution over 58 sequences in Mauritania.
Figure 2
Figure 2
Relative distribution of SARS-CoV-2 lineages in North African countries (February 2020 to September 2023) Based on whole genome sequencing (based on data downloaded from Global Initiative on Sharing All Influenza Data per 15 September 2023). The diagram illustrates the relative distribution (%) of SARS-CoV-2 lineages in North African countries. Different lineages are color-coded, and those with higher proportions are marked in black font for easy identification. (a) Represents the distribution over 5044 sequences obtained in Egypt. (b) Illustrates the distribution over 178 sequences in Libya. (c) Shows the distribution over 2455 sequences in Tunisia. (d) Depicts the distribution over 880 sequences in Algeria. (e) Displays the distribution over 2168 sequences in Morocco. (f) Represents the distribution over 58 sequences in Mauritania.
Figure 2
Figure 2
Relative distribution of SARS-CoV-2 lineages in North African countries (February 2020 to September 2023) Based on whole genome sequencing (based on data downloaded from Global Initiative on Sharing All Influenza Data per 15 September 2023). The diagram illustrates the relative distribution (%) of SARS-CoV-2 lineages in North African countries. Different lineages are color-coded, and those with higher proportions are marked in black font for easy identification. (a) Represents the distribution over 5044 sequences obtained in Egypt. (b) Illustrates the distribution over 178 sequences in Libya. (c) Shows the distribution over 2455 sequences in Tunisia. (d) Depicts the distribution over 880 sequences in Algeria. (e) Displays the distribution over 2168 sequences in Morocco. (f) Represents the distribution over 58 sequences in Mauritania.
Figure 3
Figure 3
Chronological distribution of Pango lineages among all SARS-CoV-2 genomic sequences from North African countries, retrieved from Global Initiative on Sharing All Influenza Data (accessed on 15 September 2023) spanning from February 2020 to September 2023. The upper graph illustrates the frequency (proportion) of sequences for the most prevalent lineages in North African countries per month). The lower graph presents the absolute number of identified SARS-CoV-2 lineages per month. A. Egypt. B. Libya. C. Tunisia, D. Algeria. E. Morocco. F. Mauritania.
Figure 3
Figure 3
Chronological distribution of Pango lineages among all SARS-CoV-2 genomic sequences from North African countries, retrieved from Global Initiative on Sharing All Influenza Data (accessed on 15 September 2023) spanning from February 2020 to September 2023. The upper graph illustrates the frequency (proportion) of sequences for the most prevalent lineages in North African countries per month). The lower graph presents the absolute number of identified SARS-CoV-2 lineages per month. A. Egypt. B. Libya. C. Tunisia, D. Algeria. E. Morocco. F. Mauritania.
Figure 3
Figure 3
Chronological distribution of Pango lineages among all SARS-CoV-2 genomic sequences from North African countries, retrieved from Global Initiative on Sharing All Influenza Data (accessed on 15 September 2023) spanning from February 2020 to September 2023. The upper graph illustrates the frequency (proportion) of sequences for the most prevalent lineages in North African countries per month). The lower graph presents the absolute number of identified SARS-CoV-2 lineages per month. A. Egypt. B. Libya. C. Tunisia, D. Algeria. E. Morocco. F. Mauritania.
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