Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect?
Abstract
:1. Introduction
2. Materials and Methods
2.1. Epidemiological Dynamics and Genomic Data Processing
2.2. Sequence Alignment and Phylogenetic Analysis of Algerian Genomes
2.3. Mutation Signature and Clade Assignment Analysis
3. Results
3.1. Epidemiology of SARS-CoV-2 in Algeria and North Africa
3.2. Phylogenetic Analysis of SARS-CoV-2 Genomes in Algeria
3.3. Distribution of SARS-CoV-2 Lineages and Clades in North Africa
3.3.1. Egypt
3.3.2. Libya
3.3.3. Morocco
3.3.4. Sudan
3.3.5. Tunisia
3.4. Phylogenetic Analysis of Omicron Genome Sequences from North Africa
3.5. Genomic Variation and Mutation Signature
3.6. Variant Analysis of Omicron SARS-CoV-2 Genomes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Country | Total Cases | Sequenced Genomes | Analyzed Genomes |
---|---|---|---|
Algeria | 214,592 | 85 | 36 |
Egypt | 375,330 | 1418 | 971 |
Libya | 381,749 | 56 | 38 |
Morocco | 952,814 | 609 | 352 |
Sudan | 45,112 | 116 | 31 |
Tunisia | 721,031 | 315 | 241 |
Western Sahara | 10 | ND | ND |
Total | 2,690,638 | 2599 | 1669 |
Genomic Coordinate | Effect | N Samples | Class | Genomic Region |
---|---|---|---|---|
A23403G | S:D614G | 25 | SNP | Spike protein |
G23948T | S:D796Y | 25 | ||
C23202A | S:T547K | 25 | ||
C24130A | S:N856K | 25 | ||
T23599G | S:N679K | 25 | ||
T24469A | S:N969K | 25 | ||
C23604A | S:P681H | 25 | ||
C24503T | S:L981F | 25 | ||
A24424T | S:Q954H | 24 | ||
C23854A | S:N764K | 24 | ||
C23525T | S:H655Y | 24 | ||
G22813T | S:K417N | 24 | ||
G22578A | S:G339D | 24 | ||
T22195G | S:N211K | 23 | ||
A23040G | S:Q493R | 22 | ||
TC22673CT | S:S371L | 22 | ||
T22679C | S:S373P | 22 | ||
C22686T | S:S375F | 22 | ||
G22992A | S:S477N | 22 | ||
C22995A | S:T478K | 22 | ||
A23013C | S:E484A | 22 | ||
G22898A | S:G446S | 21 | ||
C10029T | NSP4:T492I | 25 | SNP SNP | Transmembrane protein |
A11537G | NSP6:I189V | 25 | ||
11286TGTCTGGTT | NSP6:L105 | 24 | Deletion | |
G8393A | NSP3:A1892T | 25 | SNP | Predicted phosphoesterase |
A2832G | NSP3:K38R | 24 | SNP | |
6513GTT | NSP3:S1265 | 24 | Deletion | |
C28311T | N:P13L | 24 | SNP | Nucleocapsid protein |
GGG2881AAC | N:RG203KR | 24 | ||
G26709A | M:A63T | 24 | SNP | Membrane |
A26530G | M:D3G | 22 | ||
C26577G | M:Q19E | 24 | ||
C26270T | E:T9I | 25 | SNP | Envelope |
A18163G | NSP14:I42V | 22 | SNP | 3′-to-5′ exonuclease |
C10449A | NSP5:P132H | 24 | SNP | 3C-like proteinase |
C14408T | NSP12b:P314L | 25 | SNP | RNA-dependent RNA polymerase |
A28271T | 3′UTR:28271 | 25 | Extragenic | 3′ Untranslated Region |
C241T | 5′UTR:241 | 24 | Extragenic | 5′ Untranslated Region |
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Menasria, T.; Aguilera, M. Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Microorganisms 2022, 10, 467. https://doi.org/10.3390/microorganisms10020467
Menasria T, Aguilera M. Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Microorganisms. 2022; 10(2):467. https://doi.org/10.3390/microorganisms10020467
Chicago/Turabian StyleMenasria, Taha, and Margarita Aguilera. 2022. "Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect?" Microorganisms 10, no. 2: 467. https://doi.org/10.3390/microorganisms10020467