Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection
2.2. Whole-Genome Sequencing
2.3. Genome Assembly
2.4. Variant Detection by Partial Sequencing of the S Gene
2.5. Variant Detection by Real-Time RT-PCR
2.6. Clade and Lineage Assignment
2.7. Phylogenetic Analysis
3. Results
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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Wave 1 | Wave 2 | Wave 3 | Begining of Wave 4 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
WHO | GISAID Clade | Nextstrain Clade | Methodolgy | Pango Lineage | Mar-20 | Apr-20 | Jun-20 | Jul-20 | Aug-20 | Sep-20 | Oct-20 | Nov-20 | Dec-20 | Jan-21 | Feb-21 | Mar-21 | Apr-21 | May-21 | Jun-21 | Jul-21 | Total |
WGS | B.1.153 | 1 | 1 | 2 | |||||||||||||||||
WGS | B.1.1 * | 1 | 4 | 5 | 6 | 1 | 5 | 2 | 1 | 1 | 26 | ||||||||||
20A | WGS | B.1.36.10 | 1 | 1 | |||||||||||||||||
WGS | B.1 * | 12 | 9 | 2 | 1 | 7 | 4 | 4 | 13 | 1 | 12 | 5 | 7 | 8 | 7 | 92 | |||||
WGS | B.1.520 | 1 | 1 | ||||||||||||||||||
19A | WGS | B.4 | 3 | 3 | |||||||||||||||||
20A | WGS | B.1.36 | 1 | 1 | |||||||||||||||||
20A | WGS | B.1.398 | 1 | 1 | |||||||||||||||||
20A | WGS | B.1.214 | 2 | 2 | |||||||||||||||||
20B | WGS | B.1.1.50 | 6 | 1 | 7 | ||||||||||||||||
20C | WGS | B.1.597 | 1 | 1 | 2 | ||||||||||||||||
20D | WGS | B.1.1.1 | 1 | 1 | 2 | ||||||||||||||||
20A | WGS | B.1.22 | 2 | 1 | 2 | 5 | |||||||||||||||
20C | WGS | B.1.428.2 | 2 | 2 | 6 | 3 | 2 | 1 | 16 | ||||||||||||
20B | WGS | B.1.1.25 | 2 | 2 | |||||||||||||||||
20B | WGS | B.1.1.198 | 1 | 2 | 1 | 1 | 1 | 6 | |||||||||||||
20B | WGS | B.1.1.189 | 1 | 3 | 4 | ||||||||||||||||
WGS | B.1.1.354 | 1 | 1 | ||||||||||||||||||
20E | WGS | B.1.177 | 2 | 7 | 6 | 2 | 6 | 4 | 7 | 4 | 38 | ||||||||||
20A | WGS | B.1.160 | 3 | 15 | 15 | 3 | 11 | 13 | 26 | 1 | 1 | 88 | |||||||||
WGS | B.1.111 | 1 | 1 | 2 | |||||||||||||||||
20A | WGS | B.1.389 | 1 | 1 | |||||||||||||||||
WGS | B.1.575 | 1 | 2 | 1 | 4 | ||||||||||||||||
20A | WGS | B.1.473 | 1 | 1 | |||||||||||||||||
20C | WGS | B.1.595 | 1 | 1 | |||||||||||||||||
WGS | B.1.623 | 1 | 1 | ||||||||||||||||||
20A | WGS | B.1.236 | 1 | 1 | 2 | ||||||||||||||||
WGS | B.1.535 | 1 | 1 | ||||||||||||||||||
20A | WGS | B.1.533 | 1 | 1 | 2 | ||||||||||||||||
Alpha | GRY | 20I | WGS | B.1.1.7 | 1 | 25 | 79 | 11 | 6 | 1 | 713 | ||||||||||
PS/qRT-PCR | 1 | 3 | 113 | 79 | 277 | 112 | 5 | ||||||||||||||
20A | WGS | B.1.416 | 1 | 1 | 2 | ||||||||||||||||
WGS | B * | 1 | 1 | ||||||||||||||||||
20A | WGS | B.1.243 | 1 | 1 | |||||||||||||||||
Zeta | 20B | WGS | P.2 | 4 | 1 | 5 | |||||||||||||||
19B | WGS | A.27 | 8 | 6 | 3 | 23 | |||||||||||||||
PS | 3 | 2 | 1 | ||||||||||||||||||
19B | WGS | A.23.1 | 1 | 1 | 2 | ||||||||||||||||
WGS | B.1.415.1 | 1 | 1 | ||||||||||||||||||
Eta | G/484K.V3 | 21D | WGS | B.1.525 | 2 | 6 | 1 | 1 | 20 | ||||||||||||
PS | 3 | 5 | 2 | ||||||||||||||||||
20A | WGS | B.1.160.14 | 2 | 2 | |||||||||||||||||
20A | WGS | B.1.160.28 | 2 | 2 | |||||||||||||||||
Beta | GH/501Y.V2 | 20H | WGS | B.1.351 | 1 | 2 | |||||||||||||||
PS | 1 | ||||||||||||||||||||
WGS | B.1.1.178 | 1 | 1 | ||||||||||||||||||
G | 20A/S:126A | WGS | B.1.620 | 2 | 1 | 3 | |||||||||||||||
20E | WGS | B.1.1.318 | 2 | 6 | 1 | 9 | |||||||||||||||
20G | WGS | B.1.2 | 2 | 2 | |||||||||||||||||
Delta | G/478K.V1 | 21A,21I,21J | WGS | B.1.617.2 | 4 | 84 | 16 | 253 | |||||||||||||
PS | 6 | 92 | 51 | ||||||||||||||||||
20C/S:80Y | WGS | B.1.367 | 1 | 1 | |||||||||||||||||
WGS | B.1.629 | 1 | 1 | ||||||||||||||||||
Total | 15 | 18 | 6 | 7 | 20 | 21 | 43 | 49 | 10 | 36 | 46 | 197 | 193 | 313 | 310 | 74 | 1359 |
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Chouikha, A.; Fares, W.; Laamari, A.; Haddad-Boubaker, S.; Belaiba, Z.; Ghedira, K.; Kammoun Rebai, W.; Ayouni, K.; Khedhiri, M.; Ben Halima, S.; et al. Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19. Viruses 2022, 14, 624. https://doi.org/10.3390/v14030624
Chouikha A, Fares W, Laamari A, Haddad-Boubaker S, Belaiba Z, Ghedira K, Kammoun Rebai W, Ayouni K, Khedhiri M, Ben Halima S, et al. Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19. Viruses. 2022; 14(3):624. https://doi.org/10.3390/v14030624
Chicago/Turabian StyleChouikha, Anissa, Wasfi Fares, Asma Laamari, Sondes Haddad-Boubaker, Zeineb Belaiba, Kais Ghedira, Wafa Kammoun Rebai, Kaouther Ayouni, Marwa Khedhiri, Samar Ben Halima, and et al. 2022. "Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19" Viruses 14, no. 3: 624. https://doi.org/10.3390/v14030624
APA StyleChouikha, A., Fares, W., Laamari, A., Haddad-Boubaker, S., Belaiba, Z., Ghedira, K., Kammoun Rebai, W., Ayouni, K., Khedhiri, M., Ben Halima, S., Krichen, H., Touzi, H., Ben Dhifallah, I., Guerfali, F. Z., Atri, C., Azouz, S., Khamessi, O., Ardhaoui, M., Safer, M., ... Triki, H. (2022). Molecular Epidemiology of SARS-CoV-2 in Tunisia (North Africa) through Several Successive Waves of COVID-19. Viruses, 14(3), 624. https://doi.org/10.3390/v14030624