Comparison of Circulating Variants during the Beginning, Middle and the End of the 4th Wave of COVID-19 in Tehran Province, Iran in 2021
-
Akram Sadat Ahmadi
,
Nazanin Zahra Shafiei–Jandaghi
,
Kaveh Sadeghi
,
Ahmad Nejati
,
Sevrin Zadheidar
,
Talat Mokhtari-Azad
,
Jila Yavarian
Abstract
Background: Whole viral genome sequencing with next generation sequencing (NGS) technique is useful tool for determining the diversity of variants and mutations of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2). In this study we have attempted to characterize the mutations and circulating variants of the SARS-CoV-2 genome during the 4th wave of COVID-19 pandemic in Tehran, Iran in 2021.
Methods: We performed complete genome sequencing of 15 SARS-CoV-2 detected from 15 COVID-19 patients during the 4th wave of COVID-19 pandemic with NGS. Three groups of the patients at the beginning, middle and the end of the 4th wave were compared together.
Results: We detected alpha and delta variants during the 4th wave of the pandemic. The results illustrated a dominance of amino acid substitution D614G in spike, and the most frequent mutants were N-R203K, G204R, S235F, nsp12-P323L, nsp6-G106del, G107del and F108del.
Conclusion: The detection of the virus mutations is a useful procedure for identifying the virus behavior and its genetic evolution in order to improve the efficacy of the monitoring strategies and therapeutic measures.
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2. Yavarian J, Shafiei-Jandaghi N-Z, Sadeghi K, et al (2020). First cases of SARS-CoV-2 in Iran, 2020: case series report. Iran J Public Health, 49(8):1564-1568.
3. Yavarian J, Nejati A, Salimi V, et al (2022). Whole genome sequencing of SARS-CoV2 strains circulating in Iran during five waves of pandemic. PLoS One,17(5):e0267847.
4. Sadeghi K, Zadheidar S, Zebardast A, et al (2023). Genomic surveillance of SARS‐CoV‐2 strains circulating in Iran during six waves of the pandemic. Influenza Other Respir Viruses, 17(4):e13135.
5. Yadav PD, Nyayanit DA, Majumdar T, et al (2021). An epidemiological analysis of SARS-CoV-2 genomic sequences from different regions of India. Viruses, 13(5):925.
6. Pachetti M, Marini B, Benedetti F, et al (2020). Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med, 18(1):179.
7. Menasria T, Aguilera M. (2022). Genomic Diversity of SARS-CoV-2 in Algeria and North African Countries: What We Know So Far and What We Expect? Microorganisms, 10(2):467.
8. Anwar MZ, Lodhi MS, Khan MT, et al (2022). Coronavirus Genomes and Unique Mutations in Structural and Non-Structural Proteins in Pakistani SARS-CoV-2 Delta Variants during the Fourth Wave of the Pandemic. Genes (Basel), 13(3):552.
9. WHO. Tracking-SARS-CoV-2-variants 2022 [Acsseded on 3 December 2022]
10. Mboowa G, Mwesigwa S, Kateete D, et al (2021). Whole-genome sequencing of SARS-CoV-2 in Uganda: imple-mentation of the low-cost ARTIC pro-tocol in resource-limited settings. F1000Res, 10:598.
11. Fibriani A, Stephanie R, Alfiantie AA, et al (2021). Analysis of SARS-CoV-2 Genomes from West Java, Indonesia. Viruses, 13(10):2097.
12. Victor Corman TB, Sebastian Brünink, Christian Drosten. Diagnostic detection of 2019-nCoV by real-time RT-PCR-Protocol and preliminary evaluation as of Jan 17, 2020-. In: Charité Virology B, Germany, editor. Berlin, Germany 2020.
13. Shu Y, McCauley J (2017). GISAID: Global initiative on sharing all influen-za data–from vision to reality. Euro Surveill, 22(13):30494.
14. Flores-Vega VR, Monroy-Molina JV, Ji-ménez-Hernández LE, et al. (2022). SARS-CoV-2: Evolution and Emer-gence of New Viral Variants. Virus-es,14(4):653.
15. Tian D, Sun Y, Zhou J, Ye Q (2021). The global epidemic of the SARS-CoV-2 delta variant, key spike muta-tions and immune escape. Front Immu-nol, 12:751778.
16. Saito A, Nasser H, Uriu K, et al. (2021). SARS-CoV-2 spike P681R mutation enhances and accelerates viral fusion. bioRxiv, Published online June. 17:2021.06.
17. Groves DC, Rowland-Jones SL, Angyal A (2021). The D614G mutations in the SARS-CoV-2 spike protein: Implications for viral infectivity, disease severity and vaccine design. Biochem Biophys Res Commun, 538:104-107.
18. Wu H, Xing N, Meng K, et al (2021). Nucleocapsid mutations R203K/G204R increase the infectivity, fitness, and virulence of SARS-CoV-2. Cell Host Microbe, 29(12):1788-1801. e6.
19. Shen L, Bard JD, Triche TJ, et al (2021). Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications. Emerg Microbes Infect,10(1):885-93.
20. Kangarshahi ZT, Lak S, Ghadam M, et al (2021). The proteins of sars-cov-2 and their functions. Mil Med Sci Lett (Voj. Zdrav. Listy), 90(4):172-190
21. Fooladinezhad H, Shahidi M, Mahmanzar M, et al. (2022). SARS-CoV-2 NSP3, NSP4 and NSP6 mutations and Epistasis during the pandemic in the world: Evolutionary Trends and Natural Selections in Six Continents. medRxiv 2022.05.22.22275422.
22. Mazhari S, Alavifard H, Rahimian K, et al (2021). SARS-CoV-2 NSP-12 mutations survey during the pandemic in the world. 2021. Preprint from Research Square, 22 Sep 2021. https://doi.org/10.21203/rs.3.rs-877078/v1
23. Chand GB, Banerjee A, Azad GK ( 2020). Identification of novel mutations in RNA-dependent RNA polymerases of SARS-CoV-2 and their implications on its protein structure. PeerJ, 8:e9492.
24. Mari A, Roloff T, Stange M, et al (2021). Global genomic analysis of SARS-CoV-2 RNA dependent RNA polymerase evolution and antiviral drug resistance. Microorganisms, 9(5):1094.
25. Pitts J, Li J, Perry JK, et al (2022). Remdesivir and GS-441524 retain antiviral activity against Delta, Omicron, and other emergent SARS-CoV-2 variants. Antimicrob Agents Chemother, 66(6):e0022222.
26. Redondo N, Zaldívar-López S, Garrido JJ, Montoya M (2021). SARS-CoV-2 accessory proteins in viral pathogenesis: knowns and unknowns. Front Immunol, 12:708264.
27. Nguyen TT, Pathirana PN, Nguyen T, et al (2021). Genomic mutations and changes in protein secondary structure and solvent accessibility of SARS-CoV-2 (COVID-19 virus). Sci Rep,11(1):3487.
28. Mahmood TB, Saha A, Hossan MI, et al (2021). A next generation sequencing (NGS) analysis to reveal genomic and proteomic mutation landscapes of SARS-CoV-2 in South Asia. Curr Res Microb Sci, 2:100065.
| Files | ||
| Issue | Vol 52 No 12 (2023) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijph.v52i12.14323 | |
| Keywords | ||
| SARS-CoV-2 Genome sequencing Mutation Variant COVID-19 | ||
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How to Cite
1.
Ahmadi AS, Shafiei–Jandaghi NZ, Sadeghi K, Nejati A, Zadheidar S, Mokhtari-Azad T, Yavarian J. Comparison of Circulating Variants during the Beginning, Middle and the End of the 4th Wave of COVID-19 in Tehran Province, Iran in 2021. Iran J Public Health. 2023;52(12):2621-2629.
