Pasteur Institute of Iran
Journal of Medical Microbiology and Infectious Diseases
Thu, Apr 25, 2024
Volume 10, Issue 3 (9-2022)
JoMMID 2022, 10(3): 141-145 |
Back to browse issues page
Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:
Maleki A, Fereydouni Z, Tavakoli M, Ezani A, Hosseini M, Nemati A H, et al . Novel Mutations Associated with N-Gene Target Failure in SARS-COV-2 Genome in Iran, Case Series. JoMMID 2022; 10 (3) :141-145
URL: http://jommid.pasteur.ac.ir/article-1-484-en.html
URL: http://jommid.pasteur.ac.ir/article-1-484-en.html
Ali Maleki 
, Zahra Fereydouni , Mahsa Tavakoli , Akram Ezani , Mirshamsedin Hosseini , Amir Hesam Nemati , Parastoo Yektay Sanat , Tahmineh Jalali , Mohammad Hassan Pouriayevali , Mostafa Salehi-Vaziri
, Zahra Fereydouni , Mahsa Tavakoli , Akram Ezani , Mirshamsedin Hosseini , Amir Hesam Nemati , Parastoo Yektay Sanat , Tahmineh Jalali , Mohammad Hassan Pouriayevali , Mostafa Salehi-Vaziri
COVID-19 National Reference Laboratory, Pasteur Institute of Iran, Pasteur Ave., 1316943551, Tehran, Iran
Abstract: (842 Views)
Precision tracking and monitoring viral genome mutations are critical during a viral pandemic such as COVID-19. As molecular assays for diagnosing numerous infectious agents are being developed, RT-PCR is still deployed as the gold standard for detecting SARS-CoV-2. Despite its proofreading capability, SARS-CoV-2, like other RNA viruses, adopts several changes in its genome. If these mutations, especially deletions, occur in the target areas of primers and probes, they will hinder molecular detection methods from identifying the given gene. The authors describe the cases in which, despite the lack of the N gene detection, the ORF1ab gene was discovered with a relatively low cycle of threshold (Ct). Following sequencing, changes were discovered in the annealing region of the forward and reverse primers and probes used in the SARS-CoV-2 detection kit. Among the most significant mutations is a large deletion of 15 nucleotides in the N gene, which has never been seen in prior variants. This highlights the importance of persistent monitoring of hypervariable regions in the SARS-CoV-2 genome through sequencing and updating the molecular detection kits during the COVID-19 pandemic.
Type of Study: Case Report |
Subject:
Infectious diseases and public health
Received: 2022/07/6 | Accepted: 2022/09/19 | Published: 2022/10/12
Received: 2022/07/6 | Accepted: 2022/09/19 | Published: 2022/10/12
References
1. WHO. COVID-19 weekly epidemiological update, 29 Jun 2022. World Health Organization. 2022; Edition 98.
2. Robson F, Khan KS, Le TK, Paris C, Demirbag S, Barfuss P, et al. Coronavirus RNA Proofreading: Molecular Basis and Therapeutic Targeting. Molecular Cell. 2020; 79 (5): 710-27. [DOI:10.1016/j.molcel.2020.07.027]
3. Koyama T, Platt D, Parida L. Variant analysis of SARS-CoV-2 genomes. Bull World Health Organ. 2020; 98 (7): 495-504. [DOI:10.2471/BLT.20.253591]
4. Tegally H, Wilkinson E, Giovanetti M, Iranzadeh A, Fonseca V, Giandhari J, et al. Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa. medRxiv. 2020:2020.12.21.20248640. [DOI:10.1101/2020.12.21.20248640]
5. Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, et al. Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data. medRxiv. 2021:2020.12.30.20249034. [DOI:10.1101/2020.12.30.20249034]
6. Salehi-Vaziri M, Fazlalipour M, Seyed Khorrami SM, Azadmanesh K, Pouriayevali MH, Jalali T, et al. The ins and outs of SARS-CoV-2 variants of concern (VOCs). Arch Virol. 2022; 167 (2): 327-44. [DOI:10.1007/s00705-022-05365-2]
7. Naveca F, da Costa C, Nascimento V, Souza V, Corado A, Nascimento F, et al. SARS-CoV-2 reinfection by the new
8. Variant of Concern (VOC) P. 1 in Amazonas, Brazil. virological org Preprint available at: https://virological org/t/sars-cov-2-reinfection-by-thenew-variant-of-concern-voc-p-1-in-amazonas-brazil/596 Available at: https://virological org/t/sars-cov-2-reinfection-by-the-new-variant-of-concern-voc-p-1-in-amazonas-brazil/596. 2021.
9. Ferreira I, Datir R, Papa G, Kemp S, Meng B, Rakshit P, et al. SARS-CoV-2 B.1.617 emergence and sensitivity to vaccine-elicited antibodies. bioRxiv. 2021: 2021.05.08.443253.
10. Weisblum Y, Schmidt F, Zhang F, DaSilva J, Poston D, Lorenzi JC, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife. 2020; 9: e61312. [DOI:10.7554/eLife.61312]
11. Lu R, Niu P, Zhao L, Wang H, Wang W, Tan W. Sequencing the complete genome of COVID-19 virus from clinical samples using the Sanger Method. China CDC Wkly. 2020;2 (25): 447-52. [DOI:10.46234/ccdcw2020.088]
12. Salehi-Vaziri M, Jalali T, Farahmand B, Fotouhi F, Banifazl M, Pouriayevali MH, et al. Clinical characteristics of SARS-CoV-2 by re-infection vs. reactivation: a case series from Iran. Eur J Clin Microbiol Infect Dis. 2021; 40 (8): 1713-9. [DOI:10.1007/s10096-021-04221-6]
13. Hu B, Guo H, Zhou P, Shi Z-L. Characteristics of SARS-CoV-2 and COVID-19. Nat Rev Microbiol. 2021; 19 (3): 141-54. [DOI:10.1038/s41579-020-00459-7]
14. wwwgovuk [Internet]2020. [cited 2020]. Available from: https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/961299/Variants_of_Concern_VOC_Technical_Briefing_6_England-1.pdf.
15. Dutta NK, Mazumdar K, Gordy JT. The Nucleocapsid Protein of SARS-CoV-2: a Target for Vaccine Development. J Virol. 2020; 94 (13): e00647-20. [DOI:10.1128/JVI.00647-20]
16. Le Bert N, Tan AT, Kunasegaran K, Tham CYL, Hafezi M, Chia A, et al. SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls. Nature. 2020; 584 (7821): 457-62. [DOI:10.1038/s41586-020-2550-z]
17. Bohn MK, Mancini N, Loh TP, Wang C-B, Grimmler M, Gramegna M, et al. IFCC interim guidelines on molecular testing of SARS-CoV-2 infection. Clin Chem Lab Med. 2020; 58 (12): 1993-2000. [DOI:10.1515/cclm-2020-1412]
18. Vogels C, Fauver J, Grubaugh N. Multiplexed RT-qPCR to screen for SARS-COV-2 B. 1.1. 7. B.1:1.
19. Bozidis P, Tsaousi ET, Kostoulas C, Sakaloglou P, Gouni A, Koumpouli D, et al. Unusual N Gene Dropout and Ct Value Shift in Commercial Multiplex PCR Assays Caused by Mutated SARS-CoV-2 Strain. Diagnostics. 2022; 12 (4): 973. [DOI:10.3390/diagnostics12040973]
20. Wollschläger P, Todt D, Gerlitz N, Pfaender S, Bollinger T, Sing A, et al. SARS-CoV-2 N gene dropout and N gene Ct value shift as indicator for the presence of B.1.1.7 lineage in a commercial multiplex PCR assay. Clin Microbiol Infect. 2021; 27 (9): 1353.e1-.e5. [DOI:10.1016/j.cmi.2021.05.025]
21. Sánchez-Calvo JM, Alados Arboledas JC, Ros Vidal L, de Francisco JL, López Prieto MD. Diagnostic pre-screening method based on N-gene dropout or delay to increase feasibility of SARS-CoV-2 VOC B.1.1.7 detection. Diagn Microbiol Infect Dis. 2021; 101 (4): 115491. [DOI:10.1016/j.diagmicrobio.2021.115491]
22. Jung Y, Park G-S, Moon JH, Ku K, Beak S-H, Lee C-S, et al. Comparative Analysis of Primer-Probe Sets for RT-qPCR of COVID-19 Causative Virus (SARS-CoV-2). ACS Infect Dis. 2020; 6 (9): 2513-23. [DOI:10.1021/acsinfecdis.0c00464]
23. Hadfield J, Megill C, Bell SM, Huddleston J, Potter B, Callender C, et al. Nextstrain: real-time tracking of pathogen evolution. Bioinformatics. 2018; 34 (23): 4121-3. [DOI:10.1093/bioinformatics/bty407]
Send email to the article author
| Rights and permissions | |
 |
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.