Determine the Whole Genome Sequences of SARS-COV-2 Isolated from Iraqi Patients Using NGS Method
DOI:
https://doi.org/10.54133/ajms.v6i2.777Keywords:
SARS corona virus-2, WGS, NGSAbstract
Background: Next-generation sequencing (NGS) can monitor the transmission of COVID-19 and viral alterations. Objectives: To provide information about testing techniques and infection control measures, as well as to direct the development of vaccines and treatments for the Corona virus. Methods: Six Iraqi SARS-CoV-2 strains were investigated using whole-genome sequencing using the next-generation sequencing method. The sequencing was carried out with an Illumina MiSeq system, and phylogenetic analysis was carried out for all Iraqi sequences retrieved from GISAID. Results: The analysis of the isolates from this study showed that all the sequences from the most recent wave, which happened in the summer of 2022, were primarily clustered in the 20A clades and the 21K, 21L (Omicron) clades, as determined by the GISAID and Nextclade systems. On the other hand, the PANGO system revealed that six sequences were of the BA.1 lineage in Iraq, while four were of the BA.2 lineage. We found that throughout the country's subsequent pandemic waves, SARS-CoV-2 clades and their lineages exhibited circulation patterns and dominance. Conclusions: NGS continues to supply vital COVID-19 evidence to academics, vaccine and medication makers, and public health regulators.
Downloads
References
Sulayman N. Deep learning-based predictive model of mRNA vaccine deterioration: An analysis of the stanford COVID-19 mRNA vaccine dataset. Baghdad Sci J. 2023;20(4 (SI)):1451-1458. doi: 10.21123/bsj.2023.8504.
Zhu FC, Li YH, Guan XH, Hou LH, Wang WJ, Li JX, et al. Safety, tolerability, and immunogenicity of a recombinant adenovirus type-5 vectored COVID-19 vaccine: a dose-escalation, open-label, non-randomised, first-in-human trial. Lancet. 2020;395(10240):1845-1854. doi: 10.1016/S0140-6736(20)31208-3.
Hamid MK. Impact of COVID-19 vaccine on hearing status of young ages (Medical College students as a sample). Baghdad Sci J. 2023;20(4):1498-1506. doi: 10.21123/bsj.2023.8694.
Yousif MG, Hashim K, Rawaf S. Post COVID-19 effect on medical staff and doctors' productivity analysed by machine learning. Baghdad Sci J. 2023;20(4):1507-1519. doi: 10.21123/bsj.2023.8875.
Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. nature. 2020;579(7798):270-273. doi: 10.1038/s41586-020-2012-7.
Almashhadani AD, AL-Thwani AN. Determination of angiotensin-converting enzyme 2 (ACE2) receptor level in samples of Iraqi patients infected with COVID-19. Iraqi J Biotechnol. 2022;21(2)178-182.
Auda IG, Auda J, Salih RH. SARS-CoV-2 and other Coronaviruses: A matter of variations. Al-Kindy Coll Med J. 2023;19(1):5-10.doi: 10.47723/kcmj.v19i1.927.
Guo YR, Cao QD, Hong ZS, Tan YY, Chen SD, Jin HJ, et al. The origin, transmission and clinical therapies on coronavirus disease 2019 (COVID-19) outbreak–an update on the status. Military Med Res. 2020;7:1-10. doi: 10.1186/s40779-020-00240-0.
Abduallah ZS, AL-Thwani AN, Almashhadani AD, Mohsin MI. Estimation of CRP and some hematological parameters with COVID-19 patients using ANOVA as a statistical tool. Nat Volatile Essent Oils. 2021;8(5):8915-8919.
Zalzala HH. Diagnosis of COVID-19: facts and challenges. New Microbes New Infect. 2020;38:100761. doi: 10.1016/j.nmni.2020.100761.
Kradi AM, Al-Faisal AHM, Turki AM. Alteration of M and N genes of corona virus 2 (SARS-CoV-2). Iraqi J Biotechnol. 2022;21(2):39-45.
Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T, Erichsen S, et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 2020;181(2):271-280. doi: 10.1016/j.cell.2020.02.052.
Oude Munnink BB, Nieuwenhuijse DF, Stein M, O’Toole Á, Haverkate M, Mollers M, et al. Rapid SARS-CoV-2 whole-genome sequencing and analysis for informed public health decision-making in the Netherlands. Nature Med. 2020;26(9):1405-1410. doi: 10.1038/s41591-020-0997-y.
Alpdagtas S, Ilhan E, Uysal E, Sengor M, Ustundag CB, Gunduz O. Evaluation of current diagnostic methods for COVID-19. APL Bioengineer. 2020;4(4):041506. doi: 10.1063/5.0021554.
Elbe S, Buckland‐Merrett G. Data, disease, and diplomacy: GISAID's innovative contribution to global health. Global Challenges. 2017;1(1):33-46. doi: 10.1002/gch2.1018.
Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data–from vision to reality. Eurosurveillance. 2017;22(13):30494. doi: 10.2807/1560-7917.ES.2017.22.13.30494.
Ghazzi JJ, Fadhil HY, Aufi IM. Impact of SARS-COV-2 Variants on the Infection Severity among Iraqi Patients. Iraqi J Sci. 2023:3263-3272. doi: 10.24996/ijs.2023.64.7.7.
Al-Janabi MK, Al-Ahmer SD, Al-Ganabi AD, Aufi IM, editors. Rapid and accurate molecular detection of adenovirus associated with gastroenteritis children in Baghdad city. AIP Conference Proceedings. 2022; 2398(1). doi: 10.1063/5.0093770.
Andrews S. Fast QC: a quality control tool for high throughput sequence data. Cambridge, United Kingdom; 2010.
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114-2120. doi: 10.1093/bioinformatics/btu170.
Li H, Durbin R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics. 2009;25(14):1754-1760. doi: 10.1093/bioinformatics/btu170.
Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, et al. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579(7798):265-269. doi: 10.1038/s41586-020-2008-3.
Database resources of the national genomics data center in 2020. Nucleic Acids Res. 2020;48(D1):D24-D33. doi: 10.1093/nar/gkz913.
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):4121-4123. doi: 10.1093/bioinformatics/bty407.
Katoh K, Asimenos G, Toh H. Multiple alignment of DNA sequences with MAFFT. Methods in Molecular Biology (Clifton, N.J.). 2009:537:39-64. doi: 10.1007/978-1-59745-251-9_3.
Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evolu. 2015;32(1):268-274. doi: 10.1093/molbev/msu300.
Rambaut A, Holmes EC, O’Toole Á, Hill V, McCrone JT, Ruis C, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nature Microbiol. 2020;5(11):1403-1407. doi: 10.1038/s41564-020-0770-5.
GISAID. lineage nomenclature aids in genomic epidemiology studies of active hCoV-19 viruses. Clade and Lineage Nomenclature, March 2, 2021. Available at: https://gisaid.org/resources/statements-clarifications/clade-and-lineage-nomenclature-aids-in-genomic-epidemiology-of-active-hcov-19-viruses/
Alhussien TAA, Fadhil HY. Analysis of mutations in conserved and susceptible regions across the whole genome sequencing analysis for SARS-CoV-2 in Iraqi patients. Iraqi J Sci. 2023:56-64. doi: 10.24996/ijs.2023.64.1.6.
Dearlove B, Lewitus E, Bai H, Li Y, Reeves DB, Joyce MG, et al. A SARS-CoV-2 vaccine candidate would likely match all currently circulating variants. Proc Natl Acad Sci USA. 2020;117(38):23652-23662. doi: 10.1073/pnas.2008281117.
Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, et al. Tracking changes in SARS-CoV-2 spike evidence that D614G increases infectivity of the COVID-19 virus. Cell. 2020;182(4):812-827. doi: 10.1016/j.cell.2020.06.043.
Cleemput S, Dumon W, Fonseca V, Abdool Karim W, Giovanetti M, Alcantara LC, et al. Genome detective coronavirus typing tool for rapid identification and characterization of novel coronavirus genomes. Bioinformatics. 2020;36(11):3552-3555. doi: 10.1093/bioinformatics/btaa145.
Michel CJ, Mayer C, Poch O, Thompson JD. Characterization of accessory genes in coronavirus genomes. Virol J. 2020;17:1-13. doi: 10.1186/s12985-020-01402-1.
Mahmood ZS, Fadhil HY, Hussein TAA, Ad'hiah AH. The severity of coronavirus disease 19: Profile of inflammatory markers and ACE (rs4646994) and ACE2 (rs2285666) gene polymorphisms in Iraqi patients. Meta Gene. 2022;31:101014. doi: 10.1016/j.mgene.2022.101014.
Downloads
Published
How to Cite
Issue
Section
License
Copyright (c) 2024 Al-Rafidain Journal of Medical Sciences ( ISSN 2789-3219 )
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Published by Al-Rafidain University College. This is an open access journal issued under the CC BY-NC-SA 4.0 license (https://creativecommons.org/licenses/by-nc-sa/4.0/).