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ORIGINAL RESEARCH

Mutational Analysis of Circulating Omicron SARS-CoV-2 Lineages in the Al-Baha Region of Saudi Arabia

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Pages 2117-2136 | Received 31 May 2023, Accepted 20 Jul 2023, Published online: 27 Jul 2023

References

  • Chen B, Tian E-K, He B, et al. Overview of lethal human coronaviruses. Signal Transduction Targeted Therapy. 2020;5(1):89.
  • Tabibzadeh A, Zamani F, Laali A, et al. SARS-CoV-2 molecular and phylogenetic analysis in COVID-19 patients: a preliminary report from Iran. Infect Genetics Evolution. 2020;84:104387.
  • Hui DS, Azhar EI, Madani TA, et al. The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health—The latest 2019 novel coronavirus outbreak in Wuhan, China. Int j Infectious Dis. 2020;91:264–266.
  • Tan W, Zhao X, Ma X, et al. A novel coronavirus genome identified in a cluster of pneumonia cases—Wuhan, China 2019− 2020. China CDC Weekly. 2020;2(4):61–62.
  • Zhu N, Zhang D, Wang W, et al. A novel coronavirus from patients with pneumonia in China, 2019. N Eng j Med. 2020;2:643.
  • Linka K, Peirlinck M, Kuhl E. The reproduction number of COVID-19 and its correlation with public health interventions. Computational Mechanics. 2020;66:1035–1050.
  • Brant AC, Tian W, Majerciak V, Yang W, Zheng Z-M. SARS-CoV-2: from its discovery to genome structure, transcription, and replication. Cell Biosci. 2021;11(1):1–17.
  • Chan JF-W, Kok K-H, Zhu Z, et al. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan. Em Microbes Infections. 2020;9(1):221–236.
  • Rohaim MA, El Naggar RF, Clayton E, Munir M. Structural and functional insights into non-structural proteins of coronaviruses. Microb Pathog. 2021;150:104641.
  • Atzrodt CL, Maknojia I, McCarthy RD, et al. A Guide to COVID‐19: a global pandemic caused by the novel coronavirus SARS‐CoV‐2. FEBS J. 2020;287(17):3633–3650.
  • Su S, Wong G, Shi W, et al. Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends Microbiol. 2016;24(6):490–502.
  • Amicone M, Borges V, Alves MJ, et al. Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolution. Evolution Med Public Health. 2022;10(1):142–155.
  • Callaway E. The Coronavirus is mutating—does It Matter? Nature Publishing Group; 2020.
  • Telenti A, Arvin A, Corey L, et al. After the pandemic: perspectives on the future trajectory of COVID-19. Nature. 2021;596(7873):495–504.
  • Harvey WT, Carabelli AM, Jackson B, et al. SARS-CoV-2 variants, spike mutations and immune escape. Nat Rev Microbiol. 2021;19(7):409–424.
  • World Health Organization. Tracking SARS-Cov-2 Variants. Available from: https://Www.Who.Int/En/Activities/Tracking-SARS-Cov-2-Variants/. Accessed July 24, 2023.
  • Zhang Y, Zhang H, Zhang W. SARS-CoV-2 variants, immune escape, and countermeasures. Front Med. 2022;16(2):196–207.
  • Kandeel M, Mohamed ME, El‐Lateef HM A, Venugopala KN, El‐Beltagi HS. Omicron variant genome evolution and phylogenetics. J Med Virol. 2022;94(4):1627–1632.
  • Gao SJ, Guo H, Luo G. Omicron variant (B. 1.1. 529) of SARS‐CoV‐2, a global urgent public health alert! J Med Virol. 2022;94(4):1255.
  • Kumar A, Parashar R, Kumar S, et al. Emerging SARS‐CoV‐2 variants can potentially break set epidemiological barriers in COVID‐19. J Med Virol. 2022;94(4):1300–1314.
  • Brookman S, Cook J, Zucherman M, Broughton S, Harman K, Gupta A. Effect of the new SARS-CoV-2 variant B. 1.1. 7 on children and young people. Lancet Child Adolescent Health. 2021;5(4):e9.
  • Kustin T, Harel N, Finkel U, et al. Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2-mRNA-vaccinated individuals. Nat Med. 2021;27(8):1379–1384.
  • Gao Q, Hu Y, Dai Z, Xiao F, Wang J, Wu J. The epidemiological characteristics of 2019 novel coronavirus diseases (COVID-19) in Jingmen, Hubei, China. Medicine. 2020;99(23):e20605. doi:10.1097/md.0000000000020605
  • Van Der Made CI, Simons A, Schuurs-Hoeijmakers J, et al. Presence of genetic variants among young men with severe COVID-19. JAMA. 2020;324(7):663–673.
  • Caputo E, Mandrich L. Structural and Phylogenetic Analysis of SARS-CoV-2 Spike Glycoprotein from the Most Widespread Variants. Life. 2022;12(8):74.
  • Tian D, Sun Y, Xu H, Ye Q. The emergence and epidemic characteristics of the highly mutated SARS-CoV-2 Omicron variant. J Med Virol. 2022;94(6):2376–2383. doi:10.1002/jmv.27643
  • Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. bioRxiv. 2021. 10.1101/2020.10.12.336644.
  • Braeye T, Catteau L, Brondeel R, et al. Vaccine effectiveness against onward transmission of SARS-CoV2-infection by variant of concern and time since vaccination, Belgian contact tracing, 2021. Vaccine. 2022;40(22):3027–3037. doi:10.1016/j.vaccine.2022.04.025
  • Parlikar A, Kalia K, Sinha S, et al. Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2. PeerJ. 2020;8:e9576. doi:10.7717/peerj.9576
  • McLean G, Kamil J, Lee B, et al. The impact of evolving SARS-CoV-2 mutations and variants on COVID-19 vaccines. MBio. 2022;13(2):e02979–21.
  • Wang P, Nair MS, Liu L, et al. Antibody resistance of SARS-CoV-2 variants B. 1.351 and B. 1.1. 7. Nature. 2021;593(7857):130–135.
  • Shen X, Tang H, McDanal C, et al. SARS-CoV-2 variant B. 1.1. 7 is susceptible to neutralizing antibodies elicited by ancestral spike vaccines. Cell Host Microbe. 2021;29(4):529–539. e3.
  • Edara VV, Hudson WH, Xie X, Ahmed R, Suthar MS. Neutralizing antibodies against SARS-CoV-2 variants after infection and vaccination. JAMA. 2021;325(18):1896–1898.
  • Corman VM, Landt O, Kaiser M, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Euro Surveillance. 2020;25:54.
  • Oliveira RRM, Costa Negri T, Nunes G, et al. PipeCoV: a pipeline for SARS-CoV-2 genome assembly, annotation and variant identification. PeerJ. 2022;10:e13300. doi:10.7717/peerj.13300
  • Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–477. doi:10.1089/cmb.2012.0021
  • Merkel D. Docker: lightweight Linux containers for consistent development and deployment. Linux Journal. 2014;2014:2.
  • O’Toole Á, Pybus OG, Abram ME, Kelly EJ, Rambaut A. Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences. BMC Genomics. 2022;23(1):121. doi:10.1186/s12864-022-08358-2
  • Robert CE. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32(5):1792–1797.
  • Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22(13):1658–1659.
  • Pettersen EF, Goddard TD, Huang CC, et al. UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem. 2004;25(13):1605–1612.
  • Singh H, Dahiya N, Yadav M, Sehrawat N. Emergence of SARS-CoV-2 New Variants and Their Clinical Significance. Canadian j Infect Dis Med Microbiol. 2022;2022:7336309. doi:10.1155/2022/7336309
  • Mannar D, Saville JW, Zhu X, et al. SARS-CoV-2 Omicron variant: antibody evasion and cryo-EM structure of spike protein-ACE2 complex. Science. 2022;375(6582):760–764. doi:10.1126/science.abn7760
  • Harris E. Study: no New SARS-CoV-2 Variants in Recent Outbreak in China. JAMA. 2023;329(10):788. doi:10.1001/jama.2023.2089
  • Silva S, Kohl A, Pena L, Pardee K. Recent insights into SARS-CoV-2 omicron variant. Rev Med Virol. 2023;33(1):e2373. doi:10.1002/rmv.2373
  • Vieillard-Baron A, Flicoteaux R, Salmona M, et al. Omicron Variant in the Critical Care Units of the Paris Metropolitan Area: the Reality Research Group. Am J Respir Crit Care Med. 2022;206(3):349–363. doi:10.1164/rccm.202202-0411LE
  • Mohseni Afshar Z, Tavakoli Pirzaman A, Karim B, et al. SARS-CoV-2 Omicron (B.1.1.529) Variant: a Challenge with COVID-19. Diagnostics. 2023;13(3):43.
  • Mourier T, Shuaib M, Hala S, et al. SARS-CoV-2 genomes from Saudi Arabia implicate nucleocapsid mutations in host response and increased viral load. Nat Commun. 2022;13(1):601. doi:10.1038/s41467-022-28287-8
  • Darwish DBE. Insight into SARS-CoV-2 Omicron variants in Saudi Arabian genomic isolates. Saudi Med J. 2022;43(11):1276–1279. doi:10.15537/smj.2022.43.11.20220381
  • Fonager J, Bennedbæk M, Bager P, et al. Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022. Euro Surveillance. 2022;27(10). doi:10.2807/1560-7917.es.2022.27.10.2200181
  • Yao L, Zhu KL, Jiang XL, et al. Omicron subvariants escape antibodies elicited by vaccination and BA.2.2 infection. Lancet Infect Dis. 2022;22(8):1116–1117. doi:10.1016/s1473-3099(22)00410-8
  • Tegally H, Moir M, Everatt J, et al. Emergence of SARS-CoV-2 Omicron lineages BA.4 and BA.5 in South Africa. Nat Med. 2022;28(9):1785–1790. doi:10.1038/s41591-022-01911-2
  • Feng Z, Shen Y, Li S, et al. The First Outbreak of Omicron Subvariant BA.5.2 - Beijing Municipality, China, July 4, 2022. China CDC Wkly. 2022;4(30):667–668. doi:10.46234/ccdcw2022.136
  • Ong CP, Ye ZW, Tang K, et al. Comparative analysis of SARS-CoV-2 Omicron BA.2.12.1 and BA.5.2 variants. J Med Virol. 2023;95(1):e28326. doi:10.1002/jmv.28326
  • Cao Y, Yisimayi A, Jian F, et al. BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature. 2022;608(7923):593–602. doi:10.1038/s41586-022-04980-y
  • Shrestha LB, Foster C, Rawlinson W, Tedla N, Bull RA. Evolution of the SARS-CoV-2 omicron variants BA.1 to BA.5: implications for immune escape and transmission. Rev Med Virol. 2022;32(5):e2381. doi:10.1002/rmv.2381
  • Zhao F, Ma Q, Yue Q, Chen H. SARS-CoV-2 Infection and Lung Regeneration. Clin Microbiol Rev. 2022;35(2):e0018821. doi:10.1128/cmr.00188-21
  • Pinto D, Park YJ, Beltramello M, et al. Cross-neutralization of SARS-CoV-2 by a human monoclonal SARS-CoV antibody. Nature. 2020;583(7815):290–295. doi:10.1038/s41586-020-2349-y
  • Callaway E. Heavily mutated Omicron variant puts scientists on alert. Nature. 2021;600(7887):21. doi:10.1038/d41586-021-03552-w
  • Cui Z, Liu P, Wang N, et al. Structural and functional characterizations of infectivity and immune evasion of SARS-CoV-2 Omicron. Cell. 2022;185(5):860–871.e13. doi:10.1016/j.cell.2022.01.019
  • Wang L, Cheng G. Sequence analysis of the emerging SARS-CoV-2 variant Omicron in South Africa. J Med Virol. 2022;94(4):1728–1733. doi:10.1002/jmv.27516
  • Benvenuto D, Angeletti S, Giovanetti M, et al. Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy. J Infect. 2020;81(1):e24–e27. doi:10.1016/j.jinf.2020.03.058
  • Ippoliti C, De Maio F, Santarelli G, et al. Rapid Detection of the Omicron (B.1.1.529) SARS-CoV-2 Variant Using a COVID-19 Diagnostic PCR Assay. Microbiology Spectrum. 2022;10(4):e0099022. doi:10.1128/spectrum.00990-22
  • Willett BJ, Grove J, MacLean OA, et al. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology. 2022;7(8):1161–1179. doi:10.1038/s41564-022-01143-7
  • Zahradník J, Marciano S, Shemesh M, et al. SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Nature Microbiology. 2021;6(9):1188–1198. doi:10.1038/s41564-021-00954-4
  • Korber B, Fischer WM, Gnanakaran S, 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.e19. doi:10.1016/j.cell.2020.06.043
  • Huang F, Chen L, Guo W, et al. Identifying COVID-19 Severity-Related SARS-CoV-2 Mutation Using a Machine Learning Method. Life. 2022;12:6.
  • Alquraan L, Alzoubi KH, Rababa’h SY. Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity. Inform Med Unlocked. 2023;39:101256. doi:10.1016/j.imu.2023.101256
  • Wise J. Covid-19: the E484K mutation and the risks it poses. BMJ. 2021;372:n359. doi:10.1136/bmj.n359
  • Liu Z, VanBlargan LA, Bloyet LM, et al. Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization. Cell Host Microbe. 2021;29(3):477–488.e4. doi:10.1016/j.chom.2021.01.014
  • Lan J, He X, Ren Y, et al. Structural insights into the SARS-CoV-2 Omicron RBD-ACE2 interaction. Cell Res. 2022;32(6):593–595. doi:10.1038/s41422-022-00644-8
  • Singh A, Steinkellner G, Köchl K, Gruber K, Gruber CC. Serine 477 plays a crucial role in the interaction of the SARS-CoV-2 spike protein with the human receptor ACE2. Sci Rep. 2021;11(1):4320. doi:10.1038/s41598-021-83761-5
  • Barnes CO, West AP Jr, Huey-Tubman KE, et al. Structures of Human Antibodies Bound to SARS-CoV-2 Spike Reveal Common Epitopes and Recurrent Features of Antibodies. Cell. 2020;182(4):828–842.e16. doi:10.1016/j.cell.2020.06.025
  • Vo GV, Bagyinszky E, An SSA. COVID-19 Genetic Variants and Their Potential Impact in Vaccine Development. Microorganisms. 2022;10(3):e46. doi:10.3390/microorganisms10030598