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Research Articles

Genetic diversity and evolutionary dynamics of the Omicron variant of SARS-CoV-2 in Morocco

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References

  • Dhawan M, Saied ARA, Mitra S, et al. Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2? Biomed Pharmacother. 2022 Oct 1;154:113522. Elsevier Masson s.r.l. doi: 10.1016/j.biopha.2022.113522
  • Alquraan L, Alzoubi KH, Rababa’h SY. Mutations of SARS-CoV-2 and their impact on disease diagnosis and severity. Inf Med Unlocked. 2023;39:101256. doi: 10.1016/j.imu.2023.101256
  • Galani A, Markou A, Dimitrakopoulos L, et al. Delta SARS-CoV-2 variant is entirely substituted by the omicron variant during the fifth COVID-19 wave in Attica region. Sci Total Environ. 2023 Jan;856:159062.
  • El Mazouri S, Bendani H, Boumajdi N, et al. Report of SARS-CoV-2 BA.1 lineage in Morocco. Microbiol Resour Announc. 2022 May;11(5). doi: 10.1128/mra.00169-22
  • Ren W, Zhu Y, Lan J, et al. Susceptibilities of human ACE2 genetic variants in Coronavirus infection. J Virol. 2022;96(1):e0149221. doi: 10.1128/JVI.01492-21
  • He X, Hong W, Pan X, et al. SARS-CoV-2 Omicron variant: characteristics and prevention. MedComm. 2(4): Blackwell Publishing Inc.:838–845. 2021 Dec 1. doi: 10.1002/mco2.110
  • Weng S, Shang J, Cheng Y, et al. Genetic differentiation and diversity of SARS-CoV-2 Omicron variant in its early outbreak. Biosaf Heal. 2022 Jun;4(3):171–178. doi: 10.1016/J.BSHEAL.2022.04.004
  • Oude Munnink BB, Worp N, Nieuwenhuijse DF, et al. The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology. Nature Med. 2021 Sep 1;27(9): 1518–1524. Nature Research. doi: 10.1038/s41591-021-01472-w.
  • El Mazouri S, Bendani H, Boumajdi N, et al. Phylogeography and genomic analysis of sars-cov-2 delta variant in morocco. J Infect Dev Ctries. 2022;16(8):1258–1268. doi: 10.3855/jidc.16513
  • Wilkinson E, Giovanetti M, Tegally H, et al. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science. 2021;374(6566):423–431. doi: 10.1126/science.abj4336
  • Meriem L, Essabbar A, Alouane T, et al. Do the Moroccan SARS-CoV-2 genetic diversity hamper the use of the developed universal vaccines in Morocco? bioRxiv [Preprint]. 2020. doi: 10.1101/2020.06.30.181123
  • Chaouni B, Allali I, Sehli S, et al. Genomic evidence of multiple SARS-CoV-2 introductions into Morocco. J Obstet Gynaecol. 2020 Jul;9:679.
  • Badaoui B, Sadki K, Talbi C, et al. Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco. Biosaf Heal. 2021 Apr;3(2):124–127. doi: 10.1016/J.BSHEAL.2021.01.003
  • Patel RK, Jain M, Liu Z. NGS QC toolkit: a toolkit for quality control of next generation sequencing data. PLoS One. 2012;7(2):e30619. doi: 10.1371/journal.pone.0030619
  • Shepard SS, Meno S, Bahl J, et al. Viral deep sequencing needs an adaptive approach: IRMA, the iterative refinement meta-assembler. BMC Genomics. 2016;17(1). doi: 10.1186/s12864-016-3030-6
  • Aanniz T, Ouadghiri M, Bendahou MA, et al. First Report of a SARS-CoV-2 genome sequence with a Spike His69-Val70 deletion and an Asn439Lys mutation in Morocco; 2021. doi: 10.3390/pathogens9100829.
  • Hadfield J, Megill C, Bell SM, et al. NextStrain: real-time tracking of pathogen evolution. Bioinformatics. 2018 Dec;34(23):4121–4123. doi: 10.1093/bioinformatics/bty407
  • Cardona G, Rosselló F, Valiente G. Extended Newick: it is time for a standard representation of phylogenetic networks. BMC Bioinf. 2008 Dec;9: doi:10.1186/1471-2105-9-532
  • Rambaut A, Holmes EC, O’Toole Á, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol. 2020 Nov;5(11):1403–1407. doi: 10.1038/s41564-020-0770-5
  • “GISAID - Audacity instant app.” ( Cited 2023 Jul 4). https://gisaid.org/database-features/audacity-instant-app/.
  • Essabbar A, Kartti S, Alouane T, et al. IDbSV: an open-access repository for monitoring SARS-CoV-2 variations and evolution. Front Med. 2021 Dec;8. doi:10.3389/fmed.2021.765249
  • Greaney AJ, Loes AN, Crawford KHD, et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host Microbe. 2021 Mar;29(3):463–476.e6. doi: 10.1016/J.CHOM.2021.02.003
  • Wickham H, Averick M, Bryan J, et al. Welcome to the Tidyverse. J Open Source Softw. 2019 Nov;4(43):1686. doi: 10.21105/JOSS.01686
  • Wickham H. ggplot2. Wiley Interdiscip Rev Comput Stat. 2011 Mar;3(2):180–185. doi: 10.1002/WICS.147
  • Bloom JD, Beichman AC, Neher RA, et al. Evolution of the SARS-CoV-2 mutational spectrum. bioRxiv [Preprint]. 2022. doi: 10.1101/2022.11.19.517207
  • Mouna O, Aanniz T, Essabbar A, et al. Report of SARS-CoV-2 B1.1.7 lineage in Morocco. Microbiol Resour Announc. 2021 Apr;10(16):e00240–21. doi: 10.1128/MRA.00240-21
  • Rodriguez JA, Gonzalez J, Arboleda-Bustos CE, et al. Computational modeling of the effect of five mutations on the structure of the ACE2 receptor and their correlation with infectivity and virulence of some emerged variants of SARS-CoV-2 suggests mechanisms of binding affinity dysregulation. Chem Biol Interact. 2022 Dec;368:110244. doi: 10.1016/J.CBI.2022.110244.
  • Chan MC, Chan KK, Procko E, et al. Machine learning guided design of high affinity ACE2 decoys for SARS-CoV-2 neutralization. bioRxiv Prepr Serv Biol. 2021 Dec. doi: 10.1101/2021.12.22.473902
  • Haslwanter D, Dieterle ME, Wec AZ, et al. A combination of receptor-binding domain and N-Terminal domain neutralizing antibodies limits the generation of SARS-CoV-2 Spike neutralization-escape mutants. MBio. 2021;12(5):e0247321. doi: 10.1128/mBio
  • Cao Y, Jian F, Wang J, et al. Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution. Nature. 2022. doi: 10.1101/2022.09.15.507787.
  • Qu P, Evans JP, Faraone JN, et al. Distinct neutralizing antibody escape of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7 and BA.2.75.2. bioRxiv Prepr Serv Biol. 2022. doi: 10.1101/2022.10.19.512891
  • Kaku CI, Starr TN, Zhou P, et al. Evolution of antibody immunity following Omicron BA.1 breakthrough infection. bioRxiv [Preprint]. 2022. doi: 10.1101/2022.09.21.508922
  • Qu P, Evans JP, Faraone JN, et al. Enhanced neutralization resistance of SARS-CoV-2 Omicron subvariants BQ.1, BQ.1.1, BA.4.6, BF.7, and BA.2.75.2. Cell Host Microbe. 2022 Nov;31(1):9–17.e3. doi: 10.1016/J.CHOM.2022.11.012
  • Greaney AJ, Starr TN, Bloom JD. An antibody-escape estimator for mutations to the SARS-CoV-2 receptor-binding domain. Virus Evol. 2022;8(1): doi: 10.1093/ve/veac021
  • Wang Z, Schmidt F, Weisblum Y, et al. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature. 2021 Apr;592(7855):616–622. doi: 10.1038/s41586-021-03324-6
  • Zahradník J, Marciano S, Shemesh M, et al. SARS-CoV-2 variant prediction and antiviral drug design are enabled by RBD in vitro evolution. Nat Microbiol. 2021 Sep;6(9):1188–1198. doi: 10.1038/s41564-021-00954-4
  • Frye CJ, Shine M, Makowski JA, et al. Bioinformatics analysis of the s2m mutations within the SARS-CoV-2 Omicron lineages. J med virol. 2022;95(1): John Wiley and Sons Inc. doi: 10.1002/jmv.28141
  • Imperatore JA, Cunningham CL, Pellegrene KA, et al. Highly conserved s2m element of SARS-CoV-2 dimerizes via a kissing complex and interacts with host miRNA-1307-3p. Nucleic Acids Res. 2022 Jan;50(2):1017–1032. doi: 10.1093/nar/gkab1226
  • Chaudhari A, Chaudhari M, Mahera S, et al. In-silico analysis reveals lower transcription efficiency of C241T variant of SARS-CoV-2 with host replication factors MADP1 and hnRNP-1. IMU. 2021 Jan;25:100670.
  • Jian F, Yu Y, Song W, et al. Further humoral immunity evasion of emerging SARS-CoV-2 BA.4 and BA.5 subvariants. Lancet Infect Dis. 2022 Nov 1;22(11): 1535–1537. NLM (Medline). doi: 10.1016/S1473-3099(22)00642-9.
  • Wolter N, Jassat W, Walaza S, et al. Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study. Lancet. 2022 Jan;399(10323):437–446. doi: 10.1016/S0140-6736(22)00017-4
  • Bao J, Sun R, Ai J, et al. Proteomic characterization of Omicron SARS-CoV-2 host response. Cell Discov. 2022;8(1):46. doi: 10.1038/s41421-022-00418-x
  • Attwood SW, Hill SC, Aanensen DM, et al. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nat Rev Genet. 2022;23(9):547–562. doi: 10.1038/s41576-022-00483-8
  • Duault H, Durand B, Canini L. Methods combining genomic and epidemiological data in the reconstruction of transmission trees: a systematic review. Pathogens. 2022;11(2):252. doi: 10.3390/pathogens11020252

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