Phylogeography and genomic analysis of SARS-CoV-2 delta variant in Morocco

  • Safae El Mazouri Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
  • Houda Bendani Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
  • Nasma Boumajdi Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco https://orcid.org/0000-0002-8226-2244
  • Tarik Aanniz Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco https://orcid.org/0000-0003-3308-2607
  • Ilham Kandoussi Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
  • Saaïd Amzazi Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
  • Lahcen Belyamani Emergency Department, Military Hospital Mohammed V, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco https://orcid.org/0000-0003-1464-6649
  • Azeddine Ibrahimi Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
  • Mouna Ouadghiri Laboratory of Biotechnology, Medical and Pharmacy School, Mohammed V University, Rabat, Morocco https://orcid.org/0000-0002-2306-9364
Keywords: SARS-CoV-2, delta variant, AY.33, mutation analysis, spike, phylogeography

Abstract

Introduction: Since the COVID-19 pandemic began in December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved with many variants of concern emerging across the world.

Methodology: In order to monitor the evolution of these variants in Morocco, we analyzed a total of 2130 genomes of the delta variant circulating around the world. We also included 164 Moroccan delta variant sequences in our analysis.

Results: Our findings suggest at least four introductions from multiple international sources and a rise of a dominant delta sub-lineage AY.33 in Morocco. Moreover, we report three mutations in the N-terminal domain of the S protein specific to the Moroccan AY.33 isolates, T29A, T250I and T299I. The effect of these mutations on the secondary structure and the dynamic behavior of the S protein N-terminal domain was further determined.

Conclusions: We conclude that these mutations might have functional consequences on the S protein of SARS-CoV-2.

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Published
2022-08-30
How to Cite
1.
El MazouriS, Bendani H, Boumajdi N, Aanniz T, Kandoussi I, Amzazi S, Belyamani L, Ibrahimi A, Ouadghiri M (2022) Phylogeography and genomic analysis of SARS-CoV-2 delta variant in Morocco. J Infect Dev Ctries 16:1258-1268. doi: 10.3855/jidc.16513
Section
Coronavirus Pandemic