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

ABSTRACT

Among the numerous variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that have been reported worldwide, the emergence of the Omicron variant has drastically changed the landscape of the coronavirus disease (COVID-19) pandemic. Here, we analyzed the genetic diversity of Moroccan SARS-CoV-2 genomes with a focus on Omicron variant after one year of its detection in Morocco in order to understand its genomic dynamics, features and its potential introduction sources. From 937 Omicron genomes, we identified a total of 999 non-unique mutations distributed across 92 Omicron lineages, of which 13 were specific to the country. Our findings suggest multiple introductory sources of the Omicron variant to Morocco. In addition, we found that four Omicron clades are more infectious in comparison to other Omicron clades. Remarkably, a clade of Omicron is particularly more transmissible and has become the dominant variant worldwide. Moreover, our assessment of Receptor-Binding Domain (RBD) mutations showed that the Spike K444T and N460K mutations enabled a clade higher ability of immune vaccine escape. In conclusion, our analysis highlights the unique genetic diversity of the Omicron variant in Moroccan SARS-CoV-2 genomes, with multiple introductory sources and the emergence of highly transmissible clades. The distinctiveness of the Moroccan strains compared to global ones underscores the importance of ongoing surveillance and understanding of local genomic dynamics for effective response strategies in the evolving COVID-19 pandemic.

KEYWORDS:

• SARS-CoV-2 genomic surveillance
• variants of concern
• omicron
• phylogenetic analysis
• spike protein
• next-generation sequencing

Acknowledgements

This work was carried out with the assistance of national funding from the Moroccan Ministry of Higher Education and Scientific Research (COVID-19 program) to A.I. and scholarship of excellence from the National Center for Scientific and Technical Research in Morocco. We would like to acknowledge the GISAID database for providing publicly available data, which greatly contributed to our research.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Data availability statement

The data generated during the current study are available from the

Supplementary material

Supplemental data for this article can be accessed online at https://doi.org/10.1080/20477724.2023.2250942

Additional information

Funding

This research was funded by Moroccan Ministry of Higher Education and Scientific Research (COVID-19 Program).