Rabat – For the first time, Moroccan researchers have drawn a detailed map tracing how COVID-19 mutated and spread across the country between 2021 and 2024.
The landmark study, carried out by the Pasteur Institute of Morocco in collaboration with Ibn Rochd University Hospital in Casablanca, has been published in NPJ Viruses, part of the Nature group of scientific journals.
The paper, titled “Genomic surveillance in Morocco tracks SARS-CoV-2 variant shift from Alpha to Omicron sublineage JN1,” is the first comprehensive Moroccan research to examine the virus’s evolution through real-time genomic monitoring.
Backed by the Africa Centers for Disease Control and Prevention, the team analyzed 235 patient samples, providing a precise view of how the virus changed over time within the country.
A shifting viral landscape
The study paints a striking picture of how quickly the pandemic changed course. In 2021, Alpha and Delta variants each represented around 38% of recorded infections, while Omicron appeared earlier than expected, already accounting for 21%.
By 2022, the situation had transformed. Omicron and its subvariants completely displaced the others, representing all cases in Morocco by 2024.
“The newer Omicron strains, especially JN.1.45 detected last year, carry up to 89 mutations. This shows how remarkably the virus adapts to escape immune defenses,” said Oumaima Bouddahab, the lead researcher.
Although Delta was more likely to cause severe illness, Omicron proved more transmissible. The researchers found that nearly eight in ten patients developed significant symptoms, particularly within the 20 to 40 age group.
Morocco’s strategic position
The findings also suggest that Morocco was not just a victim of global trends but an active hub in viral transmission.
Genetic maps revealed exchanges of variants with Europe, Sub-Saharan Africa, and Asia, a pattern explained by Morocco’s role as a crossroads for trade and travel.
Key mutations such as E484K and N501Y, known to weaken vaccine protection, were detected in local samples. These mutations had earlier driven major outbreaks in countries like Brazil and India, reinforcing concerns about the need for updated vaccines.
Lessons for future preparedness
The researchers concluded their study with three recommendations aimed at protecting Morocco and the wider region from future pandemics.
They called for permanent monitoring centers at borders and transport hubs, investment in vaccine platforms that can be rapidly adapted, and stronger cooperation across North Africa with the support of the World Health Organization (WHO).
The study insists that genomic surveillance is essential, not optional. “Viruses do not stop at borders,” the researchers warned, noting the importance of building local scientific capacity rather than depending solely on global data.