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COVID-19: First case of the BA.2.86 variant detected in France
As part of the genomic surveillance of SARS-CoV-2, led by Santé publique France in collaboration with the National Reference Center for Respiratory Infections, and the activities of the EMERGEN consortium, a case of the BA.2.86 variant has been detected in the Grand Est region, based on samples from the latest weekly Flash survey conducted on August 21, 2023. Investigations are underway to gather additional information on this first case.
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What do we know about this new BA.2.86 variant?
BA.2.86 is a new variant within the Omicron family and has been classified as a Variant Under Monitoring (VUM) by the World Health Organization. It is receiving particular attention internationally due to its atypical genetic profile and the significant number of mutations it carries.
As of noon on August 31, 2023, there were 25 sequences of this sublineage worldwide, distributed across several countries: ten sequences in Denmark, four in the United States, four in Sweden, two in South Africa, two in Portugal, one in the United Kingdom, one in Israel, and one in Canada; In addition to these 25 sequences is the one detected for the first time in France on August 31, 2023, by the CNR Virus des Infections Respiratoires from a sample obtained from a private laboratory in the Grand Est region and from the latest Flash survey dated August 21, 2023.
At this stage, the emergence of the BA.2.86 variant is still too recent to assess its characteristics and impact. However, the immune status of the global population is very different from what it was at the time of Omicron’s emergence, with a significant proportion of people who have been vaccinated or infected by different successive variants, allowing for some level of protection to be maintained, particularly against severe forms of the disease.
Genomic surveillance: a cornerstone for detecting emerging variants
Genomic surveillance of SARS-CoV-2 is now one of the cornerstones of the fight against the COVID-19 pandemic at both the national and international levels. Whole-genome sequencing of the virus remains the only technique capable of confirming variants, detecting emerging variants, and identifying the mutations that characterize them.
In France, this surveillance falls under the purview of the National Reference Center (CNR) for Respiratory Infections (Hospices Civils de Lyon) and its associated laboratories (Institut Pasteur, Institut Pasteur de la Guyane, and CHU de La Réunion); it is conducted in close collaboration with Santé publique France and its partners in the EMERGEN consortium.
EMERGEN at a Glance
The EMERGEN project, coordinated by Santé publique France and ANRS|MIE, was launched in January 2021 in the context of the COVID-19 pandemic following the emergence of the first variant of concern of SARS-CoV-2 (Alpha, first detected in the United Kingdom in November 2020). Its primary mission was to deploy a nationwide genomic surveillance system for SARS-CoV-2 to monitor the emergence and/or introduction of variants of concern more proactively.
Since its inception, the EMERGEN project has been based on a multidisciplinary consortium bringing together complementary expertise: sample collection, sample preparation and sequencing, bioinformatic analysis of genomes, publication of sequencing results in national and international databases, analysis for surveillance purposes (Flash surveys) or risk assessment (classification of variants as variants of concern, to be monitored, or under evaluation), potential discovery and functional characterization of new variants, and research on their epidemiological and functional impact. In 2023, the consortium’s activities will continue to focus on SARS-CoV-2, primarily utilizing the sequencing capabilities of the CNR Respiratory Infections Virus. Work is underway to gradually expand its surveillance and research activities to other emerging infectious diseases (viral, as well as bacterial, fungal, or parasitic).
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