Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature

We investigate the emergence, mutation profile, and dissemination of SARS-CoV-2 lineage B.1.214.2, first identified in Belgium in January 2021. This variant, featuring a 3-amino acid insertion in the spike protein similar to the Omicron variant, was speculated to enhance transmissibility or immune evasion. Initially detected in international travelers, it substantially transmitted in Central Africa, Belgium, Switzerland, and France, peaking in April 2021. Our travel-aware phylogeographic analysis, incorporating travel history, estimated the origin to the Republic of the Congo, with primary European entry through France and Belgium, and multiple smaller introductions during the epidemic. We correlate its spread with human travel patterns and air passenger data. Further, upon reviewing national reports of SARS-CoV-2 outbreaks in Belgian nursing homes, we found this strain caused moderately severe outcomes (8.7% case fatality ratio). A distinct nasopharyngeal immune response was observed in elderly patients, characterized by 80% unique signatures, higher B- and T-cell activation, increased type I IFN signaling, and reduced NK, Th17, and complement system activation, compared to similar outbreaks. This unique immune response may explain the variant's epidemiological behavior and underscores the need for nasal vaccine strategies against emerging variants.

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Publication Details

Journal
BMC Infectious Diseases
Published
2024-10-10
DOI
https://doi.org/10.1186/s12879-024-09967-w
Citations
2
Primary Topic
SARS-CoV-2 and COVID-19 Research
Type
article
Field-Weighted Citation Impact
0.78

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article

Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature

Emmanuel André, Piet Maes, Frédéric Rousseau, Gijs Van Pottelbergh et al.
2 citations
BMC Infectious Diseases
SARS-CoV-2 and COVID-19 Research
0.78
article

Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature

Emmanuel André, Piet Maes, Frédéric Rousseau, Gijs Van Pottelbergh, Gytis Dudas, Bruno Verhasselt, Veerle Matheeussen, Soraya Maria Menezes, Marco Gerdol, Truus Goegebuer, Brigitte Maes, Bert Vanmechelen, Johan Van Weyenbergh, Dagmar Obbels, Keith Durkin, Joost Schymkowitz, Wim Laffut, Tom Wenseleers, Samuel L. Hong, Marc A. Suchard, Elke Wollants, Geert A. Martens, Rob van der Kant, Bram Van Holm, Guy Baele, Carl Vael, Francine Ntoumi, Pieter Vermeersch, Lize Cuypers, Jérémie Gras, Aine Niamh O’Toole, Barney Potter, Simon Dellicour, Andrew Holtz, Ann‐Sophie Jacob, Tony Wawina-Bokalanga, Luís Serrano, Vincent Bours, Andrew Rambaut, Javier Delgado, Claujens Chastel Mfoutou Mapanguy, Katja Soubotko
article en
2 citations

Abstract

We investigate the emergence, mutation profile, and dissemination of SARS-CoV-2 lineage B.1.214.2, first identified in Belgium in January 2021. This variant, featuring a 3-amino acid insertion in the spike protein similar to the Omicron variant, was speculated to enhance transmissibility or immune evasion. Initially detected in international travelers, it substantially transmitted in Central Africa, Belgium, Switzerland, and France, peaking in April 2021. Our travel-aware phylogeographic analysis, incorporating travel history, estimated the origin to the Republic of the Congo, with primary European entry through France and Belgium, and multiple smaller introductions during the epidemic. We correlate its spread with human travel patterns and air passenger data. Further, upon reviewing national reports of SARS-CoV-2 outbreaks in Belgian nursing homes, we found this strain caused moderately severe outcomes (8.7% case fatality ratio). A distinct nasopharyngeal immune response was observed in elderly patients, characterized by 80% unique signatures, higher B- and T-cell activation, increased type I IFN signaling, and reduced NK, Th17, and complement system activation, compared to similar outbreaks. This unique immune response may explain the variant's epidemiological behavior and underscores the need for nasal vaccine strategies against emerging variants.

BMC Infectious DiseasesVol. 24(1)
Institució Catalana de Recerca i Estudis Avançats (ES), Université Libre de Bruxelles (BE), University of Trieste (IT), University of Antwerp (BE), Institut Pasteur (FR), University of Liège (BE), University of California, Los Angeles (US), Universitat Pompeu Fabra (ES), Vilnius University (LT), Université Paris Cité (FR), Rega Institute for Medical Research (BE), Ghent University Hospital (BE), AZ Klina (BE), Jessa Hospital (BE), Institute of Pathology and Genetics (BE), Antwerp University Hospital (BE), Fondation Congolaise Pour La Recherche Médicale (CG), Barcelona Institute of Science and Technology (ES), Centre for Genomic Regulation (ES), AZ Delta (BE), VIB-KU Leuven Center for Brain & Disease Research (BE), AZ Sint-Lucas (BE), Marien Ngouabi University (CG), University of Tübingen (DE), Hasselt University (BE), University of Edinburgh (GB), KU Leuven (BE)
European Commission, Agence Nationale de la Recherche, Fonds De La Recherche Scientifique - FNRS, Fonds Wetenschappelijk Onderzoek, KU Leuven, Vlaamse regering, National Institutes of Health, Universitaire Ziekenhuizen Leuven, KU Leuven
Good health and well-being
Openalex Percentile: Top 27%
SARS-CoV-2 and COVID-19 Research
0.78
DOIOpen Access PDFOpenAlex
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