[en] 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.
Disciplines :
Immunology & infectious disease
Author, co-author :
Holtz, Andrew; Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, Paris, France. andrew.holtz@pasteur.fr
Van Weyenbergh, Johan; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium. johan.vanweyenbergh@kuleuven.be
Hong, Samuel L; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Cuypers, Lize; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium ; Department of Laboratory Medicine, University Hospitals Leuven, National Reference Centre for Respiratory Pathogens, Leuven, Belgium
O'Toole, Áine; Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
Dudas, Gytis; Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
Gerdol, Marco; Department of Life Sciences, University of Trieste, Trieste, Italy
Potter, Barney I; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Ntoumi, Francine; Fondation Congolaise Pour La Recherche Médicale, Brazzaville, Republic of Congo ; Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany
Mapanguy, Claujens Chastel Mfoutou; Fondation Congolaise Pour La Recherche Médicale, Brazzaville, Republic of Congo ; Faculty of Sciences and Techniques, University Marien Ngouabi, Brazzaville, Republic of Congo
Vanmechelen, Bert; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Wawina-Bokalanga, Tony; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Van Holm, Bram; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Menezes, Soraya Maria; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Soubotko, Katja; General Practice Heiberg, Leuven, Belgium
Van Pottelbergh, Gijs; Department of Public Health and Primary Care, KU Leuven, Leuven, Belgium
Wollants, Elke; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Vermeersch, Pieter; Department of Laboratory Medicine, University Hospitals Leuven, National Reference Centre for Respiratory Pathogens, Leuven, Belgium
Jacob, Ann-Sophie; Department of Laboratory Medicine, University Hospitals Leuven, National Reference Centre for Respiratory Pathogens, Leuven, Belgium
Maes, Brigitte; Laboratory for Molecular Diagnostics, Jessa Hospital, Hasselt, Belgium ; Hasselt University, Hasselt, Belgium ; Limburg Clinical Research Center, Hasselt, Belgium
Obbels, Dagmar; University of Ghent, Ghent, Belgium
Matheeussen, Veerle; Department of Laboratory Medicine, Antwerp University Hospital (UZA), Edegem, Belgium ; Laboratory of Medical Biochemistry and Laboratory of Medical Microbiology, University of Antwerp, Wilrijk, Belgium
Martens, Geert; Department of Laboratory Medicine, AZ Delta General Hospital, Roeselare, Belgium
Gras, Jérémie; Institut de Pathologie Et de Génétique, Gosselies, Belgium
Verhasselt, Bruno; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Laffut, Wim; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Vael, Carl; Department of Laboratory Medicine, KLINA General Hospital, Brasschaat, AZ, Belgium
Goegebuer, Truus; AZ Sint-Maarten, Mechelen, Belgium
van der Kant, Rob; Switch Laboratory, VIB Center for Brain and Disease Research and Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium ; Molecular Medicine, KU Leuven, Leuven, Belgium
Rousseau, Frederic; Switch Laboratory, VIB Center for Brain and Disease Research and Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium ; Molecular Medicine, KU Leuven, Leuven, Belgium
Schymkowitz, Joost; Switch Laboratory, VIB Center for Brain and Disease Research and Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium ; Molecular Medicine, KU Leuven, Leuven, Belgium
Serrano, Luis; Center for Genomic Regulation, Barcelona Institute for Science and Technology, 08003, Barcelona, Spain ; Universitat Pompeu Fabra, 08002, Barcelona, Spain ; Institució Catalana de Recerca I Estudis Avançats, 08010, Barcelona, Spain
Delgado, Javier; Center for Genomic Regulation, Barcelona Institute for Science and Technology, 08003, Barcelona, Spain
Wenseleers, Tom; Department of Biology, KU Leuven, Leuven, Belgium
Bours, Vincent ; Université de Liège - ULiège > GIGA > GIGA Cancer - Human Genetics
André, Emmanuel; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Suchard, Marc A; Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, CA, USA
Rambaut, Andrew; Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
Dellicour, Simon; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium ; Université Libre de Bruxelles, Brussels, Belgium
Maes, Piet ✱; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
Durkin, Keith ✱; Université de Liège - ULiège > Département des sciences biomédicales et précliniques ; Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
Baele, Guy ✱; Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
