BMC Infectious Diseases (Oct 2024)
Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature
- Andrew Holtz,
- Johan Van Weyenbergh,
- Samuel L. Hong,
- Lize Cuypers,
- Áine O’Toole,
- Gytis Dudas,
- Marco Gerdol,
- Barney I. Potter,
- Francine Ntoumi,
- Claujens Chastel Mfoutou Mapanguy,
- Bert Vanmechelen,
- Tony Wawina-Bokalanga,
- Bram Van Holm,
- Soraya Maria Menezes,
- Katja Soubotko,
- Gijs Van Pottelbergh,
- Elke Wollants,
- Pieter Vermeersch,
- Ann-Sophie Jacob,
- Brigitte Maes,
- Dagmar Obbels,
- Veerle Matheeussen,
- Geert Martens,
- Jérémie Gras,
- Bruno Verhasselt,
- Wim Laffut,
- Carl Vael,
- Truus Goegebuer,
- Rob van der Kant,
- Frederic Rousseau,
- Joost Schymkowitz,
- Luis Serrano,
- Javier Delgado,
- Tom Wenseleers,
- Vincent Bours,
- Emmanuel André,
- Marc A. Suchard,
- Andrew Rambaut,
- Simon Dellicour,
- Piet Maes,
- Keith Durkin,
- Guy Baele
Affiliations
- Andrew Holtz
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité
- Johan Van Weyenbergh
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Lize Cuypers
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Áine O’Toole
- Institute of Ecology and Evolution, University of Edinburgh
- Gytis Dudas
- Institute of Biotechnology, Life Sciences Center, Vilnius University
- Marco Gerdol
- Department of Life Sciences, University of Trieste
- Barney I. Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Francine Ntoumi
- Fondation Congolaise Pour La Recherche Médicale
- Claujens Chastel Mfoutou Mapanguy
- Fondation Congolaise Pour La Recherche Médicale
- Bert Vanmechelen
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Tony Wawina-Bokalanga
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Bram Van Holm
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Soraya Maria Menezes
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Katja Soubotko
- General Practice Heiberg
- Gijs Van Pottelbergh
- Department of Public Health and Primary Care, KU Leuven
- Elke Wollants
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Pieter Vermeersch
- Department of Laboratory Medicine, University Hospitals Leuven, National Reference Centre for Respiratory Pathogens
- Ann-Sophie Jacob
- Department of Laboratory Medicine, University Hospitals Leuven, National Reference Centre for Respiratory Pathogens
- Brigitte Maes
- Laboratory for Molecular Diagnostics, Jessa Hospital
- Dagmar Obbels
- University of Ghent
- Veerle Matheeussen
- Department of Laboratory Medicine, Antwerp University Hospital (UZA)
- Geert Martens
- Department of Laboratory Medicine, AZ Delta General Hospital
- Jérémie Gras
- Institut de Pathologie Et de Génétique
- Bruno Verhasselt
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Wim Laffut
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Carl Vael
- Department of Laboratory Medicine, KLINA General Hospital
- Truus Goegebuer
- AZ Sint-Maarten
- Rob van der Kant
- Switch Laboratory, VIB Center for Brain and Disease Research and Department of Cellular and Molecular Medicine, KU Leuven
- Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research and Department of Cellular and Molecular Medicine, KU Leuven
- Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research and Department of Cellular and Molecular Medicine, KU Leuven
- Luis Serrano
- Center for Genomic Regulation, Barcelona Institute for Science and Technology
- Javier Delgado
- Center for Genomic Regulation, Barcelona Institute for Science and Technology
- Tom Wenseleers
- Department of Biology, KU Leuven
- Vincent Bours
- Department of Medical Genetics, CHU Liege
- Emmanuel André
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Marc A. Suchard
- Department of Biostatistics, Fielding School of Public Health, University of California
- Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh
- Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Piet Maes
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- Keith Durkin
- Laboratory of Human Genetics, GIGA Research Institute
- Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven
- DOI
- https://doi.org/10.1186/s12879-024-09967-w
- Journal volume & issue
-
Vol. 24,
no. 1
pp. 1 – 18
Abstract
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.
Keywords
