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

DOI
https://doi.org/10.1186/s12879-024-09967-w
Journal volume & issue
Vol. 24, no. 1
pp. 1 – 18

Abstract

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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.

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