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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, Aine O'Toole, Gytis Dudas, Marco Gerdol, Barney I. Potter, Francine Ntoumi, Claujens Chastel Mfoutou Mapanguy, et al.
(2024) BMC INFECTIOUS DISEASES. 24(1).
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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.
Keywords
SARS-CoV-2, Genomic epidemiology, Phylogeography, Phylodynamics, Disease spread, COVID-19, ESCAPE

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MLA
Holtz, Andrew, et al. “Emergence of the B.1.214.2 SARS-CoV-2 Lineage with an Omicron-like Spike Insertion and a Unique Upper Airway Immune Signature.” BMC INFECTIOUS DISEASES, vol. 24, no. 1, 2024, doi:10.1186/s12879-024-09967-w.
APA
Holtz, A., Van Weyenbergh, J., Hong, S. L., Cuypers, L., O’Toole, A., Dudas, G., … Baele, G. (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. BMC INFECTIOUS DISEASES, 24(1). https://doi.org/10.1186/s12879-024-09967-w
Chicago author-date
Holtz, Andrew, Johan Van Weyenbergh, Samuel L. Hong, Lize Cuypers, Aine O’Toole, Gytis Dudas, Marco Gerdol, et al. 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.” BMC INFECTIOUS DISEASES 24 (1). https://doi.org/10.1186/s12879-024-09967-w.
Chicago author-date (all authors)
Holtz, Andrew, Johan Van Weyenbergh, Samuel L. Hong, Lize Cuypers, Aine 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, Jeremie 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 Andre, Marc A. Suchard, Andrew Rambaut, Simon Dellicour, Piet Maes, Keith Durkin, and Guy Baele. 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.” BMC INFECTIOUS DISEASES 24 (1). doi:10.1186/s12879-024-09967-w.
Vancouver
1.
Holtz A, Van Weyenbergh J, Hong SL, Cuypers L, O’Toole A, Dudas G, et al. Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature. BMC INFECTIOUS DISEASES. 2024;24(1).
IEEE
[1]
A. Holtz et al., “Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature,” BMC INFECTIOUS DISEASES, vol. 24, no. 1, 2024.
@article{01JN6FJRE71JXH7VSN2F7T2APM,
  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.}},
  articleno    = {{1139}},
  author       = {{Holtz, Andrew and Van Weyenbergh, Johan and Hong, Samuel L. and Cuypers, Lize and O'Toole, Aine and Dudas, Gytis and Gerdol, Marco and Potter, Barney I. and Ntoumi, Francine and Mapanguy, Claujens Chastel Mfoutou and Vanmechelen, Bert and Wawina-Bokalanga, Tony and Van Holm, Bram and Menezes, Soraya Maria and Soubotko, Katja and Van Pottelbergh, Gijs and Wollants, Elke and Vermeersch, Pieter and Jacob, Ann-Sophie and Maes, Brigitte and Obbels, Dagmar and Matheeussen, Veerle and Martens, Geert and Gras, Jeremie and Verhasselt, Bruno and Laffut, Wim and Vael, Carl and Goegebuer, Truus and van der Kant, Rob and Rousseau, Frederic and Schymkowitz, Joost and Serrano, Luis and Delgado, Javier and Wenseleers, Tom and Bours, Vincent and Andre, Emmanuel and Suchard, Marc A. and Rambaut, Andrew and Dellicour, Simon and Maes, Piet and Durkin, Keith and Baele, Guy}},
  issn         = {{1471-2334}},
  journal      = {{BMC INFECTIOUS DISEASES}},
  keywords     = {{SARS-CoV-2,Genomic epidemiology,Phylogeography,Phylodynamics,Disease spread,COVID-19,ESCAPE}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{18}},
  title        = {{Emergence of the B.1.214.2 SARS-CoV-2 lineage with an Omicron-like spike insertion and a unique upper airway immune signature}},
  url          = {{http://doi.org/10.1186/s12879-024-09967-w}},
  volume       = {{24}},
  year         = {{2024}},
}
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