Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion

Delphine Planas (), Isabelle Staropoli, Vincent Michel, Frederic Lemoine, Flora Donati, Matthieu Prot, Francoise Porrot, Florence Guivel-Benhassine, Banujaa Jeyarajah, Angela Brisebarre, Océane Dehan, Léa Avon, William Henry Bolland, Mathieu Hubert, Julian Buchrieser, Thibault Vanhoucke, Pierre Rosenbaum, David Veyer, Hélène Péré, Bruno Lina, Sophie Trouillet-Assant, Laurent Hocqueloux, Thierry Prazuck, Etienne Simon-Loriere () and Olivier Schwartz ()
Additional contact information
Delphine Planas: Université Paris Cité
Isabelle Staropoli: Université Paris Cité
Vincent Michel: INSERM
Frederic Lemoine: Université Paris Cité
Flora Donati: Université Paris Cité
Matthieu Prot: Université Paris Cité
Francoise Porrot: Université Paris Cité
Florence Guivel-Benhassine: Université Paris Cité
Banujaa Jeyarajah: Institut Pasteur
Angela Brisebarre: Institut Pasteur
Océane Dehan: Institut Pasteur
Léa Avon: Institut Pasteur
William Henry Bolland: Université Paris Cité
Mathieu Hubert: Université Paris Cité
Julian Buchrieser: Université Paris Cité
Thibault Vanhoucke: Université Paris Cité
Pierre Rosenbaum: Université Paris Cité
David Veyer: Hôpital Européen Georges Pompidou
Hélène Péré: Hôpital Européen Georges Pompidou
Bruno Lina: Hospices Civils de Lyon
Sophie Trouillet-Assant: Hospices Civils de Lyon
Laurent Hocqueloux: Service de Maladies Infectieuses
Thierry Prazuck: Service de Maladies Infectieuses
Etienne Simon-Loriere: Université Paris Cité
Olivier Schwartz: Université Paris Cité

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: Abstract The unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolate and characterize XBB.1, XBB.1.5, XBB.1.9.1, XBB.1.16.1, EG.5.1.1, EG.5.1.3, XBF, BA.2.86.1 and JN.1 variants, representing >80% of circulating variants in January 2024. The XBB subvariants carry few but recurrent mutations in the spike, whereas BA.2.86.1 and JN.1 harbor >30 additional changes. These variants replicate in IGROV-1 but no longer in Vero E6 and are not markedly fusogenic. They potently infect nasal epithelial cells, with EG.5.1.3 exhibiting the highest fitness. Antivirals remain active. Neutralizing antibody (NAb) responses from vaccinees and BA.1/BA.2-infected individuals are markedly lower compared to BA.1, without major differences between variants. An XBB breakthrough infection enhances NAb responses against both XBB and BA.2.86 variants. JN.1 displays lower affinity to ACE2 and higher immune evasion properties compared to BA.2.86.1. Thus, while distinct, the evolutionary trajectory of these variants combines increased fitness and antibody evasion.

Date: 2024
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DOI: 10.1038/s41467-024-46490-7

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