Rapid characterization of a Delta-Omicron SARS-CoV-2 recombinant detected in Europe

Etienne Simon-Loriere (1) , Xavier Montagutelli (2) , Frederic Lemoine (1) , Flora Donati (3) , Franck Touret (4) , Jerome Bourret (3) , Matthieu Prot (1) , Sandie Munier (1) , Mikael Attia (1) , Laurine Conquet (2) , Scott Nguyen , Faustine Amara (1) , Anna Maisa (5) , Lucie Fournier (5) , Angela Brisbarre , Oceane Dehan (3) , Laurine Levillayer (1) , Vithiagaran Gunalan , Jannik Fonager , Morten Rasmussen (6) , Stephan Kemeny (7) , Abdelali Zrhidri , Thomas Duret , Sylvie Behillil (8) , Vincent Enouf (9) , Christophe Rodriguez , Slim Fourati , Jean-Michel Pawlotsky , Nicolas Capron , Hugues Leroy , Elodie Alessandri-Gradt , Florian Juszczak , Laetitia Gheysen , Véronique Brodard , Hélène Moret , Martine Bos , Matthijs Welkers , Claus Scholz , Sofia Paraskevopoulou (10) , Laurence Josset (11) , Claire Cervi , Brigitte Couzon , Stéphanie Marque-Juillet , Deborah Delaune (1) , Slim El Khiari (12) , Julien Fumey (12) , Marie-Charlotte Hallouin-Bernard , Félix Rey (13) , Yazdan Yazdanpanah (14) , Bruno Coignard , Xavier de Lamballerie (4) , Sylvie van Der Werf (8) , Axelle Paquin (15)

1 Génomique évolutive des virus à ARN - Evolutionary genomics of RNA viruses
2 Génétique de la souris - Mouse Genetics
3 CNR - laboratoire coordonnateur - Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris]
4 UVE - Unité des Virus Emergents
5 Santé publique France - French National Public Health Agency [Saint-Maurice, France]
6 UCPH - University of Copenhagen = Københavns Universitet
7 Gen-Bio
8 GMV-ARN (UMR_3569 / U-Pasteur_2) - Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses
9 P2M - Plateforme de Microbiologie Mutualisée - Mutualized Platform for Microbiology
10 RKI - Robert Koch Institute [Berlin]
11 CHU Lyon
12 Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB
13 Virologie Structurale - Structural Virology
14 ANRS - MIE - ANRS - Maladies infectieuses émergentes
15 CH Laval - Centre Hospitalier de Laval

Abstract Recombination is a crucial process in the evolution of many organisms. Although the evolutionary reasons behind its occurrence in RNA viruses are debated, this phenomenon has been associated with major epidemiological events such as virus host range expansion, antigenic shift or variation in virulence 1,2, and this process occurs frequently in positive strand RNA viruses such as coronaviruses. The SARS-CoV-2 pandemic has been associated with the repeated emergence of variants of concern presenting increased transmissibility, severity or immune escape 3. The recent extensive circulation of Delta worldwide and its subsequent replacement by viruses of the Omicron lineage 4 (BA.1 then BA.2), have created conditions for genetic exchanges between viruses with both genetic diversity and phenotypic specificities 5-7. Here we report the identification and in vitro and in vivo characterization of a Delta-Omicron recombinant in Europe. This recombinant exhibits immune escape properties similar to Omicron, while its behavior in mice expressing the human ACE2 receptor is more similar to Delta. This recombinant provides a unique and natural opportunity to better understand the genotype to phenotype links in SARS-CoV-2.

Domaines: Santé publique et épidémiologie

Etienne Simon-Loriere, Xavier Montagutelli, Frederic Lemoine, Flora Donati, Franck Touret, et al.. Rapid characterization of a Delta-Omicron SARS-CoV-2 recombinant detected in Europe. 2022. ⟨pasteur-04067089⟩