Back to Search Start Over

Culture and identification of a 'Deltamicron' SARS‐CoV‐2 in a three cases cluster in southern France

Authors :
Philippe Colson
Pierre‐Edouard Fournier
Jeremy Delerce
Matthieu Million
Marielle Bedotto
Linda Houhamdi
Nouara Yahi
Jeremy Bayette
Anthony Levasseur
Jacques Fantini
Didier Raoult
Bernard La Scola
COMBE, Isabelle
Microbes évolution phylogénie et infections (MEPHI)
Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)
Institut Hospitalier Universitaire Méditerranée Infection (IHU Marseille)
Vecteurs - Infections tropicales et méditerranéennes (VITROME)
Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées (IRBA)
Unité de Neurobiologie des canaux Ioniques et de la Synapse (UNIS - Inserm U1072)
Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)
Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut de Recherche Biomédicale des Armées [Brétigny-sur-Orge] (IRBA)
Source :
Journal of Medical Virology, Journal of Medical Virology, 2022, ⟨10.1002/jmv.27789⟩
Publication Year :
2022
Publisher :
Wiley, 2022.

Abstract

Multiple SARS-CoV-2 variants have successively, or concommitantly spread worldwide since summer 2020. A few co-infections with different variants were reported and genetic recombinations, common among coronaviruses, were reported or suspected based on co-detection of signature mutations of different variants in a given genome. Here we report three infections in southern France with a Delta 21J/AY.4-Omicron 21K/BA.1 “Deltamicron” recombinant. The hybrid genome harbors signature mutations of the two lineages, supported by a mean sequencing depth of 1,163-1,421 reads and mean nucleotide diversity of 0.1-0.6%. It is composed of the near full-length spike gene (from codons 156-179) of an Omicron 21K/BA.1 variant in a Delta 21J/AY.4 lineage backbone. Importantly, we cultured an isolate of this recombinant and sequenced its genome. It was observed by scanning electron microscopy. As it is misidentified with current variant screening qPCR, we designed and implemented for routine diagnosis a specific duplex qPCR. Finally, structural analysis of the recombinant spike suggested its hybrid content could optimize viral binding to the host cell membrane. These findings prompt further studies of the virological, epidemiological, and clinical features of this recombinant.

Details

ISSN :
10969071 and 01466615
Volume :
94
Database :
OpenAIRE
Journal :
Journal of Medical Virology
Accession number :
edsair.doi.dedup.....d4ccaf15e9d290dab106902a0ef0ffc1