tetano
Editor, Senior Moderator
J Med Virol
. 2022 Apr 25.
doi: 10.1002/jmv.27789. Online ahead of print.
Culture and identification of a "Deltamicron" SARS-CoV-2 in a three cases cluster in southern France
Philippe Colson[SUP] 1 2 3 [/SUP], Pierre-Edouard Fournier[SUP] 1 2 4 [/SUP], Jeremy Delerce[SUP] 1 [/SUP], Matthieu Million[SUP] 1 2 3 [/SUP], Marielle Bedotto[SUP] 1 [/SUP], Linda Houhamdi[SUP] 1 [/SUP], Nouara Yahi[SUP] 5 [/SUP], Jeremy Bayette[SUP] 6 [/SUP], Anthony Levasseur[SUP] 1 2 [/SUP], Jacques Fantini[SUP] 5 [/SUP], Didier Raoult[SUP] 1 2 [/SUP], Bernard La Scola[SUP] 1 2 3 [/SUP]
Affiliations
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. This article is protected by copyright. All rights reserved.
Keywords: Delta; Deltamicron; Omicron; SARS-CoV-2; epidemic; lineage; recombinant; variant.
. 2022 Apr 25.
doi: 10.1002/jmv.27789. Online ahead of print.
Culture and identification of a "Deltamicron" SARS-CoV-2 in a three cases cluster in southern France
Philippe Colson[SUP] 1 2 3 [/SUP], Pierre-Edouard Fournier[SUP] 1 2 4 [/SUP], Jeremy Delerce[SUP] 1 [/SUP], Matthieu Million[SUP] 1 2 3 [/SUP], Marielle Bedotto[SUP] 1 [/SUP], Linda Houhamdi[SUP] 1 [/SUP], Nouara Yahi[SUP] 5 [/SUP], Jeremy Bayette[SUP] 6 [/SUP], Anthony Levasseur[SUP] 1 2 [/SUP], Jacques Fantini[SUP] 5 [/SUP], Didier Raoult[SUP] 1 2 [/SUP], Bernard La Scola[SUP] 1 2 3 [/SUP]
Affiliations
- PMID: 35467028
- DOI: 10.1002/jmv.27789
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. This article is protected by copyright. All rights reserved.
Keywords: Delta; Deltamicron; Omicron; SARS-CoV-2; epidemic; lineage; recombinant; variant.
