Culture and identification of a "Deltamicron" SARS-CoV-2 in a three cases cluster in southern France

Abstract

Multiple SARS-CoV-2 variants have successively, or concomitantly spread worldwide since the summer of 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 1163-1421 reads and a 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 quantitative polymerase chain reaction (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.

Keywords: Omicron; SARS-CoV-2; delta; deltamicron; epidemic; lineage; recombinant; variant.

Figure 1

Schematic of the SARS‐CoV‐2 Delta 21J_AY.4‐Omicron 21K/BA.1 recombinant genome, and phylogenetic trees based on different regions of the Deltamicron genome reflecting the origin of most of the viral genome from a Delta 21J_AY.4 variant and the origin of a region spanning a large part of the spike gene from an Omicron 21K/BA.1 variant. (A) Map of the SARS‐CoV‐2 genome. (B) Schematic representation of parental and recombinant genomes. (C) Mutations in the three Delta 21J_AY.4‐Omicron 21K/BA1 recombinant genomes. Adapted from screenshots of the nextclade web application output (https://clades.nextstrain.org)., Color codes for nucleotide mutations are as follows: Green: U; yellow: G; blue: C; red: A; light grey: deletions; dark grey: uncovered regions. Genomes are labeled with the identifiers of the NCBI GenBank (https://www.ncbi.nlm.nih.gov/genbank/) and IHU Méditerranée Infection (https://www.mediterranee-infection.com/tout-sur-le-coronavirus/sequencage-genomique-sars-cov-2/) sequence databases. (D, E) Phylogenetic trees based on different regions of the Deltamicron genomes showing the origin of most of the viral genome from a Delta 21J_AY.4 variant (D) and the origin of a region spanning a large part of the spike gene from an Omicron 21K/BA.1 variant (E). The 10 genomes the most similar genetically to these regions of the recombinant genomes obtained here were selected from the sequence database of our institute through a BLAST search, then were incorporated in the phylogeny together with the genome of the Wuhan‐Hu‐1 isolate. Sequences from recombinant genomes are indicated by green or orange backgrounds. Sequences are labeled with identifiers from the GenBank (https://www.ncbi.nlm.nih.gov/genbank/) and IHU Méditerranée Infection sequence databases.

Figure 2

Microscopy images of the virus cytopathic effect (A, B) and of a viral particle (C) in the culture of the SARS‐CoV‐2 Delta 21J_AY.4‐Omicron 21K/BA.1 recombinant on Vero E6 cells. (A) Absence of cytopathic effect (negative control: absence of virus). (B) Cytopathic effect observed 4 days postinoculation on Vero E6 cells of the respiratory sample of the first patient for whom the SARS‐CoV‐2 Delta 21J_AY.4‐Omicron 21K/BA.1 recombinant was identified. (C) Scanning electron microscopy image was obtained with a SU5000 microscope (Hitachi High‐Technologies Corporation)

Figure 3

Schematic of the predicted structure of the spike protein of the SARS‐CoV‐2 Delta 21J_AY.4‐Omicron 21K/BA.1 recombinant (A) Overall structure of the recombinant spike protein. The secondary structure is in grey, mutated amino acids are in blue. NTD, N‐terminal domain; RBD, receptor‐binding domain; S1‐S2, cleavage site. (B) Superimposition of the secondary structure of the Omicron 21K/BA.1 variant (in cyan) and recombinant (in red) spike proteins. NTD, N‐terminal domain; RBD, receptor‐binding domain. (C) Comparison of the electrostatic surface potential of the spike proteins in Delta 21J_AY.4 lineage, Omicron 21K/BA.1 variant, and in the recombinant. The color scale (negative in red, positive in blue, neutral in white) is indicated. NTD, N‐terminal domain; RBD, receptor‐binding domain