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.

Deltacron: Apprehending a new phase of the COVID-19 pandemic

“…Importantly, scientists are now much more convinced that the new strain from France is a true recombinant and the genetic sequencing data was clear. The Institute Pasteur team claims to have cultivated the virus in the lab, proving that it is not a cross-contamination product [ 5 , 6 ].…”

“…An international database of viral sequences recorded 33 cases of the new variant in France, eight in Denmark, one in Germany, and one in the Netherlands in a March 10 update. According to the UK Health Security Agency, around 30 cases have been reported in the UK (UKHSA) [ 6 , 11 ]. Although the World Health Organization (WHO) designated certain strains in the Netherlands and Denmark on March 9, the Deltacron has not been identified as a variant of concern due to the small number of confirmed cases [ 6 , 11 , 12 ].…”

“…According to the UK Health Security Agency, around 30 cases have been reported in the UK (UKHSA) [ 6 , 11 ]. Although the World Health Organization (WHO) designated certain strains in the Netherlands and Denmark on March 9, the Deltacron has not been identified as a variant of concern due to the small number of confirmed cases [ 6 , 11 , 12 ].…”

“…The recombinant spike protein's basic form was determined. When overlaid with the Omicron 21K/BA spike, one variant mutation was found in the N-terminal domain (NTD) [ 6 , 13 ]. The recombinant's receptor-binding domain (RBD) is definitely derived from the Omicron 21K/BA.1 variant.…”

“…The recombinant's receptor-binding domain (RBD) is definitely derived from the Omicron 21K/BA.1 variant. As a whole, this structural analysis shows that the recombinant virus was chosen based on kinetic properties imparted by a convergent rise in the electrostatic potential of both the NTD and the RBD, as well as an expansion of the NTD surface [ 6 , 11 ]. As a result, the emergence of novel recombined viruses may lead to increased disease transmission or immune evasion [ 7 ].…”