Not Over Yet: Researchers Identify “Deltacron” Hybrid COVID-19 Variant

A Delta and Omicron hybrid coronavirus strain has been identified in the US, the UK, the Netherlands, France, and Denmark.

Delta 21J/AY.4-Omicron 21K/BA.1, which many are calling “Deltacron,” is known as a recombinant virus because it contains genes from both variants. Recombinants occur when more than 1 variant infects the same person and replicates in the same cells. One study estimates up to 5% of SARS-CoV-2, the virus that causes coronavirus, could be recombinants.

A recent study, preprinted in MedRxiv, identified the Deltacron strain while conducting SARS-CoV-2 genotypic surveillance in France. The study period ran from December 27, 2021-February 14, 2022, and the variant was first sequenced in January 2022.

Deltacron has nearly the full-length spike protein of Omicron and a Delta backbone, or “body.” The hybrid genome is supported by a mean sequencing depth of 1163-1421 reads and a mean nucleotide diversity of 0.1-0.6%.

Philippe Colson of IHU Mediterranee Infection in Marseille, France, the lead author of the study, said the team designed and implemented a specific duplex qPCR for routine diagnosis. The variant appears to have been circulating since the beginning of 2022, suggesting it may be less infectious than previous strains.

So far, only 17 patients in the US have been infected with Deltacron, and approximately 30 in the UK. The Deltacron cases identified in France, Denmark, and the Netherlands are fairly similar and may be the same recombinant, but the Deltacron infections in the US and UK appear to combine different aspects of the Delta and Omicron parent variants.

It is still too early to know whether Deltacron will be highly transmissible, like Omicron, or cause severe illness, like Delta. One cause for concern is the structural arrangement of the recombinant spike protein; the hybrid content could optimize viral binding to the host cell membrane. However, researchers anticipate it will not elevate to a variant of concern (VOC), as it initially does not appear to spread as easily as prior strains.

Recombinant variants are not an anomaly, and often occur when 1 variant overtakes another, previously dominant, variant. Previous Delta and Omicron waves and highly effective COVID-19 vaccinations mean there will likely be some degree of protection against Deltacron.