Emerging Diseases report on SARS-CoV-2 Delta–Omicron recombinant viruses

May 16, 2022

To detect new and changing SARS-CoV-2 variants, the Centers for Disease Control and Prevention (CDC) investigated candidate Delta–Omicron recombinant genomes national genomic surveillance. Laboratory and bioinformatic investigations identified and validated 9 genetically related SARS-CoV-2 viruses with a hybrid Delta–Omicron spike protein, according to a new Emerging Diseases report.

Emerging variants of SARS-CoV-2 are characterized and monitored closely by national genomic surveillance. In addition to sequencing efforts from US public health, academic, and commercial laboratories, the CDC collects and sequences SARS-CoV-2 specimens from 64 partners across state, tribal, local, and territorial public health agencies through the National SARS-CoV-2 Strain Surveillance program and funds SARS-CoV-2 sequencing through a nationwide network of commercial laboratory testing companies.

To date, these efforts have contributed 1.8 million SARS-CoV-2 genomes from the United States to public repositories. The purpose of this genomic surveillance system is to detect and respond dynamically to new and changing SARS-CoV-2 variants.

The results provide evidence of a recombinant SARS-CoV-2 genome containing a hybrid spike protein derived from a Delta (AY.119.2)–Omicron (BA.1.1) recombination event. However, the ability to effectively identify and confirm additional recombinant viruses remains challenging because of the range of sequence quality available in the public domain. These limitations are a result of amplification inefficiency and consensus-calling algorithmic error, as well as cases of co-infection or potential sample contamination.

Despite recombinant viruses with a hybrid spike protein having been detected over the course of 6 weeks, the number of resulting cases remains low. Most cases were identified within the mid-Atlantic region of the United States. However, epidemiologic linkage cannot be determined because CDC does not collect identifying information for these samples.

Recombination is an evolutionary mechanism frequently observed in coronaviruses, and it can lead to rapid accumulation of mutations and heightened transmissibility. SARS-CoV-2 recombination events have also been found to arise disproportionately in the spike. Recombination between Alpha and Delta SARS-CoV-2 variants has been documented.

Given the divergence of the Delta and Omicron variant genomes, as well as the known immune-escape properties of Omicron, a Delta–Omicron recombinant strain could alter the landscape of vaccine and therapeutic effectiveness.

In early 2022, viruses resulting from recombination between Delta and Omicron were reported, but further inspection indicated that these claims seemed to have resulted from laboratory artifact or co-infections. With this study, we identified candidate Delta–Omicron recombinant genomes from the CDC national genomic surveillance and attempted to rule out laboratory contamination or sequencing error.

Systematic virus surveillance is essential for long-term monitoring of SARS-CoV-2 evolution. Given the potential public health consequences of new variants emerging from recombination, investigations involving laboratory and bioinformatic components, such as the one presented here, are critical for correctly identifying and tracking these viruses.

Link to the Emerging Infectious Disease report from the CDC

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