News Medical: Nine Possible Omicron + Delta Recombinant Viruses Found in CDC National Genomic Monitoring Dataset
From News Medical found here on the web and quoted below, from their March 28, 2022, “Omicron+Delta recombinant hints emergence of supervirus, expert warns; explains key features of next COVID variant”:
Scott Nguyen, bioinformatician at the Public Health Laboratory in Washington, told NPR, the variant seems to be optimizing the combinations – picking the best traits from each for infectiousness and immune evasion.
Nguyen found a recombinant variant that’s mostly delta but contains the spike protein of omicron. “So a good chunk of the virus’ spike protein is omicron but the body of the virus is still delta,” Nguyen says.
“From the variant’s perspective, it has the best of worlds.”
From News Medical found here on the web and quoted below, from their March 24, 2022 story:
In a recent study posted to the bioRxiv* preprint server, researchers reported a novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron and Delta recombinant virus in the United States (US).
In the present study, the authors reported SARS-CoV-2 with recombinant genomes that feature hallmark mutations of the Omicron and Delta VOCs from the CDC national genomic surveillance system. The team also outlines attempts to eliminate sequencing of laboratory contamination. A quick interclade recombination identification technique named Bolotie was employed in the investigation.
Raw data of the identified SARS-CoV-2 recombinant sequences were developed using the amplicon and molecular loop-based sequencing approaches to rule out bioinformatic errors, Omicron-Delta coinfections, and laboratory contaminations. The sequencing techniques employed in the study were Nanopore, Pacific Bioscience (PacBio), and Illumina sequencing. The results demonstrated the discovery of a collection of nine possible SARS-CoV-2 recombinant sequences from the CDC national genomic monitoring dataset. The nine sequences were EPI_ISL_10389336, EPI_ISL_10389339, EPI_ISL_8981712, EPI_ISL_9088187, EPI_ISL_8981824, EPI_ISL_8981459, EPI_ISL_9147935, EPI_ISL_9147438, and EPI_ISL_8720194. These sequences were discovered as possible recombinant genomes with one parent in Omicron (Clade 21K) and another in Delta (Clade 21J) using Bolotie. Among nucleotide (nt) positions 22577 and 22035 (referenced to Genbank accession NC_045512.2), Bolotie defined a single breakpoint. No differential mutations were observed among 21K and 21J clades.
These sequences harbored signature mutation patterns from SARS-CoV-2 Omicron and Delta lineages, moving from Delta-related alterations to Omicron-linked substitutions among 158 and 339 spike (S) amino acids. This breakpoint differs from the breakpoint upstream of S in the ORF1ab gene found in two clusters of putative Delta-Omicron recombinants discovered in the United Kingdom (UK).