Delta and Omicron recombinant SARS-CoV-2 detected in the US

A study headed by the Centers for Disease Control and Prevention in the US has detected nine SARS-CoV-2 viruses with genetic information from the Delta (AY.119.2) and Omicron (BA.1.1) variants in several mid-Atlantic states of the US.

The states where the recombinants were detected are New Jersey, Tennesse, Massachusetts, and Pennsylvania.

RNA viruses like the SARS-CoV-2, which causes COVID-19,  frequently mutate. In the presence of more than one variant, hybrid viruses may result.

The Centers for Disease Control and Prevention (CDC) collects and sequences SARS-CoV-2 specimens from 64 states and jurisdictions via the National SARS-CoV-2
Strain Surveillance Program (NS3). The CDC also funds SARS-CoV-2 sequencing via commercial laboratory testing companies nationwide. This program has resulted in 1.8 million SARS-CoV-2 genomes collected from the United States since January 2021.

The genomic surveillance system aims to detect and respond dynamically to new and changing SARS-CoV-2 variants that can result in highly infectious or deadlier variants. The authors made sure they were not from laboratory artifacts or coinfections.

The nine samples contained recombination within the Spike gene, containing substitutions common to Delta lineages at the 5’ end and Omicron lineages at the 3’ end. The samples they isolated are different from the Delta-Omicron recombinants identified in the United Kingdom.

The table below shows the recombinant strains isolated by the National SARS-CoV-2
Strain Surveillance Program (NS3). GISAID is a global science initiative that provides open access to genomic data of influenza viruses and coronaviruses.

Source: Lacek et al., 2022

Luckily, the new recombinant viruses are not more infectious than the previous. According to the authors

Despite being detected over the course of 6 weeks, the number of cases resulting from these hybrid Spike recombinant viruses remains low.

The study is available as a preprint at medRxiv.

Hopefully, we will see the end of this COVID-19 soon. I think everyone had enough of this pandemic.

 

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