Solving a Genetic Mystery at the Heart of the COVID-19 Pandemic

Stylized Novel Coronavirus SARS-CoV-2

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This scanning electron microscopic lense image reveals SARS-CoV-2 emerging from the surface area of cells (blue/pink) cultured in the laboratory. Credit: National Institute of Allergy and Infectious Diseases-Rocky Mountain Laboratories, NIH

Computational biologists go into the origins of the single distinct protein in the SARS-CoV-2 family tree.

As the COVID-19 pandemic enters its 2nd year, researchers are still working to comprehend how the SARS-CoV-2 stress progressed, and how it ended up being a lot more harmful than other coronaviruses, which human beings have actually been living together with for centuries.

Virologists and epidemiologists worldwide have actually hypothesized for months that a protein called ORF8 most likely holds the response, and a current research study by Berkeley Lab researchers has actually assisted validate this hypothesis.

In a paper released in mBio, lead author Russell Neches and his associates reveal that ORF8 progressed from another coronavirus protein called ORF7a, which both proteins have folds comparable to that of a human antibody. This finding assists to describe how the infection prevents immune detection and has the ability to intensify into an extreme infection in some hosts.

“By exploring the structural and functional characteristics of ORF8, and using supercomputers to look at the genomes of over 200,000 viruses, we discovered a striking and highly unusual evolutionary strategy,” stated co-author Nikos Kyrpides, a computational biologist at the DOE Joint Genome Institute (JGI). “Amazingly, it seems that within the SARS clade, the gene encoding ORF7a is used as a ‘template’ gene, remaining stable, with a duplicate copy of this gene evolving to a point almost beyond recognition.” SARS-CoV-2 occurred and blew up into a pandemic when a SARS stress’s replicate ORF7a gene took place to alter resulting in a brand-new protein (which we now call ORF8) that offered it the capability to hinder immune cells.

According to the group, a comparable occasion happened in the SARS-CoV stress that triggered the SARS epidemic in the early 2000s. In that circumstances, a copy of the ORF7a gene split into 2, leading to ORF8a and ORF8b proteins.

Christos Ouzounis, senior author of the research study and a JGI affiliate researcher, kept in mind that the connection in between ORF8 and ORF7a was at first rather hard to make, due to how little was understood about this set of genes and their encoded proteins compared to the existing understanding about surface area proteins (such as the notorious spike protein), and due to the fact that ORF8 and ORF7a presently appear hugely various. ORF7a is extremely steady, anomaly resistant protein that engages with extremely couple of mammalian host proteins, whereas ORF8 is encoded by the most anomaly susceptible gene in the viral genome, and is now understood to be associated with lots of interactions in the body.

“Our findings – and their confirmation by parallel sequence and structure studies – reveal ORF8 to be an evolutionary hotspot in the SARS lineage. The lack of knowledge about the role of these genes has diverted attention to the more well-understood genes, but we now know more about this gene and hopefully it will receive more attention from the community,” stated Kyrpides.

Reference: “Atypical Divergence of SARS-CoV-2 Orf8 from Orf7a within the Coronavirus Lineage Suggests Potential Stealthy Viral Strategies in Immune Evasion” by Russell Y. Neches, Nikos C. Kyrpides and Christos A. Ouzounis, 19 January 2021, mBio.
DOI: 10.1128/mBio.03014-20

This work was supported by the ExaBiome Project, a Berkeley Lab-led partnership that establishes supercomputing tools for microbiome analysis. JGI is an Office of Science user center.

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