Researchers found new hidden overlapping gene in SARS-CoV-2 virus

Prashasti Awasthi Mumbai | Updated on November 11, 2020

An undated scanning electron microscope image shows SARS-CoV-2 (yellow), also known as novel coronavirus, the virus that causes Covid-19, isolated from a patient in the U.S., emerging from the surface of cells (blue/pink) cultured in the lab.   -  Reuters

Overlapping genes may be one of an arsenal of ways in which coronaviruses have evolved to replicate efficiently, thwart host immunity, or get themselves transmitted.

Researchers have found a new “hidden” gene in the SARS-CoV-2 virus that may have contributed to its unique biology that has triggered pandemic in the world.

The study mentioned that the virus has about 15 genes in total, and this unique gene that they have found overlaps these genes (genes within genes). The findings were published in the journal eLife.

Lead author Chase Nelson, a postdoctoral researcher at Academia Sinica in Taiwan said: "Overlapping genes may be one of an arsenal of ways in which coronaviruses have evolved to replicate efficiently, thwart host immunity, or get themselves transmitted."

He added: "Knowing that overlapping genes exist and how they function may reveal new avenues for coronavirus control, for example, through antiviral drugs.".

They found that this gene -- ORF3d -- is also present in a previously discovered pangolin coronavirus. This could answer repeated loss or gain of this gene during the evolution of SARS-CoV-2 and related viruses.

Additionally, ORF3d has been independently identified and shown to elicit a strong antibody response in Covid-19 patients. This also demonstrated that the new gene's protein is manufactured during human infection.

Nelson elaborated: "We don't yet know its function or if there's clinical significance. But we predict this gene is relatively unlikely to be detected by a T-cell response, in contrast to the antibody response. And maybe that has something to do with how the gene was able to arise."

According to researchers, overlapping genes are hard to identify, and most scientific computer programs are not designed to find them. However, they are common in viruses.

The study reasoned that this is partly because RNA viruses have a high mutation rate, so they tend to keep their gene count low to prevent a large number of mutations. As a result, viruses have evolved a sort of data compression system in which one letter in its genome can contribute to two or even three different genes.

"Missing overlapping genes puts us in peril of overlooking important aspects of viral biology. In terms of genome size, SARS-CoV-2 and its relatives are among the longest RNA viruses that exist. They are thus perhaps more prone to 'genomic trickery' than other RNA viruses," Nelson added.

Published on November 11, 2020

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