Researchers identify a new “hidden” gene in SARS-CoV-2

A team of researchers announced that they have identified an “overlapping gene” in the SARS-CoV-2 genome. The facility could contribute to its unique biology and pandemic potential. Details of the study are published in the journal eLife.

Understand the threat better

The newly identified gene – called ORF3d – is an example of what geneticists call an “overlapping gene,” which partially or totally overlaps another gene, expressing a protein other than the latter. These structures are difficult to identify in genetic sequences, as the genomic scanning systems, responsible for traversing the chains of the genetic code, are not programmed to isolate them.

This announcement is not “extraordinary” in itself. RNA viruses are in fact prone to harbor overlapping genes due to their high mutation rate. As a result, they try to keep their gene count low to avoid a large number of mutations. As a result, they are developing a kind of “data compression system” in which one letter of the genome can contribute to two or even three different genes.

That said, the discovery is important. In a virus that has fifteen or so genes, understanding its genomic structure better could have a significant impact on how we fight the pathogen.

“Overlapping genes may be one of the many ways coronaviruses have evolved to replicate effectively, counter host immunity, or be passed on.“, Explains Chase Nelson, of Academia Sinica in Taiwan and lead author of the study. “Knowing these genes exist and how they work can reveal new pathways for coronavirus control, for example through antiviral drugs“.

Still in the dark

As for ORF3d, there is still a lot to learn about the reason for its presence. “We do not yet know its function or if there is any clinical significance“, Continues Chase Nelson. Browsing through the genomic databases, the researchers still discovered that the gene had already been identified, but only in a variant of the coronavirus that affects pangolins (found in Guangxi, China).

We also know that it was previously misclassified as an unrelated gene – ORF3b – found in other coronaviruses, including SARS-CoV-2. In reality, “ORF3d and ORF3b they are unrelated and encode completely different proteins“, Continues the researcher. “This means that our knowledge of SARS-CoV ORF3b should not be applied to SARS-CoV-2 ORF3d“.

Finally, based on previous blood tests performed on human COVID-19 patients, it would appear that ORF3d is the cause strong antibody response. This shows that the protein for this new “mysterious” gene is produced when SARS-CoV-2 infects humans.

So far this is all we know. Research will now continue to better understand the genomic structure of this virus. In this way, we could then develop other ways to protect ourselves from it.