Researchers identify new ‘hidden’ gene in SARS-CoV-2 | COVID Research

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

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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 different from the latter. These structures are difficult to identify in genetic sequences, since the genomic scanning systems, responsible for traversing the chains of genetic code, are not programmed to isolate them.

This announcement is not “extraordinary” in itself. RNA viruses are indeed prone to harbor overlapping genes due to their high mutation rate. Therefore, they seek to keep their number of genes 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 genes, the fact of a better understanding of its genomic structure could have a significant impact on the way in which we fight the pathogen.

” Overlapping genes may be one of the many ways in which coronaviruses have evolved to replicate effectively, thwart host immunity, or transmit themselves, ” says Chase Nelson, of Academia Sinica at Taiwan and lead author of the study. “ Knowing that these genes exist and how they work may reveal new avenues for controlling coronaviruses, 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 don’t yet know its function or if there is the clinical significance, ” Chase Nelson continues. Browsing through genomic databases, the researchers still found 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 wrongly classified as an unrelated gene – ORF3b – found in other coronaviruses, including SARS-CoV-2. In fact, “ ORF3d and ORF3b are not linked and encode entirely different proteins ”, continues the researcher. “ This means that our knowledge about SARS-CoV ORF3b should not be applied to SARS-CoV-2 ORF3d ”.

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

So far that’s all we know. The research will now continue in order to better understand the genomic structure of this virus. In this way, we could then develop other ways to protect ourselves from it.

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