Researchers have uncovered a mysterious gene in the genetic code of the coronavirus SARS-CoV-2 – which is virtually hidden from view in the genome of the virus, and yet largely ignored.
The newly called gene – is called ORF3d An example of this is the so-called overlapping gene: a type of ‘gene inside a gene’ that is effectively hidden in a string of nucleotides, as it overlaps the coded sequences of other genes.
“In terms of genome size, SARS-Covy-2 and its relatives are one of the longest-lived RNA viruses,” explains Chase Nelson, a bioenformatist at the American Museum of Natural History.
“They are probably more susceptible to ‘genomic tricks’ than other RNA viruses.”
Viruses are actually quite likely to host overlapping genes, so it’s not exactly a shocking discovery. Even if ORF3d Genomic Trickery represents what really remains to be seen, but in any case, it’s hard to see for sure.
The overlapping genes are difficult to identify in the genetic sequence, as genomic scan systems can often miss them when running through the strings of the genetic code: programmed to select individual genes, but not overlaid the nucleotides of adjacent genes in the index.
In the case of viruses such as SARS-Covy-2, which can be a serious blind spot. Since the beginning of this year, scientists have been scrambling to understand as much as possible about this deadly virus, and while some aspects of its genetic make-up have been clarified (including Pay’s consent that it was not made in a laboratory). Remains that we do not yet know.
“The disappearance of overlapping genes puts us at risk for important aspects of viral biology,” says Nelson.
“An overlapping gene can be an arsenal in a way in which the coronavirus has evolved to effectively mimic, fail the host’s immunity, or infect itself.”
For no ORF3d, Hidden in the genome and wrapping other genes, there is still a lot to learn about why it is.
By scanning through genomic databases, the researchers found that the gene had been identified before, but only in one type of coronavirus affecting pangolins (found in Guangxi, China).
It has also previously been classified as an unrelated gene, ORF3b – which is present in other coronaviruses, including SARS-Covy – but it’s not really the same thing.
“The two genes are unrelated and encode completely different proteins,” Says Nelson. “This means knowledge about SARS-COV ORF3b SARS-CoV-2 should not be applied ORF3d“
One of the mysterious genes we know of, based on previous blood work with human covid-19 patients, is ORF3d Strong antibody response.
Whether or not the T-cell will also be triggered – or what other viral purpose overlapping occurs ORF3d Maybe – we’re still in the dark. It can be relatively benign. It can’t be.
“We don’t yet know if it has any medical significance,” says Nelson.
“But we speculate that unlike the antibody response, it is not possible for this gene to be detected by the T-cell response. And perhaps it has something to do with how the gene was able to emerge.”
One thing is for sure. In a virus that contains only 15 known genes, the discovery of another one – let alone an overlapping gene – is an important development. Just how remarkable, scientists will now try to find out.
These findings are reported Elife.
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