'Hidden' gene discovered in Covid-19 virus could give more insight into its ability to spread

  • Scientists have discovered a 'hidden' gene in the genetic code of SARS-CoV-2
  • This overlapping gene, the team said, is unlikely to be detected by the human body's T-cells
  • Earlier findings have also found mysterious genes, all helpful in the search for treatments and vaccines 

Researchers from the American Museum of Natural History have identified a new "hidden" gene in SARS-CoV-2, the virus that causes Covid-19, and say this may explain why it is so highly infectious.

The discovery of the “overlapping gene”, named ORF3d, could have a significant impact on how we combat the virus, the research team wrote. Overlapping genes (OLGs) are a type of 'gene within a gene', effectively concealed in a string of nucleotides, ScienceAlert explains.

"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," said lead author Chase Nelson, a postdoctoral researcher at Academia Sinica in Taiwan and a visiting scientist at the American Museum of Natural History.

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

Their findings were published in the journal eLife.

ORF3d unlikely to be detected by T-cells

According to the team’s findings, the newly discovered gene is present in a previously discovered pangolin coronavirus. This, they say, possibly reveals repeated loss or gain of this gene during the evolution of the new coronavirus, as well as related viruses.

The gene has also shown to elicit a strong antibody response in Covid-19 patients, the researchers said, demonstrating that its protein is manufactured during human infection.

"We don't yet know its function or if there's clinical significance," Nelson said. "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."

T-cells are “natural killers”, whose job is to find infected cells in the human body and destroy them, Professor Thomas Scriba, deputy director of immunology and laboratory director at the South African Tuberculosis Vaccine Initiative, University of Cape Town, previously told Health24

Mysterious genes explained

Overlapping genes are hard to spot, the researchers explained, as they are virtually hidden from view in the virus's genome, and therefore easily overlooked.

Most scientific computer programmes are not designed to find them, they said, although OLGs are relatively common in DNA and RNA viruses – partly because RNA viruses (such as SARS-CoV-2) have a high mutation rate.

"Missing overlapping genes puts us in peril of overlooking important aspects of viral biology," Nelson said.

"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."

Previous discoveries on hidden mutations

Earlier this year, scientists from a separate study also suggested that SARS-CoV-2 exploits a rare, ‘silent’ (hidden) gene mutation in certain people, and said it may provide clarity on why two young and healthy individuals can be so differently affected by the virus, Health24 reported

In another breakthrough study, researchers uncovered a second receptor, called neuropilin-1, which may explain why the virus is so highly infectious.

This receptor is widespread in human tissues, they said, and explained that the new coronavirus has a convenient advantage when infecting human cells. These discoveries are all critical in the race to develop a vaccine and treatment for Covid-19.

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Image: Getty/Andriy Onufriyenko

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