Mysterious New “Hidden” Gene Discovered in COVID-19 Virus

DNA Genetics

Researchers have discovered a new “hidden” gene in SARS-CoV-2 — the virus that causes COVID-19 — that may have contributed to its unique biology and pandemic potential. In a virus that only has about 15 genes in total, knowing more about this and other overlapping genes — or “genes within genes” — could have a significant impact on how we combat the virus. The new gene is described today in the journal eLife.

“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.”

The research team identified ORF3d, a new overlapping gene in SARS-CoV-2 that has the potential to encode a protein that is longer than expected by chance alone. They found that this gene is also present in a previously discovered pangolin coronavirus, perhaps reflecting repeated loss or gain of this gene during the evolution of SARS-CoV-2 and related viruses. In addition, ORF3d has been independently identified and shown to elicit a strong antibody response in COVID-19 patients, demonstrating that the new gene’s 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.”

At first glance, genes can seem like written language in that they are made of strings of letters (in RNA viruses, the nucleotides A, U, G, and C) that convey information. But while the units of language (words) are discrete and non-overlapping, genes can be overlapping and multifunctional, with information cryptically encoded depending on where you start “reading.” Overlapping genes are hard to spot, and most scientific computer programs are not designed to find them. However, they are common in viruses. 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,” said Nelson. “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.”

Prior to the pandemic, while working at the Museum as a Gerstner Scholar in Bioinformatics and Computational Biology, Nelson developed a computer program that screens genomes for patterns of genetic change that are unique to overlapping genes. For this study, Nelson teamed up with colleagues from institutions including the Technical University of Munich and the University of California, Berkeley, to apply this software and other methods to the wealth of new sequence data available for SARS-CoV-2. The group is hopeful that other scientists will investigate the gene they discovered in the lab to define its function and possibly determine what role it might have played in the emergence of the pandemic virus.

Reference: “Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic” by Chase W Nelson, Zachary Ardern, Tony L Goldberg, Chen Meng, Chen-Hao Kuo, Christina Ludwig, Sergios-Orestis Kolokotronis and Xinzhu Wei, 1 October 2020, eLife.
DOI: 10.7554/eLife.59633

Funding for this work was provided in part by Academia Sinica, the Bavarian State Government and 12 National Philanthropic Trust, the U.S. National Science Foundation (grant numbers 1755370 and 1758800, and the University of Wisconsin-Madison.

17 Comments on "Mysterious New “Hidden” Gene Discovered in COVID-19 Virus"

  1. I’m all for science, but the coronavirus hysteria has brought “superstitious science” into the collective consciousness. Articles like this only make matters worse.

  2. Rassalas, this article plainly describes a new research study. This is the kind of stuff scientists read every day. I don’t see any superstition or hype here.

  3. Gerry Nightingale | November 11, 2020 at 9:56 pm | Reply

    The article is failing to mention just ‘what’ comprises the supposed genomes in a viral entity.
    The notion of intrinsic genetic coding in a viral-body is completely suppositional as there is NO direct conclusive evidence to support intrinsic genetic ‘codes’ in a virus that are on a par
    with actual living cells!
    “Actions/Reactions” do not validate suppositional analogues.

  4. Do any of you know of similarities in any way with morgellons fiber disease which I have though America failed to find it( and didn’t test me properly for it either) I have bad case and a strain 3 Europeans have yet to find in there comparative base studies alien like things in every camera I get hyroglyphs popping up on furniture etc. I clean. My phones monitoring all I do music recording all vocal videos crazy. I am sane degree and intelligence above normal but I am being shown things that may come to pass. Paul revere approach not working. Nobody takes me serious.just like CDC did not when I tried to get them samples of my various body fluids skin etc. Let me know cause I am sure they are tied in as was Sars and?? My Europeans have told me their findings.let me know what you think? Thanks Scottish gut going home cause of various reasons. Cheers jock..

  5. Well you all are familiar with designer genes! Asinine, guanine, urasil and cytosine. What fun! And you thought Ian Flemming’s villains were scary!

  6. So wait your saying scientist trying to figure this thing out is a conspiracy right? Everything is a conspiracy right? Here’s a thought maybe conspiracy folks are lazy failures looking for excuses.
    Or maybe that’s what they want us to think🤣

  7. Sounds like this hidden gene provides proof that this virus was created!

  8. David Goldberg | November 12, 2020 at 7:39 am | Reply

    Well here we go..the smoking bullet. The virus was engineered.

  9. ATGC, not AUGC

  10. No, it doesn’t prove engineering of the gene. Read the article closely. So-called “hidden” genes are common in viruses and are simply difficult to spot.

  11. Conspiracy theorists could read this article forward,backwards, print it out and eat it! It wouldn’t matter because people see what they believe instead of believing what they see. Work on that folks. #reality

  12. Criticalthinker | November 12, 2020 at 2:51 pm | Reply

    I am by no means a scientist or virologist but what I do know is the timing of the virus has proven to be very profitable for certain factions of our society. Both financially and politically. The virus could not have come at a better time for some to exploit it for their own diabolical purposes if that makes me a conspiracy theorist so be it. Whether it came about organically or was manufactured in lab the virus has destroyed many lives and not just of the people who have contracted it. The reaction to it has destroyed just as many lives if not more and the results will be felt for a generation.

  13. Criticalthinker | November 12, 2020 at 2:54 pm | Reply

    I am by no means a scientist or virologist but what I do know is the timing of the virus has proven to be very profitable for certain factions of our society. Both financially and politically. The virus could not have come at a better time for some to exploit it . Whether it came about organically or was manufactured in lab the virus has destroyed many lives and not just of the people who have contracted it. The reaction to it has destroyed just as many lives if not more and the results will be felt for a generation.

  14. Criticalthinkerunite | November 12, 2020 at 2:55 pm | Reply

    I am by no means a scientist or virologist but what I do know is the timing of the virus has proven to be very profitable for certain factions of our society. Both financially and politically. The virus could not have come at a better time for some to exploit it . Whether it came about organically or was manufactured in lab the virus has destroyed many lives and not just of the people who have contracted it. The reaction to it has destroyed just as many lives if not more and the results will be felt for a generation.

  15. Razzmatazz who in the hell got rich from the pandemic?!?! 30 million Americans unemployed, small businesses closing, large company layoff, halt of world travel. Drug companies?!? Well not until they develop a vaccine and who cares if it works!

  16. kamir bouchareb st | November 15, 2020 at 11:24 pm | Reply

    good article

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