A mysterious gene is hidden in the coronavirus: it could give rise to the entire pandemic

Coronavirus hides a gene that could give rise to the entire pandemic

The researchers found a hidden gene in the coronavirus that causes the COVID-19. Perhaps it was that mysterious gene that laid the foundation for the unique biology of a rapidly spreading pandemic. The virus has only 15 genes, and more information on new overlapping genes could have a significant impact on the researchers' fight against a dangerous disease. Overlapping genes could be one way for coronaviruses to evolve to replicate efficiently, suppress host immunity, or transmit themselves.

So says Chase Nelson, a research fellow at Sinica Academy in Taiwan. In his opinion, knowledge about which overlapping genes can exist and how they behave in the human body opens up new opportunities to combat not only the COVID-19, but also other coronavirus infections.


The mysterious new gene was named ORF3d. Its peculiarity lies in the fact that it can encode a protein that is actually longer than the rest. The same gene was found in the body of pangolins, which, it is believed, could become a carrier of coronavirus from the animal world to the human world.

Independent identification of the ORF3d gene demonstrated that the gene can elicit the strongest antibody response in patients with the coronavirus, while showing that the new gene's protein is produced during human infection. According to the researchers, there is very little information about the functions of the new protein and its clinical significance.

But there are predictions that the gene has a small likelihood of being detected by a T-cell response as opposed to detecting antibodies. Perhaps it is due to the fact that the gene could arise that way. Overlapping genes are difficult to detect, and most of the scientific programs used to find them are not designed.


But for the viruses, that situation is considered traditional. The RNA viruses have a high mutation rate and they strive to maintain a certain number of genes without changing the number, using a gene overlap system. When such genes are absent, it is indicative of a dangerous viral biology.

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