Researchers discover new hidden gene in COVID-19

A team of researchers from Taiwan’s Academia Sinica have discovered a “hidden gene” in the novel coronavirus. This hidden gene in SARS-CoV-2, virus causing COVID-19, may have contributed to its unique biology and potential of the pandemic. Discovery of a gene for a virus that already has 15 genes in total could have a significant impact on how we will fight against the virus.

Key Points

  • This study has been published in the magazine eLife. The lead author of the study is Chase Nelson who is a postdoctoral researcher at Academia Sinica and a visiting scientist at the American Museum of Natural History.
  • The researchers have found a new overlapping gene, ORF3d, in SARS-CoV-2. This new gene has a potential to encode a protein which lasts longer than expected by chance alone.
  • The team also found that this gene is also present in previously discovered pangolin coronavirus.
  • The lead author said that the function or any clinical significance of gene is not known yet but it is predicted that it is unlikely to be detected by a T-cell response.
  • At the first look, the new gene appeared like a written language in which they made a string of letters for conveying information.
  • While the unit of language/information being transferred is discrete, genes are multifunctional and overlapping.
  • Overlapping genes are hard to find, and it is difficult to spot them using scientific computer programs also. This is somewhat 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 system of data compression in which one letter in its genome contributes to 2 or even 3 different genes.
  • Nelson highlighted that “Missing overlapping genes puts us in a great danger of overlooking major aspects of viral biology”.

Before COVID-19, Nelson has developed a computer program for screening genomes for patterns of genetic change that are unique to overlapping genes.

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