‘Hidden’ gene with unknown purpose found in SARS-CoV-2

11 Nov 2020

Image: © creativeneko/Stock.adobe.com

Researchers have discovered an overlapping gene in the novel coronavirus SARS-CoV-2 that may have contributed to its pandemic potential.

As efforts continue to develop a vaccine for Covid-19, scientists are continuing to learn more about the SARS-CoV-2 virus that causes the disease. Publishing to eLife, an international team of researchers announced the discovery of a gene in the virus that has not been seen before.

With only around 15 genes in the virus, knowing more about this and other overlapping genes – or genes within genes – could have a significant impact on how scientists combat the virus.

This overlapping gene, dubbed ORF3d, has the potential to encode a protein that is longer than expected. This same gene is also present in a previously discovered pangolin coronavirus.

Furthermore, ORF3d has been independently shown to produce a strong antibody response in patients diagnosed with Covid-19. This shows that the new gene’s protein is manufactured during human infection.

“We don’t yet know its function or if there’s clinical significance,” said Chase Nelson, a postdoctoral researcher at Academia Sinica in Taiwan and a visiting scientist at the American Museum of Natural History.

“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.”

Prone to ‘genomic trickery’

Overlapping genes can be multifunctional, with viruses evolving to create a biological data compression system where one nucleotide letter – A, U, G or C – can contribute to two or even three different genes.

This makes it difficult for researchers as overlapping genes are hard to spot and most scientific computer programs are not designed to find them, despite being common in viruses.

“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.”

However, using a new program and working with the Technical University of Munich and the University of California, Berkeley, the research team was able to screen genomes for patterns of genetic change that are unique to overlapping genes. It is now hoped other scientists will be able to examine the newly discovered gene and determine what possible role it may have had in the rise of the pandemic.

Colm Gorey was a senior journalist with Silicon Republic