Researchers have discovered a mysterious gene in the SARS-CoV-2 coronavirus code. Until now, the segment was invisible to the human eye.

The gene was called ORF3d and is known as overlapping gene: a kind of gene within a gene, which is hidden in a nucleotide chain due to the way it overlaps the encoded sequences of other genes.

“In terms of genome size, SARS-CoV-2 and its relatives are among the largest RNA viruses out there,” explains bioinformatician Chase Nelson from the American Museum of Natural History.

Viruses are quite prone to harboring overlapping genes, but in a virus that only has about 15 known genes, the discovery of one more is a significant development. 

Overlapping genes are difficult to identify in genetic sequences, as genomic scanning systems can often miss them when traversing the strands of the genetic code. It is because they are programmed to pick up individual genes, but without necessarily seeing the general schemes. In the context of a virus-like SARS-CoV-2, that could be a serious blind spot. 

“Ignoring overlapping genes puts us at risk of ignoring important aspects of viral biology. Gene overlap can be one of the ways coronaviruses have evolved to replicate efficiently, thwart host immunity, or spread,” Nelson stresses.

One thing that is known about the mysterious gene is that ORF3d causes a strong antibody response, but if T cells are also triggered or what other purposes it can serve is yet to be investigated, scientists conclude in their report for eLife.