Science‘s COVID-19 reporting is supported by the Pulitzer Center and the Heising-Simons Foundation.
It’s only a tiny change. At some point early in the pandemic, one of the 30,000 letters in the genome of SARS-CoV-2 changed from an A to a G. Today, that mutation, at position 23,403, has spread around the world. It is found in the vast majority of newly sequenced viruses and has become the center of a burning scientific question: Has the mutation become so common because it helps the virus spread faster? Or is it just coincidence?
More than 6 months into the pandemic, the virus’ potential to evolve in a nastier direction—or, if we’re lucky, become more benign—is unclear. In part that’s because it changes more slowly than most other viruses, giving virologists fewer mutations to study. But some virologists also raise an intriguing possibility: that SARS-CoV-2 was already well adapted to humans when it burst onto the world stage at the end of 2019, having quietly honed its ability to infect people beforehand.
On average, the coronavirus accumulates about two changes per month in its genome. Sequencing SARS-CoV-2 genomes helps researchers follow how the virus spreads. Most of the changes don’t affect how the virus behaves, but a few may change the disease’s transmissibility or severity.
One of the earliest candidates was the wholesale deletion of 382 base pairs in a gene called ORF8, whose function is unknown. First reported by Linfa Wang and others at the Duke-NUS Medical School in Singapore in a March preprint, the deletion has since been reported from Taiwan as well. A deletion in the same gene occurred early in the 2003 severe acute respiratory syndrome (SARS) outbreak, caused by a closely related coronavirus; lab experiments later showed that variant replicates less efficiently than its parent, suggesting the mutation may have slowed the SARS epidemic. Cell culture experiments suggest the mutation does not have the same benign effect in SARS-CoV-2, Wang says, “but there are indications that it may cause milder disease in patients.”