How dangerous Omicron is, won’t be known for weeks
At 7.30 a.m. on Wednesday, Kristian Andersen, an infectious disease researcher at Scripps Research in San Diego, received a message on Slack: “This variant is completely insane.” Andrew Rambaut of the University of Edinburgh was reacting to a new SARS-CoV-2 genome sequence found in three samples collected in Botswana on 11 November and one picked up a week later in a traveler from South Africa to Hong Kong.
Andersen looked at the data and then replied: “Holy shit—that is quite something. The length of that branch…” A few minutes later he added: “Just had a look at the list of mutations—so nuts.”
They were talking about what is now called Omicron, a new variant of concern, and the long branch Andersen noticed refers to its distance to every other known virus on SARS-CoV-2’s evolutionary tree. The variant seemed to have picked up dozens of mutations, many of them known to be important in evading immunity or increasing transmissibility, with no intermediate sequences in the database of millions of viral genomes. On Tuesday, after spotting the odd sequences in a global database, Tom Peacock, a virologist at Imperial College London, had already posted his own verdict on GitHub: “This could be of real concern.”
Now, once again, the world is watching as researchers work nights and weekends to learn what a new variant has in store for humanity. Is Omicron more infectious? More deadly? Is it better at re-infecting recovered people? How well does it evade vaccine-induced immunity? And where did it come from? Finding out will take time, warns Jeremy Farrar, the head of the Wellcome Trust: “I’m afraid patience is crucial.”
Researchers in South Africa were already on the trail of this new variant. Several teams were independently trying to figure out why cases were spiking in Gauteng, a northern province that includes Johannesburg and Pretoria. And a private lab called Lancet had noticed that routine PCR tests for SARS-CoV-2 were failing to detect a key target, the S gene, in many samples, a phenomenon previously seen with Alpha, another variant of concern. When Lancet sequenced eight of these viruses, they found out why: The genome was so heavily mutated that the test missed the gene. [Continue reading…]