The computer generated image shows the omicron variant of the coronaviruses. This variant has a large number of defects, some of which are concerning.
The images are of Uma Shankar.
The discovery of omicron, a new variant of coronaviruses with a high number of concerning mutations, has kicked off a frenzy of research. Scientists are trying to figure out how transmissible this variant is.
They're wondering how omicron got created.
Two scientists are in the thick of the research. At the Fred Hutchinson Cancer Research Center in Seattle, there is a professor named Trevor Bedford. Richard Lessells is an infectious disease specialist at the University of KwaZulu-Natal in South Africa and part of the team that identified omicron in South Africa. Here's what they have to say.
There is a big surprise in Omicron's genetic family tree.
Scientists use genetic code to puzzle out the origin of a coronaviruses variant. A person who wants to find out their ancestry is the same person. The virus's genome contains clues, so they can find traces of that lineage in their genes.
"It's been very common to use an evolutionary tree to catch the introduction of the SARS-CoV-2 viruses to places like Australia and Taiwan that have not had a lot of local spread." If you look at the viral genome, you can see if it's close to where the imports are coming from.
As they continue to take samples in the new region, scientists will be able to see how each particular strain picks up more and more benign changes step-by-step until it becomes a significantly different strain.
When you look at the family tree for the omicron variant, you will see that the closest sequence is back in mid- 2020. That is very rare to see.
Scientists can tell that this variant evolved from a strain that was circulating in mid-2020, but there's been no trace of the intermediate versions that would have been expected.
"It doesn't tie into anything that was circulating recently," says Bedford. It is a long way from the 2020 strain.
How do I explain this?
The animal source is hypothesis number one.
It's possible that the mid-2020 strain evolved as it spread among them and has just recently spilled over into humans.
The hypothesis is not likely to prove true, according to Bedford. He says this is getting technical. You'd expect to see signs of the animal's genetic material in the genome, but instead there's an addition of human RNA that was evolving in a human.
hypothesis 2:Cryptic spread in an unmonitored region
There is a chance that the mid-2020 strain started circulating in a location where there hasn't been a lot of monitoring. The virus would be able to evolve under the radar. It will pick up enough mutations by the time you get to 2021, and then explode onto the scene at that point.
He finds that scenario hard to believe. The earlier versions of the virus would have spread more widely if it were on its way to becoming omicron. It would have been noticed in countries that have robust systems.
Lessells agrees. On the other hand, he notes that there are countries in Africa where there has not been a lot of sampling of the coronaviruses. He says that South Africa's labs picked up a variant that hadn't been seen before in a traveler from Tanzania, where they weren't measuring the epidemic very well.
"That variant never really took off in any area," he said. We don't know what the significance of that was and we don't know how much it was circulating. He says that the episodes show that a variant is less likely to be identified once it reaches South Africa. He says that there are sevengenomics hubs that are connected to the public and private diagnostic labs.
Omicron causes a notable signature in the tests that are done on a routine basis to confirm infections. Lessells and his colleagues were alert to the warning flag by a private lab last month so that they could sequence the samples in which they discovered omicron. "If you can respond quickly to what you're observing in the cases in the diagnostic lab, then you can pick up some of the early variant that are at a relatively early stage," he says. You would have to have a big blind spot to be missing something that's really evolving over a period of months.
Incubation in a person with an illness.
The virus could have been hiding inside the body of a single person, which would have been a blind spot for health officials. A person whose immune system was suppressed because of an HIV infection. The person's immune system is strong enough to prevent the coronaviruses from killing them. It isn't strong enough to completely clear the virus. The virus stays inside the person for a long time. There's a chance that it will acquire a better way to evade the person's immune cells.
"It creates a game where the immune response is chasing and the virus is running, and that's what it does." At the end of the year, if you look in these individuals, you can see that they have evolved a quite evolved virus.
Lessells is one of several researchers who have demonstrated this phenomenon by retroactively analyzing a series of samples of the coronaviruses that had been taken over a period of about six months from a woman who had HIV. She was not being properly treated for her HIV infection during that time because of a series of unfortunate mistakes in her medical care, even as she was participating in a larger study for which samples were being taken of the coronaviruses that she harbored.
"Because we had samples from a few different time points over that six month period, we were able to show how the virus evolved and how it changed over time," Lessells said.
If this is how omicron was created, then it's likely that the virus was spread from one person to another.
Why wouldn't this spread happen at earlier points in the evolution of the immune system?
"That's a good question and a legitimate one," says BEDFORD. I don't have an obvious answer. He considers this scenario the most plausible explanation of omicron's emergence.
Knowing omicron's source is important.
Both scientists said that the scientific investigation of omicron is happening in real time, with new information coming out so fast that their views on its origins could change.
In the short run, making educated guesses as to omicron's source can inform assessment of how seriously to treat the threat from the variant. If omicron had been evolving out of sight in a large group of humans, this suggests it's not transmissible. He says that they've only seen a handful of travel cases. It's taken a little while to ramp up to this level, so that would suggest that it hasn't been spreading rapidly.
If omicron evolved in one person's body and only recently spread to a wider population, this means the level of circulation that is now being detected. This would suggest that the variant is more transmissible.
The larger point is that there needs to be more HIV treatment.
Regardless of the origin of omicron, the emergence of it is a reminder of the dangers of the virus in an immune compromised person. This is especially important when it comes to the millions of people in Southern Africa who are not on medication for HIV. The point is not to blame people in this situation, but to recognize that helping them is a key to ending the coronaviruses epidemic. The intervention here is clear. We need to strengthen our HIV response and get as many people as possible on effective treatment.
