This increase in sequencing is helping scientists to map in more detail the mutational landscape of coronaviruses that circulate across the country. Therefore, it is not surprising that they are beginning to appear more surprises. But as the pace of genomic data generation accelerates, there has not yet been a similar and coordinated breakthrough in what is called “variant characterization”.
Sequencing can help you identify mutations that it could be problematic. But he cannot say whether these mutations make that version of the virus behave differently than others. For this, it is necessary to carry out studies with antibodies, living human cells and animal models. Each type of experiment or analysis requires a unique set of skills and there are many different methods for measuring the same things. You need immunologists, structural biologists, virologists and a lot of other -ologists as well. And ideally, you want everyone to follow the same scientific standards so that you can compare one variant with the next and determine whether a new strain is a public health concern or just interesting.
In the USA, the CDC is the primary body with the authority to designate any emerging strains as “variants of interest” or “variants of concern”. Exceeding this limit requires strong evidence that a particular constellation of mutations gives you the ability to do any of the four things: spread faster and more easily, inflict more serious illnesses, weaken the effectiveness of treatments with Covid-19 or avoid antibodies produced by vaccination or during a previous infection with an older version of the virus.
So far, the agency has raised only three new versions of SARS-CoV-2 to the category of most concern: B.1.1.7, which was first detected in the United Kingdom, B.1.351 in South Africa and P.1 in Brazil. . (While there is an ongoing struggle over which code nomenclature system to use, most scientists have agreed to avoid the “insert the name of the place here” nomenclature for its imprecision and stigmatizing effect. For simplicity, let’s refer to B.1.1. 7, B.1.351 and P.1 hereafter as the Big Three.)
But the agency is currently tracking other variants of interest – including B.1.256 in New York and B.1427 / 429 in California – and tracking ongoing studies to assess the ability of these strains to escape immune responses and erode the protections offered by existing vaccines. As new data becomes available, the agency may raise any variants of particular concern to this higher level. “The threshold for designating a variant of interest should be relatively low to monitor potentially important variants,” a CDC spokesman told WIRED via email. “However, the limit for designating a variant of concern must be high in order to focus resources on variants with the greatest public health implications.”
The spokesman did not provide details on what the agency considers “strong evidence”, but said the CDC has been engaging with international partners, including the World Health Organization, in discussing criteria for designating variants.
In other words, it is not just a matter of finding new variants, it is a matter of characterizing your biological behavior – what does it mean for someone to become infected with one or the other? “Getting sequences is just the beginning of the story,” says Topol. “There is a lot more science that needs to happen to know if a mutation is significant. And now, many labs that are publishing about it are just looking at part of the story, because it’s the quickest thing to do. But what is fast can also be misleading. “
For example, several studies in the past few weeks have shown that antibodies trained to attack older versions of the virus have a much harder time recognizing variants B.1.351 and P.1. This raised alarms about the vaccine’s effectiveness. But just because the antibodies don’t fight these new mutants in a test tube too, it doesn’t mean that your immune system will have the same problems in a real-world Final Boss Fight. The immune system is more than antibodies, and far fewer laboratories have the experience to conduct tests with live T cells, the other major player in developing immunity against Covid-19. These cells, which eliminate the virus by eliminating herds of infected cells, are difficult to grow outside the human body. So it took a little longer to understand how they respond to variants. But new data suggests that they respond very well.