This sequence of sequences helps scientists map the mutation landscape of the coronviruses in the country in finer detail. It is therefore not surprising that they are starting to pick up more surprises. But because the pace of generating genomic data has accelerated, there has not yet been a similar, collaborative advance in what is called ‘variant characterization’.
Sequence can help you identify mutations maybe be problematic. But you can not tell if the mutations cause the version of the virus to behave differently from others. For that, you need to do 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 also need immunologists, structural biologists, virologists and a whole host of other biologists. And ideally, you want them all to meet the same scientific standards so that you can compare one variant with the next and determine if a new strain is related to a public health point of view or is merely interesting.
In the US, the CDC is the primary body with authority to designate emerging tribes as ‘variants of interest’ or ‘variants of concern’. To exceed this threshold, strong evidence is needed that a particular constellation of mutations gives the ability to do one of four things: spread faster and easier, administer worse diseases, impair the effectiveness of Covid-19 treatments, or evade antibodies produced by vaccination. or during previous infection with an older version of the virus.
So far, the agency has increased only three new versions of SARS-CoV-2 to the most worrying category: B.1.1.7, first detected in the UK, B.1.351 from South Africa and P.1 from Brazil. (Although there is a constant battle over the code-naming system to be used, most scientists have agreed to keep the name ‘insert-place-here-here’ away because of its inaccuracy and stigmatization. For simplicity, we will refer to B.1.1.7, B.1.351 and P.1 from here as the Big Three.)
But the agency is currently discontinuing additional interesting variants – including B.1.256 from New York and B.1427 / 429 in California – and is monitoring ongoing studies to assess the ability of these strains to evade immune responses and the protection afforded by existing vaccines. As new data becomes available, the agency may push any concerns of variants to this top level. “The threshold for indicating a variant of interest must be relatively low to monitor potentially important variants,” a CDC spokesman told WIRED by email. “However, the threshold for designating a source of concern must be high in order to concentrate resources on the variant with the highest health consequences for the public.”
The spokesman did not provide details on what the agency considered “strong evidence”, but said the CDC was involved with international partners, including the World Health Organization, in discussing criteria for designating variants.
In other words, it’s not just about finding new variants, but also about characterizing their biological behavior – what does it mean for someone to become infected with something? “Getting series is just the beginning of the story,” says Topol. ‘There is a lot more science that needs to happen to know if a mutation makes sense. And right now, a lot of labs that publish about this are only looking at one part of the story, because that’s the quick thing to do. But what is fast can also be misleading. ”
For example, a number of studies in recent weeks have shown that antibodies trained to attack older versions of the virus are much more difficult to recognize the B.1.351 and P.1 variants. This raised alarm about the effectiveness of the vaccine. But just because antibodies do not fight these new mutants in a test tube does not mean that your immune system will have the same problems in a real Final Boss Fight. The immune system is more than antibodies, and far fewer laboratories have the necessary expertise to perform tests with live T cells, the other major player in the development of Covid-19 immunity. These cells, which clear the virus by eradicating herds of infected cells, grow outside the human body. It therefore took a while longer to understand how they respond to the variants. But new data suggests they are just responding well.