Coronavirus variants: the name game
You might know them as the "UK variant" or "South African variant" - but what are they really called, and why? Phil Sansom has your coronavirus variants field guide, with help from head of the COVID-19 Genomics UK Consortium, Sharon Peacock...
Phil - To an extent, any talk of new coronavirus variants is slightly misleading.
Sharon - Looking for new variants is like looking for a needle in a haystack because there are thousands and thousands of new mutations in the virus. And so looking for one that's important can be very challenging.
Phil - That’s Sharon Peacock, talking to Chris Smith on the Naked Scientists in January. She runs a consortium called COVID-19 Genomics UK, or COG-UK. They feverishly sequence the full genetic code - the whole genome - of the samples of coronavirus they get sent, and so far have more than 200,000 sequences under their belt.
Phil - The point she’s making is that it’s easy to find a new variant - it’s much trickier to find a variant that’s both new and more dangerous. There are a few methods.
Sharon - First of all, we can look at spread between populations. We can also look at the population of genetic information that we have to demonstrate whether, for example, a particular lineage or line is expanding more rapidly than we expected. But laboratory experiments are really critical here, they provide crucial evidence, and there's different types of laboratory experiments that we would want to do. First of all, we'd look at how the virus interacts with cells that are grown in the laboratory: are they more likely to adhere to those cells and get entry into them? We'd also want to see how the virus interacts with antibodies that have been raised by people who've had a natural infection or been vaccinated, to see whether that interaction is what we would expect or not.
Phil - All of these techniques became very useful in the UK at the end of last year, when they discovered what later came to be known as the UK variant, the Kent variant, or B.1.1.7.
Sharon - It was only really in mid to late November when it really became clear that there seemed to be spread of cases in the South of England, whereas there wasn't spread in other parts of the country that were under similar cut a lockdown rules. There are range of explanations for that, but one of them is that the virus could be somewhat different in its behaviour. And so at that point, in the beginning of December, analysts who understand the genomes very well realised that the two could be related: an increasingly transmissible virus linked to a very specific genome.
Phil - B.1.1.7’s genome is specific by 23 mutations, and it’s also not clear where exactly it came from - it wasn’t particularly related to other variants going round the UK. That was in December. A few days later, South Africa announced they’d found their own concerning variant. Then within the space of a month, two were found in Brazil. Turns out pandemic gut punches sometimes come like buses. But Sharon would question the way we’ve been referring to them.
Sharon - I think it's really important that we avoid labelling variants based on where they've been first detected, because where they've been first detected doesn't necessarily mean where they've emerged. And nobody can really be held responsible for an act of nature - for a mutation.
Phil - Sharon Peacock, head of COG-UK. So bearing that in mind - can we decode the names these variants have got? They tend to be complicated because genetics is complicated, and the WHO hasn’t yet come up with a standard naming system. Into this void, a few main systems have emerged. The open access-database GISAID uses one system; the group Nextstrain that we featured on Naked Genetics back in April uses a second.
The third is my favourite, and it’s where the name B.1.1.7 comes from. It’s a system proposed last year with the acronym PANGOLIN. Here, instead of defining a variant by what’s in it, you define it based on events in its past. Those events will usually be: it arriving in a new place, and expanding and multiplying through the area.
Using their website, we can explain why it’s called B.1.1.7. “B” was an escape from China at the end of 2019; the first "1" is a big expansion through Europe at the time of the Italian outbreak at the start of 2020. The second “1” is a more specific European wave, and the “7” is the bad news variant we’re dealing with now.
Let’s translate the other key variants now. The South African variant in PANGOLIN is B.1.351. The Brazilian variants are called P.1 and P.2, which are shortened versions of longer names in the B.1 group.
These names are clearly many times less memorable than naming them by countries. We’ll just have to do our best to repeat them until we remember: B.1.1.7, B.1.351, and P.1 and P.2.