The new variants of the virus can spread like wildfire, and all of us have a role to play in keeping them out of the community.
I have to admit, when I first heard UK prime minister Boris Johnson talking about a new, more transmissible strain of SARS-CoV-2, the virus responsible for Covid-19, part of me did wonder whether he was doing a bit of his trademark exaggerating to help explain away he and his government’s woeful pandemic response.
The only data we were given at the time was that the new variant, referred to as B1.1.7, 501Y.V1, or VUI-202012/01, was rapidly growing in proportion when you looked at the different SARS-CoV-2 strains people in London and the south of England were testing positive with. This rise coincided with the beginning of the northern hemisphere winter as well as the Christmas shopping season. That means B1.1.7/501Y.V1 could have become more dominant because of what we call the “founder effect”, which is when a mutant takes off not because it is more infectious, but because it is the one that people who are infectious happen to have.
Still, Johnson’s announcement had everyone spooked. Within days many countries were restricting travel from the UK to stop the new variant from spreading. But the horse had already bolted. The B1.1.7/501Y.V1 variant has now been reported in over 50 countries. For those that are doing genomic sequencing and submitting those sequences to Nextstrain, there are now over 13,000 B1.1.7/501Y.V1 SARS-CoV-2 sequences in the database. They come from 30 countries, including throughout Europe as well as from the United States, Israel, India, Brazil, Jamaica, and Hong Kong.
In many of these countries, the cases of B1.1.7/501Y.V1 are directly linked to travel from the UK. But for some, like the US, there are reports of cases where people haven’t travelled recently, suggesting the new variant is already spreading in the community there. If it is more infectious, that doesn’t bode well for the US given its equally terrible pandemic response and soaring case numbers.
You might have missed this over the Christmas holiday, but the B1.1.7/501Y.V1 variant was soon joined by another potentially more infectious variant of SARS-CoV-2 identified in South Africa – B.1.351 or 501Y.V2. There are now over 400 genome sequences from this variant in the database, submitted by 12 countries including the UK, Botswana, Australia, Germany, Ireland, Switzerland, France, Sweden, and South Korea. And just in the last few days, there’s talk of more concerning variants that have been identified in Brazil.
What’s the evidence these variants are more infectious?
Given the accelerated pace of Covid-19 research, a lot has happened since the B1.1.7/501Y.V1 and B1.351/501Y.V2 variants were first announced. Before I get into what we know about them now, I want to give a shoutout to Dr Emma Hodcroft (@firefoxx66 on Twitter) from the Institute of Social and Preventive Medicine at the University of Bern in Switzerland. Dr Hodcroft is maintaining this very cool repository of SARS-CoV-2 mutations and variants of interest. As she’s based in Europe and working with European data, the repository is mainly focused on those mutations/variants spreading there. It comes complete with spinning protein structures showing where the mutations of interest are.
Lots of the evidence for these variants being more infectious is indirect, but it’s all beginning to point in the same direction. First up we have this neat study that evolved the spike protein in the lab, looking to see which mutations arose, and then looking at how well the mutated spike proteins were able to bind to their receptor, ACE2. In these experiments, several mutants rapidly arose including S477N, E484K, and N501Y. The number codes are for the specific location of the mutation on the genome, and the letters for the amino acid that mutates. So N501Y means the mutation is located at position 501 and it changes an asparagine (N) to a tyrosine (Y). Where in a protein an amino acid is that changes, and what it changes to, can have a huge effect on how a protein works.
The B1.1.7/501Y.V1 and B1.351/501Y.V2 variants have that N501Y change. In the lab, the N501Y mutation causes the SARS-CoV-2 spike protein to bind about 2.5 times better to its receptor ACE. But there are combinations of mutations that increase that even further. For example, a spike protein with both the E484K and the N501Y mutations binds 13 times better! That’s the combination the B1.351/501Y.V2 variant has, as well as a Brazilian variant called P.1, on top of other mutations.
OK, so they bind better to their receptor. What else? The next bit of evidence, at least for the UK variant, comes from a technical briefing from Public Health England. It shows that the B1.1.7/501Y.V1 variant is becoming more prevalent all over the country. In other words, it looks like it’s outcompeting the other variants. From the contact tracing data it also looks like this variant’s attack rate is higher. That’s the number of exposed people who become infected. It goes from 11.4% to 15.6% for people who have contact face-to-face (within one metre), skin-to-skin, or are coughed, sneezed or spat on. And it goes from 6% to 8.4% for those who were within one to two metres of an infectious person for 15 minutes or more over 24 hours.
Lastly, a couple of new statistical analyses that have just been released. You can read them here and here. They use different approaches to model the R number for the B1.1.7/501Y.V1 variant compared to other variants in the UK as England was putting restrictions in place. Both found that when they looked across all English regions, in the overwhelming majority the number of B1.1.7/501Y.V1 cases expands during their (not restrictive enough) restrictions, while other lineages contract. That means that while their so-called “lockdowns” have been enough to suppress the older variants of SARS-CoV-2, they don’t work as well with B.1.1.7/501Y.V1. As an aside, until recently, England was using a regional three-tier system of restrictions. The highest tier had churches, gyms, shops, schools and universities open. The country is now having what they are calling a national lockdown. It’s less restrictive than our alert level three, so who knows how well it will work at containing B.1.1.7/501Y.V1.
So, what do these new variants mean for us here in New Zealand? Well, with citizens, permanent residents and other workers continuing to arrive here, we can expect the variants to arrive too. Everyone working in MIQ needs to be on full alert. Those in charge need to be constantly assessing the risks and ensuring all the appropriate measures are being taken, including that the most appropriate PPE is being worn by everyone who needs it. This is a virus we now know transmits through the air, through close contact, and through touching contaminated inanimate surfaces.
Which brings me to my final point. It’s all well and good expecting everyone working in MIQ to be doing their bit to keep New Zealand safe from Covid-19. But the rest of us have a role to play in this too. If any variants of the virus got out, never mind these more infectious ones, they would spread like wildfire. The cost of living at alert level one is that we still need to be doing all we can to ensure that any outbreak can be contained as quickly as possible. And it’s not even that hard. Remember the Swiss cheese model that Toby Morris and I talked about last year? Use the Covid Tracer App. Switch on Bluetooth. And see about getting tested if you have any symptoms that could be Covid-19. Don’t brush it off as a cold or hay fever.
The more complacent we are, the more sorry we will be.