New mutations of Sars-Cov2 are around 50% more infectious

New mutations of Sars-Cov2 are estimated to be around 50% more infectious, which makes suppressing spread of the virus 50% harder, and herd immunity harder to achieve with vaccination.

The virus Sars-Cov2 mutates all the time – although it doesn’t mutate as fast as the flu, it has been mutating all year – that’s how we are able to use genomic testing to help contact tracing identify the way outbreaks spread.

But lately, there have been two more variants identified which are significantly more different than most mutations of the virus, and both in the lab and in the wild, seem to spread much faster. The UK variant  is rapidly becoming the most common variant there, particularly in London and the South East. The South African version hasn’t been studied as much, but seems to have similar characteristics.

Two comprehensive studies in the UK (Centre for Mathematical modelling of infectious diseases and Imperial College) conclude, with some very sophisticated modelling, that this new variant is around 40-60% more infectious than previous variants, but no more deadly.

What are the implications of 50% more transmissibility? Mathematically, there are two main implications:

• The average number of people infected by any one person increases by 50%. That means that a Reff (the measure of transmissibility) of 0.9, which eventually would see an outbreak dying out, would now become 1.4, with an outbreak continuing to grow. Or a person who would previously have infected 2 people, would now infect 3.
• Herd immunity requires more infection (or vaccination) to achieve – mathematically herd immunity is related to the Reff. So herd immunity would require around 75% of the population to have been infected or vaccinated, rather than 60%.

And these two mathematical implications lead to more implications for managing the pandemic around the world as this variation is increasingly the main variant:

• Every aspect of public health management needs to become stricter to stamp out an outbreak. Lockdowns (if required) have to be more severe, reducing ways for people to interact with each other. Contact tracing needs to be even faster to find more people before they transmit the virus further. Masks need to be mandated in more places. Every slice of the swiss cheese model of management needs to be in play.
• Vaccines will have to be rolled out faster to have the same effect of achieving herd immunity – it takes longer to get to 75% of the population than 60%.
• Places in the world, like parts of Brazil, that have (sadly) achieved herd immunity through 60% of the population being infected become vulnerable to the virus again
• It is even more important to ensure that the whole world is vaccinated – the more infectious the virus us, the harder it will be to contain with quarantine strategies – a more infectious disease means all countries are reliant on each other’s management of the virus
• Fast rollout of vaccine everywhere in the world becomes even more important to avoid further mutation of the virus (mutations are more likely to arise if lots of people are infected) – the next mutation might reduce efficacy of the vaccines that have already been developed, even if this one hasn’t.

The mathematical modellers authoring this paper compared a mathematical model of the actual spread of Covid19 across 7 regions of the UK (including a number of factors and outcomes – hospital admissions, ICU occupancy, and proportion of each variant in the positive tests) with what they could actually observe of all of those outcomes. They varied a number of different possible features of the new mutation – infectiousness, likelihood of reinfection, susceptibility of children and quicker incubation periods.

We use this model to capture the emergence of VOC 202012/01 and consider its potential impact. To understand possible biological mechanisms for the observed dynamics associated with VOC 202012/01, we considered four alternative hypotheses for why the new variant might be spreading more efficiently: increased infectiousness; immune escape; increased susceptibility among children; and shorter generation time.

The best fit of all these alternatives was increased transmissibility, of around 50%, which can been seen in the graphs of all of the outcomes of the model – the first row (which looks at increased transmissibility) has the purple line (the model results) fitting the observed outcomes (the black lines).

The fitted model based upon increased transmissibility, which reproduces observed epidemiological dynamics and increases in relative prevalence of VOC 202012/01, suggests no clear evidence of a difference in odds of hospitalisation or relative risk of death, but finds strong evidence of higher relative transmissibility, estimated at 56% higher than preexisting variants (95% CrI across three regions: 50-74%).

Links about Vaccines

Here is a link to all the latest about vaccines around the world – which ones are being rolled out, and which ones are in late stage trials. This roundup has a special focus on the Astra Zeneca vaccine, which has been approved in the UK:

Last night, the UK authorities approved this vaccine for distribution there. Of special interest is the intent to give as many people as possible a first shot, without holding back supplies for the second round. I think that this is simultaneously the correct decision for them to make and also very bad news.

How should we best roll vaccines out around the world? What are the potential potholes? Helen Branswell from Statnews has a long article, with a lot of potential potholes along the road, including going too fast, losing the confidence of the public, and many more.

But if we’re not careful, we could fail to take full advantage of the opportunity scientists and governments, pharmaceutical companies and philanthropic foundations have created for us. And there’s a possibility that the pandemic off-ramp doesn’t merge with a straight road back to Normalville, but instead becomes a meandering country lane with the occasional detour. We may need to choose the right turns and avoid the potholes as we make our way to our destination. It will require patience.

And an article from Australia, suggesting that we should be vaccinating people around hotel quarantine as our first priority:

Can we further reduce the probability of the virus sneaking through the border and quarantine, without stopping people arriving at all? Yes. Firstly, by utterly pedantic and thorough processes in quarantine – although I suspect we may be close to hitting the ceiling here on how much better this can get. Secondly, we have a “trick” we can use – tighten up the border more by vaccinating first all border, quarantine, airline and airport staff. That is, the first 200,000 or so doses of vaccine go here – not to healthcare workers.

Why? Because if – and this is a big “if” – the vaccine not only stops people getting sick from Sars-CoV-2, but also stops them getting infected in the first place (or if infected, not being very infectious to others), then we achieve an extra barrier to stop the virus getting back in.

Life Glimpses

Now that 2020 is finished, I’m remembering some of the 2020 highlights that happened because of Covid19 for me.

• One particularly memorable evening rehearsing with my choir in our local park there was a massive thunderstorm. We were under cover, but we got to sing while watching the lightning crack all around us – the gospel classic The Storm is passing over.
• I saw waratahs in the wild for the first time – the symbol of this region, and the symbol of my favourite part of the year here – Ngoonungi, or early spring.
• My role as sous-chef in the quest for the perfect cupcake – we may not have reached perfection, but we had a lot of fun trying.

This blog, and all of my readers and commenters, have helped me become better at noticing the highlights. Thanks to all of you for coming on the journey with me, and appreciating the beauty that we could see in our every day this year.

Bit of beauty

This tree at Bradley’s Head is doing its best to grow out of the wall where it has found itself – seems a good picture for where we find ourselves at the beginning of 2021. Here’s to a 2021 of thriving within whatever constraints we find ourselves in.