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Covid Mutations

Yes its real interesting stuff and I am a fan of the work of Emma Hodcroft.

I usually just end up busting tired pandemic mutation cliches though, since the actual implications of various mutations are not easy for them to establish. So its hard for example to understand at this point whether there are any serious implications to the 'new variant' that Hancock made a big deal of recently.

Speaking of that variant, I do note that one of the links from that github page is to the initial article about the new variant that the Covid-19 Genomics UK Consortium published. They need to investigate further so there is nothing earth-shattering in their report, but it might provide a useful starter to the subject:


In the absence of firm understanding of any implications from specific mutations, the genome tracking stuff is also of interest when attempting to establish a picture of how this virus spreads. Here is another of their articles which discusses transmission in Scotland and Wales. Contains important and interesting but also obvious conclusions. Basically stuff that backs the idea that border controls and attempts at full viral suppression are things to do. But of course there is no 'political will' for England to go for that approach, no matter what other countries deploy that approach and get results.


A striking observation was that following the first lockdown, the majority of virus lineages that had been circulating in the population in Scotland appeared to become extinguished. Very few lineages persisted over the summer. This supports the idea that it is possible to eradicate the virus from a country when stringent public health measures are in place. What was then observed going into the second wave is that disease was caused by new lineages that has been introduced into the country, many of which could be traced to introductions from countries outside of the UK. Summer holidays and other travel abroad taken at a time when disease was under control in Scotland, but less so elsewhere, has had a predictable outcome.

In Wales, the analysis identified that the current population of circulating SARS-CoV-2 is also different to the lineages that were present in March and April 2020. Early on in the pandemic, a high proportion of cases could be linked to imports into Wales, with a drop in both the number of extant lineages and new introductions following the first lockdown. Like Scotland, Wales observed that the majority of lineages circulating in Wales appeared to become extinguished following the package of measures introduced in Wales as part of the first lockdown.

Wales also observed that after the easing of the first lockdown, the rise in cases forming the start of the second wave was driven by imports — from other parts of the UK and the wider world. The Welsh analysis also examined transmission on a more local level, identifying that cases in areas of high population density (cities) were more likely to result from local chains of transmission, whereas those in less urban areas were more likely to be associated with imports from elsewhere and rarely led to local onward transmission.

So, what can we conclude? Perhaps the obvious. The pandemic in Scotland and Wales has been driven by importations. This provides indisputable evidence for the importance of border controls, including effective screening and isolation policies. Once introduced, spread is driven by travel, and then onward spread by population density. Genomics data permits us to quantify the number of these introductions and better understand spread from one geographical region to another, providing invaluable information that can help shape policy and practice.
 
VUI – 202012/01 - I really hope this doesn't put me in the realm of conspiracy theorist but I really dont believe the 70% more transmissible idea yet.

From the gov website:
NERVTAG’s early analysis suggests the new variant could increase R by 0.4 or greater. Although there is considerable uncertainty, it may be up to 70% more transmissible than the old variant.

I havent seen that in the data yet. I'm thinking its a scare story to get people to take matters seriously again. I really hope it isnt correct because it would have big implications on how the situation develops.
 
VUI – 202012/01 - I really hope this doesn't put me in the realm of conspiracy theorist but I really dont believe the 70% more transmissible idea yet.

From the gov website:


I havent seen that in the data yet. I'm thinking its a scare story to get people to take matters seriously again. I really hope it isnt correct because it would have big implications on how the situation develops.

I think my approach is to split the subject into at least 3 subjects that I then feel free to think about and talk about without my attitude towards one theme affecting all the other in ways that may be a mistake.

eg I can make noises about the timing, the politics, the public health messaging, entirely separate from whatever the reliability of the claims turns out to be.

Those angles do not detract from whatever the implications of this strain are or arent. Im still in the middle of watching the Scottish press conference and since unlike England they have less fear of bringing up the subject of hospital infections, my thoughts on the picture they may have seen and analysed can now include the possibility they have seen alarming patterns of transmission with this strain in relation to some hospital outbreaks. But I'm not strongly wedded to this theme yet because I've not seen any data or their calculations and analysis.

So for now I am fairly neutral as to whether this strain will cement itself as a great big new deal in this pandemic, or just ends up as temporary framing that wont stand the test of time. If there were not so many other things that can influence R (including vaccine good news that may have affected attitudes) and very much including all the potential seasonal factors that we havent had to deal with before with this virus, then I would probably be leaning more strongly towards this strain being notably more transmissible and being behind much of the trajectories seen in the south. Those other factors and potentially important variables do not give me any reasons to doubt the implications of this new strain, they are not something I would use to refute other compelling evidence, but they do obscure the picture and mean that I will have to take an even more cautious approach to reaching conclusions about the new strain.
 
One of the subjects I'd split off is about levels of genomic surveillance in different countries, and indeed in the UK. I already moaned earlier that the info they gave today that I've seen so far did not include percentages of samples from areas other than the southern ones which have more of the new strain. So my list of questions involves the figures for other areas over time, and also far more info about the nature of our genomic surveillance systems and what sorts of settings the samples come from. And very much about how even the geographic spread of samples used is, eg are there more samples in general from the South being subject to genomic testing, are there any obvious areas of much more limited surveillance that could be blind spots.
 
It could be based on early estimates of the ability of this strain to hitch a ride on scotch egg breath.

I believe the wording used today was often of the 'up to 70%' variety so I expect they have a range in mind that they didnt feel like sharing.
 
Well I dont think I will be presenting that data. Because my initial thoughts when looking at it are that it is unfortunate that the increases they are seeing in percentage terms in some regions happen during a period where the overall number of samples analysed seems to have been falling quite a lot. So at a minimum I think I will wait for other sources to state their opinions of this data.
 
I spoke to Dr Emma Hodcroft about that ONS data and it does seem like a reasonable way to quickly and roughly track the growth of this variant by proxy.

Although as the blurb in the ONS data (in the results tab) does explain that there are other reasons why the S bit of the test may not go positive (eg not enough viral load in the sample), and so they cannot use that data as a new strain indicator until about mid-November, presumably because other agencies have told them that this is the time period when prevalence of the new strain is known via proper genomic analysis to have increased enough that its become a strong enough signal in this data to stand clear of the usual background noise thats always there when using that methodology. But this continues to make me wary of interpreting their data on the other, so far less affected regions where this data has not shown a clear increase over time. I might just end up graphing noise!
 
This is a big problem resulting from the herd immunity / DGAF approach, the larger the infected population the greater the opportunity for mutations to occur.

Someone was speculating that is partly why this mutation has arisen successfully here as it's been 'squeezed' from both ends - a high % infection rate in the population, and yet also some restrictions that force it to need to mutate as well.

Beyond my understanding if that has any truth to it though....
 
Someone was speculating that is partly why this mutation has arisen successfully here as it's been 'squeezed' from both ends - a high % infection rate in the population, and yet also some restrictions that force it to need to mutate as well.

Beyond my understanding if that has any truth to it though....
The equivalent of not finishing your antibiotic course innit
 
Its already been mentioned in the main UK thread but the NERVTAG minutes on this subject are here:


Includes:

  • It was noted that whilst previous variants have successfully emerged in periods of low prevalence without clear evidence of having a selective advantage, the emergence and subsequent dominance of VUI-202012/01 in a period of relatively high prevalence suggests VUI-202012/01 does have a selective advantage over other variants.
 
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If anyone fancies digging into this, there's a vid of a three hour plus COG-UK online conference that happened a few days ago.


Thank you to all the speakers, chairs, attendees and organisers of the very first COG-UK Showcase Event: SARS-CoV-2 sequencing to inform clinical care, public health interventions and policy decisions.
The afternoon was filled with an array of thought-provoking talks, covering stimulating topics and research areas related to SARS-CoV-2 genome sequencing and what it has taught us to date about the ongoing COVID-19 pandemic.
The event featured an exceptional line-up of speakers, covering the focal themes of mutations and their implications for transmission, disease severity, therapeutics and vaccines; genomic-informed evidence on transmission in specific environments; and an overview of SARS-CoV-2 lineage introduction and transmission.

Recommend watching the last hour
 
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Thanks for that. I didnt hae a spare hour so I just skimmed that bit and chanced upon the section where convalescent plasma and Spike mediated immune evasion was being mentioned.

Thanks to 2hats on the main UK thread, I was pointed to the paper in question.


When combined with the other detail that has emerged so far, I am no longer neutral in regards my concerns about this new variant. There are multiple reasons for them to worry about it. If only one or two of their concerns are validated the implications are still of concern. Not that every legitimate concern during viral surveillance comes to fruition, but even so, not good.
 
VUI – 202012/01 - I really hope this doesn't put me in the realm of conspiracy theorist but I really dont believe the 70% more transmissible idea yet.

I haven't been playing really close attention to be fair, but I don't know what they mean by "70% more transmissible".
Is this an estimation based on estimated proportion in particular areas, and the changes in the estimated R rate, I wonder...
 
And another PHE document, which I've also just mentioned on the main UK thread because its part of the current newsworthy government decision making and response.


Contains detail such as:

Of the 962 cases in the cluster, data was available for 915 individuals; most specimen dates were in November (828/915) followed by October (79/915), with a small number of cases in September (4/915). Distribution of cases by patient sex is similar (51% female, 49% male). By age, just under 90% of individuals are aged <60 years; work is being undertaken to compare this age distribution to relevant comparators. Six of the 915 cases are deceased.
 
As it seems to have emerged from near Dover, (before spreading through the SE and London) it is possible it came in with cross channel traffic, or went out with the same, either way it seems quite likely to be present on the continent.

Fails to explain Wales though.
 
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