New coronavirus variant: What do we know?

Ewan Birney (deputy directory of EMBL European Molecular Biology Laboratory)&#x27;s Twitter is a really good source of first class scientific information on this.<p>You need to scroll back about 2 days to get the latest info (and he refers to the Twitter accounts of others in the field who can give more information).<p>His Twitter profile is @ <a href="https:&#x2F;&#x2F;twitter.com&#x2F;ewanbirney&#x2F;" rel="nofollow">https:&#x2F;&#x2F;twitter.com&#x2F;ewanbirney&#x2F;</a><p>(Ewan is awesome - he is also (co)director of EMBL-EBI European Bioinformatics Institute, and I had the honour (as a Computer Scientist) of working there for nine years)

Wouldn&#x27;t there be an element of cherry picking to this whole variant story? Like, don&#x27;t viruses mutate constantly, we just don&#x27;t analyze them in a disciplined manner most of the time, so if you start doing that you&#x27;re bound to find something like this, but so would anyone else conducting a similar analysis anywhere else and at any other point in the pandemic?

Based on the precedent of all other endemic human coronaviruses, there is reason to guess that the winning mutations will be less dangerous. This is also consistent with theory:<p><a href="https:&#x2F;&#x2F;www.ncbi.nlm.nih.gov&#x2F;pmc&#x2F;articles&#x2F;PMC4873896&#x2F;" rel="nofollow">https:&#x2F;&#x2F;www.ncbi.nlm.nih.gov&#x2F;pmc&#x2F;articles&#x2F;PMC4873896&#x2F;</a><p>&gt; By far, the most widely studied trade-off involves transmission and virulence (Anderson and May, 1982; Frank, 1996; Alizon et al. 2009).

I find it completely disappointing and disheartening that the west has done almost nothing to curb the virus, thus increasing the chance of mutation and continued spread. It&#x27;s just hard to see the pointing of fingers at China that&#x27;s happened, especially in hindsight when it&#x27;s unclear if it even began in China (which doesn&#x27;t really matter anyway if it was a naturally occurring zoonotic crossover event) and not somewhere else like Italy, but the west has just rolled over to the threat of the virus in its response. Meanwhile, life in China has been basically normal for a while.<p>It further drives me crazy because I am still disconnected from my family because the U.S. <i>still</i> refuses to allow my fiancée to travel back (she lives and works in the U.S.) from the country best dealing with this to to the worst. It&#x27;s just sickening there&#x27;s no support for people like us, and now it looks like it can only get worse in the west.

A good visualization of the mutations, including the South African one that isn&#x27;t related, but also increasing:<p><a href="https:&#x2F;&#x2F;nextstrain.org&#x2F;groups&#x2F;neherlab&#x2F;ncov&#x2F;S.N501?c=gt-S_501,69&amp;p=grid&amp;r=country" rel="nofollow">https:&#x2F;&#x2F;nextstrain.org&#x2F;groups&#x2F;neherlab&#x2F;ncov&#x2F;S.N501?c=gt-S_50...</a>

Two sources: <a href="https:&#x2F;&#x2F;www.cogconsortium.uk&#x2F;wp-content&#x2F;uploads&#x2F;2020&#x2F;12&#x2F;Report-1_COG-UK_19-December-2020_SARS-CoV-2-Mutations.pdf" rel="nofollow">https:&#x2F;&#x2F;www.cogconsortium.uk&#x2F;wp-content&#x2F;uploads&#x2F;2020&#x2F;12&#x2F;Repo...</a> <a href="https:&#x2F;&#x2F;www.bmj.com&#x2F;content&#x2F;371&#x2F;bmj.m4857" rel="nofollow">https:&#x2F;&#x2F;www.bmj.com&#x2F;content&#x2F;371&#x2F;bmj.m4857</a>

I think most people seem to be underestimating just how bad this is. During the recent 4-week lockdown it was already clear that something odd was going on in Kent; whilst case counts were dropping in the rest of the country, they continued to rise significantly there. Something was clearly different.<p>Now high case counts are spreading from the South East into the rest of the country. We don&#x27;t know whether we can even stop the growth. During the last lockdown schools remained open; I suspect that it may be necessary to close them in order to just stop the growth. A significant reduction in cases looks impossible.<p>This strain has probably already spread to tens of other countries. Every country which is just about holding things together, whatever their strategy, is going to struggle with a significantly more transmissible variant of the virus.

My worry is this: If you take a population where a virus is widespread and start vaccinating then the likelihood for a mutation that escapes the vaccination is much higher, had you instead taken a population where the virus not widespread and vaccinated there.<p>Is this correct?<p>UK has a widespread ongoing outbreak and is the first nation to deliver vaccinations at a big scale.

VUI – 202012&#x2F;01 on Wikipedia [1]:<p>&gt; The first Variant Under Investigation in December 2020 (VUI – 202012&#x2F;01), also known as lineage B.1.1.7, is a variant of SARS-CoV-2, the virus that causes COVID-19. The variant was first detected in the United Kingdom in October 2020 from a sample taken the previous month, and it quickly began to spread by mid-December. It is correlated with a significant increase in the rate of COVID-19 infection in England; this increase is thought to be at least partly because of mutation N501Y inside the spike glycoprotein&#x27;s receptor-binding domain, which is needed for binding to ACE2 in human cells.<p>Correlation does not equal causation. Most of the northern hemisphere is experiencing a significant increase in cases, i.e., a second wave. It has not yet been established whether this variant exhibits a unique pathogenesis.<p>[1] <a href="https:&#x2F;&#x2F;en.m.wikipedia.org&#x2F;wiki&#x2F;VUI_–_202012&#x2F;01" rel="nofollow">https:&#x2F;&#x2F;en.m.wikipedia.org&#x2F;wiki&#x2F;VUI_–_202012&#x2F;01</a>

This Report from the COVID-19 Genomics UK Consortium gives a good summary of the prevalent genotypes with UK COVID-19 cases. You can see how the B.1.1.7 mutations N501Y + Δ69-70 and N501Y are very recent and mostly showed up during the last 28 days.<p><a href="https:&#x2F;&#x2F;www.cogconsortium.uk&#x2F;wp-content&#x2F;uploads&#x2F;2020&#x2F;12&#x2F;Report-1_COG-UK_19-December-2020_SARS-CoV-2-Mutations.pdf" rel="nofollow">https:&#x2F;&#x2F;www.cogconsortium.uk&#x2F;wp-content&#x2F;uploads&#x2F;2020&#x2F;12&#x2F;Repo...</a>

The best reaction to this would be to pressure the NIH to lift the ban on the Astrazeneca vaccine. There is enough stockpiled supply to vaccinate most of the UK quickly and they would have a first mover advantage to getting a bunch of that vaccine. Evidence suggests this varient still has the same spike protein and seems like it would be still prevented by most if not all the vaccines.

Is there anyway to know if the vaccines are effective against the new strains?

The question I&#x27;m most curious about: Does the vaccine(s) we&#x27;ve hustled to get developed, produced, and distributed over the last few months basically get invalidated because of the new strain?

My state has an Rt as high as London and people are running around like there is no epidemic at all. It&#x27;s very frustrating.<p><a href="https:&#x2F;&#x2F;rt.live&#x2F;" rel="nofollow">https:&#x2F;&#x2F;rt.live&#x2F;</a>

<a href="https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;VUI_%E2%80%93_202012&#x2F;01" rel="nofollow">https:&#x2F;&#x2F;en.wikipedia.org&#x2F;wiki&#x2F;VUI_%E2%80%93_202012&#x2F;01</a>

The telegraph reckons it was spotted in Brazil earlier this year<p><a href="https:&#x2F;&#x2F;www.telegraph.co.uk&#x2F;news&#x2F;2020&#x2F;12&#x2F;21&#x2F;supercharged-covid-mutation-spotted-brazil-last-spring&#x2F;" rel="nofollow">https:&#x2F;&#x2F;www.telegraph.co.uk&#x2F;news&#x2F;2020&#x2F;12&#x2F;21&#x2F;supercharged-cov...</a>

Viruses mutate constantly.<p>Vaccines target subsequences of amino acids on proteins which both variants most likely have.<p>Mark my words that this a non story&#x2F;media sensationalism and will be out of the news in a few weeks.

I feel embarassed because people vilified my comment about Boris using this piece of news with a political cover motive. I am sorry, saying this is different than being a negationist. I hope more people get it now that I honestly try to explain myself better. Thanks.

The talk of the virus potentially being on a path to vaccine escape is very worrying. Sounds like we might end up in a situation where we have seasonal COVID like we do with the flu :(

I know I&#x27;m less afraid of it. More contagious generally means less deadly.

There&#x27;s so many questions that this raises.<p>- Is it more infectious or just bypasses current immunities?<p>- Will the vaccines basically be voided by this?<p>- Is it less lethal? Could it create more general immunity in communities without killing?<p>- Has is spread yet? I&#x27;ve read the UK gov knew about this in october... seems like it&#x27;s probably everywhere by now

I am now suitably terrified. The vaccine won’t be deployed fast enough. Coronavirus and humanity are in for a roller-coaster ride over the next few years...

There&#x27;s been a certain amount of public arguments between the government in the UK (yay Christmas) and scientists (boo Christmas). I really hope that this is not a tactical exaggeration used by the latter to get their way that&#x27;s got way out of hand ...

Very suspicious that this story breaks just as Boris needs to lock down the country over christmas.<p>&quot;everyone is going to hate me, quick think of something to blame.&quot;.... Eureka .... &quot;There&#x27;s a new virus strain, totally unforeseeable, don&#x27;t blame me for the lock downs&quot;<p>Just sayin&#x27;