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New coronavirus strain up to 70% more transmissible
- dm319 6y agoSomething strange was happening in the UK rates in the last few weeks. Despite a second lockdown, cases in London started increasing again, and areas in 'Tier 3' (highest tier restrictions) also started increasing cases post-lockdown. This was despite other areas continuing to drop cases despite having the same measures. Apparently the areas that had started rising were correlated with percentage prevalence of this new strain, which at the moment is known to be present in the UK, but might have come from abroad, or travelled already. As a result of this, I can see the vaccination programme getting a huge rocket, as it looks like lockdown and highest restrictions aren't decreasing cases - which is potentially disastrous for containing the virus, and stopping the hospitals get overwhelmed at a time when they normally operate at full capacity. Christmas relaxation rules have been cancelled in the UK, which has caused much disappointment to my family and friends. Understandable, but no less disappointing.
- CodeGlitch 6y agoYes I just watched Boris Johnson's announcement. I know there's a lot of criticism about his leadership, but I'm still glad they are following the science.
- dm319 6y agoHe's had a lot of criticism, but I don't think he has done too badly. And that's coming from someone who is normally left-leaning, and not a fan of him. There were definite mistakes at the beginning, and a blase attitude resulted in a bad first wave for the UK. It's still not completely clear why the death rate was so high - may be related to the way the coronavirus ripped through care homes early on, or simply because the UK could have locked down a week or two earlier. Not to mention the mess up with ventilators and PPE. But since then, the UK has handled the second wave reasonably well. People aren't talking about the crazy high rates in France and Spain which were exceeding the US for much for time, and with a corresponding high death rate too. I don't know what's going on with Germany, but their previously pristine record looks like it's being shattered at the moment... I think something changed after Boris went to hospital.
- AndrewDucker 6y agoExcept for the government's advisers recommending a lockdown in September and being ignored. https://www.bbc.co.uk/news/uk-54518002 https://www.bbc.co.uk/news/uk-54518002
- dm319 6y agoYes, he's definitely not been great. We're talking B- here, not A+. Maybe C++.
- AndrewDucker 6y agoThere are definitely worse!
- tandr 6y agoWell, C is not always worse than C++ I will see myself out.
- gnusty_gnurc 6y ago> as it looks like lockdown and highest restrictions aren't decreasing cases This has been apparent since the beginning. It's a highly contagious seasonal virus. When it declined in the northeast of the US as the spring led into summer, people proclaimed their expert advice was successful...ignoring that it's seasonal virus. Cuomo wrote even wrote a freaking book about his success.
- dm319 6y agoNo that has not been apparent. The first lockdown got cases down to very low levels (10s/million/day). It turned around a sky-rocketing increase in cases - it's not like the seasons changed between April and May. The second lockdown in the UK was a tiered approach, and has managed the levels (at least up to 3 weeks ago) better than France, Belgium or Spain. Not quite as good as Germany or Italy, and nowhere near the Scandinavian countries (excluding Sweden). Are you really trying to tell me that the variation in COVID rates is only down to seasons?
- gnusty_gnurc 6y agoLargely yes
- jasonlaramburu 6y agoIf it’s a seasonal virus why have states like Texas had multiple spikes in the same year?
- gnusty_gnurc 6y agoYou should be smart enough to know that a respiratory virus could be seasonal but still spread throughout the year. And the further complexity of being presented with this huge US graph, which in reality is the aggregated result of so many communities with varying levels of prevalence/previous exposure. Hope-Simpson studied this with flu, fig. 2 on pg. 5 shows some recognizable trends that line up with latitude: https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2134066&blobtype=pdf https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2134...
- jt2190 6y agoThis article is very light on details. Here’s a better one: “Update on new SARS-CoV-2 variant and how COG-UK tracks emerging mutations” Dec 14, 2020 https://www.cogconsortium.uk/news_item/update-on-new-sars-cov-2-variant-and-how-cog-uk-tracks-emerging-mutations/ https://www.cogconsortium.uk/news_item/update-on-new-sars-co... Edit: Here’s a report: “Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations” Recently a distinct phylogenetic cluster (named lineage B.1.1.7) was detected within the COG-UK surveillance dataset. This cluster has been growing rapidly over the past 4 weeks and since been observed in other UK locations, indicating further spread. Several aspects of this cluster are noteworthy for epidemiological and biological reasons and we report preliminary findings below. In summary: • The B.1.1.7 lineage accounts for an increasing proportion of cases in parts of England. • The number of B.1.1.7 cases, and the number of regions reporting B.1.1.7 infections, are growing. • B.1.1.7 has an unusually large number of genetic changes, particularly in the spike protein. https://virological.org/t/preliminary-genomic-characterisation-of-an-emergent-sars-cov-2-lineage-in-the-uk-defined-by-a-novel-set-of-spike-mutations/563 https://virological.org/t/preliminary-genomic-characterisati...
- yread 6y ago> Mutation N501Y is one of six key contact residues within the receptor-binding domain (RBD) and has been identified as increasing binding affinity to human and murine ACE2. > The spike deletion 69-70del has been described in the context of evasion to the human immune response but has also occurred a number of times in association with other RBD changes. > Mutation P681H is immediately adjacent to the furin cleavage site, a known location of biological significance.... > nucleotide changes on this branch are predominantly amino acid-altering (14 non-synonymous mutations and 3 deletions). There are 6 synonymous mutations on the branch. This is suggestive of a process involving adaptive molecular evolution > These include spike position 501, one of the key contact residues in the receptor binding domain (RBD), and experimental data suggests mutation N501Y can increase ACE2 receptor affinity (Starr et al. 2020) and P681H, one of 4 residues comprising the insertion that creates a furin cleavage site between S1 and S2 in spike. The S1/S2 furin cleavage site of SARS-CoV-2 is not found in closely related coronaviruses and has been shown to promote entry into respiratory epithelial cells and transmission in animal models (Hoffmann, Kleine-Weber, and Pöhlmann 2020; Peacock et al. 2020; Zhu et al. 2020). N501Y has been associated with increased infectivity and virulence in a mouse model (Gu et al. 2020). Both N501Y and P681H have been observed independently but not to our knowledge in combination before now. > deletion of two amino acids at sites 69-70 in spike ... arose in the mink-associated outbreak in Denmark on the background of the Y453F RBD mutation This doesn't sound good
- mehrdadn 6y agoWhat does 70% more transmissible mean?
- kordlessagain 6y agoR number changed when that one nucleotide change increased the number of spikes on the surface by 5-8X. This modification was seen occurring in multiple locations, so maybe not a single linage change. Maybe more like an increase in probability that one nucleotide would "flip" in multiple organisms, with enough organisms at hand. The spike itself attacks/props open ACE2 receptors, like those found on your eyes, and is mostly encoded using ~39 some odd nucleotides borrowed from a South Asian fish. Plotting the number of "words" repeated in the genome (~30K nucleotides) yields a phi-like curve, with the words/codons in the spike occurring more statistically significantly than others. The mutation is not expected to cause more severe cases, but is more infectious due to more spikes needing to be neutralized to fend off the infection. In bloodstream plant lectins have been shown to be effective at this, as well as llama nanoparticles. All of this is Googlable using the right key terms. Fish DNA in the spike: https://dnascience.plos.org/2020/02/20/covid-19-vaccine-will-close-in-on-the-spikes/ https://dnascience.plos.org/2020/02/20/covid-19-vaccine-will... One nucleotide changes number of spikes: https://www.washingtonpost.com/science/2020/06/29/coronavirus-mutation-science/?arc404=true https://www.washingtonpost.com/science/2020/06/29/coronaviru...
- mehrdadn 6y agoOh thanks, I was just trying to understand what it's measuring. So are they saying its R factor is now 1.7R?
- kordlessagain 6y agoNot sure on the new R number. Not a lot of data yet. Check this out, however: https://www.sciencedaily.com/releases/2020/11/201112144040.htm https://www.sciencedaily.com/releases/2020/11/201112144040.h... > Kawaoka and Halfmann contributed their unique coronavirus study model, which uses hamsters. The University of Wisconsin-Madison team -- including Shiho Chiba, who ran the hamster experiments -- performed replication and airborne transmission studies with both the original virus and the mutated version created by Baric and Hou. > They found that the mutated virus not only replicates about 10 times faster -- it's also much more infectious. > Hamsters were inoculated with one virus or the other. The next day, eight uninfected hamsters were placed into cages next to infected hamsters. There was a divider between them so they could not touch, but air could pass between the cages. > Researchers began looking for replication of the virus in the uninfected animals on day two. Both viruses passed between animals via airborne transmission, but the timing was different. > With the mutant virus, the researchers saw transmission to six out of eight hamsters within two days, and to all the hamsters by day four. With the original virus, they saw no transmission on day two, though all of the exposed animals were infected by day four. > "We saw that the mutant virus transmits better airborne than the [original] virus, which may explain why this virus dominated in humans," Kawaoka said.
- CodeGlitch 6y agoOne wonders if the virus is now "airborne"? Is that something viruses can actually do, ontop of being passed on through water droplets after coughing/sneezing.
- aphextron 6y ago>One wonders if the virus is now "airborne"? Is that something viruses can actually do, ontop of being passed on through water droplets after coughing/sneezing. It always has been. The virus is aerosolized through exhalation, and spreads much like secondhand smoke [0]. [0] https://www.sciencedirect.com/science/article/pii/S0925753520302630#p0175 https://www.sciencedirect.com/science/article/pii/S092575352...
- throwitaway1235 6y agoI remember a listening to a podcast interviewing a physician from a major hospital who made sure to explain the difference between an airborne pathogen and one that is respiratory active. Jogging my memory. Airborne meaning a virus that a person exhales in an elevator (example) will still be present and transmissible x amount of time later. Respiratory active meaning transmissible by coughing/exhaling in the presence of someone else. These are important distinctions if true and still relevant.
- Exmoor 6y agoIn the sense of your explanation it COVID-19 is indeed airborne.
- jobigoud 6y agoAs far as I understand it lives in droplets heavier than air that fall to the ground in a matter of a few seconds. The next person entering the elevator won't breathe it. Truly airborne viruses can be lifted by regular air turbulences and travel kilometers before landing on someone else.
- aphextron 6y agoImportant to note that this has been known since early summer. There are multiple strains of SARS-Cov-2, and the original Wuhan strain is almost nonexistent in the US at this point. The mutated strain, while much more infectious, is actually much less deadly at the same time.
- bart_spoon 6y agoMost of this isn’t true. This particular mutation is relatively new, only having been spreading much in the last few months. Also, there is little to no evidence that this strain is more or less deadly than any other strain, though there does seem to be indications that it is more infectious.
- eznzt 6y agoWhat is the chance this particular strain has been manually engineered?
- dm319 6y agoHighly unlikely. You overestimate our ability to genetically edit things and predict what the outcome will be. The virus is mutating at a rate of about one mutation/month - that's fairly standard.
- rolph 6y agoeven if, the virus was engineered, the mutation rate would incur deviation from the engineered character, at the same rate as we are seeing with this naturally occuring virus. An engineered SARS would quickly be subject to selection.
- piercebot 6y agoI wonder how much of this was caused by natural selection brought on by changes in human behavior; masks wearing, social distancing, etc.
- dm319 6y agoI'm sure this is likely. It's quite concerning, as it may mean that we need a full lock-down (as in people not going to work) until we have a majority of the population vaccinated.
- raarts 6y agoI don't think that's even possible. I read somewhere that just about 40% of the population has the type of job that can be done from home. A lot of the rest is sitting at home due to restaurants, stores closing, but a fair amount of people is required to take care of the ones at home. Bringing them stuff, transporting it all. I doubt we can win from a virus other than adapting our immune system (and some people dying). Even vaccination might just encourage the virus to evolve.
- dm319 6y agoBy full lockdown I mean similar to the first-wave lockdown in the UK. No travelling for non-essential work, only key workers. Vaccination _is_ adapting the immune system, and exactly combats viral evolution by shutting down the transmission.
- rurban 6y agoNo, this is normal for every RNA virus. It was already detected in May, that subsequent dominant strains (remember, the virus mutated with every single generation, every 10 days) have much more deletions than mutations, and are thus as such much less dangerous and much more transmissible, as their hosts don't detect it. This time UK got their sensationalist headline. In fact those are more dangerous, R is higher, and mortality is very low and insignificant. But reaching the vulnerable better makes it more dangerous in the end.
- davidhyde 6y ago> “If allowed to go unchecked, the new variant of the virus could increase the country’s R rate, which is estimated to be between 1.1 and 1.2, by 0.4 per cent.” I wonder if the author actually meant 40%.
- skookum 6y agoMaybe they meant to say 0.4, without any qualifier - i.e. that the rate went from 0.7-0.8 to 1.1-1.2? A change from the lower end of the old range to the higher end of the new range would match the 70% increase in transmissibility. (though that would require an increase of almost 0.5)
- davidhyde 6y agoYou nailed it, I think that’s what they meant.
- up6w6 6y agoIf some relevant mutation happens and we are forced to update the vaccines, which seems to not be so difficult for the new mRNA vaccines (pfizer and moderna ones), will it need to pass through all clinical tests again ?
- carlmr 6y agoI mean if the virus mutates at a speed like this it may be useful to allow mRNA as a platform (at least for this virus). So that we can get the vaccines out faster than the virus mutates. (Assuming effectiveness of the vaccine is impacted)