New strain, potentially more contagious - Printable Version
+- The CardBoard (https://thecardboard.org/board)
+-- Forum: Emergency (https://thecardboard.org/board/forum-11.html)
+--- Forum: Covid-19 (https://thecardboard.org/board/forum-12.html)
+--- Thread: New strain, potentially more contagious (/thread-21213.html)
+- The CardBoard (https://thecardboard.org/board)
+-- Forum: Emergency (https://thecardboard.org/board/forum-11.html)
+--- Forum: Covid-19 (https://thecardboard.org/board/forum-12.html)
+--- Thread: New strain, potentially more contagious (/thread-21213.html)
New strain, potentially more contagious - magnus - 12-19-2020
There's a new strain detected in southeast England that scientists believe is more contagious.
https://www.cnn.com/world/live-news/coronavirus-pandemic-vaccine-updates-12-19-20/h_6f7a8c59cac8f9419cec869bc6df2227
Unknown whether the mutations will affect vaccine effectiveness but most likely still effective.
lex24 - lex24 - 12-19-2020
Johnson was moving towards loosening restrictions for Xmas. Now this. Interesting to see where this leads.
Query: Any support for this theory from other scientists? Lot of folks analyzing this .
RE: New strain, potentially more contagious - M T - 12-19-2020
Deja vu all over again..
July 2 (UK): "New, more infectious strain of COVID-19 now dominates global cases of virus: study" Study. [Strain D614G]
Sept (US): "Massive genetic study shows coronavirus mutating and potentially evolving amid rapid US spread" [Strain D614G in Houston]
Oct (US) "Coronavirus Mutation May Have Made It More Contagious" Paper [Strain D614G is 99.9% of infections in Houston]
This new new strain is apparently being called "VUI – 202012/01" for now. It was identified in September.
RE: New strain, potentially more contagious - dabigv13 - 12-19-2020
Hard to know what to make of it. A similar but genetically distant mutated strain occurred in South Africa and is increasing in prevalence at expense of other strains as well, and both have the same protein change in the spike epitope. Whether this has clinical significance, too early to tell. But it would not be unusual for a virus out in the wild for more than a year to develop a more transmissible mutation.
RE: New strain, potentially more contagious - Goose - 12-19-2020
UK is certainly responding to a surge in infections by locking down London and Southwest England. They are attributing this surge to the new strain of virus, although whether that is true is hard to know ATM. Good excuse though. Case counts certainly concerning in those areas.
RE: New strain, potentially more contagious - Hurlburt88 - 12-20-2020
I posted on this in another thread. I have also asked myself the question if this new strain is a good "excuse" for governments to ask the citizenry to double-down on SIP during the holidays. As I talk to my team in the UK, they have been pretty loose socially over the last 2 months even with high numbers.
RE: New strain, potentially more contagious - BostonCard - 12-20-2020
A population geneticist made this analogy to me some time ago, and I think it is apt here.
Imagine a drunk person at a street corner. The distance that drunk person moves from the street corner represents the rise of new genetic variants. If there is a slight grade to that street (a genetic advantage), the drunk will tend, over time, to move downhill. But even if there is no grade to the street, over time the drunk will through chance, wind up some distance away from their original position.
The bottom line is that if you had a mutation that made the virus more transmissible, you would see it slowly become more prevalent. However, it doesn't work the other way around; the fact that a strain with a mutation has become more prevalent doesn't mean that the mutation necessarily made the virus more transmissible. Over time, even under what is called "neutral selection" you would expect some mutations to become more prevalent due to chance.
This paper makes the case that there is no evidence of increased transmission from various COVID-19 mutations:
https://www.nature.com/articles/s41467-020-19818-2
On D641G specifically:
Quote:A much discussed mutation in the context of demographic confounding is D614G (nucleotide position 23,403), a non-synonymous change in the SARS-CoV-2 Spike protein. Korber et al. suggested that D614G increases transmissibility but with no measurable effect on patient infection outcome21. Other studies have suggested associations with increased infectivity in vitro18,40 and antigenicity41. Here we conversely find that D614G does not associate with significantly increased viral transmission (median log10(RoHO) = 0, paired t test p = 0.28; Supplementary Data 4), in line with our results for all other tested recurrent mutations. Though clearly, different choices of methodology may lead to different conclusions. A recent study on a sample of 25,000 whole-genome sequences exclusively from the UK used different approaches to investigate D614G. Not all analyses found a conclusive signal for D614G, and effects on transmission, when detected, appeared relatively moderate39.
These apparently contrasting results for D614G should be considered carefully. What is, however, indisputable is that D614G emerged early in the pandemic and is now found at high frequency globally, with 36,347 assemblies in our data set (77.8%) carrying the derived allele (Fig. 1a and Supplementary Data 3). However, D614G is also in linkage disequilibrium (LD) with three other derived mutations (nucleotide positions 241, 3037, and 14,408) that have experienced highly similar expansions, as 98.9% of accessions with D614G also carry these derived alleles (35,954/36,347). It should be noted that the D614G mutation displays only five independent emergences that qualify for inclusion in our analyses (fewer than the other three sites it is associated with). While this limits our power to detect a statistically significant association with transmissibility, the low number of independent emergences suggests to us that the abundance of D614G is more probably a demographic artefact: D614G went up in frequency as the SARS-CoV-2 population expanded, largely due to a founder effect originating from one of the deepest branches in the global phylogeny, rather than being a driver of transmission itself.
If I can translate that, they don't think that D614G is more transmissible than other mutations (but also can't prove the negative).
BC
RE: New strain, potentially more contagious - DocSavage87 - 12-20-2020
(12-20-2020, 11:53 AM)BostonCard Wrote: If I can translate that, they don't think that D614G is more transmissible than other mutations (but also can't prove the negative).
A more recent paper concludes "data show that the D614G substitution enhances SARS-CoV-2 infectivity, competitive fitness, and transmission in primary human cells and animal models."
https://science.sciencemag.org/content/370/6523/1464
Here's a tweet thread from a molecular biologist on the set of mutations in the UK variant.
[tweet]
https://twitter.com/AliNouriPhD/status/1340505791841841152?s=20
[/tweet]
RE: New strain, potentially more contagious - magnus - 12-20-2020
Many countries now closing their borders to UK residents.
RE: New strain, potentially more contagious - M T - 12-20-2020
If it wasn't clear from my note earlier, the "new strain" in England is not D614G. (But when D614G was spreading, it was considered the same sort of event.)
RE: New strain, potentially more contagious - DocSavage87 - 12-20-2020
(12-20-2020, 04:38 PM)M T Wrote: If it wasn't clear from my note earlier, the "new strain" in England is not D614G. (But when D614G was spreading, it was considered the same sort of event.)
Not sure if that was directed towards me, but the tweet thread clarifies that the UK variant has "mutations [that] are accumulating in the backdrop of another mutation, D614G, which has become dominant, globally, and has enhanced infectivity and replication fitness. It's even been shown, experimentally, to transmit faster through droplets & aerosols in hamsters."
Griffins78 - Griffins78 - 12-26-2020
It looks like the variant in the UK is called B.1.1.7. Here’s what William Haseltine, PhD, chair and president of the global health think tank, ACCESS Health International wrote on CNN, “Opinion: Here’s what’s worrying about the coronavirus variant” with a link to this paper, “Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations”
He says, “this new variant tells us important things about the virus: it can adapt to become more easily transmissible and may be able to become more difficult to neutralize and may possibly be able to outsmart the vaccine to a small extent.”
The paper concludes, “We report a rapidly growing lineage in the UK associated with an unexpectedly large number of genetic changes including in the receptor-binding domain and associated with the furin cleavage site. Given (i) the experimentally-predicted and plausible phenotypic consequences of some of these mutations, (ii) their unknown effects when present in combination, and (iii) the high growth rate of B.1.1.7 in the UK, this novel lineage requires urgent laboratory characterisation and enhanced genomic surveillance worldwide.”
RE: Griffins78 - Goose - 12-26-2020
(12-26-2020, 09:52 AM)Griffins78 Wrote: It looks like the variant in the UK is called B.1.1.7. Here’s what William Haseltine, PhD, chair and president of the global health think tank, ACCESS Health International wrote on CNN, “Opinion: Here’s what’s worrying about the coronavirus variant” with a link to this paper, “Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations”Let it simply be said that anything written by William Haseltine should be taken with many grains of salt. He has been characterized as "controversial" by some and in much less flattering ways by others. That doesn't make him wrong, but it does raise questions.
He says, “this new variant tells us important things about the virus: it can adapt to become more easily transmissible and may be able to become more difficult to neutralize and may possibly be able to outsmart the vaccine to a small extent.”
The paper concludes, “We report a rapidly growing lineage in the UK associated with an unexpectedly large number of genetic changes including in the receptor-binding domain and associated with the furin cleavage site. Given (i) the experimentally-predicted and plausible phenotypic consequences of some of these mutations, (ii) their unknown effects when present in combination, and (iii) the high growth rate of B.1.1.7 in the UK, this novel lineage requires urgent laboratory characterisation and enhanced genomic surveillance worldwide.”
RE: New strain, potentially more contagious - dabigv13 - 12-30-2020
The variant is in SoCal. Hopefully some local academic institutions decide to up their game with genomic sequencing so we can find out how prevalent this is. Hardly a surprise, but very unwelcome.
https://www.sfchronicle.com/coronavirus/article/Coronavirus-live-updates-news-bay-area-15237940.php
More here-
[Tweet]https://twitter.com/K_G_Andersen/status/1344397421023961090[/tweet]
RE: New strain, potentially more contagious - magnus - 12-31-2020
I saw they found it in Florida too. No travel history.
Most likely this is just getting started in the US but that also means that if it really is the driving force for the UKs surge, our winter is going to be horrible as we not only try to get the November surge under control but will likely face the widespread infection of this new strain in the next couple months. =(
RE: New strain, potentially more contagious - OutsiderFan - 12-31-2020
It was a 100% certainty the new virus was or would be in the U.S., just based on how the pandemic started. It's a lot more places than are known right now also.
I pray it is in Santa Clara County and responsible for the seemingly absurd number of cases over the last month in the county. If it isn't yet here and isn't yet responsible for the spike, it is going to get really, really bad for our hospitals and health workers when it does arrive. Sure, they might get vaccinated so they don't get sick, but that doesn't relieve stress of dealing with so many sick people at once. Possibly having to ration care and decide people who might otherwise live, must die, is a choice no health care worker wants to make.
Also praying we don't have a major e.... No, not gonna say it.