New Variant Covid-19 VUI 202012/01

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Woodchopper
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Dec 24, 2020 8:03 pm

New NERVTAG meeting, now has high confidence it spreads faster:
https://m.box.com/shared_item/https%3A% ... 6964987830

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Dec 24, 2020 8:30 pm

Data update. Cases and hospital occupancy surging in Tier 4 areas of England.
https://twitter.com/jburnmurdoch/status ... 37793?s=21

15% of tests in London now positive, hospital occupancy also increasing Sweden, US and Croatia.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Dec 24, 2020 8:33 pm

Rapid evaluation confirms lateral flow devices effective in detecting new COVID-19 variant
https://www.gov.uk/government/news/rapi ... 19-variant

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Dec 24, 2020 8:46 pm

Woodchopper wrote:
Thu Dec 24, 2020 7:54 pm
Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England

https://cmmid.github.io/topics/covid19/ ... riant.html

We estimate that VOC 202012/01 is 56% more transmissible (95% credible interval across three regions 50-74%) than preexisting variants of SARS-CoV-2. We were unable to find clear evidence that VOC 202012/01 results in greater or lesser severity of disease than preexisting variants. Nevertheless, the increase in transmissibility is likely to lead to a large increase in incidence, with COVID-19 hospitalisations and deaths projected to reach higher levels in 2021 than were observed in 2020, even if regional tiered restrictions implemented before 19 December are maintained. Our estimates suggest that control measures of a similar stringency to the national lockdown implemented in England in November 2020 are unlikely to reduce the effective reproduction number Rt to less than 1, unless primary schools, secondary schools, and universities are also closed. We project that large resurgences of the virus are likely to occur following easing of control measures. It may be necessary to greatly accelerate vaccine roll-out to have an appreciable impact in suppressing the resulting disease burden.
Good thread summarizing the paper: https://twitter.com/billhanage/status/1 ... 81063?s=21

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Dec 25, 2020 9:37 am

Is the new SARS-CoV-2 UK variant (B.1.1.7) already in the US? Maybe.

The Helix® COVID-19 Test includes amplification of three viral genes: Orf1ab, N and the S gene. A recent preprint has shown that deletion of H69 and V70 can be characterized by a dropout of the S gene in standard and widely used RT-PCR SARS-CoV-2 tests. This analysis technique can therefore serve as a proxy to detect infections driven by these newly emerging sequence variants. Given the new information about the link between S gene dropout and the H69del/V70del mutation, together with the concern over increased transmissibility of the B.1.1.7 strain, we examined the prevalence of S gene dropout in 2 million samples from across the US tested at Helix.

We observe a rise in S gene dropout starting in early October, with 0.25% of our daily COVID-19-positive tests exhibiting this pattern during the first week. The rate of positive samples with S gene dropout has grown slowly over time, with last week exhibiting the highest level yet at 0.5% of COVID-19-positive tests that are consistent with the H69del/V70del variant.
https://blog.helix.com/sars-cov2_uk-variant/

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Fri Dec 25, 2020 9:53 am

Woodchopper wrote:
Fri Dec 25, 2020 9:37 am
Is the new SARS-CoV-2 UK variant (B.1.1.7) already in the US? Maybe.

The Helix® COVID-19 Test includes amplification of three viral genes: Orf1ab, N and the S gene. A recent preprint has shown that deletion of H69 and V70 can be characterized by a dropout of the S gene in standard and widely used RT-PCR SARS-CoV-2 tests. This analysis technique can therefore serve as a proxy to detect infections driven by these newly emerging sequence variants. Given the new information about the link between S gene dropout and the H69del/V70del mutation, together with the concern over increased transmissibility of the B.1.1.7 strain, we examined the prevalence of S gene dropout in 2 million samples from across the US tested at Helix.

We observe a rise in S gene dropout starting in early October, with 0.25% of our daily COVID-19-positive tests exhibiting this pattern during the first week. The rate of positive samples with S gene dropout has grown slowly over time, with last week exhibiting the highest level yet at 0.5% of COVID-19-positive tests that are consistent with the H69del/V70del variant.
https://blog.helix.com/sars-cov2_uk-variant/
So while the total rate of positive tests increased quite a lot in that period, the proportion with the S gene dropout doubled from 0.25% to 0.5% in two months, and since H69del/V70del is a relatively common mutation and only one of the features of B.1.1.7, well, I don't think this is really B.1.1.7. The data from the UK shows it going from ~1% to ~10% in about 3 weeks.
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Dec 25, 2020 10:10 am

shpalman wrote:
Fri Dec 25, 2020 9:53 am
Woodchopper wrote:
Fri Dec 25, 2020 9:37 am
Is the new SARS-CoV-2 UK variant (B.1.1.7) already in the US? Maybe.

The Helix® COVID-19 Test includes amplification of three viral genes: Orf1ab, N and the S gene. A recent preprint has shown that deletion of H69 and V70 can be characterized by a dropout of the S gene in standard and widely used RT-PCR SARS-CoV-2 tests. This analysis technique can therefore serve as a proxy to detect infections driven by these newly emerging sequence variants. Given the new information about the link between S gene dropout and the H69del/V70del mutation, together with the concern over increased transmissibility of the B.1.1.7 strain, we examined the prevalence of S gene dropout in 2 million samples from across the US tested at Helix.

We observe a rise in S gene dropout starting in early October, with 0.25% of our daily COVID-19-positive tests exhibiting this pattern during the first week. The rate of positive samples with S gene dropout has grown slowly over time, with last week exhibiting the highest level yet at 0.5% of COVID-19-positive tests that are consistent with the H69del/V70del variant.
https://blog.helix.com/sars-cov2_uk-variant/
So while the total rate of positive tests increased quite a lot in that period, the proportion with the S gene dropout doubled from 0.25% to 0.5% in two months, and since H69del/V70del is a relatively common mutation and only one of the features of B.1.1.7, well, I don't think this is really B.1.1.7. The data from the UK shows it going from ~1% to ~10% in about 3 weeks.
True, but S gene dropout is used as a proxy by the Public Health England report: https://assets.publishing.service.gov.u ... L2_SH2.pdf

Possible explanations appear to be:

- it’s the same variant, spreading slower in the US.
- it’s the same variant, and there’s a threshold effect whereby it doesn’t grow explosively when it’s at very low levels.
- it’s a different variant which is still more transmissible.
- noise.

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Fri Dec 25, 2020 10:32 am

Well, wot I reckon is that B.1.1.7 isn't that much more transmissible and its spread has been facilitated in the UK by of poorly implemented tiers (i.e. leaving London in tier 2 right next to Kent in tier 3) and other countries won't have a particular issue with it, but I think one of your links did test all the various hypotheses and decided that more transmissibility was the most plausible one.
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Dec 25, 2020 10:40 am

shpalman wrote:
Fri Dec 25, 2020 10:32 am
Well, wot I reckon is that B.1.1.7 isn't that much more transmissible and its spread has been facilitated in the UK by of poorly implemented tiers (i.e. leaving London in tier 2 right next to Kent in tier 3) and other countries won't have a particular issue with it, but I think one of your links did test all the various hypotheses and decided that more transmissibility was the most plausible one.
Yes it did.

We could look into that with the Google and Apple mobility data. But I’m on my phone and don’t have much time now.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Dec 25, 2020 9:11 pm

B.1.1.7 aka VUI2020/01 amounts to 31% of all UK 🦠 virus genomes collected since Dec 1.. and 501Y.V2 represents 53% of all genomes from S. Africa since Nov 1
https://twitter.com/macroliter/status/1 ... 55744?s=21

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Dec 26, 2020 3:57 am

U.K. variant puts spotlight on immunocompromised patients’ role in the COVID-19 pandemic
https://www.sciencemag.org/news/2020/12 ... 9-pandemic

Neutralising antibodies drive Spike mediated SARS-CoV-2 evasion
https://www.medrxiv.org/content/10.1101 ... 20241927v2

Second link on a similar subject. I thought I’d posted the first earlier, but couldn’t find it.

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sat Dec 26, 2020 10:56 am

The UK's covid dashboard is actually really good, as long as it actually gets updated. In particular, you can quickly get to the normalized infection rates for any area from a country level all the way down to local authorities. And then there's the interactive map.

Conversely, it's easy for me to git pull all the data for Italy which gives me cases at the comune level and declared-covid-free and deaths at the regional level but I can't seem to find a dashboard which plots those and I'm not sure if I can be bothered to greatly expand my spreadsheet.

The official version just seems to give graphs for the whole nation and the current numbers for any region or comune you want to click on, and this one just seems to plot cumulative cases for each region.

Anyway, something seems to be driving the case rates in Veneto and Friuli-Venezia-Giulia to not come down the same way that the rest of the nation has, but looking at that list I wanted to see if Le Marche was also having trouble coming down since that's where we probably have community transmission of the new variant (since it was detected in someone who has no obvious direct link to the UK). It might be the case, actually, since there isn't such an obvious change of gradient on those graphs as compared to e.g. Lombardy. But I don't think that region was ever declared a red zone.

I'll probably have to investigate the python scripts bundled with the git repository.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sat Dec 26, 2020 11:12 am

Oh and France has found it now, in someone recently arrived from London.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sat Dec 26, 2020 7:36 pm

Italy has found a few cases, in people recently arrived from London. Of course they aren't really looking for it in recent positives with no connection to the UK, let alone looking for anyone positive-asymptomatic with it in the general population.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sat Dec 26, 2020 7:39 pm

having that swing is a necessary but not sufficient condition for it meaning a thing
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Dec 26, 2020 8:03 pm

shpalman wrote:
Sat Dec 26, 2020 7:39 pm
Spain and Sweden too
Yes, and several other places: Denmark, Belgium, France, Ireland, Netherlands, Japan, Singapore, Lebanon, South Africa and Australia.

It’s probably safe to assume that it’s everywhere Britons travel to. Though they seem to be small numbers and associated with people who’ve been in Britain. ETA though that could just be where people are looking.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Dec 26, 2020 10:06 pm

Woodchopper wrote:
Sat Dec 26, 2020 8:03 pm
shpalman wrote:
Sat Dec 26, 2020 7:39 pm
Spain and Sweden too
Yes, and several other places: Denmark, Belgium, France, Ireland, Netherlands, Japan, Singapore, Lebanon, South Africa and Australia.

It’s probably safe to assume that it’s everywhere Britons travel to. Though they seem to be small numbers and associated with people who’ve been in Britain. ETA though that could just be where people are looking.

And Canada
https://twitter.com/reuters/status/1342 ... 50376?s=21

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Dec 27, 2020 3:56 am

Japan will ban entry from all countries to prevent the spread of the more contagious U.K. strain of the coronavirus, the government announced Saturday.

The ban takes effect Monday and continues through the end of January. Japanese nationals and foreigners living in Japan will be permitted to return to the country. A 14-day quarantine request will apply to all without exception.

Japan currently bans entry from 152 nations, but since October, it has allowed in foreign students or business professionals planning long-term stays. Now the issuance of those visas will be suspended, but those who have already acquired visas can enter even after Monday.

New entry from the U.K. and South Africa -- two countries where the new variant is spreading -- has already been suspended.

To avoid disruptions to economic activity, bilateral business travel arrangements with 11 countries including China and South Korea will be maintained. Since many foreigners are entering Japan through this arrangement, the latest travel ban may have little impact on limiting foreign arrivals.

As of Friday, five people who traveled from Britain were confirmed to be infected with the new strain, according to the government.

Those arriving from countries where the new variant has been detected will be required to present proof of negative tests taken within 72 hours of departure. They also must take PCR tests upon arrival.
https://asia.nikkei.com/Spotlight/Coron ... n-s-spread

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Dec 27, 2020 1:10 pm

Summary of where it’s spread: https://cov-lineages.org/global_report.html

Media reports suggest other countries as well.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Dec 27, 2020 1:16 pm

Instead of going into quarantine after the new variant was announced, about 200 Britons at a Swiss ski resort disappeared and could not be contacted by Swiss authorities.
https://www.20min.ch/story/200-briten-v ... 6183998060

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sun Dec 27, 2020 1:23 pm

Woodchopper wrote:
Sun Dec 27, 2020 1:16 pm
Instead of going into quarantine after the new variant was announced, about 200 Britons at a Swiss ski resort disappeared and could not be contacted by Swiss authorities.
https://www.20min.ch/story/200-briten-v ... 6183998060
Switzerland so far has been giving relatively little of a sh.t about covid, I mean, that they had their ski resorts open at all.
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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Sun Dec 27, 2020 1:26 pm

Woodchopper wrote:
Sun Dec 27, 2020 1:10 pm
Summary of where it’s spread: https://cov-lineages.org/global_report.html

Media reports suggest other countries as well.
Interesting. As far as I know, Italy only found one case which wasn't obviously someone just back from the UK, but then they wouldn't be looking.
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Dec 27, 2020 2:27 pm

S-variant SARS-CoV-2 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-PCR
Birmingham University Turnkey laboratory is part of the Lighthouse network responsible for testing clinical samples under the UK government Test & Trace scheme. Samples are analysed for the presence of SARS-CoV-2 in respiratory samples using the Thermofisher TaqPath RT-PCR test, which is designed to co-amplify sections of three SARS-CoV-2 viral genes. Since more recent information became available regarding the presence of SARS-CoV-2 variants of concern (S-VoC), which can show a suboptimal profile in RT-PCR tests such as the ThermoFisher TaqPath used at the majority of Lighthouse laboratories, we analysed recently published data for trends and significance of the S-gene dropout variant. Results showed that: (i) the population of S-gene dropout samples had significantly lower median Ct values of ORF and N-gene targets compared to samples where S-gene was detected (ii) on a population basis, S-gene dropout samples clustered around very low Ct values for ORF and N targets (iii) linked Ct values for individual samples showed that a low Ct for ORF and N were clearly associated with an S-dropout characteristic (iv) when conservatively inferring relative viral load from Ct values, approximately 35% of S-dropout samples had high viral loads between 10 and 10,000-fold greater than 1 x 106, compared to 10% of S-positive samples. This analysis suggests that patients whose samples exhibit the S-dropout profile in the TaqPath test are more likely to have high viral loads at the time of sampling. The relevance of this to epidemiological reports of fast spread of the SARS-CoV-2 in regions of the UK is discussed.  
https://www.medrxiv.org/content/10.1101 ... 20248834v1

ETA note that S gene dropout is the proxy used by Public Health England to estimate new variant prevalence. See link above.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Dec 27, 2020 3:43 pm

And in Norway, among two people who’d travelled from the UK.
Hopefully they took the mandatory quarantine period seriously. https://www.fhi.no/nyheter/2020/engelsk ... til-norge/

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sun Dec 27, 2020 4:00 pm

And Portugal, also from travelers from Britain
https://www.reuters.com/article/health- ... SKBN2910IB

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