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 » Sun Dec 27, 2020 10:10 pm

Two more in Canada: https://www.cbc.ca/news/canada/coronavi ... -1.5855459

The big question now is why haven’t they discovered any in the US?

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Dec 28, 2020 1:17 pm

Woodchopper wrote:
Sun Dec 27, 2020 10:10 pm
Two more in Canada: https://www.cbc.ca/news/canada/coronavi ... -1.5855459

The big question now is why haven’t they discovered any in the US?
As of Wednesday, the United States had sequenced 37 coronavirus samples in all of December.
molto tricky

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Mon Dec 28, 2020 5:25 pm

I'm hearing that Italy made its own new variant in August.

But then it's fairly typical for Italians to claim they did something first and that their version is better and the anglo-american world just copied them.

and here is a link to some guy saying it
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Re: New Variant Covid-19 VUI 202012/01

Post by Bird on a Fire » Mon Dec 28, 2020 6:39 pm

Woodchopper wrote:
Sun Dec 27, 2020 4:00 pm
And Portugal, also from travelers from Britain
https://www.reuters.com/article/health- ... SKBN2910IB
This is interesting, as Madeira has been demanding negative PCR tests from visitors all year, whereas the mainland has only just started.

Could be the "not looking" effect in action, or could suggest that pre-travel PCR isn't super useful.
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Re: New Variant Covid-19 VUI 202012/01

Post by bob sterman » Mon Dec 28, 2020 11:05 pm

Woodchopper wrote:
Sun Dec 27, 2020 10:10 pm
Two more in Canada: https://www.cbc.ca/news/canada/coronavi ... -1.5855459

The big question now is why haven’t they discovered any in the US?
Early signs of this variant came from labs using three-target PCR tests including the S gene. Samples with the new variant were matching only 2 of the 3 - i.e. exhibiting "S gene dropout".

If labs across the US are generally using two-target PCR tests that don't include the S gene - they wouldn't have spotted it early on.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Dec 29, 2020 12:38 pm

Updated Public Health England briefing
Investigation of novel SARS-CoV-2 variant
Variant of Concern 202012/01
Technical briefing 2

A matched cohort study was undertaken to inform a preliminary assessment of outcomes of hospitalisation and case fatality associated with VOC 202012/01

[...]

Review of hospital admissions data from the NHS identified that of the 3,538 cases, 42 individuals had a record of hospital admission after the date of specimen. Fewer variant cases (16 cases (0.9%)) were admitted to hospital compared to wild-type comparator cases(26 cases (1.5%))but the difference was not significant (Chi-squared test p=0.162). Due to potential time delays for receipt of hospital admissions data, the identified hospital admissions should be regarded as a minimum number of hospital admissions and further admissions data are likely to be received into this NHS dataset in the future.

The 28-day case fatality was assessed for variant cases and comparator cases. Analysis was restricted to 2,700cases with a full 28 days elapsed since the specimen date. Among variant cases,12of 1,340(0.89%)variant cases died within 28 days of their specimen date compared with 10of 1,360(0.73%)wild-type comparator cases; this difference was not signfiicant(Odds ratio:1.21, p=0.65).
https://assets.publishing.service.gov.u ... _FINAL.pdf

More at the link.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Dec 29, 2020 1:02 pm

MK Lighthouse lab @Biocentre_UK testing data showing a large increase in positive rate over the lest few days. New variant B117 stabilizing at ~80% of all new positives.
https://twitter.com/The_Soup_Dragon/sta ... 66336?s=20

Tweet by "CEO, NIHR National Biosample Centre and the Milton Keynes "Lighthouse" Coronavirus Testing Mega-Lab
@Biocentre_UK"

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Re: New Variant Covid-19 VUI 202012/01

Post by shpalman » Tue Dec 29, 2020 1:59 pm

It's been in Germany since November at least:
The new coronavirus variant sweeping Britain has been in Germany since November, health officials said on Tuesday, after detecting the variant in a patient who died in the north of the country.

Researchers were “able to sequence the variant of the B117 virus in a person infected in November this year”, the health ministry of Lower Saxony said in a statement referring to the new variant.
If there's a hotspot in Germany, it's in the other Saxony, the one near Czechia.

Germany covid dashboard
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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Dec 29, 2020 2:14 pm

THREAD: Some information on the spread of the new Covid variant across England from @ONS
infection survey - ONLY goes up to 18th December. We urgently need last week's data. BUT up to 18th Dec this is where we were:
https://twitter.com/chrischirp/status/1 ... 8819404802

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

Post by Woodchopper » Tue Dec 29, 2020 3:30 pm

Woodchopper wrote:
Sun Dec 27, 2020 10:10 pm
Two more in Canada: https://www.cbc.ca/news/canada/coronavi ... -1.5855459

The big question now is why haven’t they discovered any in the US?
Thread by Trevor Bedford on US testing, he assumes that it hasn't been found because it isn't very common.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Tue Dec 29, 2020 11:08 pm


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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Wed Dec 30, 2020 12:22 am

Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England
https://cmmid.github.io/topics/covid19/ ... Cq23eWr_j0

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Wed Dec 30, 2020 9:07 am

Thread contains lots more: https://twitter.com/trvrb/status/134403 ... 47683?s=20
With data that has emerged in the last week, I'm now 80-90% convinced that infections by the UK variant virus (Pangolin lineage B.1.1.7,
@nextstrain clade 20B/501Y.V1) result in, on average, more onward infections, ie are more transmissible.


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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Dec 31, 2020 5:47 am

A new strain of COVID-19 that reached Ireland from the United Kingdom is spreading faster than the country’s most pessimistic forecasts, Prime Minister Micheal Martin said on Wednesday.
https://www.reuters.com/article/uk-heal ... KKBN29422L

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Dec 31, 2020 5:09 pm

Report 42 - Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: insights from linking epidemiological and genetic data

We examine epidemiological evidence for this VOC having a transmission advantage from several perspectives. First, whole genome sequence data collected from community-based diagnostic testing provides an indication of changing prevalence of different genetic variants through time. Phylodynamic modelling additionally indicates that genetic diversity of this lineage has changed in a manner consistent with exponential growth. Second, we find that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S-gene target failures (SGTF) in community-based diagnostic PCR testing. Third, we examine growth trends in SGTF and non-SGTF case numbers at local area level across England, and show that the VOC has higher transmissibility than non-VOC lineages, even if the VOC has a different latent period or generation time. Available SGTF data indicate a shift in the age composition of reported cases, with a larger share of under 20 year olds among reported VOC than non-VOC cases.

[On the final point]

Share of age groups among VOC and non-VOC cases
To assess differences in the age distribution of VOC versus non-VOC cases, we considered S- and S+ case numbers in weeks 46-51 across NHS STP regions. Case numbers were standardised for differences in the population age composition in each area, weighted to compare S- cases from each NHS STP region and each epidemiological week with an equal number of S+ cases from that same STP and week (a case-control design), and aggregated over STP weeks. Accounting for binomial sampling variation and variation by area and week, we observe significantly more S- cases, our biomarker of VOC cases, among individuals aged 0-19 as compared to S+ cases, and significantly fewer S- cases among individuals aged 60-79 (Figure 4). This trend is seen in each of the regions of England most affected by the VOC thus far (East of England, London, South East and Midlands), and similar differences are seen between the raw (non-case control weighted, and non-age-standardised) age distributions of S+ and S- cases.
https://www.imperial.ac.uk/mrc-global-i ... 2-variant/

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Dec 31, 2020 5:51 pm


Lineage-specific growth of SARS-CoV-2 B.1.1.7 during the English national lockdown

[...]

Findings: We find strong and consistent evidence that B.1.1.7 proliferated (R>1) during the English lockdown in 87% (213/244) of lower tier local authorities with an average R value of 1.25. At the same time other lineages contracted (R<1) at an average R value of 0.85 in most regions, leading to 83% (203/244) of regions showing B.1.1.7 proliferation while other lineages diminished.

Implications: The emerging B.1.1.7 SARS-CoV-2 lineage spreads faster than its predecessors. It continued to grow during a lockdown in which other lineages shrank. These analyses suggest that stricter measures are required to contain the B.1.1.7 lineage.
https://virological.org/t/lineage-speci ... ckdown/575

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Thu Dec 31, 2020 11:52 pm

Disco mentioned this earlier:
Ms Sturgeon warned people of the "severity of the threat" in the new coronavirus strain.


She confirmed that 42.8% of positive tests analysed at the Lighthouse Laboratories were from the new strain.

Ms Sturgeon said this variant was "fast becoming the" dominant strain", adding this was a "real concern as it is thought to be significantly more transmissible".
https://www.glasgowlive.co.uk/news/nico ... e-19537548

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 01, 2021 8:13 pm

Our previous report showed relatively high rates of S gene dropout in viral samples collected from Massachusetts (MA), Ohio (OH), and FL. However, in our initial sequencing analysis, we find that these do not directly correlate with B.1.1.7 strain detection in the US. Of the samples with S gene dropout that were sequenced, only one of twelve in FL, and zero of seven in MA were B.1.1.7. We have not yet obtained viral sequences from samples in OH.

The results of this analysis highlight that while S gene dropout may be a reliable predictor of B.1.1.7 in the UK and France, it is a less specific indicator in the US today, given the current viral landscape. Furthermore, while the B.1.1.7 strain is present in multiple US states, other strains that cause S gene dropout are more prevalent in the US. However, with the overall high incidence of viral transmission and the higher transmissibility (here and here) of this strain, the proportions of different strains in the US could readily change.

Leveraging our nationwide SARS-CoV-2 testing footprint, with Illumina and the CDC, we will continue to sequence additional samples to monitor the spread of B.1.1.7 and/or the emergence of other strains in the US.
https://blog.helix.com/sars-cov-2-uk-va ... alifornia/

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Re: New Variant Covid-19 VUI 202012/01

Post by discovolante » Fri Jan 01, 2021 8:59 pm

Woodchopper wrote:
Thu Dec 31, 2020 11:52 pm
Disco mentioned this earlier:
Ms Sturgeon warned people of the "severity of the threat" in the new coronavirus strain.


She confirmed that 42.8% of positive tests analysed at the Lighthouse Laboratories were from the new strain.

Ms Sturgeon said this variant was "fast becoming the" dominant strain", adding this was a "real concern as it is thought to be significantly more transmissible".
https://www.glasgowlive.co.uk/news/nico ... e-19537548
Yes I put it in the wrong thread, sorry.

I was asking how it is spreading, mainly. From 17 detected cases in Scotland to nearly half in about a week. Schools were open during most of that period though I think. I hope we get more info soon, as there seems to me to be a difference between catching it more easily in school and say, it not being safe to go to the supermarket.
don't get any big ideas, they're not gonna happen

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 01, 2021 9:33 pm

discovolante wrote:
Fri Jan 01, 2021 8:59 pm
Woodchopper wrote:
Thu Dec 31, 2020 11:52 pm
Disco mentioned this earlier:
Ms Sturgeon warned people of the "severity of the threat" in the new coronavirus strain.


She confirmed that 42.8% of positive tests analysed at the Lighthouse Laboratories were from the new strain.

Ms Sturgeon said this variant was "fast becoming the" dominant strain", adding this was a "real concern as it is thought to be significantly more transmissible".
https://www.glasgowlive.co.uk/news/nico ... e-19537548
Yes I put it in the wrong thread, sorry.

I was asking how it is spreading, mainly. From 17 detected cases in Scotland to nearly half in about a week. Schools were open during most of that period though I think. I hope we get more info soon, as there seems to me to be a difference between catching it more easily in school and say, it not being safe to go to the supermarket.
I don’t think it was in the wrong thread. It’s a relevant in several threads.

There’s some info here on positive cases: https://beta.microreact.org/project/aik ... -in-the-uk

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Re: New Variant Covid-19 VUI 202012/01

Post by discovolante » Fri Jan 01, 2021 9:41 pm

Woodchopper wrote:
Fri Jan 01, 2021 9:33 pm
discovolante wrote:
Fri Jan 01, 2021 8:59 pm
Woodchopper wrote:
Thu Dec 31, 2020 11:52 pm
Disco mentioned this earlier:


https://www.glasgowlive.co.uk/news/nico ... e-19537548
Yes I put it in the wrong thread, sorry.

I was asking how it is spreading, mainly. From 17 detected cases in Scotland to nearly half in about a week. Schools were open during most of that period though I think. I hope we get more info soon, as there seems to me to be a difference between catching it more easily in school and say, it not being safe to go to the supermarket.
I don’t think it was in the wrong thread. It’s a relevant in several threads.

There’s some info here on positive cases: https://beta.microreact.org/project/aik ... -in-the-uk
Thanks :) not sure my phone can handle that site (although I'm not that confident about my laptop either!) So will try later!
don't get any big ideas, they're not gonna happen

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Fri Jan 01, 2021 9:46 pm

discovolante wrote:
Fri Jan 01, 2021 9:41 pm
Woodchopper wrote:
Fri Jan 01, 2021 9:33 pm
discovolante wrote:
Fri Jan 01, 2021 8:59 pm


Yes I put it in the wrong thread, sorry.

I was asking how it is spreading, mainly. From 17 detected cases in Scotland to nearly half in about a week. Schools were open during most of that period though I think. I hope we get more info soon, as there seems to me to be a difference between catching it more easily in school and say, it not being safe to go to the supermarket.
I don’t think it was in the wrong thread. It’s a relevant in several threads.

There’s some info here on positive cases: https://beta.microreact.org/project/aik ... -in-the-uk
Thanks :) not sure my phone can handle that site (although I'm not that confident about my laptop either!) So will try later!
Here’s the full statement.
Analysis done by Public Health Scotland shows that, yesterday, 42.8% of positive tests processed for Scotland in the Lighthouse Laboratory Network had the S gene drop out that is indicative of the new strain.

That is a higher than the 38% suggested by ONS analysis for week beginning 14 December. And that in turn compared to just six per cent at the end of November.

So this new strain appears to be fast becoming the dominant one in Scotland.
https://www.gov.scot/publications/coron ... mber-2020/

That’s looking bad.

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 8:10 am

Updated data from COG-UK, as well as Pillar 2 testing data from Public Health England, now show that the frequency of the variant has grown substantially in all regions of England.
[...]

The spread of this variant is now apparent from both sequencing data from COG-UK and S gene target failure data from Pillar 2 testing (Fig U1). There is a pattern of spread in two distinct phases, involving south-east England followed by the north of England (Fig U2, U3).
https://cmmid.github.io/topics/covid19/ ... date_1.pdf

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Re: New Variant Covid-19 VUI 202012/01

Post by Woodchopper » Sat Jan 02, 2021 8:16 am

The new variant has, or is becoming, the dominant variant across England and Scotland.

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