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Alpha B.1.1.7 Variant of COVID19 coronavirus thread

Genetics experts worry coronavirus vaccines might not work quite as well against UK variant
By Elizabeth Cohen, CNN Senior Medical Correspondent
Updated 10:28 PM ET, Wed December 23, 2020

(CNN)Michael Worobey, a biologist at the University of Arizona, has seen more than 100,000 different strains of the virus that causes Covid-19. But when he saw the new variant from the UK, he noticed something different.

"This is the first variant I've seen during the whole pandemic where I took a step back and said: 'Whoa,' " he remembers.
Health officials have downplayed the possibility that the coronavirus vaccines won't work against the UK strain, but Worobey and other scientists thinks it's a possibility -- and it's just a possibility -- that this new variant might, to a small extent, outsmart the vaccines.

<snip>

https://www.cnn.com/2020/12/23/heal...es-less-effective-prevent-covid-19/index.html
 
New COVID variant reaches Germany from UK

Date 24.12.2020

German authorities on Thursday confirmed the presence of the new coronavirus variant on German soil, adding to fears that the it could start spreading beyond the UK and South Africa.

A woman who flew in from London Heathrow this Sunday tested positive at the Frankfurt airport. Further genetic analysis of the sample at a lab in Berlin identified a case of B.1.1.7, as the variant is known, said authorities in the German state of Baden-W?rttenberg in a statement.

"It is the first known case in Germany," they said.

https://www.dw.com/en/new-covid-variant-reaches-germany-from-uk/a-56054140
 
Interesting thread on S gene dropouts in PCR tests that are increasing in the US. Indicative that the B.1.1.7 variant may be
present as it has this effect on PCR tests. The UK used the same technique to track the variant there.
- we observe S gene drop out since mid October in US. Up to 0.5% last week.
t looks like the highly contagious UK COVID-19 variant (B.1.1.7) is probably undergoing community
transmission in at least MA, OH, and FL, based on prevalence of S-dropout tests increasing over
time. If the 0.25% increase is representative, that’d be ~500 cases/day vs. UK’s 15k.
----------------------------------------------------------------------------------------
Two new sequences of B.1.1.7 lineage from Hongkong and one from Israel. One of the genome
from Hongkong doesn't have HV69-70 and Y144 deletion (GISAID: EPI_ISL_733577).
-----------------------------------------------------------------------------------------
that looks as if it was imported through the tunnel
https://twitter.com/DrEricDing/statu...596544/photo/1
--------------------------------------------------------------------------------------------
 
CDC (USA) to Require Negative COVID-19 Test from Air Travelers from the UK since Dec.28
 
Look at the time. 11:09 PM



From: "Media@cdc.gov (CDC)" <sohco@CDC.GOV>
To: MMWR-MEDIA@LISTSERV.CDC.GOV
Subject: CDC Media Statement: CDC to Require Negative COVID-19 Test from Air Travelers from United Kingdom
Date: Dec 24, 2020 11:09 PM



Media Statement

For Immediate Release
Thursday, December 24, 2020
Contact: CDC Media Relations
(404) 639-3286

CDC to Require Negative COVID-19 Test from Air Travelers from the United Kingdom


Today, President Trump is taking another step to protect the health of the American people by requiring air passengers arriving from the United Kingdom (U.K.) to test negative, via PCR or Antigen test, no more than 72 hours before departure from the U.K. to the United States.

The public health authorities in the United Kingdom recently announced the discovery of a new variant of SARS-CoV-2. Viruses constantly change through mutation, and preliminary analysis in the U.K. suggests that this new variant may be up to 70% more transmissible than previously circulating variants.

On March 14, President Trump issued a Presidential Proclamation to suspend the entry of foreign nationals who visited the United Kingdom in the past 14 days. This has reduced air travel to the U.S. from the U.K. by about 90%. This additional testing requirement will fortify our protection of the American public to improve their health and safety and ensure responsible international travel. The order is consistent with existing CDC testing guidance and U.S. Department of Transportation / Federal Aviation Administration guidance in the “Roadway to Recovery” document.

This new order is consistent with the measures that have been taken so far to increase our ability to detect and contain COVID-19 proactively and aggressively.

Passengers are required to get a viral test (i.e., a test for current infection) within the 3 days before their flight from the U.K. to the U.S. departs, and provide written documentation of their laboratory test result (in hard copy or electronic) to the airline. Airlines must confirm the negative test result for all passengers before they board. If a passenger chooses not to take a test, the airline must deny boarding to the passenger.

This order will be signed tomorrow, December 25, and become effective on December 28, 2020.
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sharon sanders said:
Look at the time. 11:09 PM



From: "Media@cdc.gov (CDC)" <sohco@CDC.GOV>
To: MMWR-MEDIA@LISTSERV.CDC.GOV
Subject: CDC Media Statement: CDC to Require Negative COVID-19 Test from Air Travelers from United Kingdom
Date: Dec 24, 2020 11:09 PM



Media Statement

For Immediate Release
Thursday, December 24, 2020
Contact: CDC Media Relations
(404) 639-3286

CDC to Require Negative COVID-19 Test from Air Travelers from the United Kingdom


Today, President Trump is taking another step to protect the health of the American people by requiring air passengers arriving from the United Kingdom (U.K.) to test negative, via PCR or Antigen test, no more than 72 hours before departure from the U.K. to the United States.

The public health authorities in the United Kingdom recently announced the discovery of a new variant of SARS-CoV-2. Viruses constantly change through mutation, and preliminary analysis in the U.K. suggests that this new variant may be up to 70% more transmissible than previously circulating variants.

On March 14, President Trump issued a Presidential Proclamation to suspend the entry of foreign nationals who visited the United Kingdom in the past 14 days. This has reduced air travel to the U.S. from the U.K. by about 90%. This additional testing requirement will fortify our protection of the American public to improve their health and safety and ensure responsible international travel. The order is consistent with existing CDC testing guidance and U.S. Department of Transportation / Federal Aviation Administration guidance in the “Roadway to Recovery” document.

This new order is consistent with the measures that have been taken so far to increase our ability to detect and contain COVID-19 proactively and aggressively.

Passengers are required to get a viral test (i.e., a test for current infection) within the 3 days before their flight from the U.K. to the U.S. departs, and provide written documentation of their laboratory test result (in hard copy or electronic) to the airline. Airlines must confirm the negative test result for all passengers before they board. If a passenger chooses not to take a test, the airline must deny boarding to the passenger.

This order will be signed tomorrow, December 25, and become effective on December 28, 2020.
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Click to expand...

Too late.
 
> My husband and I oversee a few labs with high volume Covid testing.
> We have been watching for S gene drop-outs in the tests that we know
> don’t cover the S gene in B.1.1.7 but would detect ORF1ab and N gene.
> None detected by far in our US-based labs. It’ll be here soon.
------------------------------------------------------------
I wonder what that dropout means, is it like this 218-"deletion" that we see in
>England/ALDP-C497BF/2020,UK,UK-ENG,2020-12-12,50,B.1.351,1.0,G,N,L,A,Y,Y,T,P,Q,ref
{South Africa -variant}
at position 22323-22540 ? the other 2 deletions are at 11288-11296 and 22281-22289
---------------------------------------------------------
when the dropout is easy to detect, that may be a method to find and eliminate the
new English variant, {but not the others in South Africa, Nigeria? and all the future ones ?!}
-------------------------------------------------
 
Last edited:
@Cedders68
Should a PCR test be developed to look specifically for the 501Y spike RNA?
That would allow batch testing for the new variant among multiple samples where
occurrence of the variant is low? S drop-out doesn't
----------------------------------------------------------
 
New variant report 2020-12-27

Data source and processing

All whole genome SARS-CoV-2 sequences were pulled from GISAID at 2020-12-27 12:19 GMT. The genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.

The sequences were then assigned lineages with pangolin v2.1.3, pangoLEARN version 2020-12-17.

Pangolin assigns B.1.1.7 to sequences with more than 4 of the 17 defining B.1.1.7 SNPs – defined here – and B.1.351 to any sequences with more than 3 of the 5 defining B.1.351 SNPs.

https://cov-lineages.org/global_report.html
 
@alanmcn1
Our % positive has jumped from 2 to 8 % over Xmas weekend.
S drop out sitting at 80% of those positives
(Birmingham)
 
Update: New UK, South African variant Covid strains detected in Finland

Three people have been diagnosed with two different strains of the virus.

Three people who recently returned to Finland from abroad have been diagnosed with new strains of the coronavirus, according to a joint press release from the Ministry of Social Affairs and Health (STM), the Finnish Institute for Health and Welfare (THL) and the Helsinki University Hospital District (HUS).

Two of the infections are a variant of the coronavirus that was recently identified in the UK and one has been confirmed to have been infected by the variant found in South Africa.

The strains were identified in a collaboration between the HUS and the virology laboratories of the University of Helsinki.

According to the joint statement, the infected patients are presently in good condition and are being treated in isolation. People who may have been exposed to the new virus variants have been quarantined and have been asked to undergo a coronavirus test.

<snip>

https://yle.fi/uutiset/osasto/news/...nt_covid_strains_detected_in_finland/11716211
 
@theosanderson
https://assets.publishing.service.g...cal_Briefing_VOC202012-2_Briefing_2_FINAL.pdf
S dropout now appears a very good indication of B.1.1.7 in all regions.
Roughly a third of swab tests are carried out with the TaqPath assay that serendipitously
allows this S dropout detection of B.1.1.7.
No differences seen in reinfections (small N in each case)
Big increase seen in secondary attack rate, consistent with increased transmission
(And an impressively powered analysis)
---------------------------------------------
@youyanggu
I estimate that by the end of January, just 2% of the US population will have gained
full immunity by vaccination alone
---------------------------------------------------------
@TWenseleers
More infectious SARS-CoV2 VOC 202012/01 strain is spreading at a similar rate across
the whole UK. Clearly not a founder effect. >90% of all infections will be by this strain
across the UK by February 1st.
------
The study also calculated that either much stricter measures (such as prolonged remote
education) or vaccinating 0.4% of the whole population per day would be required to contain it.
The severity & infection fatality rate is most likely similar to that of the original type.
-----------
 
@HewittPete
This is worth watching. So far Denmark - which has a superb virus sequencing programme -
isn't seeing B117 growing faster than other lineages. T
-----------------------------------
 
> Three people have been diagnosed with two different strains of the virus.

no double-infections, but just 3 people with a new lineage
-----------------------------------------------------------------
UK's new COVID-19 variant found in Nigeria, scientists say
-------------------------------------------------------------
 
Last edited:
TWiV700,
02:40 , PHE technical briefing #2 ,
0900 wild-type def.
11:00 transmissible
16:07-16:59 silent = censored ? ,
1800 "allegedly" ,
{so proud he(VR) found a new word to obfuscate probability estimates ...
also "may" - but not "proof" , he is OK with possible (likely?) -but not proven-
increased transmissibility of b117}
25:00 never seen in an outbreak a virus becomes more and more transmissible
doesn't make sense to me
{but that's what usually happens, IMO, see seasonal flu}
41:00 immunocompromised
47:20 Daniel Griffin ... different topic
 

MRC Centre for Global Infectious Disease Analysis

Dec 31, 2020
UPDATE #COVID19 new variant VOC202012/01 in England

VOC growing rapidly

Transmission advantage for VOC of 0.4 to 0.7 difference in reproduction number compared to non-VOC variant

VOC affecting a greater proportion of under 20s

Report https://imperial.ac.uk/mrc-global-infectious-disease-analysis/covid-19/report-42-sars-cov-2-variant/…


11m
Prof
@axel_gandy
on
@BBCRadio4
this morning speaking about the latest report on the new #SARSCoV2 variant of concern in England

https://bbc.co.uk/sounds/play/m000qnj6… (from 48:15)
@imperialcollege
Quote Tweet
vAvGCtjF_normal.jpeg

MRC Centre for Global Infectious Disease Analysis

Dec 31, 2020
UPDATE #COVID19 new variant VOC202012/01 in England

VOC growing rapidly

Transmission advantage for VOC of 0.4 to 0.7 difference in reproduction number compared to non-VOC variant

VOC affecting a greater proportion of under 20s

Report https://imperial.ac.uk/mrc-global-in...ariant/…
 
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