nCoV_info

https://flutrackers.com/forum/forum/europe-aj/europe-covid-19-sept-13-2020-may-31-2021/901351-england-new-variant-of-covid19-coronavirus-may-be-causing-faster-spread-in-some-areas-december-14-2020-wales-scotland-denmark






twitter-thread from @Chjulian , translated from Spanish :

 Update: Headlines announce the identification of a "new variant" of the coronavirus in the UK.
 It is not clear if the new variant is responsible for the increase in cases.
However, this variant is interesting. And here I tell you why 37 / n
@Chjulian
·
First, we need to understand that our immune system uses specialized mechanisms
to recognize and eliminate the virus, preventing its spread and ending disease.
The infectious period is the time in which we can transmit SARS-CoV-2 to another person

In the case of COVID19, the infectious period begins a couple of days before symptoms
develop and can last up to a couple of weeks (more details here https://bmjopen.bmj.com/content/10/8/e039856
). The disease is generally acute, short-lived bone 39 / n

An Immunocompetent individual has a normal
immune response. When our immune
system is weakened, we say it is immunosuppressed. Immunosuppressed individuals
may have persistent infections that last for longer periods of time (months!) 40 / n

Under these conditions, SARS-CoV-2 can accumulate many more mutations than we
would expect (in a single individual) and which could be transmitted if the transmission
is successful after a long time 41 / n

Remember that it is normal for viruses to mutate and SARS-CoV-2 accumulates
(on average) one or two mutations per month at the population level 42 / n
[##  1.43 per month , ua5m1.gif {gsgs} ]

The new variant (named B.1.1.7) has 17 mutations (woah!). And it is speculated that
it could have originated in an individual with a persistent infection (for example,
an immunosuppressed individual, but we have no information about it) 43 / n

It is important to mention that our immune system goes to the battlefield as quickly
 as possible to avoid an arms race at the molecular level, reducing the chances that
the virus will produce a mutation that allows it to evade our immune response 44 / n

If the hypothesis turns out to be true, it can have important consequences for treatment.
 A persistent infection accumulates diversity and depending on how we treat it, we may
or may not cause an arms race at the molecular level 45 / n

That is, to select mutations with unknown epidemiological potential. There is no need
 to be alarmed, I just want to show how we scientists must think and articulate our strategy
to face the battle in the short, medium and long term 46 / N

Nor can we say that a persistent infection in an immunosuppressed individual is a
greater problem than infections in immunocompetent individuals. Definitely the
evolutionary forces that "moderate" the evolution of the virus are different and ... 47 / n

... we hope that the origin of B.1.1.7 was somewhat unusual and had nothing to do
 with the increase in cases (studies continue). There is also a second hypothesis
(with less support) to explain why this variant has so many 48 / n mutations

Are you sure they remember minks? there is always the slim chance that SARS-CoV-2
will adapt to other mammals (By the way, there are no minks on farms in the UK),
but a prolonged epidemic ... 49 / n

... in the fauna around us it could result in new genetic variants that could (after a while)
jump to humans with various mutations. For this and other reasons, it is important to
evaluate what is happening at the level of the fauna around us 50 / n

t really amazes me how much we learn and the twists and turns a sprout can take! 51 / n

Fortunately, there is no evidence (to date) that this variant has an impact on the severity
of the disease or on the effectiveness of 52 / n vaccines.

2020/11/03 , genbank release 240 , Oct.15 is available

https://ftp.ncbi.nlm.nih.gov/genbank/gbrel.txt

release 239 from Aug2020 had 39 virus files with 17491 MB and 3161686 sequences and 5824026918 Bases
   and 50462 coronavirus nucleotide sequences
release 240 from Oct2020 has 44 virus files with 18889 MB and 3223498 sequences and 6442230159 Bases
   and 68651 coronavirus nucleotide sequences 33844 of which are SARS2

how to make members mods,admins
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permissions
click the number in the Members column
to add more members to that group

they have an unusually high percent of positives in UK, >40%  [only in England ?? Wales,Scot,NI]
compare with Italy,Czech,Poland,Austria :
http://magictour.free.fr/PR-0416.GIF

ONS reports weekly deaths from all causes
https://data.gov.uk/dataset/1cf2c6d1-b69b-4122-94ce-006202c323ba/weekly-provisional-figures-on-deaths-registered-in-england-and-wales

weekly provisional deaths in England and Wales
-11-,-12-,-13-,-14-  , week (mar7-apr3)
2725,2709,2786,3865, at home
4975,4770,5105,7884, hospital
0553,0551,0504,0554, hospice
2471,2335,2489,3769, care home
0044,0043,0033,0053, other communal
0249,0238,0225,0272, elsewhere

from COVID
0,1,15,120,at home
5,100,501,3110,hospital
0,0,2,31,hospice
0,2,20,195,care home
0,0,0,3,other communal
0,0,1,16,elsewhere


~2000 additional deaths at home or care home
so, add 65% to the normal COVID-reported deaths
in total deaths in England and Wales were 16397/11142 = 47% increased in week 14
this should go up in weeks 15,16 and then slowly decline.
Total excess deaths ~50000 in this wave
-----------edit----------
well, IHME is down today (2020/04/17/05:30-UTC) to 23791, [it was >60000 on Apr07]
plus 47% would be ~35000 for the UK
https://covid19.healthdata.org/united-kingdom
------------------------

In Milan or NY it was ~100% increased , in Bergamo ~500% in the peak-weeks

COVID-sequences links :
Nov20,40432+107300+631

https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049&SeqType_s=Nucleotide
https://www.cogconsortium.uk/data/
https://civnb.info/sequences/
http://www.insdc.org/
https://www.ebi.ac.uk/




-------------------------------------------------------------------------------
other links :
(https://www.viprbrc.org/brc/home.spg?decorator=vipr).

flu : https://www.ncbi.nlm.nih.gov/genomes/FLU/Database/nph-select.cgi?go=database

releases : https://ftp.ncbi.nih.gov/genbank/gbrel.txt



----------------------------------------------------------------
582 COVID-19 sequences (507 of these full genome) downloaded on Apr11 from :
[615 on Apr12)
(876 on Apr14 , 795 full)+102 full German ones from Drosten-tweet s.u.
(1207 on Apr21)

https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?VirusLineage_ss=Severe%20acute%20respiratory%20syndrome%20coronavirus%202,%20taxid:2697049&SeqType_s=Nucleotide

386 from USA , (earliest from Jan19, IL-Jan21,CA-Jan22,WA-Jan25
94 from China , (66 full , earliest from Dec.23
25 from Spain (earliest Feb26 ,
17 from Iran , (2 full, earliest Mar09
6 from Italy , (1 full, Jan30
...

dates = symptom-onset ?


mutation-picture : http://magictour.free.fr/sars2-4.GIF
rows are viruses , columns are RNA-nucleotide-positions , black pixels are mutations
horizontally and vertically sorted so to give maximum black connected components

community-spread in Washington State since at least Jan19,
one day before Zhong Nanshang raised the alarm on Chinese TV
and 4 days before Wuhan lockdown !

Jan19 was sample-collection, sequence-release date was Mar26
another sequence from WA , Jan25, release date Feb05
also already with that C27969T (my current enumeration) - mutation typical for WA

MN985325 , https://wwwnc.cdc.gov/eid/article/26/6/20-0516_article
China-traveler , symptom-onset = Jan16 , sampled Jan19 , USA-WA , genbank Mar27
https://www.ncbi.nlm.nih.gov/nuccore/MN985325
had already the C27969T mutation

---------------------------------------------

Apr05 ,  Locatelli:
>  it is essential to continue to comply with distance measures. Without it, we would have
> had 30 thousand more deaths  [instead of just 15000 official COVID-19-deaths,
6fold mortality in Mar in Bergamo]
---------------------------------------------------------------
Apr.07 , Chris Murray , UofWA  Institute for Health Metrics and Evaluation
deaths in the hundreds of thousands , peak on Apr16
estimates fewer total deaths than last week.
It assumes that strict social-distancing methods which flattened the curve in other parts
of the world will be adhered to in the U.S. Studies t
https://covid19.healthdata.org/united-states-of-america
81766  COVID-19 deaths  projected by August 4, 2020
----------------------------------------------------------------
Fox News reporter John Roberts , Apr15
Multiple sources are telling Fox News today that the United States now has high confidence that,
while the coronavirus is a naturally occurring virus, it emanated from a virology lab in Wuhan, that,
because of lax safety protocols, an intern was infected, who later infected her boyfriend, and then
went to the wet market in Wuhan, where it then began to spread,”
------------------------------
Ebright,Apr15
 “The first human infection could have occurred as a natural accident, with a virus passing from
bat to human, possibly through another animal. But the first human infection also could have
occurred as a laboratory accident, with a virus accidentally infecting a laboratory worker.”
--------------------------------
 Ebright, Jan25
“at this point there’s no reason to harbor suspicions” the lab may be linked to the virus outbreak.
-----------------------------
----------------------------------------------------------------------------
Apr30 , Trump:
I think that the World Health Organization should be ashamed of themselves because
they are like the public relations agency for China,
The US pays WHO almost $500 million a year and China pays them $38 million a year,
Whether it's a lot more, it doesn't matter. They shouldn't be making excuses when people
make horrible mistakes, especially mistakes that are causing hundreds of thousands
of people around the world to die.
----------------------------------------------------------------------
Apr30 , Pompeo
The World Health Organization simply failed to respond in this case... With respect to
the WHO, we know that they had one job, right? A single mission: To prevent the spread
of a pandemic. We know that the leader of that organization travelled to China and then
declined to declare it a pandemic until everyone in the world knew that was already true,
 

UK-"dashboard" , data from regions , download


https://www.arcgis.com/apps/opsdashb...0b19484dd4bb14
https://fingertips.phe.org.uk/docume...rd%20Data.xlsx


English charts , 8 regions relative to the average :

http://magictour.free.fr/e-0403a.GIF

you can see, how London bends down 5 days after they changed the strategy