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Discussion thread VI - COVID-19 (new coronavirus)

#85 Norway

Clarification: "The changes in the outbreak virus from Trondheim are different from the changes seen in the virus from the tourist bus from Rogaland and we are not talking about the same variant of the virus."

https://www.fhi.no/nyheter/endringer...fra-trondheim/

Added: Podcast from FHI dated 14.10.20 "The virus from the people in the bus tour has a mutation that makes it more infectious - only 6% of known mutations have an alteration of this particular spike and this is a change that is important to observe, it helps the virus to bind better to cells and give more infection. Few publications still about this mutation " They are going to observe 2 types of the virus in a lab, one without the mutation of the spike - the other with the mutation and see if one will at some point outgrow the other, indicating better adaption of one type or the other.

https://shows.acast.com/folkehelsepodden/episodes/mutasjon-i-koronaviruset
 
I checked genbank some days ago, most recent USA from Sep19
most recent non-USA were ca.10 from Malta from Sep07
https://www.ncbi.nlm.nih.gov/labs/v...navirus 2, taxid:2697049&SeqType_s=Nucleotide
The biggest sequence database is England with >48000 sequences, last update from Sep03.
https://www.cogconsortium.uk/data/
Charite/Germany has 491 sequences, latest are 1 from Sep28 and 1 from Sep25
https://civnb.info/sequences/
http://magictour.free.fr/sars2de4.ll1 {save it, open with editor, fixed character size, long lines)
mutation picture : http://magictour.free.fr/sars2de4.GIF
 
Toaster2 said:
But - and this is pure speculation - there is also something funny with the Argentina numbers (on Worldometer). Please check how the numbers of infected vs deaths deviate from each other over the last month or so. Is this a new strain taking over, hence the mortality gap ? Or is it just bad reporting of deaths ?
Click to expand...

there was a big backlog some weeks ago in Argentina, earlier deaths reported on one day
 
https://www.reuters.com/article/us-...BN2760NA?utm_medium=Social&utm_source=twitter

Deaths after flu shots in S.Korea fan fears, but authorities find no link

By Sangmi Cha

3 MIN READ

SEOUL (Reuters) - Nine people have died after getting flu shots in South Korea in the past week, raising concerns over the vaccine’s safety just as the seasonal inoculation programme is expanded to head off potential COVID-19 complications.
...
Five new deaths were reported on Wednesday alone, but authorities had no plans to suspend the vaccination programme, unless investigations, including post mortems, revealed a link, which preliminary findings had not.
Click to expand...

Not sure how much information they are going to gain from doing post mortems. Very surprised that they are forging ahead - when the covid trials are halted for illness.
 
This case could have been from loss of cold chain.

https://www.koreatimes.co.kr/www/nation/2020/10/113_297831.html
"The 17-year-old boy in the western port city of Incheon, whose identity has been withheld, died early Friday morning after receiving the flu shot on Wednesday, according to the Korea Disease Control and Prevention Agency (KDCA).

The KDCA said he was administered with one of the vaccine bottles that were shipped by Shinsung Pharm Co., a distributor of some vaccine bottles that were exposed to room temperature during shipments as part of a nationwide free flu shots program."
 
Steffi thanks for the update so now we have some information to work with.

The S S477N sequence (Norway/392/2020) is now up at Nextstrain and shows one additional AA change ORF1a L1507F but is otherwise the same as a number of other European sequences.
Norway1.JPG

The screenshot, from Nextstrain, shows Norway/3992/2020 (collection date 21 Sept. 2020) and the other sequences with S477N on this branch. In total there are a little over a hundred N447 and about 3500 S447 sequences at GISAID the bulk from Australia going back to mid March. A look at the whole phylogenic tree shows the S477N change holding its own but not out performing the wild type, it falls within the RBD.

S N439K falls outside the RBD and I can only find 6 one old one in the US and 5 from Ireland.
 
Thanks JJackson - it's interesting to see and to follow this one as Folkehelseinstituttet in Norway says symptoms develop in just 2 days.
 
that's S7579N in my amino-acid-encoding with 13 coding regions
nucleotides G22992A in the SARS2-consensus ACACACCTTG

2 German sequences :
>Berlin/570067245716,08-16,14,K1895R,M3087I,A4582S,P4720L,V5173L,K5547R,E5590D,A5775S,G5974V,S7579N,D7716G,Q8433H,M9535I,A9677T
>Ploen/ChVir8607,08-24,13,M3087I,L3606F,A4582S,P4720L,V5173L,K5547R,E5590D,S7579N,D7716G,Q8433H,M9535I,A9677T,R9686K

96 out of the 48561 from UK <Sep03 have it
and 3732 out of 24923 from my last genbank download from Sep29 , 3694 of these from Australia
Lebanon,Mar20
Florida,Apr12
Mass.Mar28
 
Steffi as gs and I have pointed out this Spike change is not new and has not been linked to rapid disease progression anywhere else. The S RBD to ACE2 binding has always been good and is therefore probably not under much selection pressure. The one change that is unique to this sequence is the ORF1a change, if this effects suppression of the host innate response in anyway then that is more likely to change the speed at which the virus gains control. I still think the most likely explanation is that this is not a genetic change with any real effect but the small sample size does not have the power to distinguish genuine change from a random cluster of cases at the lower end of the normal range.
 
this is as in 1918 , with the October wave , except that lethality is currently still low.
But ununderstood.
But unstoppable.
I'm not even sure, if lockdowns still work, Israel's lockdown stopped the "old outbreak"
not the new "October-Europe-surge"

It's mainly in Europe, but I would be surprised when it won't go around the world.
It could be related to the cold-spill in Europe on Sep.26 , but I'm not sure.

e..g. why didn't Vienna,Norway,Denmark get it (yet) , French departments

--------------------------------
they should quickly analyze this, collect the weather-data and compare with the
case-counts in Sep,Oct for big cities, for regions
I could do it, but lots of data, takes long, the task should be shared.
It's importantant to know this soon, whether it depends on cold-spills
 
Last edited:
Gsgs, for the Netherlands it might be clearest. We had an initial surge that paused for two weeks after we had better weather, before it went up into the second wave when the weather turned again
 
gs the epi-curves fro Norway, Denmark and Austria are all climbing rapidly, much like the rest of Europe.
 
Please see:

US - Important measurements of COVID-19 coronavirus situation is the trend in hospitalizations, ICU cases, deaths - 7 day moving average hospitalizations & deaths are climbing - October 23, 2020

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

There is a lot of media play about 82k new cases today.....it might as well be 100k, 110k...200k....whatever....we have 330 million people in the US. The most important numbers to follow are the hospitalizations, ICU cases, and deaths. One faulty lower testing day and the numbers will artificially give the impression that the case load is less. And conversely, a lot of testing will serve to discover what we already know - we are in a pandemic that is sweeping the world.

Assume everyone and every surface is positive for the SARSCoV2 virus.

Act accordingly.

Take care.
 
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