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Discussion thread VI - COVID-19 (new coronavirus)

OK - This is an uncomfortable discussion, but one that needs to be had.

Today I came across this article about Manaus in Brazil.

Covid-19: Brazil hospitals 'run out of oxygen' for virus patients
https://www.bbc.co.uk/news/world-latin-america-55670318


Hospitals in the Brazilian city of Manaus have reached breaking point while treating Covid-19 patients, amid reports of severe oxygen shortages and desperate staff. The city, in Amazonas state, has seen a surge of deaths and infections. Health professionals, quoted by local media, warned "many people" could die due to lack of supplies and assistance.


Now, as many of you may remember, Manaus was a major 'epicentre' for Covid back in March / April 2020. Manaus is a city with a population of @1m in a highly isolated area within the Amazon. Subsequent serology testing showed an estimated 76% of the population of this city had been infected during this first 'wave', so, if herd immunity existed anywhere on the planet, it was most likely here. Now whilst it is possible or even likely that this new outbreak is down to the new 'Brazil' mutated variant, it also shows that it is very likely that herd immunity is not an achievable goal. We would need a universal Covid vaccine, and that is at minimum, a few years away - if not longer. Scientists have been working on one of these for influenza for @ 2 decades now..

In one form or the other Covid is here to stay, and based on the above information, it is highly probable that annual vaccination is going to be required...

See https://www.the-scientist.com/news-o...rs-cov-2-68272

Given that with major efforts and a halt to economies with lockdowns it is going to take until 2022 at least (and in other countries with more limited supplies, even longer) to vaccinate everyone, then it isn't going to practical for entire national strategies to rest solely on vaccination. Vaccinating annually on this scale just isn't possible, and unless it is simultaneously done around the globe, all we will do is keep generating vaccine escape variants. We dont yet have data on how many of these hospital cases are re-infections, whether these are the same, less severe or more severe... but if hospitals are overwhelmed again, it doesn't look so good.

Also not yet factored in is the huge burden and potentially huge numbers of years of life lost that Long Covid is going to cause - it may dwarf mortality rates. The data is now pretty clear that lung damage from infections (and not just severe ones) is extensive, the numbers of people with major kidney damage etc etc is enormous. The burden to national health systems is... well, its too early to give estimates, but most certainly will be massively impactful.

Therefore, in view of all of this, it suggests to me that the longer term strategy has to evolve towards other arms of prevention in association with vaccination - nations need to be promoting self help, actively encouraging people to look after their immune system health by all means available (exercise, sleep, supplements especially zinc and vitamin D) as the data seems to point to an effective and early innate immune response limiting infection severity, and the pharmaceutical industries focus now needs to turn to early low cost intervention for mass annual usage - things that can stop the infection early, and in its tracks. We dont know enough as yet about SARS-Cov-2 virus to predict potential future mutations as we do for selecting flu strains for jabs, and vaccines are always going to be playing 'catch up'. We dont understand enough about cross immunity (or a lack thereof) to pin all our hopes that vaccination against strain A might help to limit the severity of a strain that evades the vaccine *especially* when these are limited to spike protein.

We need a rethink IMHO.
 
Universal mask use may be here to stay for some years I think.. Whilst not a panacea, its a case of the 'every little improvement' helps..
 
otoh Bergamo had much less COVID in wave 2 than e.g. Milan
Code:
           pop        dr                           Dec05  Jan10
Bergamo,  1115,6120 ,347 ,15380 , 7340  9377       25796  29224  10416   9340   .55% .03%   .58
Cremona,   359,2037 ,277 , 6811 , 4651  5887       13254  15167   6443  17950
Lodi,      230, 942 ,233 , 3699 , 3830  5063        9247  11085   5548  24120
Brescia,  1266,4391 ,211 ,16492 ,13283 17289       35682  45992  19190  15160   .35% .05%   .40
Piacenza,  287,1197 ,185 , 4675 , 5199  7095       12545  16140   7870  27420
Parma,     452,1348 ,151 , 3946 , 4275  5879       10677  13660   6731  14890

Lecco,     337, 838 ,148 , 2983 , 6249  8077       11718  14048   8735  25920
Pavia,     546,1511 ,128 , 5765 ,10942 13863       21027  26124  15262  27950
Mantova,   412, 830 ,105 , 3984 , 5660  7894       12884  17998   8900  21600
Pesaro,    359, 666 ,100 , 2943 , 1963  2863        6619  10967   3676  10240

Monza,     874,1229 , 95 , 6149 ,29350 35726       44381  49717  38232  43740
Milan,    3250,4871 , 91 ,26293,100942 123919     157873 179981 131580  40490   .15% .12%   .27
Torino,   2260,1722 , 40 ,16400 ,57294             93804 108648  92082  40740
Bologna,  1015, 636 , 33 , 6067 ,14597             28651  43349  28015  27600

province,
population in 1000
excess deaths week1-17,2020
excess deaths in % of usual deaths
COVID-cases Jan01-Aug31
COVID-cases Sep01-Nov18
COVID-cases Sep01-Nov28
COVID-cases Jan01-Nov28
COVID-cases Sep01-Nov28
COVID-cases Sep01-Nov28  / million population





Alessand,  903 , 85 , 4172 , 7504 
Biella,    345 , 82 , 1076 , 3642 
Sondrio,   288 , 79 , 1634 , 3289 
Vercelli,  307 , 78 , 1555 , 3522 
Novara,    504 , 77 , 3007 , 6925 
Trento,    609 , 72 , 5096 , 8165 
Reggio'Em, 646 , 72 , 5314 , 8716 
Como,      729 , 70 , 4365 ,17302 
Bolzano,   463 , 62 , 2935 ,15750 
Genova,   1164 , 57 , 5928 ,21106 
Rimini,    313 , 56 , 2363 , 4962 
Aosta,     134 , 55 , 1235 , 4274 
Imperia,   279 , 54 , 1576 , 3165 
Verbano-,  179 , 53 , 1182 , 2896 
Asti,      230 , 51 , 1919 , 4304 
La Spezia, 242 , 46 , 1087 , 4778 
Varese,    693 , 45 , 4181 ,30508 
Modena,    546 , 44 , 4334 ,12376 
Torino,   2260,1722 , 40 ,16400 ,57294             93804  92082  4074
Verona,    550 , 37 , 5602 ,15012 
Savona,    253 , 36 , 1791 , 3326 
Cuneo,     397 , 34 , 3104 ,14174 
Bologna,   636 , 33 , 6067 ,14597 
Ancona,    266 , 33 , 1937 , 5322 
Treviso,   416 , 31 , 3939 ,17375 
Pescara,   181 , 31 , 1694 , 2630 
Massa,     135 , 30 , 1228 , 4205 
Sassari,   170 , 28 , 1353 , 5128 
Forl,      209 , 27 , 2059 , 4464 
Macerata,  165 , 26 , 1216 , 4119 

province,
excess deaths week1-17,2020
excess deaths in % of usual deaths
COVID-cases Jan01-Aug31
COVID-cases Sep01-Nov18

Italy provinces with >25% excess deaths in weeks 1-17 , 
itatot4.png , 
eurostat,destatis,ons,nrs,nisra,ircii,cbs



London,          9814,80
West_Midlands,   7113,53
North_West,      8575,49
North_East,      3064,45
East_of_England, 6214,44
South_East,      8480,42
Yorkshire_Humber,5319,41
East_Midlands,   4244,38
Scotland,        4875,35
Wales,           2256,27
South_West,      3687,26
Northern_Ireland, 895,23


Bergamo  Italy  6120 347 2020-04-26  116
Cremona  Italy  2037 277 2020-04-26   90
Lodi     Italy   942 233 2020-04-26   78
Brescia  Italy  4391 211 2020-04-26   70
Piacenza Italy  1197 185 2020-04-26   62
Parma    Italy  1348 151 2020-04-26   50
Lecco    Italy   838 148 2020-04-26   49
CMadrid  Spain 14073 128 2020-06-14   50
Pavia    Italy  1511 128 2020-04-26   43
Mantua   Italy   830 105 2020-04-26   35
Milan    Italy  4871  91              30

Excess deaths country by country
Country 
Deaths since start of pandemic 
Expected deaths 
Excess deaths 
Excess (%) 
Latest date 
First week with excess

Spain       148940 105755 43185  41 Jun14 11
Belgium      29683  21216  8467  40 May17 11
Italy       149504 106881 42623  40 Apr26 09
Netherlands  41350  31767  9583  30 May24 11
Sweden       23373  18609  4764  26 May31 12
France      163009 135485 27524  20 May31 11
Luxembourg     671    562   109  19 Apr26 11
Portugal     25618  22708  2910  13 May24 11
Switzerland  16292  14934  1358   9 May31 11
Germany     168535 160757  7778   5 May17 12
Finland      11923  11411   512   4 May24 11
Czechia      13475  13140   335   3 Apr19 11
Denmark      14724  14598   126   1 Jun07 10
Lithuania    11470  11766  -296  -3 Jun07 09
Slovakia      9333   9646  -313  -3 Apr26 09
Bulgaria     23464  24775 -1311  -5 May31 11
Iceland        531    569   -38  -7 May31 10
Norway        9728  10932 -1204 -11 May31 10
 
Covid: 'Convalescent plasma no benefit to hospital patients'

By Philippa Roxby
3 hours ago

A potential treatment for Covid using blood plasma does not reduce deaths among hospital patients, trials show.

The results are a blow to researchers and the NHS, which led the drive to collect plasma donations.

This arm of the Recovery trial, which is investigating a number of promising Covid treatments, has now been closed.

The Oxford researchers involved say they are "incredibly grateful" for the contribution of patients across the country.

Donations of plasma have been temporarily suspended, according to NHS Blood and Transplant.

https://www.bbc.com/news/health-556...n=64&at_medium=custom7&at_custom1=[post+type]
 
Human Vaccines Project
HPV Covid Report

Can Changing COVID Vaccine Regimens End the Pandemic Faster?

January 15 2021
By Kristen Jill Abboud

With SARS-CoV-2 still infecting, sickening, and killing a staggering number of people worldwide, and only limited quantities of recently authorized vaccines available, countries are considering ways to vaccinate more people as quickly as possible.

https://mailchi.mp/humanvaccinesproject/covid-report-vaccine-development-1574777
 
There is a controversy today about whether people who have had the COVID-19, or have been vaccinated, can stop wearing a mask.

I think it is not clear yet how well the various COVID-19 vaccines actually protect people. We also do not know what the evolution of the virus means as it spreads through the populations. Unfortunately we will have to wait and see. It takes a while to fully evaluate all new vaccines once they are distributed en masse.

I have seen many vaccine "escapes" and outright failures over the years. It is probably better to err on the side of caution.

From the CDC:

"It’s important for everyone to continue using all the tools available to help stop this pandemic as we learn more about how COVID-19 vaccines work in real-world conditions. Cover your mouth and nose with a mask when around others, stay at least 6 feet away from others, avoid crowds, and wash your hands often."

https://www.cdc.gov/coronavirus/2019.../8-things.html
 
I found this (not patient zero for B.1.1.7, but similar mutations):

https://archive.fo/M1uc7#selection-375.0-379.153
a man in his 70s with lymphoma, admitted in May to a
Cambridge hospital for treatment of Covid-19.
101 days in hospital, 23 times sequenced,
69-70del, N501Y,
Dr. Kemp
Dr.Gupta

"when we saw this number of mutations we were pretty shocked" said Dr.Gupta
## they should have informed the world, tweeted about it, published the sequences

remember the accusations about the Hubei delay in informing the world
in early January.

-----------------------------------------------
as I understand there is a problem with timely publishing such findings.
Those people want to publish it later "exclusively" in a Journal,
and they are afraid that others might write about it before they do.
This "crediting the source" is presumably also the reason why there is GISAID.
But there is often a big delay (up to a year)
until something is published in a journal.
(tell me, when I'm wrong with this speculation, I'm just private,
I don't know how it goes with journals,hospitals,careers,universities.)
 
"Dachshunds" is trending on Twitter tonight but we do not provide content to Twitter anymore so I am posting here. :)

She is a great pandemic stress breaker.


Click image for larger version  Name:	image_33189.jpg Views:	6 Size:	82.3 KB ID:	904216
 
Timetree - http://www.timetree.org/

Not specifically COVID related but I have found a useful online tool (also available as an app) which solves a longtime problem I have had in finding dates on the phylogenic tree of all life. This allows you to do a number of things, enter a taxon (e.g. Vertebrate), Two taxa (Birds & Mammals - see fig. below) or build a tree from a group of taxa.

Click image for larger version  Name:	timetree.JPG Views:	1 Size:	253.7 KB ID:	904281


While I said it was not directly related to COVID I have been looking for this information as it relates to SARS-CoV-2 and our cell biology and immune system and how good various animal models are likely to be. Things like when did ACE2 receptors first appear and how much divergence occurred before bats separated from the rest of the mammals and how much divergence occurred post-separation.
 
you can ask such things in the seqanswers.com or biostars.org forums.
I wasn't there since long .... should try again.
 
Florida to start requiring proof of residency for COVID-19 vaccinations

Florida Gov. Ron DeSantis is cracking down on what's known as "vaccine tourism."

By Erin Schumaker
January 20, 2021, 3:26 PM

Starting Wednesday, people who show up for vaccines in Seminole County, Florida, will be asked to show their Florida ID or a utility bill in order to get the shot, according to ABC News Orlando affiliate WFTV. The new policy, which applies to state-run vaccination sites, will later be extended to other counties in the state.

https://abcnews.go.com/Health/flori...dency-covid-19-vaccinations/story?id=75367026
 
This YouTube link is to a good JAMA discussion that covers a number of topics relevant to this thread. They look at one dose vs two doses, the timing of the doses, vaccine availability and the reasons behind the 'vaccine in freezers problem', how many people need to be vaccinated to drastically reduce hospitalizations and, important to FluTrackers, messaging.
https://www.youtube.com/watch?v=XrHbBolmmqc
 
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