COVID-19 #13 or: How I Learned to Stop Worrying and Love the Disease

[Fragile Bird]

1 hour ago, The Great Unwashed said:

I've been watching the Russian numbers and noticed the same thing. I'm wondering if they're maxing out their testing capabilities every day because they report nearly the same numbers every day like clockwork.

Their deaths are definitely an undercount because they only report COVID-19 deaths after an autopsy has been conducted and all other possible causes have been ruled out.

A couple of weeks ago, or who knows, last week, time is fluid these days, Russian media was broadcasting the news that citizens had to brace themselves for "Italian-like" numbers of deaths.

I guess someone at the Kremlin said no effin way are we releasing those numbers.

[Mr. Chatywin et al.]

1 hour ago, Winterfell is Burning said:

Meanwhile, Brazil lost it's second Health minister in less than one month after Nelson Teich resigned- allegedly because Bolsonaro said he'll made use of cloroquine recommended for all patients, nevermind the fact that recent results shows it's eficiency it's very doubtful. Although there were other factors in play, most notably Teich learning from the press Bolsonaro issue a decree putting activities like hairdressing in the essential list- the decree was then ignored by literally every governor, even those allied to Bolsonaro. 

How are you doing in Rio?

[rotting sea cow]

2 hours ago, The Great Unwashed said:

I've been watching the Russian numbers and noticed the same thing. I'm wondering if they're maxing out their testing capabilities every day because they report nearly the same numbers every day like clockwork.

It is said that they aren't actually testing everybody individually, but doing something called "pool sampling", that is getting samples of chunks of people and mix them. If they come back negative, everything is fine, otherwise you should test them individually. I'd guess the later is not happening, which would produce interesting statistical behaviours, but it is a way to massively increase your testing capabilities at a relatively lower cost.

 

2 hours ago, The Great Unwashed said:

Their deaths are definitely an undercount because they only report COVID-19 deaths after an autopsy has been conducted and all other possible causes have been ruled out.

Well, to be fair. The Russian outbreak started to pick up steam only late in April. Giving that people take their time to die, it is not completely unsurprising that their number is still relatively low. It might also help that life's expectancy is only 72 years compared to 82 years in Italy.

[Winterfell is Burning]

2 hours ago, Tywin et al. said:

How are you doing in Rio?

Me, personally? Fine. The city itself is barely holding on.

Also, one thing I forgot to talk about: there's already dozens of people in jail, in multiple places over the country, due to corruption in buying supplies for COVID-19, and many more being investigated. That includes overpricing, buying itens like respirators from companies that have no experience or capacity of producing them, companies connected to authorities being hired without the due bidding process, companies bribing public employees and other authorities to win said bidding processes, etc, etc.  

[Mudguard]

14 hours ago, Ran said:

Following up on a paper Drosten was part of, there's new a peer-reviewed paper in Cell  (here's a general audience write-up) that finds that T-cells largely do seem to respond to SARS-CoV-2, so these nightmare scenarios of the immune system or vaccines not working are out the door. And like Drosten and co, they found T-cell cross-reactivity to SARS-CoV-2 as well, suggesting that people who have had one of the four common cold coronavirii in the past may have some partial protection which may explain situations of people having very mild or non-existent symptoms.a

The caution about not focusing vaccine efforts on training the immune system on the spike protein alone should be well-taken. I believe the Oxford vaccine, and the mRna-based one that was in phase I trials in the US, both focus on just the spike.

Although having a T-cell response is good news, it doesn't prove that a vaccine will work or that people who recover will be immune, much like showing an antibody response is good news, but doesn't prove that a vaccine will work or that people who recover will be immune.  I think the situation around immunity and vaccines hasn't changed.  For immunity, we just have to track the recovered patients over time, and see how many get reinfected.

Regarding vaccines, I have very low expectations for the Oxford vaccine and the Moderna mRNA based vaccine.  Both are based on experimental technologies that have never resulted in an approved vaccine.  At best, I think these two vaccines will provide mediocre protection, in part because as you note, the vaccine is based on a limited number of antigens, maybe just the spike protein.  Each of the approaches have a number of other problems as well. 

For example, the Oxford vaccine uses adenovirus to deliver the DNA encoding the spike protein to your cells.  If you've had an adenovirus infection in the past, and adenovirus infections are relatively common (one of the causes of the common cold), your immune system may clear the adenovirus based vaccine before it gets a chance to deliver its payload.  Or if it turns out the vaccine requires both a priming shot following by a booster shot, you generally cannot use the adenovirus based shot twice because you would have developed immunity against the adenovirus for the second shot.  You'll have to use something else for the prime.  Figuring these things out generally take years, sometimes decades, and sometimes a solution is never found.  Normally you'll want to do experiments to find out if your vaccine can generate a strong antibody response and T-cell response, and figure out the optimal dosing strategy that results in the strongest immune response, before you get into Phase III clinical trials.  I think they are essentially skipping this, or at best, are just doing extremely limited amount of optimization.  For Oxford's or Moderna's vaccine to work, it will take a huge amount of luck.

The vaccines based on traditional techniques using the whole virus, i.e. some form of inactivated virus or live attenuated virus, have the best chance of generating a strong immune response that confers lasting immunity.  These vaccines will probably take a longer time to make and test, in part because working with a dangerous virus is much more difficult than working with just one gene taken from the virus.  The number of labs qualified to do this type of work is much, much less than the number of labs that can come up with a RNA/DNA vaccine.

[rotting sea cow]

7 hours ago, Mudguard said:

Although having a T-cell response is good news, it doesn't prove that a vaccine will work or that people who recover will be immune, much like showing an antibody response is good news, but doesn't prove that a vaccine will work or that people who recover will be immune.  I think the situation around immunity and vaccines hasn't changed.  For immunity, we just have to track the recovered patients over time, and see how many get reinfected.

Regarding vaccines, I have very low expectations for the Oxford vaccine and the Moderna mRNA based vaccine.  Both are based on experimental technologies that have never resulted in an approved vaccine.  At best, I think these two vaccines will provide mediocre protection, in part because as you note, the vaccine is based on a limited number of antigens, maybe just the spike protein.  Each of the approaches have a number of other problems as well. 

For example, the Oxford vaccine uses adenovirus to deliver the DNA encoding the spike protein to your cells.  If you've had an adenovirus infection in the past, and adenovirus infections are relatively common (one of the causes of the common cold), your immune system may clear the adenovirus based vaccine before it gets a chance to deliver its payload.  Or if it turns out the vaccine requires both a priming shot following by a booster shot, you generally cannot use the adenovirus based shot twice because you would have developed immunity against the adenovirus for the second shot.  You'll have to use something else for the prime.  Figuring these things out generally take years, sometimes decades, and sometimes a solution is never found.  Normally you'll want to do experiments to find out if your vaccine can generate a strong antibody response and T-cell response, and figure out the optimal dosing strategy that results in the strongest immune response, before you get into Phase III clinical trials.  I think they are essentially skipping this, or at best, are just doing extremely limited amount of optimization.  For Oxford's or Moderna's vaccine to work, it will take a huge amount of luck.

The vaccines based on traditional techniques using the whole virus, i.e. some form of inactivated virus or live attenuated virus, have the best chance of generating a strong immune response that confers lasting immunity.  These vaccines will probably take a longer time to make and test, in part because working with a dangerous virus is much more difficult than working with just one gene taken from the virus.  The number of labs qualified to do this type of work is much, much less than the number of labs that can come up with a RNA/DNA vaccine.

Thanks for the explanations. Yes, it seems to me that the vaccine is further away than even some sober expectations. So, we need to live with the virus in the meanwhile, somehow.

BTW, since you seem to be knowledgeable on the subject. What is the probability that there is some Antibody-dependent enhancement affecting the virulence of the disease? After the news about the T-cell related immunity, some people speculated that it might be that the  common coronaviruses cold is not conferring immunity but enhancing the disease. That also brought to my mind a plot made by the anti-vaxxer crew that showed that the covid deaths per million rates are correlated with influenza vaccination rates. I don't have the plot at hand, but the numbers seemed right to me.

 

[Elaena Targaryen]

For the data junkies, Indiana is conducting a scientific study to measure the spread of covid-19 throughout the state https://fsph.iupui.edu/news-events/news/isdh-iu-partner-on-covid-19-study.html

Preliminary results show an estimated population prevalence of the virus in the state to 2.8 percent, with an estimated infection-fatality rate to 0.58 percent

 https://www.regenstrief.org/article/preliminary-findings-indiana-covid19-impact/?utm_campaign=coschedule&utm_source=twitter&utm_medium=RegenstriefNews&utm_content=IU, ISDH release preliminary findings about impact of COVID-19 in Indiana

[A True Kaniggit]

The casinos here are opening up on Monday. (Except one that has shut down permanently)

That just seems like a great way to spread the virus.

What with poker chips constantly changing hands and the constant use of slots. 

[Wilbur]

Yes, our local Indian tribes have begun to run their resort and casino operations as well.  I can't think of a more efficient way to spread germs than the near-constant, mutual handling of cards, chips and cash.  Who knew that being a croupier would suddenly thrust a person into the highest-risk of professions?

[Jeor]

It's not just the constant handling of things - there are some suggestions that time of interaction is also a significant factor in contagiousness (as opposed to brushing by someone in a grocery store) and sitting at a table for an hour or two, constantly handling chips and cards and cash that other players have touched, is kind of taunting the virus into infecting you.

On a macro level it's also pretty crazy. Casinos draw a wide variety of people in a catchment area, it's not like the local pub where you effectively have a five mile radius and that's about it. A casino could end up seeding cases across a wide region.

I'll be interested as to how many patrons they attract. Gambling is pretty inelastic demand as hardcore gamblers need to get their fix, so I think there will be some interest at the tables.

[Mr. Chatywin et al.]

On 5/15/2020 at 4:46 PM, Winterfell is Burning said:

Me, personally? Fine. The city itself is barely holding on.

Sorry for the slow reply. I've been dealing with some things, to say the least. 

Rio has to be a mess. Do you think there's much testing going on in the favelas? Or even medical care?

[Martell Spy]

China Has Quarantined 8,000 People in New COVID-19 Lockdown

https://www.thedailybeast.com/china-has-quarantined-8000-people-in-new-covid-19-lockdown?ref=home

Quote

Officials in China have locked down around 8,000 people in the northeastern city of Jilin after new clusters of COVID-19 were detected. A related cluster was also confirmed in Shulan after aggressive contract tracing led to 700 people who were potentially exposed. Anyone living in the city of Shenyang who had recently been to Jilin now has to quarantine in hospital for three weeks to mitigate potential spread. China has reported more than 89,000 cases and 4,634 deaths since the pandemic began in Wuhan late last year.

 

[Winterfell is Burning]

3 hours ago, Tywin et al. said:

Sorry for the slow reply. I've been dealing with some things, to say the least. 

Rio has to be a mess. Do you think there's much testing going on in the favelas? Or even medical care?

No. Though ICUs specifically built for COVID-19 are not at full capacity in Rio yet (just almost there), so people that get sick in favelas can, in theory, get access to treatment if they need.

And there's barely enough testing for anyone, favelas or not, due to, besides Bolsonaro's plain lack of interest, the old twin problems of blatant incompetence and shameless corruption getting in the way. Plus, the country was already broke before the virus, or Bolsonaro, came along.

[Mr. Chatywin et al.]

1 hour ago, Winterfell is Burning said:

No. Though ICUs specifically built for COVID-19 are not at full capacity in Rio yet (just almost there), so people that get sick in favelas can, in theory, get access to treatment if they need.

And there's barely enough testing for anyone, favelas or not, due to, besides Bolsonaro's plain lack of interest, the old twin problems of blatant incompetence and shameless corruption getting in the way. Plus, the country was already broke before the virus, or Bolsonaro, came along.

I have such a hard time believing that they're getting any testing, but you're closer to the situation than I am so your word is good enough for me.

But yeah, Brazil is in dire conditions, as you said, even before all of this. Can't say my beloved Argentina is doing any better though.

[Winterfell is Burning]

Yeah, Brazil is easily the major nation with the least test per capita. Basically, most of the time you're only tested if you have major symptoms.

[williamjm]

1 hour ago, Tywin et al. said:

I have such a hard time believing that they're getting any testing, but you're closer to the situation than I am so your word is good enough for me.

But yeah, Brazil is in dire conditions, as you said, even before all of this. Can't say my beloved Argentina is doing any better though.

There seems to be a dramatic difference in the numbers they are reporting, according to the Worldometers site Brazil reported more cases and deaths in a single day than Argentina have in total. Of course, there's always the question about how reliable the statistics are and neither nation seems to have done a lot of testing.

[Mr. Chatywin et al.]

17 minutes ago, williamjm said:

There seems to be a dramatic difference in the numbers they are reporting, according to the Worldometers site Brazil reported more cases and deaths in a single day than Argentina have in total. Of course, there's always the question about how reliable the statistics are and neither nation seems to have done a lot of testing.

I've only looked at Brazil, in the literal sense I looked at it across a river, but we were forbidden to go there. Uruguay. Fine. Chile. Fine. Accidentally find yourself with guns pointed at you in Paraguay. Fine. We just couldn't step foot into Brazil, and if we did, we're kicked out of the program and catch the next flight home.

But what I saw while living in Buenos Aires chilled me, and I got to live in one of the nicest places in the city, Palermo, with a rich family. The poverty in the slums is, well it breaks my heart that it is so. And I really struggle to understand how there would be any testing for people in those situations. Just for example, I've never seen child homelessness quite like that any where I've traveled to before as an adult. The situation in Brazil is the same. 

The truth is many places cannot report their actual numbers, test people, have the medical supplies they need and be honest about everything. And that includes both of our countries. 

[Winterfell is Burning]

3 hours ago, williamjm said:

There seems to be a dramatic difference in the numbers they are reporting, according to the Worldometers site Brazil reported more cases and deaths in a single day than Argentina have in total. Of course, there's always the question about how reliable the statistics are and neither nation seems to have done a lot of testing.

In Brazil, there's a dramatic undercount, as the number of deaths in general compared to last year skyrocketed, as well as cases of acute respiratory distress syndrome. It's likely the number of actual cases is much, much bigger (though to be fair, it's possible the situation is the same in Argentina, and many other places).

The difference is that Paraguay, Argentina and Uruguay adopted very strict measures early on, while Brazil didn't, and unlike the leaders that were forced to pivot, like Boris Johnson, Bolsonaro has yet refused to admit he made a mistake- probably because he gambled too highly on it blowing over fast and is too proud or afraid of losing face, specially because he thought this was the moment of making an attempt to block criminal investigations around his family and some close allies (which is typical of most recent Brazilian presidents, but none of the others was facing a pandemic) while forcing out his two most popular ministers in no small part because they were more popular than he is.

 

 

 

[rotting sea cow]

Coronavirus: France fears virus may have spread in October after military games in Wuhan

https://www.news.com.au/world/coronavirus/global/coronavirus-france-fears-virus-may-have-spread-in-october-after-military-games-in-wuhan/news-story/b55680fc3b6a11b8c258317d3454961b

Quote

France fears the killer coronavirus may have hit Europe from October as several athletes recall becoming “very sick” while competing in Wuhan back then.

Ok. But if this is the case, why tsunami of patients started to hit the hospitals only early March?

 

[DireWolfSpirit]

There's a troublesome story about some sailors (I believe it may have been the aircraft carrier crew that was in the news?) that had the virus then recovered and now are sick again.

What the hell is going on with that? Was it mistaken testing or is this confirmation that we can get the virus repeatedly or what?