Fear and Loathing, a Rat Flu Odyssey

[BGnight]

March 17, 2020 (II)

"In a study on 3000 persons, the Italian immunology professor Sergio Romagnani of the University of Florence comes to the conclusion that 50 to 75% of the test-positive persons of all age groups remain completely free of symptoms – significantly more than previously assumed."

https://swprs.org/a-swiss-doctor-on-...AZzSAnWHd9moQM

[CarlMega]

"Where are the photos of overflowing intensive care departments and the thousands of virus victims? I would add, where are the photos of the funerals and interviews with families of those who have succumbed to the virus?

These are genuine questions, it has seemed very curious to me that we have not seen endless footage of emergency vehicles arriving at packed hospitals brimming with patients in need of emergency care.

In any other situation we would be saturated with news feeds providing 24/7 coverage." -Vanessa Beeley. Investigative journalist

Sooo, where's the bodies??

https://www.huffingtonpost.co.uk/ent...eeIgaxM4F7jXcd

[splat]

[splat]

[huckbucket]

https://www.ncbi.nlm.nih.gov/pubmed/32133832

"Conclusions: In the close contacts of COVID-19 patients, nearly half or even more of the 'asymptomatic infected individuals' reported in the active nucleic acid test screening might be false positives."

Which test did they use? Try to get the full text slugger and let us know how that goes.

[splat]

[Mofro261]

This has been discussed previously but really quite sparingly.

Almost 2 weeks ago, it was discovered there are at least 2 different identified strains of this thing. An aggressive "L-type" strain and a slightly less so "S-type" strain.

https://fortune.com/2020/03/04/coron...9-wuhan-china/

https://www.cnbc.com/2020/03/04/coro...-covid-19.html

There has been enough testing done in the US to determine which strain is predominant but I can find absolutely no mention anywhere. How about Italy, Japan, Singapore, South Korea etc?

Any entity (or reporter) who believes they're qualified to be reporting positive results (CDC, WHO or otherwise) without including this pertinent info is either unaware of multiple strains and therefore unqualified IMO to be reporting, or deliberately withholding vital details which means they have an agenda other than truthful reporting and that's called fake news.

I think I posted this last week.

https://science.sciencemag.org/conte...et_cid=3242935

Immediately after Christian Drosten published a genetic sequence of the novel coronavirus online on 28 February, he issued a warning on Twitter. As the virus has raced around the world, more than 350 genome sequences have been shared on GISAID, an online platform. They offer clues to how the virus, named SARS-CoV-2, is spreading and evolving. But because the sequences represent a tiny fraction of cases and show few telltale differences, they are easy to overinterpret, as Drosten realized.


A virologist at the Charité University Hospital in Berlin, Drosten had sequenced the virus from a German patient infected in Italy. The genome looked similar to that of a virus found in a patient in Munich, the capital of Bavaria, more than 1 month earlier; both shared three mutations not seen in early sequences from China. Drosten realized the similarity could suggest the Italian outbreak was “seeded” by the one in Bavaria, which state public health officials said they had quashed by tracing and quarantining all contacts of the 14 confirmed cases. But he thought it was just as likely that a Chinese variant carrying the three mutations had taken independent routes to both countries. The newly sequenced genome “is not sufficient to claim a link between Munich and Italy,” Drosten tweeted.


His warning went unheeded. A few days later, Trevor Bedford of the Fred Hutchinson Cancer Research Center, who analyzes the stream of viral genomes, tweeted that the pattern “suggested” that the outbreak in Bavaria had not been contained after all, and had touched off the Italian outbreak. The analysis spread widely on Twitter and elsewhere—this Science correspondent retweeted the thread as well—and some Twitter users called on Germany to apologize.
Virologist Eeva Broberg of the European Centre for Disease Prevention and Control agrees with Drosten that there are more plausible scenarios for how the disease reached northern Italy than undetected spread from Bavaria. Other scientists agree. “I have to kick [Bedford's] butt a bit for this,” says Richard Neher, a computational biologist at the University of Basel who works with Bedford. “It's a cautionary tale,” says Andrew Rambaut, a molecular evolutionary biologist at the University of Edinburgh. “There is no way you can make that claim just from the phylogeny alone.” Bedford now acknowledges as much. “I think I should have been more careful with that Twitter thread.”


It was a case study in the power and pitfalls of real-time analysis of viral genomes. “This is an incredibly important disease. We need to understand how it is moving,” says Bette Korber, a biologist at the Los Alamos National Laboratory who is also studying the genome of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). But for now, scientists who analyze genomes can only make “suggestions,” she says.


The very first SARS-CoV-2 sequence, in early January, answered the most basic question about the disease: What pathogen is causing it? The genomes that followed were almost identical, suggesting the virus, which originated in an animal, had crossed into the human population just once. If it had jumped the species barrier multiple times, the first human cases would show more variety.


Some diversity is now emerging. Over the length of its 30,000-base-pair genome, SARS-CoV-2 accumulates an average of about one to two mutations per month, Rambaut says. Using these little changes, researchers draw up phylogenetic trees, much like family trees, make connections between cases, and gauge whether there might be undetected spread of the virus.


For example, the second virus genome sequenced in Washington—from a teenager diagnosed on 27 February—looked like a direct descendant of the first genome, from a case found 6 weeks earlier. Bedford tweeted that he considered it “highly unlikely” that the two genomes came from separate introductions, and said the virus must have been circulating undetected in Washington. Both patients came from Snohomish County, making the link far more persuasive than the one Bedford drew between Bavaria and Italy, Rambaut says: “It's very unlikely that this highly related virus would travel to exactly the same town in Washington.” By now the state has reported more than 160 cases, and genomes from additional patients have bolstered the link Bedford suspected.


Still, the wealth of genomes is just a tiny sample of the more than 100,000 cases worldwide, and it's uneven. On 9 March, Chinese scientists uploaded 50 new genome sequences—some of them partial—from COVID-19 patients in Guangdong province; most previous ones were from Hubei province. But overall, less than half of the published genomes are from China, which accounts for 80% of all COVID-19 cases. And sequences from around the world are still very similar, which makes drawing firm conclusions hard. “As the outbreak unfolds, we expect to see more and more diversity and more clearly distinct lineages,” Neher says. “And then it will become easier and easier to actually put things together.”


Scientists will also be scouring the genomic diversity for signs that the virus is getting more dangerous. There, too, caution is warranted. An analysis of 103 genomes published by Lu Jian of Peking University and colleagues on 3 March in the National Science Review argued they fell into one of two distinct types, named S and L, distinguished by two mutations. Because 70% of sequenced SARS-CoV-2 genomes belong to L, the newer type, the authors concluded that this type has evolved to become more aggressive and to spread faster.


“What they've done is basically seen these two branches and said, that one is bigger, [so that virus] must be more virulent or more transmissible,” Rambaut says. But other factors could be at play. “One of these lineages is going to be bigger than the other just by chance.” Some researchers have called for the paper to be retracted. “The claims made in it are clearly unfounded and risk spreading dangerous misinformation at a crucial time in the outbreak,” four scientists at the University of Glasgow wrote on www.virological.org. In a response, Lu wrote that the four had misunderstood his study.


Most genomic changes don't alter the behavior of the virus, Drosten says. The only way to confirm that a mutation has an effect is to study it in the lab and show, for instance, that it has become better at entering cells or transmitting, he says. So far, the world has been spared that piece of bad news.


.......

You can run the time analysis on GISAID. 71 geneomes seq'd thus far in the US, most are of the "S" form but both are present. I wouldn't say L is worse than S based on any data I've seen.
https://www.gisaid.org/epiflu-applic...t-hcov-19-app/

[riser4]

This is the 1st time I've ever heard ANYONE claim that a nordic country wasn't socialist...

Ya, I am bewildered.

[Danno]

BGnight = ignore list

much better

[powpig]

I think I posted this last week.

https://science.sciencemag.org/conte...et_cid=3242935

Immediately after Christian Drosten published a genetic sequence of the novel coronavirus online on 28 February, he issued a warning on Twitter. As the virus has raced around the world, more than 350 genome sequences have been shared on GISAID, an online platform. They offer clues to how the virus, named SARS-CoV-2, is spreading and evolving. But because the sequences represent a tiny fraction of cases and show few telltale differences, they are easy to overinterpret, as Drosten realized.


A virologist at the Charité University Hospital in Berlin, Drosten had sequenced the virus from a German patient infected in Italy. The genome looked similar to that of a virus found in a patient in Munich, the capital of Bavaria, more than 1 month earlier; both shared three mutations not seen in early sequences from China. Drosten realized the similarity could suggest the Italian outbreak was “seeded” by the one in Bavaria, which state public health officials said they had quashed by tracing and quarantining all contacts of the 14 confirmed cases. But he thought it was just as likely that a Chinese variant carrying the three mutations had taken independent routes to both countries. The newly sequenced genome “is not sufficient to claim a link between Munich and Italy,” Drosten tweeted.


His warning went unheeded. A few days later, Trevor Bedford of the Fred Hutchinson Cancer Research Center, who analyzes the stream of viral genomes, tweeted that the pattern “suggested” that the outbreak in Bavaria had not been contained after all, and had touched off the Italian outbreak. The analysis spread widely on Twitter and elsewhere—this Science correspondent retweeted the thread as well—and some Twitter users called on Germany to apologize.
Virologist Eeva Broberg of the European Centre for Disease Prevention and Control agrees with Drosten that there are more plausible scenarios for how the disease reached northern Italy than undetected spread from Bavaria. Other scientists agree. “I have to kick [Bedford's] butt a bit for this,” says Richard Neher, a computational biologist at the University of Basel who works with Bedford. “It's a cautionary tale,” says Andrew Rambaut, a molecular evolutionary biologist at the University of Edinburgh. “There is no way you can make that claim just from the phylogeny alone.” Bedford now acknowledges as much. “I think I should have been more careful with that Twitter thread.”


It was a case study in the power and pitfalls of real-time analysis of viral genomes. “This is an incredibly important disease. We need to understand how it is moving,” says Bette Korber, a biologist at the Los Alamos National Laboratory who is also studying the genome of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). But for now, scientists who analyze genomes can only make “suggestions,” she says.


The very first SARS-CoV-2 sequence, in early January, answered the most basic question about the disease: What pathogen is causing it? The genomes that followed were almost identical, suggesting the virus, which originated in an animal, had crossed into the human population just once. If it had jumped the species barrier multiple times, the first human cases would show more variety.


Some diversity is now emerging. Over the length of its 30,000-base-pair genome, SARS-CoV-2 accumulates an average of about one to two mutations per month, Rambaut says. Using these little changes, researchers draw up phylogenetic trees, much like family trees, make connections between cases, and gauge whether there might be undetected spread of the virus.


For example, the second virus genome sequenced in Washington—from a teenager diagnosed on 27 February—looked like a direct descendant of the first genome, from a case found 6 weeks earlier. Bedford tweeted that he considered it “highly unlikely” that the two genomes came from separate introductions, and said the virus must have been circulating undetected in Washington. Both patients came from Snohomish County, making the link far more persuasive than the one Bedford drew between Bavaria and Italy, Rambaut says: “It's very unlikely that this highly related virus would travel to exactly the same town in Washington.” By now the state has reported more than 160 cases, and genomes from additional patients have bolstered the link Bedford suspected.


Still, the wealth of genomes is just a tiny sample of the more than 100,000 cases worldwide, and it's uneven. On 9 March, Chinese scientists uploaded 50 new genome sequences—some of them partial—from COVID-19 patients in Guangdong province; most previous ones were from Hubei province. But overall, less than half of the published genomes are from China, which accounts for 80% of all COVID-19 cases. And sequences from around the world are still very similar, which makes drawing firm conclusions hard. “As the outbreak unfolds, we expect to see more and more diversity and more clearly distinct lineages,” Neher says. “And then it will become easier and easier to actually put things together.”


Scientists will also be scouring the genomic diversity for signs that the virus is getting more dangerous. There, too, caution is warranted. An analysis of 103 genomes published by Lu Jian of Peking University and colleagues on 3 March in the National Science Review argued they fell into one of two distinct types, named S and L, distinguished by two mutations. Because 70% of sequenced SARS-CoV-2 genomes belong to L, the newer type, the authors concluded that this type has evolved to become more aggressive and to spread faster.


“What they've done is basically seen these two branches and said, that one is bigger, [so that virus] must be more virulent or more transmissible,” Rambaut says. But other factors could be at play. “One of these lineages is going to be bigger than the other just by chance.” Some researchers have called for the paper to be retracted. “The claims made in it are clearly unfounded and risk spreading dangerous misinformation at a crucial time in the outbreak,” four scientists at the University of Glasgow wrote on www.virological.org. In a response, Lu wrote that the four had misunderstood his study.


Most genomic changes don't alter the behavior of the virus, Drosten says. The only way to confirm that a mutation has an effect is to study it in the lab and show, for instance, that it has become better at entering cells or transmitting, he says. So far, the world has been spared that piece of bad news.


.......

You can run the time analysis on GISAID. 71 geneomes seq'd thus far in the US, most are of the "S" form but both are present. I wouldn't say L is worse than S based on any data I've seen.
https://www.gisaid.org/epiflu-applic...t-hcov-19-app/

Thanks. That was a good & informative read.

[riser4]

Bahahahaha

[Meadow Skipper]

This is the 1st time I've ever heard ANYONE claim that a nordic country wasn't socialist...

As I mentioned way earlier, this thread is instrumental in establishing who here is an idiot.

[iceman]

I can't summarily dismiss this opinion.

https://www.statnews.com/2020/03/17/...reliable-data/


John Ioannidis is an extremely knowledgeable voice, fwiw.

FFS, why would you consider dismissing it? We are making massive public health and economic decisions essentially blind. Of course we need better data.

What would be really helpful is a test for antibodies, in order to get an idea of how many have been infected and begin to make decisons based on statistical outcomes. At this point, there's no such thing as a "death rate" there's only death totals.

[riser4]

[muted]

As I mentioned way earlier, this thread is instrumental in establishing who here is an idiot.

I've posted some dumb shit here before, but this thread is an ego boost for me.

[Toadman]

This actually happened to me as kid. Door wasn't completely shut, and dad hit a speed bump in a parking lot, and out I went. Probably doing 5-6 mph, I bounced right back up. Car ride home, dad says to my older brother and sister, "Not a word about this to your Mom." I think it was about 20 years later, us siblings were joking about it, and my Mom had this look of, WTF?

[iceman]

This is the 1st time I've ever heard ANYONE claim that a nordic country wasn't socialist...

Does the Times count? https://www.nytimes.com/2020/03/10/o...sultPosition=2

[subtle plague]

...And you are both European locals.

Hey now.. We may breed our own share of idiots over here, but these two are proudly made in `murica!

[skaredshtles]

Does the Times count? https://www.nytimes.com/2020/03/10/o...sultPosition=2

And here we get into the debate on what is "socialism" vs. "democratic socialism" vs. "an expanded welfare state"...

[Timberridge]

BGnight = ignore list

much better

I'm proud to say I have never had anyone on ignore. I can take whatever you bitches throw. Bring it on.

[iceman]

@sshl: They do have definitions. (at least the first 2). Just because people in this country routinely label anything other than pure capitalism "socialism" doesn't make it true.

[The SnowShow]

But no one gives two fucks when we have a bad flu season. The crime doesn't fit the punishment. If we banned all corporate media for 2 weeks this virus would magically disappear.

[subtle plague]

And here we get into the debate on what is "socialism" vs. "democratic socialism" vs. "an expanded welfare state"...

We prefer to call it something that roughly translates to "social capitalism" . And for the US we have a derogatory term floating around which would translate to "predatorial capitalism."
In economical theory it is the difference between ordoliberalism and libertarian ideas.

[gravitylover]

I agree. And I agree that Supreme Leader has been shocked into acting somewhat presidential after the stock market crashed. He was just muscling Cuomo into dropping state charges against him and his family, but, this new working together thing is kind of amazing. Trump realizes that he can't do this hoax bullshit anymore.

Interesting piece about Cuomo. in the NYT. Sometimes circumstances elevate politicians.

It has made some legendary to the point that all of their transgressions and foibles are dismissed unless they self destruct. Ie: Rudy People think Custer was a good guy too.


I'll tell ya, having a 93 year old father in law with worsening dementia living in a locked down assisted living facility where the residents can't leave their rooms is an interesting problem. Having nobody to talk to other than the nurses when they come in to give him his meds is making things worse. He's falling apart and afraid to eat the food trays they bring, because the dining room is closed, so he stopped eating after breakfast today. We can't visit him and he keeps turning his phone off or turning the volume off so he can't call and we can't call him so next time we do talk he's angry. We're afraid to bring him to our house because we think he's better protected and cared for where he is and he'd have to sleep on the couch so the house becomes a quiet zone 5 or 6 times a day when he naps then has to go down when he falls asleep around 7. First world problems right...

[CascadeLuke]

BGnight is the new Ron Johnson