Covid 19 virus

[iMo]

..The SARS-Covid-2 virus has a genome with about 30,000 base pairs, that means (crudely) it can only code 10,000 amino acid sequences, quite a few of which are overhead. Compare that to a computer virus with 30,000 bytes assembler instructions and 10,000 actual instructions. That little genetic material has to code for the structure of the virus, how it gets into a host cell, how it gets that host cell to manufacture more virions and so on. ..

The virus is a chunk of RNA encapsulated into "the debris" of the cell's outer membrane (the cell which burst because of the mass-produced RNA). Thus the "how to get into the cell" is not coded in the RNA itself, but specified rather by its encapsulation - and while it is made of the cell's outer membrane the barrier to enter into an another identical or "similar" cell is almost nil, imho.

[vad]

just see this:

...We hypothesize that SARS-CoV-2 does as well.

Nice hypothesis. Let me know when you’ll find a peer-reviewed article that starts its conclusion with the phrase “we established” instead of “we hypothesize”.

well if you do not like how science works you can always try cow urine 

It seems you have a lot of aspiration for science. Keep on trying, don’t give up, and take my advice. Today I am giving it away for free. When googling for something that can prove your theory, don’t search for words like “urine”. Try something different. ”Chi-squared test”, for example.

[Cerebus]

..The SARS-Covid-2 virus has a genome with about 30,000 base pairs, that means (crudely) it can only code 10,000 amino acid sequences, quite a few of which are overhead. Compare that to a computer virus with 30,000 bytes assembler instructions and 10,000 actual instructions. That little genetic material has to code for the structure of the virus, how it gets into a host cell, how it gets that host cell to manufacture more virions and so on. ..

The virus is a chunk of RNA encapsulated into "the debris" of the cell's outer membrane (the cell which burst because of the mass-produced RNA). Thus the "how to get into the cell" is not coded in the RNA itself, but specified rather by its encapsulation - and while it is made of the cell's outer membrane the barrier to enter into an another identical or "similar" cell is almost nil, imho.

I don't mean to be harsh but 'IMHO' is not a substitute for actually having studied this. A virus' protein coat is encoded in its genome, it doesn't just grab scraps of a cell's (phospholipid) membrane on the way out, it gets its host cell's ribosomes to manufacture its coat proteins. Take a look at a T4 bacteriophage and tell me how it constructs the complex protein coat (including a 'hypodermic') from a bacteria's shattered cellulose/phospholipid membrane. Getting into or out of a cell past the membranes is not a trivial task biochemically speaking, that's why cells have whole systems of proteins dedicated to active transport, ion channels in cell membranes and so on, and active mechanisms to resist 'foreign' biochemicals simply wandering into the cell.

Case in point, our friend SARS-covid-2:

Structural biology

Each SARS-CoV-2 virion is approximately 50–200 nanometres in diameter.[50] Like other coronaviruses, SARS-CoV-2 has four structural proteins, known as the S (spike), E (envelope), M (membrane), and N (nucleocapsid) proteins; the N protein holds the RNA genome, and the S, E, and M proteins together create the viral envelope.[51] The spike protein is responsible for allowing the virus to attach to the membrane of a host cell.[51]

Note in particular that very last bit about the virus' spike proteins. The structural similarity of the spike protein to antibodies is no accident, it performs a similar task to 'recognise' and attach to surface expressed proteins on a target cell. Why would it code for a membrane protein if it was just going to snatch a cell's phospholipid membrane to do the job?

[nctnico]

For the first time since 1973 our PM addressed the country.
The strategy is to isolate as much as possible the elderlyand vulnerable till its over. The rest of the population should over time get the virus in a natural way, so they get immune after they recovered so they don't pose a thread anymore after a certain period of time.

Just for clarity: it wasn't the same PM as in 1973. Still it is impressive. Never thought I'd see the day but yet here it is.

His main message  was that most people will get infected at some point (which is what Merkel; the PM of Germany also stated a couple of weeks ago). The efforts are aimed to control the outbreak so health care can keep up. Makes sense to me because that seems the only way to me to keep both the economy going and reduce loss of life.

[edavid]

Does anyone know if the PCR tests being commonly done by public health services are quantitative?  How about the antibody tests?  I've read articles that mentioned both viral load and detected/not detected results.

At least in the USA, the PCR tests are pass/fail tests.  The test basically slices and dices the sample RNA, making copies each time, matching on 3 different sample patterns found in the virus.  Each one is tagged with a dye which is then measured (after each copy iteration).  This will generate a curve of the fluorescence at a specific wavelength.  They plot this on a graph and if all 3 different dye tags cross a specific threshold within a specific # of replications, its a positive test.

So how do they do an "N-gene-specific quantitative RT-PCR assay", as described in this article:

https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30113-4/fulltext

Is it a lot more difficult than the pass/fail test you describe?

[hamster_nz]

Does anyone know if the PCR tests being commonly done by public health services are quantitative?  How about the antibody tests?  I've read articles that mentioned both viral load and detected/not detected results.

At least in the USA, the PCR tests are pass/fail tests.  The test basically slices and dices the sample RNA, making copies each time, matching on 3 different sample patterns found in the virus.  Each one is tagged with a dye which is then measured (after each copy iteration).  This will generate a curve of the fluorescence at a specific wavelength.  They plot this on a graph and if all 3 different dye tags cross a specific threshold within a specific # of replications, its a positive test.

So how do they do an "N-gene-specific quantitative RT-PCR assay", as described in this article:

https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30113-4/fulltext

Is it a lot more difficult than the pass/fail test you describe?

Have a look at "Real-Time RT-PCR Panel for Detection 2019-Novel Coronavirus - Instructions for use":

https://www.cdc.gov/coronavirus/2019-ncov/downloads/rt-pcr-panel-for-detection-instructions.pdf

If anybody wants to see the proteins that are encoded, have a look at a sequenced virus:

https://www.ncbi.nlm.nih.gov/nuccore/MN908947

[Bud]

For the first time since 1973 our PM addressed the country.

What happened in 1973?

[nctnico]

For the first time since 1973 our PM addressed the country.

What happened in 1973?

That was the oil crisis.

[Nusa]

For the first time since 1973 our PM addressed the country.

What happened in 1973?

Probably the oil embargo from the Arab producers aimed at nations supporting Israel in the Yom Kipper war. Global oil prices quadrupled as a result, and many were impacted by the lack of supply, including the US (I was a teen driver at the time).

[Stray Electron]

For the first time since 1973 our PM addressed the country.
The strategy is to isolate as much as possible the elderlyand vulnerable till its over. The rest of the population should over time get the virus in a natural way, so they get immune after they recovered so they don't pose a thread anymore after a certain period of time.

Just for clarity: it wasn't the same PM as in 1973. Still it is impressive. Never thought I'd see the day but yet here it is.

His main message  was that most people will get infected at some point (which is what Merkel; the PM of Germany also stated a couple of weeks ago). The efforts are aimed to control the outbreak so health care can keep up. Makes sense to me because that seems the only way to me to keep both the economy going and reduce loss of life.

   But you've missed an important point: at this point it little matters what happens to the economy.  The entire planet is faced with the possibility of MASSIVE numbers of deaths due to overloaded medical systems.  Right now, they're making hard decisions about the best way to keep as many people alive as possible. Yes, short of some sort of vaccine being invented EVERYONE is going to get it. And even in the best medical conditions, an average of 3.4% of the infected people are dying. That's 10 million people in the US alone and about 230 million world wide. However that's going to go up drastically if we can't limit the rate of increase so that the medical systems can deal with it.  Go look at Italy right now, they CAN'T deal with the current rate of increase, Iran is just as bad, South Korea was but now seems to be getting some control on it. Spain is losing control, so is France and Germany and the US is close behind. The US could be much worse since, thanks to the incompetence of the CDC, we still don't actually know how many people are already infected. Even countries like Canada are showing a 25% increase in the number of cases just in the last 24 hours!

  https://www.worldometers.info/coronavirus/

[Nusa]

CDC did it's job with projections, but the administration refused to pay heed to their warnings for a couple months and kept them muzzled until the damage was done.

[maginnovision]

I'm in the ER and at least it isn't busy. Stricter rules than normal though.

[Bud]

Even countries like Canada are showing a 25% increase in the number of cases just in the last 24 hours!

What did you expect if Canadian idiot health officials were saying ,as the toll was rising in China, if you see a Chinese person come say you support them and shake their hand.

[hamster_nz]

However that's going to go up drastically if we can't limit the rate of increase so that the medical systems can deal with it. 

I've been chewing on this point for some time.

If we want to limit infections to the point where hospitals can deal with it (say 10k active cases at any time, in Italy), and cases take 20 day to resolve, that is a rate of about 500 serious cases per day, and with about 20% of cases needing hospitalization, that is 2,500 new cases per day of any severity.

Italy has 60,000,000 people, so to not swamp the health system it will take 60,000,000/2,500 = 24,000 days (or 65 years!) if everybody was to get it without swamping the health system.

Even if Italy was to grow the ability to have 100k cases in hospital, that is still 65 years.

Assume Italy can have 100k hospital beds, and only 10% of the population get infected. that's still 1200 days of full hospitals with a perfectly managed rate of transmission.

They way I see it, it will either get stamped out through infection control, or the hospital system will get swamped. There isn't a middle ground. Anybody who thinks "flattening the curve" is a workable long term plan probably hasn't done the math.

(any correction to assumptions gladly accepted!)

[not1xor1]

   But you've missed an important point: at this point it little matters what happens to the economy.  The entire planet is faced with the possibility of MASSIVE numbers of deaths due to overloaded medical systems.  Right now, they're making hard decisions about the best way to keep as many people alive as possible. Yes, short of some sort of vaccine being invented EVERYONE is going to get it. And even in the best medical conditions, an average of 3.4% of the infected people are dying. That's 10 million people in the US alone and about 230 million world wide. However that's going to go up drastically if we can't limit the rate of increase so that the medical systems can deal with it.  Go look at Italy right now, they CAN'T deal with the current rate of increase, Iran is just as bad, South Korea was but now seems to be getting some control on it. Spain is losing control, so is France and Ger

In Italy the infection rate is slowly getting lower and lower although the situation is not the same everywhere (there is even a province with zero cases).
It takes time to see the effect of quarantine. I'm sure anyway that we'll have to wait at least another month before getting where China is now.

[not1xor1]

That's interesting. If an animal is infected, especially a pet (that people are very likely to get close to), how can it not happen?

It's not like the virus is automatically oozing out of every pore of the dog. If it's just in certain organs or in the blood stream, that's nothing you'd usually get in contact to. If it's in a dogs' saliva, that'd be something else.
[/quote]

SARS and COVID-19 are also transmitted via feces...
I've non idea why, but AFAIK nobody observed pet-to-human transmission

[not1xor1]

Even countries like Canada are showing a 25% increase in the number of cases just in the last 24 hours!

What did you expect if Canadian idiot health officials were saying ,as the toll was rising in China, if you see a Chinese person come say you support them and shake their hand.

probably because people are so stupid to think that every Chinese is a virus carrier while there are a lot of "Aryans" who travel to China and other countries and spread the virus everywhere

discriminating Chinese people besides being unfair and immoral is counter-productive regarding the fight against virus spread

[VK3DRB]

Pensioners still cannot get basics at their supermarket. I just got back from our local supermarket. No toilet paper, no meat, no eggs, no pasta, no tissues, not nothing except junk food. The local chemist has run out of basic meds too. The supermarkets are out of control as is our government. Scott Morrison, our Prime Minister, triggered the panic by telling people to stock up.

The state government should impose limits and use the police to fine the hoarders. Better still, use batons on them. Another effective method might be to post on forum a photo of the face of their hoarders with their trolley of loot.

[thinkfat]

In Italy the infection rate is slowly getting lower and lower although the situation is not the same everywhere (there is even a province with zero cases).
It takes time to see the effect of quarantine. I'm sure anyway that we'll have to wait at least another month before getting where China is now.

I'd expect two weeks or thereabouts for the effect to become visible. Basically, incubation period.

[magic]

Meanwhile in Poland...

Even isopropanol sells for $10 per liter now

Thankfully I have some stock for personal use.

[nctnico]

In Italy the infection rate is slowly getting lower and lower although the situation is not the same everywhere (there is even a province with zero cases).
It takes time to see the effect of quarantine. I'm sure anyway that we'll have to wait at least another month before getting where China is now.

Unfortunately the infection numbers mean absolutely nothing because they solely rely on testing. In most parts of Europe the situation is so out of control that only people with severe symptoms get tested. Also a large number of people have such mild symptoms that they aren't tested at all. All in all the only real number you can use as a gauge to say anything meaningfull about the spreading of the Corona virus is the number of deaths.

[thinkfat]

All in all the only real number you can use as a gauge to say anything meaningfull about the spreading of the Corona virus is the number of deaths.

And even that varies wildly. In Germany, we have quite a number of confirmed infections (more than 7000, if you believe JHU, a little over 6000 reported to RKI) but a very low CFR (0.2%).

IMHO, this means two things:
- Germany is still at the very beginning of the wave and not many critical cases had the time to come to closure.
- We have a good test coverage.

Alternative:
- we're incredibly sloppy in our testing and the CFR is much higher in reality.

Germans, sloppy? 

[paulca]

Tune in tonight for some serious CAR CRASH TV!

Coronavirus: German Big Brother cast to be told about pandemic live on TV

https://www.bbc.co.uk/news/newsbeat-51923334

[iMo]

..
IMHO, this means two things:
- Germany is still at the very beginning of the wave and not many critical cases had the time to come to closure.
- We have a good test coverage...

In Markus Lanz talk show (11.3.) your expert said Germany CFR is low because of very early testing start and good testing coverage..

[BU508A]