COVID-19: A thread to share some thoughts and events

SARS-CoV-2 enters the alveoli "type 2 surfactant" cells (type 1 is the oxygen exchanger) by attaching to the ACE2 receptor in the walls of the type 2 cell. CHLOROQUINE inhibits ACE2 receptors. So you need to take CHLOROQUINE before you are infected. This is like malaria prevention. Another drug REMDESIVIR inhibits "RNA-dependant RNA polymerase" which is how new RNA for the new viral cells is produced by viral action inside the alveoli cell. Both these drugs sound very promising but they have side effects.

Yes and this is why I have changed my high blood pressure medication...
https://www.sciencedaily.com/releases/2020/03/200323101354.htm
 
Mercedes F1 Ventura CPAP device

Some more info now available on the Mercedes F1 CPAP device. You can find a picture of the blue hand-sized gadget about half-way down this webpage https://edition.cnn.com/2020/03/30/tech/mercedes-f1-breathing-aid-coronavirus/index.html

Here is my educated guess of how this works. It has no motor and no electronics. There are three controls (1) Flow ON/OFF switch, (2) Flow Adjustment, (3) Oxygen Adjustment. There are two "input" ports (Oxygen in and Air in) and one "output" port (to the patient mask). The Air in port has a HEPA filter attachment, not shown in the picture. The device is likely driven by the Oxygen flow using a "venturi" on the Oxygen input path. This venturi will then suck in surrounding Air from the Air input as Oxygen molecules accelarate through the venturi nozzle towards the output port to the patient. This explains why the device is called VENTURA and why Mercedes F1 engineers are ideal for optimising the design. The Oxygen flow will elevate the pressure at the patient mask above ambient, hence get the benefits of keeping the alveoli from collapsing. There is an Oxygen pressure monitor tee'd into the patient feed pipe.

The small device needs to be plugged into another "machine" which is standard in hospitals that supplies the Oxygen - hence the elaborate gas tight stainless steel connector you see in the picture. Don't strike a match anywhere near the patient or you may see some Formula 1 thrust take place :p
 
From here (German text) https://www.n-tv.de/panorama/Frankreichs-Behoerden-warnen-vor-Chloroquin-article21681668.html:

[...]The French Agency for the Safety of Medicines (ANSM) warns of side effects in Covid-19 patients caused by the malaria drug hydroxychloroquine and the HIV drug Kaletra. "A few cases of serious side effects have been reported and are currently being analysed," the ANSM said. The agency stressed that the drugs should not be taken as self-medication or on prescription from a local doctor under any circumstances. "We demand the responsibility of everyone to avoid unnecessary hospital stays due to the misuse of these drugs".

Heart problems may follow after ingestion
Hospitals have found around 30 serious side effects in their corona patients from drugs currently being tested by European researchers, said ANSM Director General Dominique Martin. Three deaths could also be linked to the treatment. In France, the treatment of Covid-19 patients with hydroxychloroquine and Kaletra is only allowed in severe cases and after coordination between several doctors.

The authority warns in particular of cardiac disorders that can occur when the antimalarial drug is used in combination with other drugs. "We remind you that to date no drug has been formally proven to be effective for the treatment or prevention of Covid-19," the authority stresses. In view of the spread of the coronavirus, it is "quite normal" that experimental treatment methods are also used. However, these must be monitored by experts.

This was particularly true for the combination of hydroxychloroquine and the antibiotic azithromycin. The simultaneous administration of these two drugs "increases the risk" of cardiac arrhythmia, which could lead to a heart attack, warned authority head Martin. This applies all the more to patients suffering from Covid-19. The regional drug authority in Bordeaux, Western France, had also warned against self-medication with active ingredients such as hydroxychloroquine. The authority referred to the severe side effects of the drug, which include cardiac arrhythmia and neurological problems. An overdose can be fatal.

A large European study called "Discovery" is currently testing several drugs against Covid-19 that have proven effective against other viral diseases. So far, however, there is no scientific evidence that they also help against the novel coronavirus. Nevertheless, the pressure is growing in France: there is a high demand in the country's pharmacies from GPs and private individuals for certain remedies, which are repeatedly mentioned as possible therapies despite the lack of knowledge.
[...]
Translated with www.DeepL.com/Translator (free version)
 
Transistors could be the answer to testing

Came across a very intriguing article today. Biological sensing transistors, known as "BioFETS" https://cardeabio.com/field-effect-biosensing-technology/. These are transistors based upon GRAPHENE rather than SILICON. The "gates" of these transistors are coated with a "receptor" and when the target bio molecule is present, it binds to the receptor and changes the charge distribution on the gate - thereby switching the state of the transistor from OFF to ON.

This sounds remarkably like the binding of SARS-CoV-2 spikes to the ACE2 receptors, which as we have learnt is the mechanism that allows the virus to enter the alveoli type 2 cell. Lets hope that this technology development is accelarated in time to help out with testing. Imagine a Teensy based such test instrument!

GRAPHENE is preferred to SILICON because SILICON is reactive when exposed to the atmosphere, whereas GRAPHENE is stable.

Apparently, there is not just one type of SARS-CoV-2 doing the rounds. At least 8 strains of the virus have been identified https://eu.usatoday.com/story/news/...rack-coronavirus-strains-mutation/5080571002/. They are all very similar and comparing the mutation changes in "code" allows tracking of the distribution of the virus around the globe. BioFETS should be capable of detecting all these strains because, presumably, of the 30,000 or so amine bases that make up the strand of RNA, it will only need to identify a particular unique sequence. This, as we know, is how most computer anti-virus programs work - looking for specific byte sequences in the chain of bytes that make up a file.

The differences between DNA and RNA is itself an interesting topic. I found this reference https://www.thoughtco.com/dna-versus-rna-608191 most enlightening. The continuous ribbon of sugar-phosphate that forms the backbone can be further understood here https://teaching.ncl.ac.uk/bms/wiki/index.php/Sugar_phosphate_backbone. Note that the difference between "oxy" and "de-oxy" is the replacement of a Hydroxyl (OH) with a simple hydrogen (H) atom at one corner of the carbon ring shown. (The carbon ring is that pentagon shape. Carbon atoms exist at the corner junctions of the pentagon, and the convention is not to show these explicitly to try simply the presentation).
 
Serious development in the UK

It has just been reported on UK news channels that Boris Johnson, our Prime Minister, has been admitted to hospital. He placed himself in self-isolation 9 days ago. We expected (if he had a mild form of the COVID-19) that he would have been back in the public arena two days ago.

The reports tonight suggest that he has been admitted into hospital for "tests", but no further info was given. It is said that he is in the same state tonight (no worse) than he was when he appeared on the steps of No.10 last Thursday in the national "clapping campaign" that periodically takes place to thank those working on the front line.

Our Health Secretary, Matt Hancock, did return to work after 7 days with mild symptoms. He now appears in robust health. He did remark on TV that in addition to the standard symptoms of fever and cough he also suffered loss of taste and smell for a period. This has been recorded by others. We now have a national database being compiled whereby sufferers can report all their symptoms, with a view to determining additional factors that could identify infected people.
 
He's one of thousands. I can't see any reason to mention politicians or prominent people.

My take is that its his role as Prime Minister which is truly significant. As if things are not bad enough, this could turn the UK upside down (again) in hours. Parliament was suspended early and has no fixed date yet for returning. Consider too that he is one of the few people responsible for a very formidable button. The security implications are scary for us all, not to mention the economics.

Its significant that he started with "mild symptoms" - as did our Health Secretary. They both went "off-line" together two weeks since. The latter is back after the expected 7 days, but the former is not. When things don't go to rule with COVID-19, then some very serious stuff can arise very quickly. I very much hope not.
 
I'm not a specialist in this subject, but from what I understand of the way the disease progresses, the first stage is characterised by sore throat, cough and fever, and here the virus is rapidly reproducing in the throat. The next phase is when the virus invades the rest of the body, especially the lungs, and that's when the immune system starts to kick in and develop the body's immune response. BoJo's system seems to be taking a bit longer that most, but we can hope that it does get there eventually - whatever you think of his politics, nobody deserves to die from this thing. As long as he doesn't progress beyond this stage, there's no reason why he shouldn't be able to carry on with his job (although perhaps a rest would do him good).

Perhaps next is more or less severe degradation of lung function, which is where the ventilators come in, and then the final phase (if it occurs) where the immune system starts to over-react just as it does with sepsis, the vital organs start to fail and the body shuts down. Just hoping that as few as possible get to this stage - it seems to happen very quickly, and it must be dreadful for all concerned.
 
Hopefully, everything will calm down till May, I believe that everybody will strictly follow the rules to make this process run faster. It is said that vaccine will be produced approximately in September. I am so sad that I cannot travel to my newly-bought property in Cyprus that I haven't used yet due to this situation. I have heard that Austria slowly becoming to open some stores and cafes. It is good news finally.
 
Hopefully, everything will calm down till May, I believe that everybody will strictly follow the rules to make this process run faster.

I wish I could share your optimism about the behaviour of people. Sadly, at least in UK, there are some who don't believe it's serious, and some more who think that the rules are for others to follow.
 
May? Never ever...
It will calm down a little bit, but we will have fun til next year.
I really hope, some things will be different then (->in 2 years), and money$$ will rule less.
 
@MatrixRat - How is your project#1 coming along? I have now logged a fair number of days of manual body temperature readings - and learnt a few things. My lowest (accurate) data recording is 35.7 degC. A fair number of 35.9's. My highest is 36.8. The low readings occur when I first get out of bed (low metabolism) and the highest was after a hot bath - though cycling for my one hour exercise can also give 36.5.

What does this tell me? At 70 years of age, I guess the mitochondria are not as efficient as maybe they were 35 years ago. But I did have two readings of 34.5 and that told me that the digithermom was suspect. Fortunately, my order for two from eBay arrived three days ago, so, now they are out of quarantine :) I'm using one of them instead. I also have two clinical mercury thermoms (and to my surprise they agree with each other) so I can employ a voting system for best out of three!

@everybody - I'd like to buy a stepper motor from eBay to experiment with Project#2 and a fan blade. Anyone got any good suggestions for which type to buy? I'd obviously like to use a Teensy as the intelligence to drive it.

@emseedee - Thanks for some very useful info in post#108. We should all take post#110 very much to heart. Dr Li Wenliang tried to warn us all in January - this is no game.

This weekend, I ran an "electrophoresis" experiment. I had this wacky idea that I might (eventually) be able to see DNA fragments, but wanted to test my "agar" production first using vegetable dyes (as in baking cakes). To my surprise, it did work and I have some photos if anyone is interested. The theory is that agar is a matrix filter where small molecules travel faster through the matrix than large ones. The next test will be to extract DNA from fruit - apparently its easy to get it from bananas and strawberries.
 
Came across this recent series of lectures on VIROLOGY which members may find interesting... https://youtu.be/lj3NhPgOoX4

Prof Racaniello makes a number of references to SARS-CoV-2, so very pertinent to today. Lecture#1 sets the scene very well, but Lecture#2 is more interesting.

A number of countries are now thinking about how to ease the lockdowns. That may mean wearing an obligatory mask in public, so perhaps Project#3 might be to design a Teensy based do-it-yourself mask? Scrolling messages come to mind :)
 
Gday @ Telephone Bill.

Distracted by the mundane, - firewood, chainsaws and garden tools and knocking a Teensy Master Midi clock together and coaxing it to drive my mental health project.
Hopefully will be connecting some more dots on the logger in coming days.


I'm curious as to the look of the data from two sensors, one on the wrist and the other on the neck so am thinking of how many inputs.. I'm building another matrix here so have more sniffing to do.
 
Interviews with Prof Racaniello

This guy Prof Vincent Racaniello is well worth listening to directly about SARS-CoV-2 and COVID-19. He did an interview with Ethan Evans (Greater Seattle Area, U.S.) about five weeks ago (https://youtu.be/NGcdLm_1h5w). It last for two hours, but is a real gem.

I've only gotten part way through this one and now discover there's a more recent follow-up three weeks ago (https://youtu.be/c0l5jV9rz0E). Looking forward to that one in turn.

Likely we have many more weeks of lockdown ahead of us, so plenty time for your sensors. Good to hear our PM is on the mend.
 
Just an FYI - I just read (or walked through) the 3D simulation from the NY Times about social distancing and how far the virus might travel from cough or sneeze...
https://www.nytimes.com/interactive...onavirus-transmission-cough-6-feet-ar-ul.html

It is a good simulation.

Here is a very good article that details the effects of wearing a face shield against cough simulants of various droplet sizes and so forth. Very comprehensive. https://www.ncbi.nlm.nih.gov/pubmed/24467190

When I went to the grocery store this morning (first time in 14 days), I wore a face shield and a mask...and I had plenty of ethyl alcohol to apply to my hands and face when I got back to the car...and of course, plenty of soap and water when I was home.

Hey but look on the bright side, I actually managed to score some TP!
 
As a very responsible citizen, I go further.
I not only cover with mask, but also plug some orifices to protect the others from an accidental exhaust.
There is still so much unknown about the spread of the virus...

Damn, all of this drives me nuts!!!
Where is my Teensy 4.1?
All I need to know if it will be in 3.6 form factor. Want to get my PCB ready. Done with the software.
 
@KurtE - Simulations are good teachers - a picture is worth a thousand words. They are good at illustrating an event that you know for certain happens, but they are poor predictors of events that you are not sure of. There are a lot of good reasons for wearing a face mask. My biggest is signalling to others that you are taking the virus seriously (so don't crowd my space!).

I just got through both interviews on YouTube with Prof Racaniello, and this man knows what he speaks about. Just watch his 3D simulation of how Endosomes are dragged along Microtubules by protein Motor Units towards the Cell Nucleus (Virology 2020 Lecture#5 Time=34:26 https://youtu.be/aMvnlAfOWec). It will blow your mind.

Prof R's interviews discuss breath, coughs and aerosols and he makes several significant points. Not all inhaled "Virions" will be active pathogens and get on the inside of a cell. Its all a question of statistics. You may need thousands to get infected (we don't yet know). Large droplets contain many more Virions than small ones. Confined spaces (Hospitals/Care Homes) increase the density. The really big droplets will drop rapidly to the floor. Previous viral studies have looked at the statistic figures, so that's why the 6 feet rule has been declared.

@DrGee - I like your "NY Times" reference. It lists the bits of the SARS-CoV-2 proteins that we know about so far. The Virology 2020 lectures will actually tell you in much more detail how these proteins work. There is a "hairpin" effect where a protein strand is folded just like a ladies hairclip. On the very end of the hairclip, and tucked away folded for protection, is a short piece thats the "Spearhead". Triggers at some point cause the hairpin to unfold. It becomes rigidly straight by forming an "alpha helix". Then the spearhead is primed and ready - erect and very strong - ready to jab into a Moby Dick target cell, like a harpoon fired by Captain Ahab. Its magic, pure magic in the molecular world.

At the end of the last interview, Prof R was asked where on a scale of 0 to 10 does this pandemic compare with previous Viral outbreaks (Ebola, "Classic SARS", MERS...). He qualified his answer as being "medical" and not "economic". Ebola scores 9. SARS-CoV-2 scores a 4 or a 5. It is likely to become "seasonal" in the future, but once the first outbreak has passed by then the next season will be a lot less damaging - as we all get some degree of immunity.

The most light hearted part of the last interview talks about what we should do to be prepared (OK, next time). He then explained that ALL human viruses come from animals. So by studying the viruses inside animals, or from their droppings, we can be ready with vaccines. It is re-assuring to know that we now have a MERS vaccine for Camels!! :cool:
 
Code:
It turns out that the Centers for Disease Control and Prevention (CDC) has known since at least 2005 that chloroquine is effective against coronaviruses.
In 2005, Martin J Vincent et al published a study in Virology Journal titled ‘Chloroquine is a potent inhibitor of SARS coronavirus infection and spread.’

ncbi.nlm.nih.gov/pmc/articles/PMC1232869/
Published online 2005 Aug 22
Chloroquine is a potent inhibitor of SARS coronavirus infection and spread
...
Results
We report, however, that chloroquine has strong antiviral effects on SARS-CoV infection of primate cells. These inhibitory effects are observed when the cells are treated with the drug either before or after exposure to the virus, suggesting both prophylactic and therapeutic advantage.
...
Conclusion
Chloroquine is effective in preventing the spread of SARS CoV in cell culture. Favorable inhibition of virus spread was observed when the cells were either treated with chloroquine prior to or after SARS CoV infection. In addition, the indirect immunofluorescence assay described herein represents a simple and rapid method for screening SARS-CoV antiviral compounds.
...
Background
Severe acute respiratory syndrome (SARS) is an emerging disease that was first reported in Guangdong Province, China, in late 2002.
...

Code:
It ought to be no surprise that chloroquine is effective against both SARS and COVID-19. After all, they are both coronaviruses and COVID-19 has often been described in medical and research sources as SARS-2.
Chloroquine works by enabling the body’s cells better to absorb zinc, which is key in preventing viral RNA transcription – and disrupting the often fatal cytokine storm.
 
The mechanism by which the drug Choroquine might work is extremely interesting... It appears to be as simple as the "antacid" control of a fluid. Chloroquine will elevate the pH of a solution.

These corona viruses have a "Capsid" container whose outer coating consists of a lipid/fatty membrane. Inside the Capsid is the "+ssmRNA" which is the "assembler machine code" that tells the lung cell Nucleus (the cpu) how to make multiple copies of the virus. The mRNA needs to get out from within the Capsid.

Once the virus has entered the outer lung cell surface, it is automatically wrapped in another lipid/fatty membrane called an Endosome, which in turn is filled with cytoplasmic liquid. The Endosome/Virus is transported (by those motor units referred to in #123) very close to the cell Nucleus that has open pores. It is dragged along a Microtubule tightrope.

As the Endosome approaches the Nucleus, the pH of the inner cytoplasm liquid is lowered from neutral (made acidic) by injection of H+ protons from a "proton pump". This is the trigger for the hairpin harpoon (see #123) to be fired into the INSIDE of the Endosome membrane from the OUTSIDE of the Capsid. Hairpin action drags the two membranes closer and closer together until they fuse. This rips a hole in the Capsid and out pops the mRNA, which then promptly disappears down the rabbit-hole pore of the Nucleus.

You can see a great diagram explaining this, and some 3D simulations, by fast forwarding to "time reference = 41:50" and then ""time reference = 48:42" here... (https://youtu.be/aMvnlAfOWec).

So, by taking Chloroquine at clinically tolerated concentrations, the pH of the Endosome cytoplasm fails to fall to the level needed to trigger the harpoon. Its basically "indigestion technology" to inhibit the release of mRNA !
 
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