On Corona Virus

Five Articles

Covid-19 - Summary

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Last Updated: Sunday, 25 October 2020 10:02

Why is Coronavirus so Deadly?

Reproduced from article by James Gallagher,
BBC Health and science correspondent

A simple virus has brought life as we know it to a screeching halt. We have faced viral threats before, including pandemics, yet the world does not shut down for every new infection or flu season. So what is it about this coronavirus? What are the quirks of its biology that pose a unique threat to our bodies and our lives?

Master of deception

In the early stages of an infection the virus is able to deceive the body. Coronavirus can be running rampant in our lungs and airways and yet our immune system thinks everything is a-ok.

"This virus is brilliant, it allows you to have a viral factory in your nose and feel completely well," says Prof Paul Lehner from the University of Cambridge. Our body's cells start releasing chemicals - called interferons - once they are being hijacked by a virus and this is a warning signal to the rest of the body and the immune system.

But the coronavirus has an "amazing capability" of switching off this chemical warning, Prof Lehner says, "it does it so well you don't even know you're ill". When you look at infected cells in the laboratory you cannot tell they have been infected and yet tests show they are "screaming with virus" and this is just one of the "joker cards" the virus can play.

It behaves like a 'hit and run' killer

The amount of virus in our body begins to peak the day before we begin to get sick. But it takes at least a week before Covid progresses to the point where people need hospital treatment.

This is a really brilliant evolutionary tactic - you don't go to bed, you go out and have a good time," says Prof Lehner.
So the virus is like a dangerous driver fleeing the scene - the virus has moved on to the next victim long before we either recover or die. In stark terms, "the virus doesn't care" if you die, says Prof Lehner, "this is a hit and run virus".

This is a massive contrast with the original Sars-coronavirus, back in 2002. It was most infectious days after people became ill, so they were easy to isolate.

It's new, so our bodies are unprepared

Remember the last pandemic? In 2009 there were huge fears about H1N1, aka swine flu. However, it turned out to be no way near as deadly as anticipated because older people already had some protection. The new strain was similar enough to some that had been encountered in the past.
There are four other human coronaviruses, which cause common cold symptoms.

Prof Tracy Hussell from the University of Manchester, said: "This is a new one, so we don't think there's much prior immunity there." The newness of Sars-CoV-2, to give it the official name, she says, can be "quite a shock to your immune system". This lack of prior-protection is comparable to when Europeans took smallpox with them to the New World, with deadly consequences.

Building an immune defence from scratch is a real problem for older people, as their immune system is slow off the mark. Learning to fight a new infection involves a lot of trial and error from the immune system. But in older age we produce a less diverse pool of T-cells - a core component of the immune system - so it is harder to find ones that can defend against Coronavirus.

It does peculiar and unexpected things to the body

Covid starts off as a lung disease (even there it does strange and unusual things) and can affect the whole body.

Prof Mauro Giacca, from King's College London, says many aspects of Covid are "unique" to the disease, indeed "it is different from any other common viral disease". He says the virus does more than simply kill lung cells, it corrupts them too. Cells have been seen fusing together into massive and malfunctioning cells - called syncytia - that seem to stick around.

Prof Giacca also says you can have "complete regeneration" of the lungs after severe flu, but "this does not happen" with Covid. "It is quite a peculiar infection," he said.

Blood clotting also goes strangely awry in Covid, with stories of doctors unable to get a line into a patient because it is immediately blocked with clotted blood. Clotting chemicals in the blood are "200 percent, 300 percent, 400 percent higher" than normal in some Covid patients, says Prof Beverly Hunt from King's College London.

She told Inside Health: "Quite honestly, in a very long career, I've never seen any group of patients with such sticky blood." These whole-body effects could be due to the cellular doorway the virus strolls through to infect our cells - called the ACE2 receptor. It is found throughout the body including in blood vessels, the liver and kidneys, as well as the lungs. The virus can cause runaway inflammation in some patients, making the immune system go into overdrive, with damaging consequences for the rest of the body.

And we're fatter than we should be

Covid is worse if you are obese, as a generous waistline increases the risk of needing intensive care, or death. This is unusual.

"Its very strong association with obesity is something we haven't seen with other viral infections. With other lung injuries, obese people often do better rather than worse," said Prof Sir Stephen O'Rahilly, from the University of Cambridge. "It looks pretty specific [to Covid] it probably happens in pandemic flu, but not regular flu."

Fat deposited throughout the body, in organs like the liver, causes a metabolic disturbance which seems to combine badly with coronavirus. Obese patients are more likely to have higher levels of inflammation in the body and proteins that can lead to clotting.

- BBC

 

Covid-19 - Vitamin D Trial

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Last Updated: Monday, 21 September 2020 17:48

Spanish Trial Results

76 patients in Spain who tested positive for Covid-19 and who were ill enough to be admitted to hospital, took part in a randomised double blind trial of Vitamin D supplementation. This means no doctors or clinical staff knew which of the patients were given a Vitamin D analogue. Apart from this all were given the best possible care and all other treatments. While the size of the trial was small, the chances of it being in error is 1 in 1000. 50 patients received the vitamin and 26 did not, creating two groups to compare.

Of the 50, only 1 required ICU care and all recovered.

Of the remaining 26, 13 were admitted to ICU, two died and 11 recovered.

The Initial dose was the equivalent of about 100,000 I.U, with follow ups of 50,000 and 10,000. 
A daily skin exposure to 10-15 minutes of around mid-day summer sunshine is about 10,000 I.U, depending on melamine levels & closeness to the equator. Typically this dose is achievable within +/- 35 degrees of the equator, or north of Taupo.  South of this, much of the population of NZ is likely deficient in Vitamin D. 

In the USA some 42% of the population is considered deficient, rising to 82% of black skinned and 70% of Hispanic.

Links for detailed information and fact checking follow:-

Dr John Campbell - Analysis

How much vitamin D to take

Association of Vitamin D & Covid-19

Spanish Trial Results

Contact Tracing

Details
Last Updated: Sunday, 25 October 2020 09:00

Tracing your contacts with others

Privacy

This is of great concern to many about Big Brother watching and legal enforcers using the info for their own purposes. Users usually fall into one of two camps.
One group may claim they have nothing to hide. They are wrong - would they reveal all their passwords to a third party?
The other opposes any form of intrusion and object to enforcers or non-authorised gaining access to encrypted data via a back-door or other method.
Fortunately, perfect forward encryption is un-crackable in any useful period of time as the keys are transient and only used once.

Where common keys are stored somewhere they can be passed on to authorities allowing data to later be decrypted. A typical example is where Apple claim that user's phones cannot be decrypted by them, which is true - the key is embedded in the phone's secure enclave chip which cannot be read, but phone backups stored at Apple are protected by their key, which authorities can request.  

The catch 22 in the time of Coronavirus is that while knowing patient identity is essential for limiting further transmission, once tracking is allowed it maybe impossible to later revoke or opt out.

A Private Solution 

Google and Apple between them have announced a solution for Android and Apple phones which is expected to be available as an API update to all their phones in May 2020. It will be up to Govt medical services to write a tracking App and to get access to that part of the API. Both have indicated that they are planning to write such an app themselves.

Rather than pass personal contact data to authorities, it advises the users themselves if they have been within range of an infected person. Neither person nor those who have been within range of them can know the identity of the other or anyone else. Authorities only get involved when transmission and infection has occurred. Thus the bulk of the data remains private to each user and authorities only see those suspected of confirmed infected and their possible contacts.

Google Maps Timeline

This is another service that is very useful and semi private to remember locations visited and the times and distance traveled. It can also be shared between others you trust, such as a partner. The author found this very useful to see each other as a dot on a map while in malls or when visiting non-familiar towns. It has also been able to avoid speed camera fines when one can prove that at the time of the alleged offence you where somewhere when checking this at a later date. (Its often very difficult to remember this even a few days later and next to impossible after a month when the ticked arrives. This happens a lot more often than you know.) Google also allows deletion of ones history after a period.

How it works

Each phone generates a permanent unique and private key at random to serve as the phones identity. Its size is so great (2^256) that a collision (two phones with the same one) won't ever occur and it's never ever revealed. This key is used to create smaller daily keys and from them tracing numbers (tokens) every 10 minutes with a time stamp. Each phone captures and saves the tokens of every other phone coming within a preset blue tooth range and time, typically 2 metres and a few minutes.  No external storage of the token immediately occurs. It remains private to each phone and tokens older than a period, typically 21 days, are deleted. Thus phone storage requirements are small, about 40 tokens per megabyte. For most people after 21 days this would amount to a single photo.

If some official was to examine your phone, these tokens are no more useful than disclosing what lotto numbers you picked in previous draws, other than knowing you bought a ticket.  i.e You came in contact with another unknown phone. (Not quite because Lotto themselves have them recorded so they know the winners and to prove that the ticket is valid, the outlet, and the time of sale. In the case of a lost ticket the EFTPOS transactions might also identify the owners bank account.)  In the case of the tokens, no-one else knows them or can identify the source phone.

For a full security analysis refer to podcast #762.   Security Now Contact Tracing    Also Available at GRC.com,  Itunes and youtube.

How does this help with tracing

When a person feels unwell and/or is tested positive for infection or antibodies, they become registered with the authorities and must then upload the captured tokens to an official server via the app. There would likely be a legal requirement to do this, possibly to get treatment. Everyone confirmed as infected has their recorded tokens made public on the official website. They are still useless without the phone they actually came from.  Only the phone that generated the token can identify them, so privacy is maintained. (i..e. Someone in NZ won lotto, but only that person and the lotteries commission know who, but everyone knows the numbers! [token]).

Periodically, daily? all phones with the app check the official server for any published tokens. Because each token was derived from their unique private ID key, only the originating phone can recognize them. If a match is found, the originating phone will immediately warn its owner that they have been in close contact with a now registered and infected person and can calculate the date and time it occurred from the token, which is now known as an exposure notification. At this point, they need to immediately self isolate and contact authorities and arrange for testing. When such a match occurs, it maybe that their phone number and details saved in the app are automatically uploaded, so they can then be identified and contacted by medical personnel. The authorities will only then know their identity along with all other phone owners who have also been in contact and who are now suspects for infection and must be tested.

Weaknesses

  • While highly unlikely, its theoretically possible for the smaller tracing numbers to be duplicated which could result in a false positive. Its not a real issue as they only exist for 14 days.
  • It requires the co-operation of the users themselves.
  • Every one must carry their phone when venturing outside their bubble and of course install the official app with Bluetooth enabled.
  • A person may be suffering from the flu or even healthy and report an infection.  However, to avoid cry wolf attempts, authorities would only make that owners' uploaded tokens public after confirmation of a genuine case. And possibly have similar penalties to falsely dialing 111.
  • Affected users loose their privacy once a reportable event occurs. It is a medical issue though and subject to confidentiality.
  • An infected person may decide to ignore their symptoms and rely on random testing, or just be asymptomatic.

Pluses and Minuses

  • - People won't load the app.
    This could be discouraged by either offering incentives or penalties. e.g Free public transport, receipt of the cash incentive, queue priority when shopping, etc. Large retailers, Bank ATM, might require to see tokens emitting when at a turnstile for entry, or even capture them for later store tracing. The tokens themselves are still of no use until someone generates an infection alert.
  • + Those receiving a tracing match could get different alert levels as appropriate. e.g Person reports sick, but the cause is unknown and those getting alerts can be advised to just self isolate pending further confirmation.
  • + Health authorities are not overwhelmed with contact tokens.
    They only get data on those of infected uses and those who have been in contact, or who maybe vulnerable and their contacts.
  • + It is expected that only approved organisations will be able to access the phone API and write apps which Google or Apple must approve of before publishing the App on their respective stores. Thus no fake sites or Apps possible. Not that the tokens are of use, but a person who registers on one as infected might be vulnerable to fraudulent offers and cures.
  • + Connections by apps to organisations sites would likely require use of a public key in the app so only the approved app can connect to the official site.
  • + Organisations might not accept token uploads until they send you a net-code or scan a QR code to further prevent cry wolf attempts.
  • - Organisations must still carry out random testing to catch asymptomatic people. Any found though could then upload their tokens for publishing and so on.
  • + Users should welcome the knowledge of finding out if they are at risk of infection.
  • - Not possible to enforce people to always carry their phone when out.
  • - Many don't yet have a phone.
  • - Increased phone battery drain may affect some. (If low energy Bluetooth is used it would be minimal.) 
  • + Its possible that the API might always enable Bluetooth in countries that have official apps available and contact tokens could be exchanged even if no app was installed. Thus these tokens could later be checked when the app is installed.
  • - The official app proposed for NZ may not use this API, in which case there will likely be no provable way such an app is genuinely private and users will need to make up their own minds in whether to trust any such claims.
  • - A tracing App alone is not enough. Using the APP is no guarantee of anything. It is subject to many false positives, such as close bluetooth proximity to a neighbour through the the wall, or someone in the next isle of a supermarket. However, the ability to identify all those possibly infected and test them is a huge advantage in reducing the R0 to manageable numbers, and that is currently the only possible option other than lock-down.
  • + The Bluetooth system developed by Apple and Google has been enhanced to reduce false positives: 
    Exposure time is now tracked in five minute intervals, with the maximum reported exposure time capped at 30 minutes.
    The API will now include information about the power level of the Bluetooth signal in the data that is exchanged between phones. This can be used in conjunction with the RSSI ("Received Signal Strength Indication") to more accurately estimate the distance between two phones when contact was made.

The NZ App

This currently does not use Bluetooth at all but is expected to be added in time, probably when phones are officially updated with the new API. For now it just allows one to locally record the details and time one enters the premises by recording the information in a QR code that the business displays.  This is similar to the Google location tracker, but more accurately identifies the business than would GPS location alone, which tend to be unreliable when indoors and signal is weak. Using them both together is probably a good idea.

CNBC Video

This 14 minute video covers much of the above and compares the various tracing systems used in various countries, some of which are very intrusive.
Google-and-apple-partner-to-fight-coronavirus-with-contact-tracing.html

        

 

Why is Covid-19 worse than the Flu

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Last Updated: Sunday, 25 October 2020 10:42

Covid-19 versus the Flu

The information presented here is subject to change as knowledge about covid-19 is rapidly evolving. Updated October 2020.

  • Covid-19 is a new virus and no one, except those after recovery may have some immunity and even then for how long it may last. There are already known cases of re-infection.
  • There are no drugs or medicines available to cure Covid-19, yet. Our bodies have to do this and keeping fit, healthy, and ones immune system in top condition, is likely the best we can do for ourselves.
  • The rate of infection is measured by the Reproduction Number (R0) which varies between countries, the level of immunity and other factors, and is continually being re-evaluated.
    R0 for various diseases are: Measles 12-18, Ebola 1.5-2.5, Smallpox 5-7, Influenza 0.9-2.1, and Covid-19 1.5-3.5 with its average being 2.5.
  • Covid-19 has an incubation period of 5-10 days. Its not clearly known when an infected person becomes contagious or when it ends, so we have assumed the worst. Latest information has this period, called the Series Interval or Si for short, at about 5-7.5 days. Si is the time between when an infected person detects symptoms and when passed on to another that they detect symptoms.  A high Si slows the speed at which the virus propagates, so when the first person infects another 3 it might be about 6 days before they become aware of it and in the meantime infect others.
  • Influenza has an incubation period of 1-2 days. Most people are home in bed before they become infectious and usually only infect one other, but with a lower Si the spread is quite fast. Many also have some immunity, either naturally or by vaccination. When R0 is less than 1 the virus slowly dies out.
  • The latest tests for Covid-19 are now effective before a person becomes ill, if at all, and getting results of tests is not yet immediate and this is what makes it so difficult to control. Our only defense is to find (contact trace), isolate, and test all contacts of a person who tests positive, hopefully before they also become spreaders. Genetic tracing of the virus strain has helped greatly in establishing those infected from the original source and therefore part of the same cluster or tree and can be eliminated.
    Wearing a mask won't necessarily protect one from catching the virus, as it might have collected on the mask surface and get transferred from there to hands an then back to the face when the mask is removed and disposed of. However, if one is already infected the ability to spread the virus to others is greatly reduced.
  • Covid-19 is more dangerous than influenza which many die form each year, but we do have a flu vaccine. Covid-19 is far more contagious and can survive on surfaces longer thus spreading to more people and being airborne makes transmission easier, but its the higher R0 and our lack of immunity that's the problem.
  • Covid-19 is known to cause deaths in people with existing conditions, as does influenza. Emerging factors are those who are obese, have heart, lung, or immune weakness. Residing in cities with high pollution levels also exacerbates lung issues.
    Some healthy people, when infected, seem to cope for 7 or so days after becoming ill and then suddenly change for the worse needing hospital care. It is thought that children's lungs may not have yet developed the type of cells that get attacked, but if infected they are still contagious. Watch the second video bellow to see how each symptom progresses onto the next.
  • Most recent research is pointing towards it being able to adapt to the weakness of individuals and seems to depend on the symptoms that manifest. For those that get seriously ill its for various reasons. Children, for example, seem to get blood issues and adults don't always get lung issues. Its now known that Covid-19 can attack in various ways other than respiratory, with brain, liver, kidney on the list as well as blood issues. This now makes it much more serious than the flu and latest research published by the CDC places the danger of Covid-19 about 5 times greater.

Math behind spreading infection and Fantastic supporting Videos