Covid-19 Diary : Thursday 19 November, 2020

Earlier today saw the US case count break through the 12 million point, less than a week after exceeding 11 million.

Or did it?  Sure, the official count, as reported by Worldometers and elsewhere, shows 12,070,712 cases as of the end of Thursday, but is this truly the actual number of cases?

There’s an enormous mystery about the true number of cases, hinging around two unknowns.  The first is how many people have asymptomatic infections, and the second is how many people have an infection but never appear in the official count.

The phenomenon of asymptomatic infections is not unique to the coronavirus.  Other viruses sometimes can be asymptomatic as well, and it just needs to be considered as one of the far ends of the scale between “mild” and “wild”, or, in medical terms, between “asymptomatic” and “fatal”.

It is also possible to appreciate how some people, even with mild cases, choose not to become part of the official healthcare system and instead just brave it out at home.  When the official response is “there’s nothing we can do for you, don’t contact us again unless you’re seriously unwell and need hospitalization”, one has to wonder how many of those people do exactly that and never get counted into the official tally.

So what with people who never know they even had an infection, and those who don’t get entered into the official system, it is easy to understand how the 12 million count could be substantially lower than the actual reality.

But.

There’s another factor to consider as well.  How do we know a person has the virus, particularly if they are asymptomatic?  How do we know a person with mild symptoms does in fact have the virus rather than some other ailment?  In both cases, the answer is “because they have been tested, and the test shows they are infected”.

You’d be excused for thinking that such a response is as clear and unequivocal as it sounds – a binary outcome, with the two results being either “you have the virus” or “you don’t have the virus”.  End of story.

But, not quite.  In actual fact, the story is much longer, and the accuracy of test results much less certain.  In simple terms, the “gold standard” PCR testing is not actually a gold standard at all; indeed the inventor of PCR testing has gone on record, years ago, as saying it was never intended as a diagnostic test.

The thing about PCR testing is that you can turn its sensitivity up or down.  You can make it not very sensitive, which means there needs to be a large number of viral particles in a sample, or you can turn it up very sensitively, which means it can detect very very few viral particles in a sample.

Its sensitivity is measured by the number of cycles of “amplification” it goes through to create a detectable result.  There is some dispute as to what the maximum number of cycles should be, because at a certain point, the test is set so sensitively that false positive readings start to happen too often.

Dr Fauci has said that at a 35 cycle setting, the chances of a positive result being correct are minuscule.  Indeed, recent testing of the PCR process in general confirms his statement – it shows that at 17 cycles, all positive results are accurate, but at 33 cycles, only one in every five positive results is actually correct, and the other four are false positives.  So is the testing done to no more than 17 cycles?  Or 20?  Or even 33?  How about 35?

It seems that most of the time tests are being done to 45 cycles (apparently a WHO recommendation, we don’t know why).  We’ve gone from having four times as many false positives as real positives to, I don’t know – 40 times false positive?  400?  4,000?  Opinions differ.

Are we basing much of our counting on a test that is falsely positive more than four times as often as it is truly positive?  The answer to that question is totally and completely yes.  As for why that is so, I’ve no idea whatsoever.

There’s one more problem too.  PCR testing simply detects the presence of viral matter.  It doesn’t distinguish between dead and living virus particles.  Maybe you breathed in some dead virus particles, and never got the disease yourself, but the super-sensitive PCR testing detected the deal particles you’d inhaled.  That is yet another type of false positive – truly detects virus particles, but they are dead particles, not an active infection.

Here is an article from a controversial source, Mercola, on the subject.  Please don’t be like some people who shut down as soon as they see a website they don’t like.  Ignore all the Mercola commentary if you wish, and just concentrate on the many cited articles in less controversial sources they provide on which to build their explanation and analysis.  Don’t confuse the messenger (Mercola) with the message (the linked articles).

But – and there’s always a but – we then find ourselves coming back to the facts that we can be moderately sure of.  Maybe the case numbers are over-counted (or under-counted!) but we then have to reconcile that with the death numbers.  Even if we totally ignore the case numbers, even if we double them or halve them, we still have almost 1500 deaths, every day in the US currently (2,065 yesterday), to explain away.

That’s a bottom line that is hard to ignore, and the further thing is that if the case numbers are greatly inflated, then for people who truly have the disease, it is much more lethal than the current slightly-more-than-1% number suggests, which makes the virus more dangerous, and are we now back at the point where we started?

Current Numbers

In the US, it is interesting to note that more new cases were added in ND between Sunday and Thursday than have occurred in VT right from the start of the virus outbreak.

In the minor country list, both Montenegro and Luxembourg moved up two places.

There were almost no changes in the major country list, but that was more than compensated for by some major changes in the death list.  Italy appeared out of nowhere and went straight to fifth place, with the UK moving up three places, and Bolivia dropping out of the list entirely.

The US is now in 9th place, which I think is the lowest it has ever been.  However, it seems certain to displace Chile before Sunday, and is advancing on Brazil too, so we expect to see it back in its regular eighth place again on Sunday.

US Best and Worst States

Top Case Rates Minor Countries

Top Case Rates Major Countries

Top Death Rate Major Countries

I Am Not a Doctor, But….

First we had Pfizer announce a 90% effectiveness rate for its vaccine.  A few days later, the Russians said “we’re at 92%”.  On Monday this week, Moderna said “We’re at 94.5%”.

So it isn’t altogether surprising to see that Pfizer has now crunched a larger set of numbers and is saying “We’re at 95%”.

The most significant part of the Pfizer announcement though is not its 95% claim, but that the company has now completed its shortened Phase Three trial (three months instead of six) and will be applying for FDA Emergency Use Authorization any day now.  In an interesting example of how priorities are a bit strange, Pfizer will be applying for the EUA shortly, and then, at some subsequent time in the future, will publish a refereed write-up of their trial results.

I don’t anticipate any glaring inconsistencies appearing in the refereed document, but I’d also like to see the third party independent scrutiny before rather than after any type of FDA approval.  Keep in mind that this is not a “normal” sort of vaccine at all.  It is using a brand new type of approach, using mRNA.

This is an interesting explainer on what mRNA is, and while I don’t want to sound needlessly anxious, this is a new way of interfering with our body’s immune system that hasn’t even gone through a regular six month Phase Three trial, let alone been studied for some years subsequently.  The linked article mentions, in passing, the potential for it to malfunction and actually make things worse not better, and while clearly that hasn’t happened to the test subjects during the three month trial, it seems reasonable that something so fundamentally new and different should be treated with care and caution.

The good news, such as it is, is that it won’t be until sometime next year, probably the second quarter, that most of us will have a chance at trying the vaccine for ourselves.  So there’ll be another four months of unofficial testing and monitoring, like it or not, before we have to decide if we want to take the vaccine too.

And if we don’t?  Well, there’s the danger of ending up in “The Pit”, which, as this article graphically tells us, is every bit as bad as it sounds.

One of the remaining unknown issues is how long a vaccine might provide useful protection for.  That’s not surprising, because the only way to really know is to wait, watch, and see.  A related variable is how long immunity lasts after having had a dose of the disease, and again, it is difficult to know due to the lack of an extended timebase.

For a long time, the medical profession refused to accept that anyone would or could get the disease a second time.  Then, when one patient was proved to have the disease twice, they said “Oh, it is only one person, it is meaningless”.  Within a week, three other confirmed cases appeared in different parts of the world….

We don’t know how commonplace it is now, but this article points out there are currently 150 cases of known reinfection in Sweden alone.

On the other hand, this article suggests immunity might last years.  Perhaps the obscured truth in that article is in the phrase “the vast majority” (of people will get long lasting immunity).  “Vast majority” is a very subjective term, and we wonder exactly what the number is that the researchers are deeming to be a vast majority.

I recently wrote about Denmark killing its entire population of mink to prevent a new mutation of the virus from getting into the human population.  Alas, as this article relates, infected people with the new mutation have already been found in 20 different countries.  That’s a vivid reminder of how quickly the virus spreads around the world, even at present with social distancing, masks, and most countries having closed borders.

The article also indicates there are over 300 infected people in Denmark alone.

Some good news about testing.  The FDA has finally relented and allowed an “at home, pregnancy-test type” virus test kit to be self-administered at home.  The bad news is the tests will cost $50 each.  At home pregnancy test strips can cost as little as 30c each, and while there’s no reason at all that virus tests should cost as little as pregnancy tests, we need a test that is not only as simple and quick as a pregnancy test, but also as inexpensive, too.

More good news – an Indian-Israeli partnership say they are now in the very last stage of releasing a new test for the virus that takes 30 seconds to product a result.  If they can get the cost down too, that will be transformative.  We have to believe that if this is being developed and subsequently manufactured in India, and intended for use in India, then probably its cost per test will be much less than $50.

Timings And Numbers

All this week, there has been only one single state with a declining rate of new cases – Mississippi.  All the other states have varying degrees of increasing case rates.

There are a fascinating series of charts partway down this gloomy article that vividly illustrates the relentless growth in new case rates across the country over the last few months.

Dr Fauci says the average American might be able to vaccinated as soon as April.  Soon?  We’re not sure that’s the right word, although for sure it is lightning fast compared to what normal vaccine development times are.

Closings and Openings

Lots of closings this week, although, as always, without any apparent rhyme or reason.  For example, in Oregon, retail stores are allowed to have up to 75% of their normal capacity numbers of customers in the store.  Cross the border into Washington, and the shops there are restricted to 25% of normal capacity.

California is categorizing counties into four color coded tiers.  The colors are, in alphabetical order, orange, purple, red, yellow.  Can you put those colors into order of severity though?  I bet you get it wrong (answer in the linked article).

Why can’t they simply call their four tiers “Good, bad, very bad, and extremely bad”?  This is another example of how “simplifying” something actually makes it much more complicated and unintuitive.

New Orleans has canceled its Mardi Gras parades for next year.

This article about Florida not imposing restrictions has the quote “we can’t have businesses dying”.  Well, yes, maybe that is true, but what about people dying?

A New York restaurant will require its patrons to take a test prior to entering its premises.  That’s not an altogether bad idea at all, and while it doesn’t guarantee people are 100% safe, it sure does improve the odds greatly.  The restaurant will charge diners $50 each to be tested.

If we could get the cost down to $5, then it could be extended even to McDonalds.  I never thought I’d miss sitting on a hard seat in a garishly colored restaurant, and chewing on a quarter pounder.

Talking about how testing doesn’t guarantee that people aren’t infected, the poster-child example of that is Seadream, with its disastrous Caribbean cruise that ended up with seven of its 53 passengers infected, notwithstanding multiple testing.

They’ve now cancelled the rest of their scheduled cruises for the balance of this year.

One slightly amusing point.  Everywhere I turn, I’ve been reading of bloggers on the cruise and their experiences.  One wonders how many of the 53 fools on board were bloggers, desperate for a free cruise, and how many were actually “real people”.   I bet Seadream is now wishing they’d not had any bloggers with audiences on board and could have kept things a bit quieter!

Shortages

This is just one of a growing number of articles of the returning shortages of items such as, yes, “bathroom stationery”.

Another shortage?  Tests.  How is it, with new test protocols seemingly springing up regularly, we still can’t test everyone who wants/needs testing?

Virus?  What Virus?

I’m tempted to say “only in Ireland” but I can think of several other national stereotypes that would also support this concept.

Air passenger numbers are steadily climbing back up to last year’s levels again.  Someone should tell them the CDC is advising people not to travel for Thanksgiving.  We’d broaden that advice to every day, not just the Thanksgiving weekend.

It also seems the CDC’s left hand doesn’t know what its right hand is doing.  The same CDC that says “don’t travel for Thanksgiving” also said, a couple of weeks, that cruise lines can reactivate their cruising programs.

Rumors

Let’s hope this chilling prediction stays in the rumors category.

Other

This is a good example of correlating two events that may not be related.  But it has both my dog and me anxious.

To close what has been a series of mixed messages on a positive note, here’s an article about an extraordinary achievement by an extraordinary middle schooler.   We expect some naysayers will insist we ignore her achievement because she isn’t a “real” scientist….

Please stay happy and healthy; all going well, I’ll be back again on Sunday.

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