Wednesday, September 30, 2020

How accurate are the different coronavirus tests?

I looked recently into the accuracy of forehead thermometers and, while I concluded that they were useful as an initial screening tool, they are not equivalent to an actual COVID-19 test.

There are two main types of tests for the coronavirus: the molecular real-time polymerase chain reaction nasopharygeal  test (usually shortened to "RT-PCR test" or just "PCR test", for obvious reaons), and the antigen test. Antibody (or serology) tests also exist, but they do not indicate an active virus, and are of more limited use for diagnosis. Some 130 different tests have been approved by the US's Federal Drug Agency (FDA) under its Emergency Use Authorization (EUA) protocol, which allows '"unapproved uses of approved medical products" in emergency situations like this, but none of them are fully approved by the FDA, with all the rigorous testing and vetting of new procedures that normally happens. And, as we shall see, some tests are definitely better than others.

The PCR test is still considered the gold standard, and here we are talking about the familiar image from countless television reports of a white-coated healthcare worker poking a long swab deep into a testee's nose. The test searches for the presence of the virus' genetic material deep in a person's nasal cavity. Done properly (i.e. deep enough to cause discomfort, to where the nasal cavity meet the pharynx at the back of the mouth), the PCR test is almost 100% accurate and effective, even in the absence of symptoms. 

However, ideally, the test should be done least 8 days after infection to ensure that sufficient viral particles are present (i.e. a test performed soon after infection is less effective and more likely to produce a false negative result). Less invasive, more shallow swabs of the nose, or of saliva from the back of the mouth,which have been authorized recently in the US, are also typically less accurate, although still quite good. False positive results, where viral particles remain long after a person has recovered from the disease, are possible, but not that common.

PCR tests must be analyzed in a lab on large specialized equipment, and it can take several days for results to become available, or even up to a week or more (theoretically, they should be available the same day, but in practice this does not happen). The other issue that is arising with extensive PCR testing is a shortage of reagents, the chemicals that are needed to analyze the tests, which in many cases is proving to be the limiting factor on how many and how fast tests can be performed. "Pooled testing" may speed things up, whereby batches of tests are analyzed together: if the result is negative, no more needs to be done, while, if the pool result is positive, individual tests can then be re-analyzed. 

The FDA has also recently approved saliva or spit tests under its EUA protocol, such as the SalivaDirect test developed by the Yale School of Public Health, among others. This is a PCR test, but using the quick and simple expedient of spitting into a container, rather than the invasive and time-consuming nasopharyngeal swab method using trained personnel. These newer tests appear to be very accurate (Yale claims 94% accuracy compared to nasopharyngeal PCR tests), as well as quicker, cheaper and less instrusive, and home kits are expected to be available soon.

The other main COVID diagnostic test, antigen testing, on the other hand, produces results within just a few hours, even minutes. However, the compromise is that that they are substantially less accurate, mainly because they require large amounts of viral material to yield a positive result. Antigen tests use nasal or throat swabs to look for the presence of certain proteins on the surface of the virus. If the test is positive, it is generally reliable, but false negatives, where the virus is present but not picked up, can occur in 20-30% of tests, even as high as 50%, making it much less effective than the PCR test.

There are also antibody tests available. Antibody tests are not diagnostic tests: they do not indicate that someone has the virus, merely that they had it at some point. They require blood samples not nasal swabs, and results are typically available within a few days, or less. 

However, COVID-19 antibodies can take several days or even weeks to develop after an infection, and the jury is still out on how long they remain active (probably just several weeks), and to what extent they would be effective on a mutating virus. Long-term T-cell analysis would be better in this regard, but no such test is easily or commercially available. 

Antigen tests are subject to false positive results, as the antibodies may occur in response to a different coronavirus. False negative rates of 20-30% have also been reported. So, the antibody test is not considered very useful or reliable, and may give a false sense of security. The presence of antibodies may not mean that a person is immune to a different (or even the same) strain of the virus.

So, it's PCR all the way, despite the slowness of results and the existence of other alternative tests, which are better used as confirmatory tests. But new saliva-based PCR tests are much quicker and cheaper, less invasive, and almost as reliable, and may be the way forward. Amid reports of 6-7 hour-long waits for traditional testing, this may be just what we need, but don't expect Canada's highly cautious and creaky old approval system to authorize them any time soon.


Well, I shouldn't speak too soon. Canada has just announcing that it is ordering nearly 8 million rapid tests from Abbott Rapid Diagnostics ULC, despite Health Canada not having approved the technology yet.

ID Now is a PCR test that has been available in the USA since March, but it yields results in just 5-13 minutes using a portable machine the size of a toaster. It still requires a qualified  health professional to collect a sample using a throat or nasal swab, but it could still speed up testing significantly. There was some concern early on in the US that the tests yielded many false negative results, but Abbott maintains that these problems have been fixed and that tests perform well when administered soon after symptoms appear.

Tuesday, September 29, 2020

How accurate are forehead thermometers, really?

I've seen several articles (like this one from the New York Times in February) suggesting that the now-ubiquitous forehead thermometers (aka infrared thermometers, temporal scanners, or just "temperature guns") are quick and easy but not actually very accurate. Now, that article also talked about how useless masks are (this was February, remember?), but my physiotherapist said the same thing just this week, so it's clearly a pretty widely-held view. Is it actually true, though?

Well, yes and no, but mainly no. There are several different types of thermometer, and they can give slightly different readings. Rectal temperature readings are generally considered the most accurate, although the drawbacks are obvious, and this method is rarely used in practice. The more usual oral thermometer tends to give a reading about 0.3-0.6°C (0.5-1.0°F) lower than a rectal thermometer, and the oral reading is the most often used (yielding the familiar 37.0°C or 98.6°F "normal" temperature). Tympanic or ear thermometers give very similar readings to rectal thermometers. Armpit thermometers tend to give temperatures 0.3-0.6°C (0.5-1.0°F) lower than oral thermometers. And so, as it turns out, do infrared forehead thermometers. 

So, while they are not 100% accurate, they are still pretty good. They are unlikely to give a reading that is wildly inaccurate in either direction. And, if they are predictably half a degree lower than oral thermometers, it is easy to make an adjustment for the discrepancy. 

Of course, whether a fever is a reliable marker of COVID-19 is another question entirely: the presence of a fever is a good (but not definitive) indicator of the virus, but the absence of a fever does not equate to the absence of the virus.

Forehead thermometers remain the easiest, quickest and least invasive test for COVID-19, and so should not be dismissed out of hand when you encounter them at a barbers or a nail salon or a school or a restaurant. But they are not reliable or definitive enough to serve as the arbiter of health at an international airport in my opinion. They are a useful initial screening tool, but no substitute for a proper COVID-19. But how accurate are THEY?

Donald J. Trump State Park is a polluted wasteland - significant?

A Guardian journalist has reported on the glories of Donald J. Trump State Park in New York state. There are some lovely state parks in New York; Donald J. Trump State Park is apparently not one of them.

It's actually just a couple of tracts of muddy, overgrown wasteland, about an hour or so north of New York City, straddling Putnam and Westchester counties. It's not easy to find - signage disappears after one on Taconic State Parkway - and, if you do find it, there's not much there, other than an empty gravel patch that serves as a parking lot, and a noticeboard warning against ticks. There is not even a bench or a trash can. A half-hearted attempt to develop it as a dog park was abandoned some years ago after asbestos was found in the decaying structures on the land. I guess it never did turn into "one of the most beautiful parks anywhere in the world" as Trump predicted back in 2006, when he donated the land to New York state.

Because this was surplus land that Trump couldn't make any money out of. His initial plans to build a golf course foundered when permission was refused on environmental grounds. So, Trump donated it to the state so that they could get the maintemamce bills and he could get the tax write-offs. He did, of course, specify that the land should always bear his glorious name. And now New York is stuck with it, although they are too embarrassed to actually list it along with their other state parks.

You can see it as an ironic statement on the state of Trump's America. Or you can see it as a piece of polluted wasteland. Luckily, you will probably never be able to find it anyway, so you may not have to see it.

Why I won't be watching the presidential debates

I don't plan on watching the first presidential debate tonight, or any of the others for that matter. I have high blood pressure, and watching Donald Trump in full flight is only going to make it worse. I tried watching daily Trump's pandemic addresses many times back in those distant, early days of April and May, when he thought that he could squeeze some political capital out of such appearances, but I usually had to move away at some point. The guy just makes me really angry.

I don't expect Joe Biden to do particularly well in the one-on-one debates. The best I am hoping for is that he holds his own and does not make any howling mistakes. This is Trump's territory. He will talk more, he will talk louder, he will goad and slash, he will make endless unsubstantiated claims, he will lie through his teeth and do it in such a way that many people will believe him. And, in the absence of any fact-checking, he will no doubt score lots of points, and may well sway some undecideds (although this apparently only makes up a surprisingly small 3-5% of those expected to vote).

But I don't feel that it would be edifying to watch this kind of bear-baiting contest. Add to that the fact that this debate is hosted by Trump's pet news channel, Fox News, which will lob him some easy partisan topics, and I think my time will be better spent reading a book or surfing Netflix. Anything really.


I'm feeling extremely vindicated right now. My wife tried to watch it and gave up after about half an hour. I'm sure I wouldn't have lasted that long.

The debate has been almost universally panned, even by conservative media outlets. Trump was completely out of control, no policies got discussed, the moderator was ineffectual, and the American public got shafted. Again.

It's tempting to think that such a shitshow can only have damaged Trump's chances. But his supporters don't tend to operate in a logical manner, and even that is not assured. All we can be thankful for is that Joe Biden survived and did not have a heart attack, although there is serious debate around whether it is in his, or anyone's, interest to go through two more of these things.

Monday, September 28, 2020

British pub curfew causing national trauma - which points to another major problem

The new 10pm curfew in Britain, a desperate attempt to reduce the alarming surge in COVID-19 cases there since lockdown has been relaxed, seems to be creating a national existential crisis.

The country is now at around 6,000 new cases a day, worse than during the dark days of April and May, snd some authotities are predicting this may go up to as much as 50,000 a day next month unless strong measures are taken. Something clearly has to be done, and the latest solution, both in Britain and elsewhere - and one which I am very unconvinced by, I have to say -  is to reduce the length of time that pubs and restaurants can serve alcohol, alcohol being one of the things that cause people to drop their guards and forget to observe social distancing rules. Ontario has also put a time limit on drinking in bars recently - last orders at 11pm, close at 12 - and this has also met with vocal opposition, despite the even less strict rule in this case. Does anyone really nees to be still drinking at midnight?

Pub owners often maintain that pubs are not the problem, and that virus transmission os more likely to happen in the home, but the evidence points to a lot of transmission in newly-reopened bars and restaurants. Socializing in an enclosed, poorly-ventilated, loud, crowded place is just not a good idea during a pandemic. The alcohol-fuelled drops in inhibitions and attention, as well as the effects of music snd dancing, only make things worse.

Many opppnents, pub owners and local politicians in Britain are arguing that if they force pubs to close at 10pm, then they are actively encouraging people to go to each others' homes or into the streets to continue the party in a more crowded and totally unregulated environment, which is only going to make the problem worse. As one politician explained, people are "coming out of a pub or restaurant at 10 o'clock, and thinking what to do next", to which I would respond, "go the hell home, don't you know there's a pandemic on. for fuck's sake?"

Many people seem to think they have a God-given right to party and to get smashed. But in a time of national, even global crisis, I'm sorry, but they may have to curtail their cosy, privileged lifestyle in the interests of the common good. I like a beer as much as the next guy - although perhaps not as much as the next guy in Britain, which has a major national alcohol problem anyway, which frankly needs to be addressed, pandemic or no pandemic. But if pubs and restaurants are part of the problem (and no-one is saying they are the whole of the problem), and people can't control their urges - yes, millennials, I'm looking at you! - then they need to allow the authorities to do what little they can to regulate those variables they can control, and not whine about how their lives are not quite perfect. 

These are non-essential activities, get used to it. 10pm last orders is not a human rights violation, it's a minor inconvenience. And maybe we need to just suck it up, and accept a bit of short-term pain to avoid long-term pain, both economic and social. Otherwise, this damned pandemic is going to go on forever!

Ooh, I didn't intend that to come out quite so stridently. I guess that's how I really feel.

Sunday, September 27, 2020

What is QAnon, and are they serious?

You may have heard passing reference to QAnon recently, probably in relation to anti-mask or anti-lockdown protests, and wondered what it is. Well, the answer probably won't satisfy you very much, but that doesn't mean the movement, if movement it can be called, can be written off as a bunch of harmless cranks.

QAnon is essentially a conspiracy theory, that seems ludicrous at first, or even second  glance, but it is apparently growing and making new connections among far-right wing groups, particularly in Gilead-style Republican America. Its base belief is that there is a shady international cabal of Satan-worshipping pedophiles that has been secretly abducting and sexually abusing children, and harvesting their blood to make a serum for eternal youth. 

The conspiracy theory maintains that this cabal, which supposedly includes high-profile individuals like Hillary Clinton and financier George Soros, is part of a secret government, or "deep state", that is controlling American and world affairs behind the scenes. Unlikely as it may seem, Donald Trump is considered by believers to be the knight in shining armour, the saviour that is leading a righteous war against this deep state. Trump, of course, is quite happy to play long with it, and has retweeted several QAnon posts in the past. There are various other ancillary beliefs to QAnon, many of them anti-semitic, and the movement is a deliberately vague, cryptic and ill-defined protean entity that can take on any shape or flavour it sees fit.

It all began in October 2017, on the sketchy social media site 4chan, the work of a single anonymous user labelled "Q". Q claimed to be a secret service operative, and he/she worked to spread a rather random and unlikely conspiracy theory, that appeared out of nowhere during the 2016 US election, that Hilary Clinton was operating a child sex ring out of a Washingto DC pizza parlour. Somehow, Q's posts struck a lodestone of interest, even after Trump was elected, and took advantage of the magical thinking that many far-right and Trump supporters are prone to. The rest, as they say, is history.

In fact, the movement has been getting more and more active on social media in recent months, and has even spread outside its American heartland. Britain is now its second-largest support base, followed by Canada, Australia and Germany. In Britain, Boris Johnson has been hailed as a potential co-saviour, along with Trump.

I know, sounds cracked, eh? And so it is, but its adherents, like the anti-vaxxers and other odd alt-right groups, can be seen popping up at any right-wing protest, and lending their support to all manner of anti-progressive causes, and so it cannot just be ignored. The FBI has gone so far as to identify QAnon as a potential terrorist threat, and you can see why: anyone that divorced from reality could potentially be capable of just about anything. Twitter and Facebook have been busy blocking QAnon-related accounts but, hydra-like, they just pop up again elsewhere.

Some acts of violence have already been linked to the belief, including the mass shooting in Hanau, Germany, in February of this year, and several QAnon supporters are even running as Republican and independent Senate candidates in the upcoming US election, which could conceivably see it move more fully into the real, offline world. Not so funny now, is it?

Wednesday, September 23, 2020

Horgan plays cynical politics in calling early election in BC

British Columbia Premier John Horgan has called an early election for October 24th 2020. This is a full year before his four year term officially expires and, despite his protestations, it is a cynical exercise in playing politics.

Horgan's minority NDP government has been held together for the last three years by an agreement with the BC Green Party, with which it has much in common. And a pretty successful partnership it has been too. Back in 2017, when thisnagreement was struck, Horgan specifically promised that he would not look to dissolve the legislature until the next scheduled election

But now, as he basks in a 19-point poll lead over the second-place Liberals, largely due to a generally favourable view of his and his government's COVID-19 management (although that could change as a second wave begins to hit BC), Horgan wants a majority. He says he "struggled mightily" with the decision, but that 19-point lead suggests otherwise. He says it is to allow the NDP a freer hand in dealing with the pandemic and the economic fallout therefrom, but his reliance on the two Green Party MPs does not seem to have hampered his policies much.

This is just a cynical power grab, pure and simple.

Canadian EV sales hampered by ... car dealerships

If the increased adoption of electric vehicles is to be a major plank in our fight against global warming, then we need to at least make sure the damned things are available. Sales of all vehicles have plummeted during the pandemic of 2020, but one of the main reasons why the take up of electric vehicles is so low is that Canada has a supply problem, and demand for EVs is outstripping supply and stocks in dealerships.

Two-thirds of Canadian dealerships had no EVs in stock at all, even before the pandemic struck. Outside of the three largest provinces - Ontario, Quebec and British Columbia - EVs are almost impossible to find. Quebec and BC still offer attractive rebates for the purchase of EVs; Ontario does not, thanks to Doug Ford's cancellation of the previous Liberal government's rebate scheme. There is also a federal financial incentive available countrywide.

There are various reasons for this, including a shortage of battery components, and manufacturers prioritizing shipments to China and Europe over North America. But there are other, less honourable, reasons too: many dealerships choose not to stock EVs because of the extra consumer education involved, the need for battery-charging infrastructure, and the loss of potential service and repair revenue, i.e. ironically, because EVs require much less service than ICE vehicles, dealerships make less money off them.

Waiting lists for EVs run from a few months to over a year, which is a ridiculous situation to be in. This in itself is another reason for dealerships not to stock EVs - why would they want to pursue a purchase with a year's delay when they can sell other cars immediately? This catch-22 situation is of their own making.

Electric vehicles are expected to become more and more popular as their battery range increases and their prices come down. For example, California has just committed to phasing out gasoline-powered cars by 2035, and where California leads, Canada usually follows eventually. But the car industry here is certainly not making things any easier, and more governmemt intervention would help there.