Covid Variant Mu

 Covid variant Mu: Some tangential thoughts.

The Guardian reports on a new “variant of interest”, labelled Mu

https://www.theguardian.com/world/2021/sep/01/who-monitoring-new-coronavirus-variant-named-mu

Mu may turn out to be a problem if it is more transmissible than Alpha or Delta, and/or can evade immune system defenses better. It all depends on whether it makes people sicker and/or kills more people. So it could be bad. Hence the monitoring.

However,  if Mu turns out to be much more transmissible yet much milder in its effects than Alpha or Delta, it could be exactly what we want: A tolerable, flu-like version of covid. For higher transmissibility would enable it to outcompete the other variants. There would still be occasional epidemics of the more serious versions, as happens with the flu, but it’s likely that better treatments would blunt their effects.

In short, a highly transmissible but mild Mu could buy the time needed to develop good treatment and even better vaccines. Hope, or wishful thinking?

                                   

Covid-19 denial by people who have it:

 

An ER nurse in South Dakota tweeted about some of her patients who deny they have covid-19.: 

How does one react to this report? I can see that some people would deny their peril in any case. We don't want to face  the near-certainty of death. But I suspect that most such denials would be versions of hope, a clinging to the near-zero chance of recovery. What this nurse reports is something else: denial triggered by politics, by ideological poison, by delusions promoted by a demagogue. What's worst about is that it prevents the comfort of family connection, of seeing and talking with loved ones.

Update: On reflection, I think that in these cases politics and ideology complicate what is a normal human reaction to the prospect of imminent death. I don' t think it's common, though.

Update 2021-09-09: I've now read stories about the Delta variant surge in Oregon and other places. The anecdotes are heartbreaking. Yet vaccine-denial and covid-denial continue, even in those places hardest hit by the latest surge in infections and death. The sad fact is that an unvaccinated person admitted to ICU has a less than 50% chance of surviving.

 

Comment on anti-vaxxers updated 2026-01-11 (link)

I've updated the post. Click on this one.

Long Covid

Comment on a report in New Scientist, October 31-November 6, 2020, pp. 10-13.

The latest data show that symptoms of covid-19 persist for up to four months in some people. Probably longer, as the study stopped at that point. The symptoms range from fatigue through “brain-fog” and memory loss through problems breathing. Blood clots threaten to provoke strokes. Headaches are common. Damage to heart, lungs, and other organs has been observed. Hospitalised people appear most likely to suffer these symptoms. The data are incomplete, but it’s likely that around 5% of people who recover from covid-19 will experience more or less serious symptoms two months or more after the onset of the infection.

I think that somewhere between one and five percent will suffer from “long covid”, defined as debilitating symptoms for two months or longer. That’s a serious consequence, since these people will need some continuing care, and/or accommodation at work. The more severe cases will be unable to work at all. The economic losses will be high, combining lost productivity and cost of care. Or, to put it another way: a significant proportion of human and other resources will be diverted from the usual economic activities.

Unanswered questions: Who is most likely to be affected, and why? What kinds of treatment will mitigate long covid? How long will it actually last?

Plagues and the Fall of Empires

 

 Plague in Marseilles, 1720

Yesterday (November 2nd), I read an article in Junior Skeptic (included in Skeptic Magazine). It told the history of plagues, of epidemics, of pandemics. How an unknown disease killed upwards of 20% of the population of Athens (404 BCE). How a plague during Marcus Aurelius’s reign (161-180 CE) killed 20% or more of the citizens of Rome. How the first wave of bubonic plague killed somewhere between 25 and 50 million people in Europe (it reached Constantinople in 542). The second plague pandemic killed about 1/3rd of the European population, and some settlements were wiped out completely. (The last plague epidemics occurred in the 1600s and 1700s.) How smallpox ravaged Europe. How the Europeans brought smallpox to the Americas, killing up to 90% of indigenous populations.

In every case, major political and economic change followed. Athens lost the Peloponnesian War. Rome became weak, and finally lost its hegemony a couple of centuries later. The bubonic plague finished off the western Roman Empire. And so on. A little extra research showed that the second and third waves of bubonic plague caused Europe-wide wars and re-arranged the remnants of the Roman Empire. Even the Spanish Flu of 1918-19 caused disruption: the Roaring 20s were as much a reaction to it as to the Great War.

And generally speaking, people forgot the great plagues almost as soon as they fizzled out. School histories tend to ignore them. In fact, I didn’t know about the Athenian epidemic until I read this article; and I thought I had learned a pretty good overview of ancient Greek history.

We don’t want to be reminded that we are subject to the random appearance of pathogens. Even now, when SARS-COV-2 is infecting people, there are many who claim it’s a hoax, or no worse than the flu, or caused by G5 phone towers, or whatever. Anything, it seems, rather than face up to the terrifying truth: we have no defences against new pathogens. And another, much less convenient, truth: that these new pathogens transfer from animals to us. Which means that as climate change alters ecosystems, it also alters the interactions between humans and other animals, and so increases the odds that a new pathogen will emerge.

One of the factors in today’s US presidential election is covid-19. Mr Trump persists in downplaying its severity and perils. Mr Biden persists in using covid-19 as a symbol for Mr Trump’s failures as a President.

We shall see what happens. But in any case, the American Empire has begun its downward trajectory.

See Wiki’s article on SARS-COV-2

Pandemic statistics: bad news, good news.

Katharine Cove, Lake Superior, 2001

 

This morning's US covid-19 death count is 231,566. Canada stands 10,262. See Johns Hopkins Covid-19 Dashboard for more. That's the bad news. The good news is that the case-fatality rate is decreasing: fewer infected people are dying. The reason is a mix of good and bad news: In both countries the infection rate of younger people has gone up. Older people die at ten times the rate (or more) of younger people. So there's what at first glance looks like a paradox: much higher daily case numbers, not many more daily deaths.

Other considerations: 

a) Younger people tend to be the wage earners, so their higher case numbers affects the labour market, which is already a mess because the pandemic has reduced demand, and so reduced the need for labour.

b) The long-term effects of covid-19 range from longish recovery times to varying degrees of physiological and cognitive damage. The data suggest that 5% or so of covid-19 recover with such in long-term effects. In the long run, that could have worse effects than the present infection rates.

c) The economy is in serious trouble, because too many people are still thinking in terms of getting back to normal. The pandemic has shown that a very large segment of our economy has relied on discretionary spending, aka as whim and desire. This segment will not return to its former profitability.

d) We hear a lot about anti-mask demonstrations, but in general, most people do wear masks, which I think means that we are generally more aware of our connections to the larger community. Which brings me to that last comment for today:

e) Most of us have found that we haven't taken the casual daily contacts, the greetings, and chats etc seriously enough. We need social connection, we need face-to-face connection. Screens and tinny voices coming from inadequate speakers aren't enough.

 

Covid-19 will become endemic (Updated 2021-08-21)

Update 2021-08-21: The Delta variant has now become the dominant strain, but apparently does no more damage than earlier variants. It is at least a hundred times more infectious than earlier variants. Since even in vaccinated people it takes time for the immune system to react, so-called "break-through" infection in vaccinated people are fairly common. But unvaccinated people are about seven times more likely to be hospitalised, and to die.

Evolutionary theory predicts this: Any mutation that improves the odds of infecting a host will eventually dominate. The same theory predicts that more variants will arise, but if they are less infectious than Delta, they will not spread. The most worrisome possibility is that Delta could morph to be more  damaging.

Since none of the vaccines prevent infection 100% of the time,  the virus (SARS-COV-19) will continue to infect people, and mutated strains will continue to arise. Sooner or later, there will be a strain that the immune response to vaccines will not be able to fight efficiently, which means that the infected people will be shedding virus longer, which will hasten the spread of that strain. There is of course the likelihood that the immune response will also change, but that change will be slow, and so such new strains will at first infect a lot of people.

So we will have a virus that  mutates regularly, and epidemics will come and go. Covid-19 will become an endemic disease like the flu. Both will cause epidemics at fairly regular intervals. The evidence so far indicates that the covid epidemics will be worse.

NB: I have corrected an omission in the discussion of false test results below. The actual effect of a test error rate depends on whether it's the same or different for positive and negative results.

Update 2021-01-25: There are two worrisome new variants of the virus. One identified in the UK, the other in South Africa. Both are more infectious, and both may be more lethal, but the vaccines apparently work as well as with the original variants. The vaccination programs have hit predictable snags in production and logistics, causing a great deal of pointless finger-pointing.

 Today WHO announced that covid-19 "may" become endemic.

Huh?????

No "may" about it. It will become endemic. The reason? Several, actually.

a) The wide range of responses to exposure to the virus, which vary from zero symptoms to serious and lethal illness to serious and lethal complications, to long-lasting after-effects. People with zero to mild symptoms are infectious.

b) Mutation. Current research on the mutated strains suggests that the virus will mutate continually, which means that by the time a vaccine or drug is developed, it may not work. Mutation also implies that vaccines and drugs would have to be updated at intervals, and that some future strains may be even more lethal than the current ones.

c) Variable immunity to the virus, which means re-infection and recurrence of the illness is certain. In fact, it's already happening. Also, the presence of antibodies does not guarantee immunity.

d) Variable incubation stage. It ranges from about 5 days to about 14 days after exposure. Also, repeated exposure seems to be a factor.

e) Variable asymptomatic but infectious stage, which follows incubation. Current data suggest two to four days.

f) Error rate of antibody test. It's about 90% accurate. Suppose an actual infection rate of 5%, then the false positive rate will close to 70%. (See the Wiki article on the base rate fallacy and the Footnote below.) This means that the anti-body test will generate a false sense of security.

These factors add up to guaranteed infections in future. The only unknowns are the future rates of infection, what factors affect those rates, and how lethal future infections will be. Experience with the flu shows that every now and then a more lethal strain will emerge. Current data suggest that covid-19 will be somewhere between twice and five times as lethal as the flu.

We will have to learn to live with it. It's likely that covid-19 will always be worse than the flu.

Footnote: Why a 90% positive accuracy isn't very good.
Suppose a 5% infection rate. Suppose a test with 90% accuracy for both positives and negatives. Then, in a population of 100,00, we will have:

Actual positives: 5,000
Detected actual positives: 4,500
Actual negatives: 95,000
Negatives detected as false positives: 9,500
Total positives detected: 9,500 + 4,500 = 14,000
Percentage of false positives: (9,500/14,000) x 100 = 67.8%

So if you get a positive test, it's more than twice as likely that you're negative than you're positive.

The state of corona virus knowledge as of today (May 3, 2020)

SARS-CoV-2 (the virus) and covid -19 (the illness)

Here’s what “we” know and don’t know as of 2020-05-01. “We” are the people who’ve collected and interpreted the data. “We know” means the data strongly support the conclusion. “We don’t know” means there are insufficient data to draw a conclusion. Compiled from reports in science news magazines, media reports, and Q & A sessions with experts.-WEK

A)    We know: Some people are infected with the virus but don’t get sick.
    We don’t know: how many.

B)    We know that the effects of the virus range from zero to death; and mild to lethal complications.
    We don’t know: Why the virus has such a wide range of effects.

C)    We know: there is a time between infection and symptoms during which a person will be infectious.
    We don’t know: the actual range of both time and severity of this infectious state.

D)    We know: that people who’ve been infected will have anti-bodies in their blood;
    We don’t know: whether the presence of antibodies gives immunity, nor what degree  of immunity, nor how long such immunity might last.

E)    We know: there will be second wave of infection, and probably a third and fourth one,
    We don’t know: how bad these subsequent waves will be.

F)    We know: that some of the economic and social effects will be permanent.
    We don’t know: which effects, nor how these effects might change over time, nor what  the knock-on effects will be.

G)    We know: covid-19 will become another infectious disease that will take its yearly toll.
    We don’t know: when that will happen, nor how common or lethal covid-19 will be.

H)    We know: that some anti-viral treatments show some activity against SARS-CoV-2.
    We don’t know: whether that activity will be good enough for effective tretament.

I)    We know: effective treatments and a vaccine will reduce the danger of covid-19 to that of the flu.
    We don’t know: which treatments will be effective.
    We don’t know: whether a vaccine is possible, and if possible, how well it is likely to work.

J)    We know: the counter-measures have reduced infection rates.
    We don’t know: how effective those counter measures actually were.

K)    We know: that a combination of dry cough and high fever, with some other signs such as difficulty breathing, indicate covid-19. But only a test can confirm the diagnosis.
    We don’t know: what other signs and symptoms may be indicators of covid-19.

Update 2020 05 04: UK doctors have observed covid-19 patients with low and extremely low blood oxygen levels, but without the usual distress. Another puzzle.

Econ 101: Why wage subsidies won’t bankrupt the country

A comment in response to the Financial Post’s worry about how much the wage subsidy program will cost. It was announced by Prime Minister Trudeau on 2020 03 30.

Since this is a wage subsidy program, most of the money will be used to pay for shelter, utilities, food, and transportation. Most of these dollars will generate sales tax revenue for  the Province (8% in Ontario) and/or the Federal government (5%) when spent.

But a dollar spent will be spent again. The consensus is that a dollar will be spent between five and seven times before all or part of it returns to the original spender. That means about 65 to 70% of the money will return to the governments.

In short, the wage subsidy will largely pay for itself. The question, “How much will the program cost?” misses the point.

Footnote: The Canadian government will provide wage subsidies of 75% on the first $59,400 of a person's wages. This will be available to all employers whose business has been impacted by covid-19. The Prime Minister also urged businesses to pay the additional 25%, and warned that any business trying to game the system will be dealt with. Many workers will eventually pay income tax on all or part of the wage subsidy.

Update 2020 03 31: My arithmetic is off, since food isn't taxed. So I estimate the payback in taxes at about 40 to 70%. However I haven't factored in the payback, financial and otherwise, of keeping the suppliers of food and transportation etc in business.

Covid-19 and self-isolation after travel abroad

Good advice for  anyone anywhere returning home from  abroad. Keep yourself as safe as possible. We're all in this together.

Social distancing and covid-19 (link)

Well-done aimation showing why social distancing matters:
https://youtu.be/dSQztKXR6k0

A comment on anti-vaxxers

I posted the following comment in response to a NYT times piece about a measles outbreak in Samoa [https://www.nytimes.com/2019/12/19/world/asia/samoa-measles.html]

The Boomer and younger generations in the West have grown up with close to zero experience of infectious diseases. Not their parents (I'm one): pretty well all of us knew friends and neighbours killed by measles, diphtheria, whooping cough, smallpox, tuberculosis, scarlet fever, polio, . . . And many of us lost family to infectious diseases. We learned to fear the silent killers, who took one unawares.

But we failed to pass on that fear, because we figured that vaccinations would limit or even eliminate these diseases. We took the new-found safety for granted, not realising that what's taken for granted is simply ignored.

That's what has left an opening for the resurgence of the anti-vaxxers, who have a 200-year long history of denying the science.

It's grim, but we have to teach people to be afraid. Not a happy prospect, but I think a necessary one.

2020-01-05: Recently, I came across the phrase “shifting expectation base-line”. It referred to the fact that we tend to assume that the world has always been as it is when we first experienced it as children. We are unaware of how much it has changed since our parents and grandparents were children. That concept applies to the perception of infectious diseases. Our children and grandchildren live in a world with almost zero infectious disease, so they assume that’s the norm.

2020-01-15: For the record, we had our flu shots as soon as they became available this season. So far, these annual vaccinations have protected us.

Update 2020 11 14 The covid-19 pandemic has begun to change people's perceptions. For the oldest generation it's largely deja vu, I think. It's like that for me, anyhow, but I'm not as terrified of covid as I was of polio when I was 10 years old. For the younger generations, it's stunning. The reactions range from enraged denial to apathy. Most people accept that intense anti-infection measures are now necessary, and compliance ranges from grudging to paranoid. The 3rd wave is inundating Canada, and continues to rise in the rest of the world. The yearning for a vaccine creates false hopes: the announcement that Pfizer and BioNTech have created one that's 90% effective has prompted reactions from a sigh of relief to suspicious skepticism. The logistics of distributing a vaccine to some 7 billion people no doubt are prompting nightmares. But the ethics are worse: who should get it first, and why?

Update 2026-01-11: The anti-0vaxxers have become a victorious political force. Measles outbreaks are becoming common. Canada ha already lost its WHO "Measles free" status. The US's federal public health agency (CDC) is in the hands of a vociferous anti-vaxxer. This will end very badly.

 

Politics 101: Proportional voting

The kerfuffle has died down, but I suspect that the rage of the extremist supporters of proportional voting will resurface during the next election in 2020. (2017-02-27)

Right now, there’s a kerfuffle about Justin Trudeau’s backtracking on changing Canada’s electoral system. He promised that 2016 would be the last election using first-past-the-post or  plurality voting. Some form of proportional representation would replace it.

A lot of people don’t like plurality voting. We have three strong parties: Conservative, Liberal, and New Democratic, each with regional strengths and weaknesses. The Green Party regularly gains 3 to 5% across all ridings (1), and wins in one. In addition we have the Bloc Quebecois, a purely local party, but which has won large numbers of Quebec seats in the past. Each major party wins majorities in some seats, and all have widely varying regional support. The Liberals tend to win in the East, and the Conservatives in the West. The NDP is mostly urban.

The result is that national support between 35 and 40% is enough to form a government. (2) If enough people vote their support rather than their opposition, we tend to get minority governments, in which no Party holds a majority of the seats.

People give various reasons for thinking this is an unfair system. Chief of these is this observation: with roughly 40% support and a roughly 60% voter turnout, about 25% of voters voted for the government, while 75% voted against it. It seems manifestly unfair that only one in four voters determine who governs. Worse, the distribution of seats does not reflect popular support. What about the values and views of those whose vote was cast differently? They will not be heard, it seems. What about people who voted for a losing party? Their vote doesn’t count, it seems. So why vote?

Let’s dispose of the unfairness argument immediately. There is in fact no fair voting system. Several mathematical proofs and demonstrations show that all systems can (and therefore sooner or later will) produce results that most voters do not like. Some will do so most of the time.

Plurality with three or more strong parties magnifies the difference between popular support and distribution of seats, which practically guarantees voter dissatisfaction.

Ranked voting tends to favour second and third choices, practically guaranteeing weak support for the government. Weak support translates into dissatisfaction very quickly.

Runoff voting, like plurality, magnifies the difference between popular support and seats won, since it masks low support for the eventual winner.  Like ranked voting, it guarantees weak support for the government.

Proportional voting almost always results in minority governments, which usually require formal or informal coalitions. Coalitions magnify the power of minority views and values, and of single-issue parties, which tend to be extreme. (3)

In short, all voting systems will skew the vote one way or another. They all cause different kinds of mismatch between what people want and what they get.

So the question becomes not, What kind of voting system do you want? but rather, What kind of skewed voting or unfairness can you accept, and why? And the complementary one, What kind of unfairness can you not tolerate, and why?

I do not like “proportional representation”, as its supporters usually term it. I have two reasons, the magnification of extreme views, and the magnification of the power of the Party.

Proportional representation encourages the formation of parties with extreme views. Three or more strong parties will result in minority government. That forces collaboration and even coalition. That’s a good thing, and if politics were on the whole a process for reasonable people to figure out what they want to do and how to do it, I’d have no qualms. But politics is about power, and in the pursuit of power people are not reasonable. To achieve a working majority, the government may have to act on extreme views from one or more small parties to ensure the votes it needs. If it can’t do that, there’s instability. (4)

I don’t like extreme views. They are always held by a minority, thus not only do not reflect the majority view, but always oppose them. Holders of extreme views are generally incapable of admitting the validity of different ones, not even those that are similar. That’s a recipe for trouble, of political and civil divisions, and, too often, bloodshed. Any voting system that gives extreme views more effective power than their numbers warrant is bad. (5) Proportional representation encourages people with extreme views to form Parties, knowing that the odds are that they will get at least a seat or two, and with luck may use those few seats to exert influence on the coalition.

Proportional representation always means slates of candidates, one way or another. (6) Slates are determined by Parties. This means that the power of the Party machine becomes stronger. The Party machine does not like local control of candidate selection, since that makes it easier for a group of  determined local voters to frustrate the will of the Party. Slates make it easier for the machine to prevent that.

I prefer the plurality system, despite its flaws, because it magnifies local control, and it forces all parties to appeal as best they can to the average voter, the so-called mushy middle. There we find a variety of political views and values, ideas that often contradict each other, and the human inconsistency that makes collaboration not only possible but necessary. Parties that have to appeal to that mushy middle don’t drift too far to the left or right. When they begin to do so, they are replaced by the other party.

Bottom line: I don’t mind that Trudeau backtracked on his promise. If I had to choose another system, I’d go with runoffs. Ranked voting does not predict run-off voting, which forces the voter to think twice, which tends to change people’s minds.

Notes:
(1) A riding is an electoral district. We elect “Members of Parliament” who sit in the House of Commons. We do not elect Senators.
(2) The Party that wins the most seats forms the government. If it has less than half the seats, it’s a “minority government”.
(3) Neither the Bolsheviks nor the Nazis won a majority of seats before they came to power.
(4) See Italy, which changes its government about every 18 months.
(5) See Israel. Most Israelis want peace with the Palestinians, but the government is hamstrung by extreme right-wing nationalist parties whose votes it needs.
(6) Slates are ranked by the Party. If your Party wins 10 seats, you’ve voted for the top 10 members of the Party list, whether you want them all or not.

Update 2020: Trudeau called an election in 2019, and achieved a minority, largely because the Conservatives had a gormless leader in Andrew Scheer, and because regional loyalties in Quebec and the West outweighed national ones. The Green elected three members, a major win for them.
     Scheer tried to look like your friendly barbecuing neighbour, but couldn't convince enough people that he enjoyed a beer. He actually looked like the hustling insurance salesman he claimed to be but wasn't. The knives came out almost immediately. Scheer also "won the popular vote", which is true if one ignores the fact that the lemming-like mass-vote for the Conservatives in Alberta and Saskatchewan made up that surplus "popular vote."
     The current covid-19 pandemic has given Canadian leaders the opportunity to act, and to look like they know what they're doing. Both Trudeau and Doug Ford (Premier of Ontario) surprised by their competence and caring. The Conservatives could have placed themselves as supportive, caring, and constructive critics of Trudeau's measures, but instead fell back on whinging about debt. The two seekers for the party leadership have not made much of a positive impression on non-Conservatives, and probably not even on Conservatives.
     Would proportional voting have made much of a difference to the current Parliament? Possibly, depending on the system adopted. That heavily regional "popular vote" win would have given Alberta and Saskatchewan too much power over the rest of Canada, which would increase the regional divisions. I doubt that a Conservative government would have rushed to create the financial supports created by the Trudeau Liberals with Bloc and NDP support. It's significant that Doug Ford, a small-c conservative by instinct, praises the co-operation between his Conservative Provincial Government and the Federal Liberals.