Because most philosophies that frown on reproduction don't survive.

Wednesday, May 13, 2020

Understanding the COVID-19 Outbreak: Part 2

This is Part 2 of my big coronavirus analysis post. You can read Part 1 here.

What Is It About Coronavirus?

Let's pause for a moment at this point to talk about why this particular virus caused countries to do such destructive things to stop its spread. Why did China carry out a shutdown which is causing it to log negative GDP growth in its official numbers for the first time since it abandoned Maoist fantasy and joined the modern world? Some people have put forward theories that this is a Chinese conspiracy to cripple the West, or a liberal conspiracy to hurt Trump or an "elite" conspiracy to exert more control over the lives of the ordinary people. Within each country and culture there are various groups reacting to this situation for various reasons of their own, but I think it's hard to see the broad reaction throughout the world as being caused by something other than the virus itself. And why this virus?

There are scarier diseases in terms of symptoms. Ebola seems like classic horror movie material in what it does to the body. And of course, there's always good old fashioned bubonic plague to fill your nightmares. However, this particular coronavirus has a set of characteristics which fit a profile sufficient to make epidemiologists and those who listen to them fairly worried.

It's fairly contagious, with the ability to pass from person to person via tiny airborne droplets of water vapor expelled from the nose and mouth when coughing, speaking, breathing, etc. It has a one to two week incubation period during which the newly infected person is contagious and thus at risk of spreading the virus without even knowing yet that he is sick. It's not so deadly as to wipe out its host population before they can pass it on to others, but it is more deadly than widespread diseases such as seasonal flu.
The SARS-CoV-2 virus which causes the disease known as COVID-19 (I must say, we are not very poetic givers of names these days) is not a malevolent force out to get us. It is a not-quite-living thing with a set of RNA code which can bond with a cell, take it over, and use the cell to manufacture duplicates of itself.  In the process of thus hijacking cells, the virus often causes a good deal of damage to the body.  This particular virus is particularly troublesome to us because it is different enough from other related viruses (called coronaviruses because of the "crown" of spiky proteins sticking out from the virus) that our bodies don't have ready-formed antibodies waiting to attack the invaders.  This doesn't mean that it's impossible for our bodies to fight it off.  Our bodies are constantly learning to identify new bacterial and viral invaders and producing new antibodies to fight them off.  However, this process of getting a large enough infestation of some new disease for our bodies to successfully learn from the attack, build antibodies, and be ready to deal with any similar invaders who show up in the future is a process that we as whole humans often identify as "getting sick."

In the case of this new coronavirus, the getting sick part can involve no symptoms at all, or a set of symptoms like a bad flu, or a set of symptoms that land you in the hospital with low oxygen levels and trouble breathing, or in perhaps 1% to 0.5% of infections: symptoms that end up killing you.  Which of these outcomes you get will depend a great deal on your age, your health, and any number of other circumstances that we don't yet fully understand.

And throughout the period during which coronaviruses are running around inside your body, hijacking cells and turning them into virus factories (while your body tools up to produce enough antibodies to wipe out the virus infestation) the newly produced viruses are finding their way into secretions in the lungs, throat, nose, and mouth which then float off through the air as little globules of moisture, which can in turn be breathed in by other people and allow the viruses that are along for the ride to colonize new cells in a new host body which doesn't yet have suitable antibodies. (If these semi-dramatized descriptions of battles going on within the body sound entertaining, your kids like ours may enjoy the Japanese animated series Cells At Work which can be found on Netflix, in which these sort of things are dramatized to the hilt.)

An important implication of all this description, which I'll get back to shortly when discussing "lockdowns" is that when we talk about how contagious a disease is, we're not talking about something which is a simple characteristic of the disease itself, but rather a result of a number of factors:
- how long the infected body is putting out viruses
- how many viruses the infected body is putting out and by what means those viruses might reach a new host
- how easily stray viruses can get into a new host body and form a viable infestation
- how often infected people are coming into contact with other people
- what percentage of people the infected host comes into contact with are themselves susceptible to infestation

If, on average, given the ability of an infected person to give off viruses and the ease with which those viruses can infect other people and how frequently people meet and how many of the people met are susceptible to infection, one infected person manages to pass the infection on to more than one other person before the infected person's body adapts and successfully wipes out the infection, the disease will continue to spread to a larger number of people and the outbreak will grow. If, on the other hand, the average infected person hands the disease on to less than one new host for the disease, the size of the outbreak will shrink. This measure of how many people the average infected person passes the infection on to is called the R(n) or R0 by epidemiologists. An R(n) which is above 1.0 means that the outbreak is spreading. One below 1.0 means it is shrinking.

COVID-19 Goes Global

The world these days is a pretty connected place, and the threads of those connections are many and tangled. If you had asked me last year where an infectious disease originating in China would spread next outside of Asia, my guess would not have been "Iran and then Italy" but that is the order of march which COVID-19 followed during January and February this year. The fact that the virus hopped from China to Iran and India reminds us that China does not just sell us cheap manufactured goods. China is working to make itself a power for development around the world, and as such they're busy acquiring companies and spreading consultants and business contacts through countries that might like an alternative to working with US companies.

It's been observed, and there's probably a fair amount of justice to this, that it was when the coronavirus outbreak in Italy got really bad that people in the US started to wake up and take notice. Yes, there are those who try to shrug off Italy as if it's a borderline third world country with a fragile health care system, but whatever stones one might choose to throw at Italy's political and medical establishments, we're talking about a modern, Western, affluent country. The hardest hit part of Italy (so far) is Lombardy, the northern province that includes the industrial powerhouse city of Milan.  Logically, we should have taken it seriously back when it was hitting China, but there was still some sense in which people could imagine it was only "over there".  Now the virus was decimating a European country.

There can be a lot of random chance in the early stages of a pandemic. One sick person goes from one city to another. Does he spend lots of time with many different people, or does he keep to himself? Does he ride the metro or take a taxi? Later on in the process it's a numbers game, but in the early stages spread can be very individual. Through whatever series of chances, Italy became central to the Western outbreak of COVID-19. On February 23rd, the Italian government shut down the Venetian Carnivale two days early, ending a major tourist event out of fears that continued gatherings would serve to spread the virus more. Looking back, having the scale of how big the outbreak would become for reference, it's perhaps impressive that they moved so fast. On Feb 23rd (according to the John Hopkins global dataset) Italy had 155 confirmed cases and 3 deaths. It wasn't until a couple weeks later on March 9th that Italy imposed a national "lockdown", asking people to stay in their homes except for essential work and errands. In those couple weeks, the counts had increased to just over 9,000 confirmed cases and nearly 500 dead. Italians took the lockdown order seriously, and indeed had been increasingly practicing "social distancing" (the phrase we now all know so well) in the period leading up to the order. However, because it takes around three weeks for someone who will eventually die of the virus to go from exposure to symptoms to death, it wasn't for another three weeks that the effects of that social distancing began to appear in the number of daily deaths leveling off and beginning to decrease.

However, although Italy copied the "lockdown" approach from China, it did not engage in the kind of aggressive tracing and quarantining of sick or exposed people that had been used by Asian nations in successfully crushing their outbreaks. The result is the lopsided curve that is seen above. What this shows is that Italy (in a pattern we've since seen in many other Western countries with major outbreaks) imposed restrictions severe enough to drastically slow the transmission of the virus, but not enough to actually wipe it out. (I performed some rudimentary modeling to demonstrate this dynamic a little while back.)  Italy saw their peak daily deaths of just over 900 back on March 27th.  As of that day, Italy had a cumulative 9,134 officially recorded COVID-19 deaths.  (Actual death totals appear to be above the official numbers.)  As of May 13th, the total officially recorded deaths are over 30,000 and still increasing by over 150 a day.  With the shape of the outbreak curve, passing the peak doesn't yet mean that you're halfway through.

There were already individual cases of COVID-19 in the US and in other Western countries as the Italian outbreak got going. We now believe the first US death due to COVID-19 was back on February 6th the result of a West Cost strain of the virus which came directly from China. But it was from Italy that the virus spread out across Europe and to New York City. And although the US had already been seeded with strains of the virus which had come with travelers directly from China, it is the New York outbreak (based on the strains which circulated in Europe) which has spread throughout the US and is the predominant source the other regional outbreaks in the US.

The US outbreak gets the lion's share of attention in our US media, partly because it's the local story, and partly because it's the "biggest". However, it's worth noting that one reason the US outbreak is the biggest is simply that the US is very big. If you look at the number of COVID-19 deaths per 1M of population, the US is high but definitely not the highest. That sad honor currently goes to Belgium, whose outbreak (due to peaking later than Italy and Spain, and not having the political implications of the outbreaks in the US and UK) doesn't get as much press.
But of course, even this is a bit of a simplistic view, because the US outbreak is really a number of highly regional outbreaks. The biggest by far is in the New York area, and if you look at New York State as if it were its own country, it would have the deadliest outbreak of any in the world. If we take some US states and mix them in with countries, all sorts of interesting comparisons arise.
New York is almost twice as bad as Belgium, with New Jersey and Connecticut also having worse outbreaks than any European country. Louisiana is neck and neck with Italy. Ohio is better than Canada and Ecuador but worse than Germany. Florida is better than Denmark but worse than Iran. Texas has had a slightly less deadly outbreak so far than Norway.

As all these countries have dealt with their outbreaks, they've mostly pursued the same "lockdown" policies, and they've all seen the same sorts of lopsided curves with a sharp increase at the beginning and a long slow decline at after the peak. The big exception is Sweden, which has asked its citizens to voluntarily pursue social distancing but has not imposed government lockdowns. These lockdowns have become a key area of controversy which I'll address in a later section. In the next section, however, I'd like to address the question of how we measure the coronavirus outbreak and get some sense of how serious it is.

Continued: Read Part 3

1 comment:

Anonymous said...

Continued sooner rather than later! The conspiracy theories are driving me crazy!!!