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Covid19, Your society and you are from the point of view of Data Science. Translated article by Jeremy Howard and Rachel Thomas (fast.ai)

Hello, Habr! I present to you the translation of the article “Covid-19, your community, and you - a data science perspective” by Jeremy Howard (Jeremy Howard) and Rachel Thomas.

From translator


In Russia, the Covid-19 problem is currently not so acute, but it is worth understanding that in Italy two weeks ago there was not such a critical situation. And it is better to inform society in advance than to regret later. In Europe, many do not take this problem seriously, and thereby put many other people at risk - as is now evident in Spain (the rapid increase in the number of cases).

Article


We are the date of Scientists, our job is to analyze and interpret the data. And the data on covid-19 is cause for excitement. The most vulnerable groups in our society, the elderly and low-income people, are in the zone of greatest risk, but to control the spread and impact of the disease, we all need to change our usual behavior. Wash your hands thoroughly and often, avoid crowding, cancel scheduled events, and do not touch your face. In this post we will explain why we are worried - and why you should also be worried. Corona in Brief, written by Ethan Alley (president of non-profit, who develops technologies to reduce the risk of pandemics) is a great article that provides all key information in a nutshell.

We need a working healthcare system


Just a couple of years ago, one of us (Rachel) was diagnosed with a brain infection that kills about a quarter of the people who get it; one third get lifelong mental breakdown. Many remain with lifelong visual and hearing damage. Rachel arrived at the hospital parking lot in a very serious condition, but she was lucky and received the necessary attention, diagnosis and treatment. Until recently, Rachel was completely healthy. With a high degree of probability, we can say that quick access to the emergency room saved her life.

Now, let's talk about covid-19 and what can happen to people in a similar situation in the coming weeks and months. The number of people infected with covid-19 doubles every 3-6 days. At a rate that doubles every 3 days, the number of infected people can increase by 100 times in two weeks (in fact, everything is not so simple, but let's not get distracted by the details). One out of 10infected people need many weeks of hospitalization, and many of them need oxygen. Despite the fact that this is only the beginning of the spread of the virus, there are already regions where hospitals do not have free places - and people cannot receive the necessary treatment (not only from coronavirus, but also from other diseases, for example, that vital therapy, which Rachel needed). For example, in Italy, where just a week ago, the administration stated that the situation was under control, now about 16 million people are locked at home (Update: 6 hours after this post, Italy locked the whole country), and similar tents are put in order to somehow cope with patient flow:

Medical tent in Italy.

Medical tent in Italy.
Dr. Antonio Pesenti, head of the regional department responsible for crisis situations in northern Italy, said : “We have no choice but to arrange intensive care in corridors, operating rooms, wards ... One of the best healthcare systems - in Lombardy - on the verge of collapse. ”

It's not like flu


Influenza mortality is estimated at 0.1%. Mark Lipstich, director of the Harvard Center for Infectious Disease Dynamics, estimates coronavirus mortality at 1–2%. The latest epidemiological modeling found a 1.6% mortality rate in February in China, 16 times higher than that of the flu (this estimate may be inaccurate, as mortality rises when the health system fails). Positive assessment: 10 times more people will die from coronavirus this year than from influenza (and the forecastElena Grewal, a former director of Data Sines at Airbnb, shows that 100 times more people can die in the worst case scenario). And this is not taking into account the huge impact exerted on the medical system, as described above. It is clear that some people are trying to convince themselves that in this situation there is nothing new and that the disease is very similar to the flu - because I really do not want to accept an unfamiliar reality.

Our brain is not designed to intuitively understand the exponential increase in the number of sick people. Therefore, we must analyze this situation as scientists, without resorting to intuition.

image
How will it look in two weeks? Two month?

On average, every person with the flu infects about 1.3 people. This is called the “R0" flu. If R0 is less than 1.0, the infection does not spread and stops. With a larger value, the infection spreads. In coronavirus, R0 today is 2-3, outside of China. The difference may seem small, but after 20 “generations” of infected people who transmit the infection, 146 people will be infected with R0 1.3, and 36 million with R0 2.5! (This, of course, is very approximate and many factors are ignored in this calculation, but this is a reasonable illustration of the relative difference between coronavirus and influenza, all other things being equal).

Note that R0 is not a fundamental parameter of the disease. It depends on the response and may change over time. It is noteworthy that in China, the R0 of the coronavirus has decreased significantly - and is now approaching 1.0! How? - you ask. Applying all the necessary measures on a scale that is difficult to imagine in a country such as, for example, the USA: completely closing megacities and developing a verification system that allows you to monitor the condition of more than a million people a week.

In social networks (including such popular profiles as Elon Musk), there is often a misunderstanding of the difference between logistic and exponential growth. Logistic growth refers to the pattern of epidemic spread of form S. Exponential growth, of course, cannot go on forever - then there would be more infected people than the entire population of the Earth! So, as a result, the rate of infection should always slow down, leading us to form S (known as sigmoid) growth over time. At the same time, a decrease in growth does not happen just like that - it is not magic. Main reasons:

  • Massive and effective actions of society.
  • A high number of infected people, which leads to a low number of potential victims due to the lack of healthy people.

So there is no logic in relying on logistic growth as a way to control a pandemic.

Another reason why it is difficult to intuitively perceive the effect of coronavirus on your local community is the significant delay between infection and hospitalization - usually about 11 days. This may seem like a short period, but by the time you notice that the hospitals are crowded, the infection will reach the level where it will be 5-10 times more infected.

Note that there are some early indicators that say the impact on your region may be somewhat dependent on climate. In the article " Temperature and latitude analysis to predict potential spread and seasonality for COVID-19"it is said that the disease has so far spread in a temperate climate (unfortunately for us, the temperature in San Francisco, where we live, lies precisely in this interval; the main centers of Europe, including London, also fall there."

"Do not panic. Keep calm ”doesn't help


One of the most common responses to calls to be vigilant on social networks is “Don't panic” or “keep calm.” This at least does not help. No one thought panic was the best way out of the situation. For some reason, however, “keep calm” is a very popular reaction in certain circles (but not among epidemiologists whose job it is to track such things). Perhaps "keep calm" helps someone to justify their own inaction or to feel superior to the people they represent in a state of panic.

But "keep calm" can easily lead to an inability to prepare and give an answer. In China, 10 million people were placed in isolation, and two new hospitals were built by the time they were in the state of today's USA. Italy waited too long, and only today (Sunday, March 8) they announced 1492 new infected and 133 dead, despite the isolation of 16 million people. Based on the best information that we can confirm at the moment, just 2-3 weeks ago, Italy was in the same situation as the USA and England today (in terms of infection statistics).
Note that almost everything associated with coronavirus is suspended in the air. We do not know either the rate of spread of infection or mortality, we do not know how long it survives on surfaces, we do not know whether it survives and how it spreads in hot climates. All that we have is our best guesses, based on the best information we could get. And remember that most of this information is in China, in Chinese. Now the best way to understand Chinese experience is to read the WHO-China Joint Mission on Coronavirus Disease 2019 report , based on a joint study of 25 experts from China, Germany, Japan, Korea, Nigeria, Russia, Singapore, the United States and WHO.

When there is some uncertainty - that, perhaps, there will be no global pandemic and that, perhaps, everything will just go away without the collapse of the hospital system - this does not mean that the right decision is to do nothing. This would be too speculative and suboptimal for any development of events. It also seems unlikely that countries like Italy and China would shut down a huge portion of their economy without good reason. And this does not coincide with what we see in infected areas where the medical system cannot cope (for example, in Italy, 462 tents are used for screening, and intensive care patients were moved from the infected areas).

Instead, a thoughtful, sensible answer is to follow the steps recommended by experts to prevent the spread of infection:

  • Avoid crowds.
  • .
  • ( ).
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  • , (!).
  • (, 9 , ).


If you are under 50 and you do not have risk factors, such as a weak immune system, cardiovascular disease, smoking, or other chronic diseases, then you can relax: it is unlikely that you will die from coronavirus. But how you react is still very important. The chance that you will become infected is still great - and if you become infected, the chance to infect others is also great. On average, each infected person infects more than two people, and they become contagious even before the onset of symptoms. If you have parents you care about or grandparents and plan to spend time with them, you may later find that you have infected them with a coronavirus. And this is a difficult burden that will remain for life.

Even if you are not in contact with people over 50, most likely you have more colleagues and acquaintances with chronic diseases than you realize. Studies show that few people talk about their health at work for fear of discrimination . We are both at risk, but many of the people we communicate with may not know this.

And, of course, this applies not only to people in your environment. This is also a very significant ethical issue. Everyone who makes efforts to slow the spread of the virus helps the whole society to reduce its spread. As Zeynep Tufekci wrote in Scientific Amercian: "Preparing for the almost inevitable global spread of the virus ... is one of the most socially useful, altruistic things you can do." She continues:
We must prepare - not because we personally feel in danger, but also to reduce the danger for each of us. We must prepare ourselves not because the end of the world is approaching, but because we can change every aspect of the risk that we face as a society. It is true that you need to prepare because your neighbors need it — especially your elderly neighbors, your neighbors who work in hospitals, your neighbors with chronic illnesses and your neighbors who cannot prepare themselves due to lack of time or resources.
It influenced us personally. The biggest and most important course we have done at fast.ai, which represents the culmination of the years of our work, was to begin at the University of San Francisco in a week. Last Wednesday (March 4), we decided to conduct the entire course online. We were one of the first courses to switch to online.. Why did we do this? Because at the beginning of last week, we realized that by conducting this course, we indirectly encourage the mass gathering of hundreds of people in a closed space, many times over several weeks. Gathering groups of people in closed spaces is the worst thing that can be done in this situation. We felt obligated to prevent this. This decision was extremely difficult. Working with students was one of the greatest joys and the most productive period every year. And our students were going to fly to this course from around the world - we did not want to disappoint them.

But we knew that this decision was right, because otherwise we, with a high probability, would increase the spread of the disease in our society.

We have to smooth the curve


This is extremely important, because if we reduce the spread of infection in society, we will give the hospitals in this society time to cope with both infected patients and regular patients whom they should treat. This is called a “smooth curve" and is clearly shown in this diagram:

image

Farzad Mostashari, the former National IT Coordinator for Healthcare, explained: “Every day there are new infected people who have no travel history or connections with known infected people, and we know that they are just the tip of the iceberg due to delays in inspections. This means that in the next two weeks the number of infected people will increase significantly ... Trying to introduce small restrictions in conditions of exponential distribution is like concentrating on sparks when a house is burning. When this happens, you need to change the strategy to mitigating preventive measures to slow the spread and reduce the impact on health. " If we can reduce the spread so that our hospitals can withstand the load, then people will have access to treatment. But if there are too many sick,many of those who need hospitalization will not receive it.

Here's what it looks like from a mathematical point of view, according to Liz Specht:
1000 2.8 . 330 . 65% . 330 (, , ). , 10% . ( , — , ). 8 . (, , .) , , 6 . 20% , ~2 . 5% — ~14 . 2.5% 20 . , , , ( ), . , .., , , , .

—


As we have already discussed, this mathematics is not accurate - China has already shown that it is possible to reduce the spread of emergency measures. Another good example of a successful reaction is Vietnam, where, among other things, national advertising (with a catchy song!) Quickly mobilized society and convinced people to change their behavior to be more acceptable in this situation.

This is not just a hypothetical situation, which was clearly visible during the Spanish in 1918. In the United States, two cities showed very different reactions to the pandemic: Philadelphia held a planned parade of 200,000 to raise funds for the war, San Luis activated a strategy to minimize social contacts to reduce the spread of the virus; all public events were canceled. And here is what the statistics on the dead in each of the cities looked like, as it is displayed inProceedings of the National Academy of Sciences :

image
Different reactions to the 1918 Spanish woman

The situation in Philadelphia quickly got out of hand to such an extent that there were not even coffins and morgues to bury so many dead.

Richard Besser, former director of the Centers for Disease Prevention and Control during the H1N1 pandemic in 2009, argues that in the US, “risk of danger and the ability to protect oneself and one's family depend on income, access to health care, immigration status and other parameters . ” He indicates that:
, . , , , . , — , , — , . . 60 , .

The US Bureau of Performance Statistics shows that less than a third of people on the lower pay level have paid sick leave.

image
Most low-income Americans do not have sick pay, so they have to go to work.

We do not have reliable information on Covid-19 in the USA


One of the biggest problems in the USA is the lack of checks; and the results of inspections are not published properly, which means that we don’t know what is really happening. Scott Gottlieb, the previous head of the Food and Drug Administration, explained that the checks were better in Seattle, so we have information about the infection in this area: “The reason we found out about Seattle's covid-19 infection is the focus of independent research. So complete surveillance in other cities has never been. So other hot spots in the US may not be found at this time. ” According to The AtlanticVice President Mike Pence has promised that around 1.5 million tests will be available this week, but in all of the US, only 2,000 people have passed the test so far. Based on work from The COVID Tracking Project , Robinson Meyer and Alexis Madrigal of The Atlantic say:
, , , covid-19 , , , . 8 , — , , . 66.650 — 10.000 .

Part of the problem is that it has reached the political level. In particular, Donald Trump clearly stated that he wants to see “numbers” (that is, the number of infected in the US) at a low level. (If you want to learn more about this topic, read the Data Science ethics article " The Problem with Metrics is a Fundamental Problem for AI "). Head of Artificial Intelligence at Google, Jeff Dean , wrote a tweet about the problem of political disinformation:
, — UNAIDS, . , , . , , (, , , , -, , ). , , , / COVID-19. , - , - , - , , . , .
Politicians don't seem to be trying to change things when it comes to transparency. Health Secretary Alex Azar, according to Wired, “started talking about the tests that medical personnel do to see if a patient is infected with a new coronavirus. The lack of these tests meant a dangerous failure in the epidemiological information regarding the spread and ferocity of the disease in the United States, aggravated by a lack of transparency on the part of the government. Hazard tried to say that new tests have already been ordered and that all that is needed is quality control to get them. ” But, they continue:
Then trump abruptly interrupted Azara. “But I think, and it is important that anyone who needs a test today or yesterday receives this test. They are here, they have tests and the tests are wonderful. Anyone who needs a check gets a check, ”Trump said. It is not true. Vice President Mike Pence told reporters that in the US, demand for tests exceeds supply.
Other countries respond much faster and more significantly than the United States. Many countries in Southeast Asia show excellent results, including Taiwan, where R0 reached 0.3 and Singapore, which was proposed as the COVID-19 Response Model . But now it is not only Asia; in France, for example, any meeting of more than 1000 people is forbidden, and schools are closed in three zones.

Conclusion


Covid-19 is an important social issue, and we can - and should - work to reduce the spread of the disease. It means:

  • Avoid large crowds
  • Cancel events
  • If possible, work from home
  • Wash hands upon arrival and exit from the house - and often outside the house.
  • Do not touch your face, especially outside the home.

Note: since it was imperative to publish this article as early as possible, we were not so careful in compiling a list of quotes and works on which we were based.

Please let us know if we missed anything.

Thanks to Sylvain Gugger and Alexis Gallagher for feedback and comments.

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