Monday, March 30, 2020

COVID-19 Tests Falling Behind in the US

Bad news: it looks like testing in the US cannot keep up with the new cases.
Confirmed new and total cases vs. tests per day

When I looked at today's case numbers before going to bad, I first was glad - can you see why?
The number of new confirmed cases for the day was larger than yesterday - but just a bit! Maybe this was a sign things were slowing down! I should have gone to bed happy right there.

But it occurred to me that I should also check the number of tests done in the US. Here are the numbers from COVID tracking project:

If you look at the last column, you'll see that the number of tests per day has been pretty stable at around 100,000 tests per day. But confirmed cases are increasing rapidly, and the percentage of positive tests is slowly creeping up.

Ideally, test capacity should increase quickly enough to allow more people to get a test, for example those with mild symptoms, or anyone who had contact with an infected person. If that would happen, the percentage of positive tests should go down. But is has gone up instead: from about 15% ten days ago to about 20% in the last two days. There are only two possible explanations for this: either the criteria for who can get a test have gotten more stringent, or the percentage of people who are infected with COVID-19 has gone up significantly.

Some politicians have applauded the recent approval of a new test platform from Abbott as a great breakthrough in testing. They pointed out that the machine can get results in only 15 minutes; but somehow, they forgot to mention that the machine can do only one test at a time, so perhaps 4 tests per hour. The alternative technique of RT-PCR is usually done in batches of 96. But's it is a great thing for Abbott: the machines cost thousands of dollars a piece, and the tests cost about $45 each, compared to about $15 for other tests. Don't get me wrong, the Abbott machines can be great at certain spots were a quick result is essential. But they were developed for doctor's offices or single tests, and it is unlikely that it will remove the bottlenecks in COVID-19 testing.

Of course, the limited number of tests that can be done (relative to the current size of the epidemic in the US) also limits the number of new cases that can be detected. That gives the impression that the growth of the epidemic has slowed down - but it is likely that this is a false impression. Without increases in testing capacity that are faster than the growth in infections, we can not know for sure.
Added 3/31/2020: The Republican governor of Maryland, Larry Hogan, stated in an interview today: 
"No state has enough testing."

Sunday, March 29, 2020

The Vampire Analogy

Let me tell you a story to illustrate some of the issues we are facing with the COVID-19 epidemic by analogy. Since most of us know more about vampires than about viruses, I'll use a vampire analogy.

In the story, the vampires have mutated from the original vampires: the sun does not bother them, so they can be out during the day. Anyone they bite also turns into a vampire, but just for a few weeks. Most people they bite simply turn back into regular people after 2 or 3 weeks, but a few of them die from vampire fever. Just like the original vampires, they are very hard to kill, and constantly want to feed. They are not afraid of crosses, but they hate the smell of garlic, and will not bite anyone who has just eaten garlic. But that's short-term protection that starts to fade after a few minutes, and is mostly gone after an hour. You can refresh it by eating more garlic.

Our story starts in a mountain town called FirstTown in Transylvania a few hundred years back. A local doctor noticed that more people than usual got sick, and some of them died. On some of them, he noticed bite marks, so he tried to warn the town about a vampire problem. But nobody really believed him, except for some local trouble makers. Everyone went along with their life as if nothing was happening. Many more got bitten by vampires and, in turn, bit their family, neighbors, friends at work, and anyone else they could find. Some people got what looked like a cold after being bitten, and people started to wonder about the new cold. But most got over it quickly, and so it seemed to be no reason to be concerned. However, the number of vampires kept increasing, and some of the new vampires got very sick. When so many people got sick that the town ran out of rooms in the local hospital, the mayor could not ignore the problem anymore. He passed a curfew where everyone had to stay home. The local guard beat and jailed everyone who did not comply, so the streets were empty after a day. Anyone who was suspected to be a vampire was locked up into a room - sometimes with other suspects, sometime alone. To keep people from starving, the mayor send his guard out to distribute food. He clad the guards in knight's armor to protect them from vampires, and closed the city gates. A couple of months later, the town was free of vampires. But some vampires had escaped before the town gates were closed, and went to neighboring towns.

The next town over, SecondTown, remembered similar vampire problems from the past. As soon as they heard about the problems in the FirstTown, they inspected every single person who wanted to enter through the city gates, and told the local doctors to watch out for any signs of vampires. Despite the controls, some vampires slipped through the gates undetected. But the doctor warned the mayor about anyone who showed the slightest signs of vampirism, and the mayor locked them up for a few weeks, just to be safe. He also warned the people living in SecondTown to not go out unless absolutely necessary, and closed the schools and some of the stores. Anyone who needed to go out to get food or visit a doctor had to eat a clove of garlic every 10 minutes to protect them from any vampires who went undetected. To make sure that there was enough garlic for everyone, the mayor told the farmers in his town to convert any corn fields to garlic fields. Fortunately, many of the farmers had done this already after the last vampire problem. Some people started to buy up garlic in large amounts, intending to sell it at a big profit to those in need, but he mayor issued new laws that had severe fines for profiteers. After the first profiteer was beheaded, and his head hung out on the market place with a big sign under it explaining his sins, the profiteering stopped.
But the mayor wanted to make sure that everyone who needed to go out would be able to get garlic, so he rationed it, and told merchants to closely track who had bought garlic, lest someone would show up at the store many times a day.
Thanks to the strict measures implemented by the mayor, and followed by almost everyone, SecondTown saw very few vampires. Every now and then, a starving vampire from FirstTown would crawl over the city walls at night undetected, but they rarely found anyone to feed on who was not reeking of garlic, so most of them just converted back after a while. Sometimes, residents of SecondTown would return home after a trip to FirstTown, but they would all be locked up for weeks until it was clear that they were not vampires, or they had reverted back into normal people.

Across the sea from SecondTown lay any another town, ThirdTown. Some people in ThirdTown had heard about the vampire problems in FirstTown, but nobody worried - everyone knew that vampires do not cross the sea! But when the first vampires were seen in ThirdTown, they remembered stories told by some crazy bard about vampires traveling in coffins. Quickly, they closed to city gates, but it was too late - some vampires had slipped in undetected, and started feeding and making new vampires quickly. The town tried to track track everyone who had been in touch with a known vampire, and put them under house arrest, but there were too many vampires that nobody knew about. Soon, the first deaths from vampire fever were reported. The mayor made a big speech on the market place, telling everyone to stay home if possible, so they would not get bitten. But many did not believe him, or thought that it was not that bad, and just ignored him. So the vampires happily kept feeding and multiplying.
As the number of vampires in ThirdTown grew, the mayor realized he needed more drastic measures to prevent the death of many people. He thought about telling everyone to eat garlic, but most garlic had been imported from FirstTown and SecondTown, and these towns kept the garlic for their own use. After talking to the farmers and realizing that there would barely be enough garlic to keep the doctors safe, the mayor told his people that regular people should not eat or buy garlic. To make the argument more convincing, he let others tell stories that garlic did not really work against vampires.
As the number of vampires in the town kept going up, the mayor kept telling people louder and louder that they should stay home; when they did not listen, he told the guard to issue fines for anyone on the street without a good excuse. What else could he do, without enough garlic and too many vampires for his guard to trace?
Eventually, the number of vampires seen in ThirdTown started to go down. New vampires still were seen, but their number did not change much, and many previous vampires were converting back to non-vampires. But the toll in ThirdTown was still tragic - many had died from vampire fever.

Across another sea lay a big city, ForceCity, also known as FC. When the first vampire was seen several weeks after the first reports in FirstTown, the FC mayor closed all ports foreigners, and then considered the city as being safe from vampires. But some vampires had slipped in already, and started biting and multiplying quickly. The FC mayor tried his best to ignore the problem, since most people were just fine a few weeks after being bitten, and all those people staying in their homes were really bad for business. When numbers kept rising, the mayor held a speech, asking people to stay home so they would not get bitten. Some people ignored him, but many tried to follow his advice. But of course, everyone had to go shopping every now and then, not realizing that vampires loved hanging around supermarkets to find new victims. Those lucky enough to keep their jobs kept going to work; that included those already converted to vampires, who found the work places a rather convenient place to feed. Vampire counters soon found that the number of vampires in FC was higher than in any other town in the world, and growing more quickly than in most other cities and towns. Numbers in ForceCity keep going up...
I am telling this story as a vampire story because viruses are such teeny little things that we can't see, and barely understand. Thanks to Bram Stoker, countless other authors, and TV, though, we all have a good idea what vampires are like. I had to modify them a bit, mostly by making vampirism temporary and by eliminating their sensitivity to sunlight, but otherwise, they have quite a few things in common with viruses - especially the tendency to exponentially multiply if left unchecked.

The towns should be easy to identify: FirstTown in the story is obviously China; SecondTown is Taiwan, but Singapore, Macau, South Korea, and Japan are similar; ThirdTown are many countries in Europe and other parts of the world; and USA = FC.

For the vampire- and virus-fighting measures, some are easier to understand than others. Staying at home works for both: neither vampires nor viruses can enter a house uninvited. Sending the city guard out to find and lock up vampires is the same as "test, track, quarantine", which is one important component in the measures in Taiwan and other asian countries that have contained the virus; but it is only possible when the number of infections is small.

The garlic eating is a rather important analogy, as is my modification that it works only a short time. The equivalent to garlic eating is widespread use of face masks by the population combined with widespread availability of public disinfection stations. Masks reduce the spread of infection by containing droplets - here's an image if you need one:
Those droplet contain a lot of virus, waiting for anyone to infect. Most of them quickly fall and settle on surfaces, waiting to be touched. Once on your fingers, it is just a question of time until they get into your mouth, nose, or eyes, and infect you. Humans touch their faces about every 2-3 minutes, and that is a habit that is very hard to break. So that's where the "garlic works just a short time" comes from: washing hands and disinfecting only works until you touch a contaminated surface, or if you disinfect hands between getting virus on them and touching your face. Face masks can help to reduce "touch transmissions" because they cover mouth and nose; public disinfection stations help by reducing the time that virus is on your hands. Both measures are an important component of a successful containment strategy, especially in the long run where "stay at home" measures cannot be sustained.

Saturday, March 28, 2020

Fact Checking Dr. Birx

The US Coronavirus Response Coordinator Dr. Birx made a number of questionable statements at the  daily Coronavirus Task Force Briefing on March 26. This post analyzes some of these statements.

Background on Dr. Birx

Dr. Deborah Birx is a well-respected medical researcher who currently serves as the "Coronavirus Response Coordinator" in the office of the US Vice President. She worked in the US Army from 1985 to 2005, and has held various leading roles in the CDC and the US government since 2005. This included different positions related to HIV/AIDS. Trained as an immunologists, Dr. Birx was well qualified for HIV-related roles, since HIV specifically targets the immune system.

In the following analysis of Dr. Birx statements, I will focus on specific statements that are incorrect. I encourage you to check the transcripts or the video of the conference to understand the context of the statements.

False Statement #1

On March 26, Dr. Birx gave the impression that computer models were not able not match the numbers observed in reality.
"... the predictions of the models don’t match the reality on the ground in either China, South Korea or Italy."




There is a large number of studies that specifically tried to model the epidemics in different countries, including Italy, South Korea, and China. These studies had to take into account the effect of government measures like "test and track", quarantine, movement restrictions, and so on. Some studies specifically tried to estimate how effective different interventions are, and have started to provide some insights that will be useful to tailor future interventions. However, virtually all studies agree that strong interventions are needed to contain the epidemic, and keep deaths and human suffering to a minimum.

False Statement #2

"There are a large group of people who are asymptomatic, who have never presented for any test."




Apparently, Dr. Birx is referring to one particular study by a group of zoologists in Oxford that had received a lot of media attention in the days before. In this particular study, the researchers found that the observed epidemics can also be modeled if the model assumes that there is a very large number of  asymptomatic individuals. If this would indeed be the case, then the majority of people in strongly affected countries would already be infected, and the epidemics in these countries would soon be over, even without any government intervention.

This study in very problematic because it ignores a large number of facts that we know about the epidemic. A well-known epidemiologist summarized "why it can't be trusted". In addition to the reasons he gives, the assumption that many asymptomatic cases exist completely ignores the data we have from "test and track" approaches in different countries, where great efforts were (and still are) undertaken to identify all possible contacts of every infected person, and test and/or quarantine everyone that had contact. One example is the intense tracking of cases in Singapore, which includes the use of antibody tests to identify people who have already recovered from the virus.

False Statement #3

On March 26, Dr. Birx stated that the researchers in the UK had "adjusted" the model which had prompted the "15 Days to Slow the Spread" guidelines, which reduced the number of predicted deaths from 500,000 to 20,000. Here is what she said (from video of the briefings, starting at 2:30:45):
"Many of you saw the recent report out of the UK about them adjusting completely their needs. This is really quite important. Remember that was the report that said there would be 500,000 death in the UK and 2.2 million deaths in the United States.
They've adjusted that number in the UK to 20,000, so half a million to 20,000.
We are looking into this in great detail to understand that adjustment."


False and misleading


The statement that the ICRF has "adjusted" numbers is false. The numbers Dr. Birx refers to can both be found in the study that was published on March 16. Here is this section of table 4:

The study explains clearly that the expected number of death is 510,000 if no interventions would happen (first column, "Do nothing"). It then shows that this number can be reduced to 19,000 deaths by a combination of interventions (third column, PC_CI_SD): closures of schools and universities (PC), isolation of all infected patients (CI), and social distancing (SD). Have a quick look at the second column, which shows what is predicted to happen when schools and other public places remain open: the number of predicted deaths jumps more than 4-fold. For the larger United States, the corresponding number would be about half a million deaths even with social distancing.

This was shown in the initial study. The data convinced the British government to dramatically change its plan of action: rather than using only social distancing measures limited to the most vulnerable groups, the UK implemented a large range of mandatory and strict measures to stop the spread of the virus, and avoid running out of ICU beds.

The results of the study were shared with the US government even before the publication; the study was publicly available since March 16.

The response by the US government has been to issue "guidelines" that are intended to stop the spread, called "15 Days to slow the spread". It's a 2-page document; here is how page 1 starts:

Everything on the first page is directed to sick people, their relatives, or members of risk groups. On page 2, there is advice for everyone that include "Avoid social gatherings in groups of more than 10 people". All those guidelines are voluntary. Experience from many countries all over the world, including the US, shows that voluntary guidelines for social distancing are often ignored. This severely limits the effectiveness of social distancing. The US guidelines correspond to the second column (CI_HQ_SD) in the table above. According to the ICRF model, these restrictions would lead to more than 400,000 deaths in the US,  assuming they were generally followed.

For comparison, here are some of the differences in the restrictions that the British government has imposed to keep the corona virus epidemic at a level that will not overwhelm hospitals:

  • Everyone is required to stay home, except for "very limited purposes" like shopping for essentials
  • Most businesses are closed, including restaurant, bars, and hotels
  • Public venues like playgrounds and churches are closed
  • All public gatherings of more than 2 people are prohibited, with minimal exceptions (e.g. for families that live together)
  • Workers must work from home whenever possible, and employers "should take every possible step to facilitate their employees working from home"
  • All restrictions are mandatory and will be enforced by police and health departments

Overall, the British restrictions are much more severe than the restrictions in US, and doubtlessly will be more effective.

I leave it to you to speculate why Dr. Birx made multiple false statements within one briefing. But if she had wanted to support the current strategy of minimal interventions by undermining the credibility of computer modeling, she could not have done a better job.

Thursday, March 26, 2020

No, It Is NOT Great

I have moved most of my COVID-19 posts onto a separate blog: But I leave any related posts that are somewhat political here, and I have to add one.

I usually do not watch the White House briefings, because I have a very low tolerance for lies and incompetence. But my friend Pierre, a mathematician, mentioned that Dr. Birx seemed to have some problems understanding the models, so I looked at that part on Youtube.

Unfortunately, she made factually wrong statements less than 2 minutes into her talk. The first one was "In no country have we seen an attack rate over 1 in a thousand". One look at the numbers for Italy (and perhaps a bit of help from a calculator) would have shown her this is wrong. Italy has 80,589 cases, which includes 6,203 new cases today. That is one confirmed case per 751 inhabitants. As I have explained in another post, the confirmed number of cases vastly understates the number of infections. The number is still going up, despite a nation-wide house arrest.
The original center of the epidemic, Wuhan, had 50,000 confirmed cases in a population of 11 million - that's 4.5 cases per 1,000. However, various studies have concluded that the actual infection rate was several times higher. One study concluded that only 1 in 6 infections showed up in the official statistics; another study estimated that roughly half of the cases were missed. One reason for the under-reporting was that testing was limited to severe cases during parts of the epidemic. This means the actual attack rate was probably between 9 and 30 in a thousand. Without the very strict interventions in Wuhan, it was estimated that the number of cases would have increased 51-fold.

I can perhaps understand if she does not understand the details about epidemic computer models. She is an immunologist, not an epidemiologist or a computer person. Still, it takes about 30 seconds to find out her statement was wrong.

But what really got to me was when she went on how she bragged about
"We do have 19 out of our 50 states that have persistently low level of cases and at this point have less than 200 cases. That's almost 40 percent of the country"
The second part is a bit misleading, to say it politely. Check the by-state list at, and you'll notice that these 19 states are also the states with the lowest population. Wyoming? Population  579,000 - about 1.4% the number for California. 56 total case, 7 new ones. Alaska? Population 732,000, or about one 25th of the population of New York.  59 cases, 17 new ones today. Other small states show similar growth in the 15% or higher range:
Look at Idaho: the number of cases doubled in a single day! Or just plug the numbers for Vermont (pop. 624,000) into a spread sheet, and extrapolate for 30 days: the number grows to 175,272. That's going from 158 cases to 25% of the state's population in 30 days! That's what exponential growth means!

Relative to the population size, Wyoming has the same number of cases as California. The governor of California clearly understands exponential growth, because he has taken strict measures to stop the spread. It is very sad to see that the US coronavirus coordinator does not understand exponential growth.

Small numbers do not mean that you are safe - they only mean that you are early in the epidemic. The only thing that indicates you are safe is if the numbers do not grow, or if the percentage growth is very low. I am pretty sure Dr. Fauci would be able to explain that to her.

What even worse is that smaller numbers also mean that containment is easier. With 200 cases, it would be possibly to trace all contacts, test them all, and quarantine everyone who tests positive. They did this very successfully in a town of 3000 people in Italy. They knew about just one infected person. They found 89 others the first time they tested, and another 6 the second time. They isolated everyone, and stopped the spread. What do you think would have happened if they had said "that's just one case, no need to worry"? By the way, this little town is an example of an attack rate of 30 in 1,000.

Rather than making statements that can be very easily proven wrong, Dr. Birx time would be better spend to study the actions various government in China, Taiwan, Hong Kong, South Korea, and Singapore have taken to stop the spread of the virus. Those actions differed a lot between countries, and the success varied somewhat, but each of these countries has managed to keep the number of new infections on a manageable level. Despite all the differences, the successful containment measures had a few things in common: they were

  • multi-pronged
  • well coordinated
  • enforced.
In stark contrast, the measures taken in the US 
  • are only based on social distancing
  • differ substantially by state and region
  • often rely on voluntary participation.

Wishful thinking has not worked so far, and will not work in the future. Please, study what has worked and is working in other countries, and implement the measures that work as soon as possible. Only a strong "Hammer" response, followed by a careful "Dance" until vaccines become available in a year or two, will work. Such an approach differs vastly from the current haphazard approach; but it is what will be best not only to minimize deaths and human suffering, but also to bring the economy back on track.

Tuesday, March 17, 2020

Dear Mr. Trump

Dear Mr. Trump, you really must work on convincing your fan base that the corona virus is very serious. If you don't, too many of your voters will die. Let me explain. Perhaps I should start with a couple of pictures? Here's one that shows who helped you defeat Mrs. Clinton in 2016:
Trump voters by age group 2016

Most countries now have realized that the new corona virus will eventually infect more than half of the population, and I think you know that now, too. Most countries have also realized that if this happens too quickly, many more people than the "usual" 0.5% or so will die, because the hospitals will be overwhelmed. Even your nice blond friend in the UK, who tried to be brave and just get all the young people infected quickly, eventually understood that!

I am sure that you are keenly aware who loves you, and who votes for you. You have proven that often enough to all of us! Hispanics almost always vote for the Democrats (even for women!), so building a wall to keep them from coming is certainly called for. But I am getting side tracked, forgive me. The real issue is older people. Folks above 50 are not just more likely to love you than those young, no-nothing liberal college kids, but they are also much more likely to vote! 

Now here's the problem: 

The stupid "imported" corona virus primarily kills older people! Even if ICU beds and ventilators are available, nearly 10% of those over 70 die. If we run out of ventilators, which is likely to happen at many places, that number goes up a lot. Let's be clear:
The virus kills your voters, Mr. Trump!

Of course, you knew that, because those scientists have been saying that for weeks now, and eventually, you just had to start believing them. They just should have said it on Fox News earlier! Now it's too late to do some things that worked so well for places like Singapore, Hong Kong, South Korea, and Taiwan. With tens or hundreds of thousands already infected, tracking all their contacts and putting them all in quarantine for 2 weeks is not possible anymore. 

So you just told everyone to stay at home if they can, and to avoid any gatherings of more than 10 people. If everyone just stayed home for a couple of weeks or perhaps months, and we close those pesky borders, then the whole thing will go away!

Funny enough, some of those almost-socialist states like New York and Massachusetts have already done things to help, like closing all restaurants and schools. Who would have thunk they'd help protect your voters? Well, there may be one little problem: your voters still believe what you told them earlier. To paraphrase Alan Dershowitz: can't they see that you were right when you call the virus harmless in February, but that you are much more right now, when you tell them it is dangerous enough to stay home?

Now, the excellent job you have done in the past three years to teach your base to only believe what you say, even if it disagrees with what almost everyone else in the world says, comes back to haunt you. Clearly, you must have known more than those pesky scientists in February! Why else would you have needed to make sure to check with you or your Vice Mike before saying anything? It all fits!

So, funny again, now the Democrats believe your new message more than the Republicans!  Funny, because just 8% of Democrats believe what you said about the virus, while 74% of Republicans believe you. But when it comes to changing plans to avoid crowds, 59% of Democrats said they had done that already, while just 40% of Republicans have. So not only are your voters more likely to die from the stupid virus because they are older - they are also more likely to be infected!

This has to change if you want to have any chance to be re-elected. Sure, some smart patriots have looked into options to delay the election, or to just declare it invalid because of the virus, but that may not work. Much better to keep your voters alive! If 60% of the population gets infected, and just 1% of the infected people die, that's still more than a couple of million voters - mostly your voters!

So, Mr. Trump, please keep hammering away at the "stay home" message until every Republican gets it. Perhaps call it "our patriotic duty" or something great you can come up with. Since we are living in the land of the free and the home of the brave, some free and brave souls will probably still go around, so please also add some other measures that have been shown to work. A lot more testing, and putting everyone who is infected or has been in contact with an infected person, in quarantine would be a good start. And how about having our great American corporations produce lots of lots of face masks to protect people? Using face masks when in public is one of the things that all the countries that really contained the virus have in common. Right now, we have don't have enough of them, so we have to reserve them for the doctors and nurses. But if we can manufacture enough masks in this great country to everyone can use them in public, then spreading the virus by coughing just won't work that well anymore. Maybe we can even put our great military to work on this!

If you get this right, your loyal fan base will love you even more, and you may even gain some of those undecided people. Sure, your fan base will still love you even if you get it wrong because they know that the Democrats are to be blamed, but there just won't be enough of them left to get you re-elected! So please, get to it!

Full disclosure: I'm not really one of your fans. But a lot of my windsurfing friends are in the 70s, and therefore at increased risk. Some have spouses with pre-existing conditions that are at even higher risk. I'd really hate to loose friends to this virus, so even if doing the right thing now may help you to get re-elected, I still want you to do the right thing. So perhaps cancel that next golf trip, and go to work instead!