Friday, October 30, 2020

New Evidence That Face Masks Work

 In the last couple of weeks, several new scientific studies were published that provide solid evidence that face masks can reduce COVID-19 transmissions significantly. In this post, I'll briefly describe several studies, as well as other evidence from trends in the US.

Face mask mandates reduced COVID-19 growth in Missouri counties

One study that was published as a preprint compared the COVID-10 growths in 5 metropolitan regions in Missouri. Two of the regions, St. Louis City and St. Louis County, implement mask mandates in July, while the three other regions did not. Comparing the COVID-19 growth rates between the "mask mandate" regions and the "maskless" regions, the authors found significantly slower growths of COVID-19 cases in the mask mandate regions: 1.36% per day, almost 2-fold lower than the 2.42% observed in the maskless regions. This difference was significantly larger than the difference in growth seem in the weeks before the mask mandates were issued.

To see if this trend persisted after the time analyzed in the study, I downloaded per-county level data from Johns Hopkins University, and looked at the growth in COVID-19 cases from July 1 to October 27:

 The counties with a mask mandate (in blue) had about 3 to 4-fold more total COVID-19 cases at the end of the period than at the beginning; the counties without mask mandates showed about 10 to 12-fold growths. This indicates that the mask mandates cut COVID-19 infections to about one third.

Face masks reduce in-flight transmission of COVID-19 dramatically

A second recent study examined how well face masks work in flights. It reviewed a number of previous studies, including one where a single passenger in business class had infected 12 other passengers in the business class cabin:

The originally infected passenger ("patient 0") was on seat 5K, shown in red. The passengers she infected during the flight (shown in orange) were mostly seated behind her, and/or to the side. Several of the infected passengers were more than 6 feet away from patient 0. The flight happened early in the epidemic, and the infected passengers did not wear face masks. The review also lists several other flights with in-flight transmission before the use of face masks on flights became common.

In stark contrast to this "superspreader event" flight is a series of flights with Emirates that arrived in Hong Kong in June and July. Overall, 8 flights transported 58 passengers who were COVID-19 infected during the flight. The flights were 8 hours long, and had a total of 1500 to 2000 passengers, who were quarantined and repeatedly tested for COVID-19 in Hong Kong. The testing showed that not a single transmissions happened on those flights. Emirates had a strict face mask policy in place at the time of the flights, which was enforced during the flights by flight attendants.

The review also describes a number of other flights, both with and without mandatory face masks, which show that the use of face masks during flights dramatically reduces the number of COVID-19 transmissions on flights.

Evidence from face masks mandates in Germany

While face masks mandates were common in Germany from the early phase of the COVID-19 epidemic on, the dates when mask mandates were issues varied by location. Two separate studies examined the resulting differences in COVID-19 transmissions, with focus on Jena, a city that implemented mask mandates early. One study presents qualitative evidence that face masks mandates reduced transmissions in Jena. The second study used "synthetic control methods" and data from 401 German regions to derive quantitative estimate, concluding that face mask mandates reduced the daily growth in COVID-19 infections by about 40%.

More evidence from US regions and states

A number of studies have focused on US states or regions, and come to similar conclusions as the studies above.  Here is a figure from one of these studies that shows a drop in COVID-19 infections after the introduction of mask mandates:

The effect shown is not as pronounced as in some of the other studies, which may be due to varying levels of adherence to the mandates, especially since enforcement of mask mandates in many US regions is lax or non-existent. Sadly, the use of face masks has become politicized in the US. Many Republican governors have refused to issue face masks; Republican law enforcement has been reluctant to actually enforce mask laws; and many Republicans refuse to wear face masks. 

The effect of the "Republican refusal" can be seen when comparing which US states have the most COVID-19 cases over time. Here are a couple of screen shots from an illustrative animation:

In early June, the most affected states were a roughly even mix of blue and red states. But by late October, the picture had changed dramatically:

Now, Republican states dominate the distribution. Of course, other factors like early re-openings and resistance against new containment measures are also likely to play a role, but negative attitudes towards face mask wearing and face mask mandates are certainly a big factor in this development.

The evidence is very clear - face masks reduce COVID-19 transmissions and save lives. Scientists have a pretty good idea why and how face masks work. I have discussed why misguided "herd immunity" strategies won't work, using Texas as an example. For the US as a whole, just "letting it take it's natural course" would cost more than a million additional lives; when taking into account that death rates increase significantly when hospitals are overloaded, the number of additional deaths in the US would more likely exceed 2 million. Anyone who still believes that COVID-19 deaths are overstated in the US needs to have a close look at excess death calculations, which show that the official COVID-19 numbers represent only 2 out of 3 COVID-19 linked deaths.

So, please, if you go to an indoor space where other people are, or if you are outdoors in a crowd, or closer than 6 feet to someone else who does not live with you: wear a mask!

Tuesday, October 27, 2020

Misleading COVID-19 Information in Florida

This page describes a systematic pattern of misrepresenting information about COVID-19 by officials in Florida. These officials include the governor Ron Desantis, the governor's spokesman Fred Piccolo Jr.,  Florida's Surgeon General, Dr. Scott A. Rivkees, and Republicans in the Florida House.

A Red Flag: Is COVID-19 Becoming More Deadly in Florida?

 What started my investigation was a strange observation: based on reported COVID-19 confirmed case numbers and deaths, it appeared that COVID-19 is becoming more deadly in Florida than it has been during the summer peak. One way of looking at this is by looking at the relation between reported case numbers and reported death rates; since deaths are typically delayed by several weeks relative to test results, I am comparing death rates to case rates two weeks earlier, using 2-week averages for both deaths and cases:

While the time-adjusted case fatality ratio (CFR) for the US remained almost constant for the US between July and October, it increased  from about 1.3% to about 4% for Florida. This peculiar increase prompted me to look for possible explanations.

The Florida COVID-19 Dashboard: How to Understate COVID-19 Deaths

One of the first stops was Florida's official COVID-19 dashboard. The graphs on the right side that depict cases and deaths are interesting:

The top graph shows the new cases, which show an increase over the last month. The bottom graph shows COVID-19 deaths, and the immediate impression is that things must be getting a lot better - the graph shows a clear downward trend in deaths! Wonderful - but in direct contradiction to the increasing fatality rates we had seen in the previous figure. What gives?

The first hint comes from the title "Resident Deaths by Date of Death". That seems reasonable enough - until you read the fine print: "The Deaths by Day chart shows the total number of Florida residents with confirmed COVID-19 that died on each calendar day (12:00 AM - 11:59 PM). Death data often has significant delays in reporting, so data within the past two weeks will be updated frequently."

The key here is that "death data often have significant delays in reporting". That means that the numbers for the last several weeks understate the actual death substantially; the number for the last few days show only a small fraction of the deaths that actually occurred. But rather than stating this clearly, the fine print states that data "will be updated frequently". Perhaps understating the actual death toll may be a bad thing, but updating frequently must be a good thing, right?

But the Florida government had a reason to choose the "death by day" reporting: it will always show a positive trend in deaths, since there will always be fewer cases for the last few days. Anyone who looks at the graph without reading and understanding the fine print will always conclude that the COVID-19 situation in Florida is improving. Always. And who reads the fine print?

For an example, we can use the screen shots of the Florida COVID-19 dashboard that the COVID Tracking Project has captured.  Here is what the death graph looked on 8/2/2020:

Death by day 8/2/20

For comparison, here is what the graph looks like when plotting the number of new death reported:

That's a very different picture for the last two weeks of July! If we look at the screenshot of the Florida dashboard from 8/15, it gives a very different picture for these weeks:

Florida dashboard as of 8/15

Note that the cases around 7/20 now hover around 160 per day, instead of the 120 per day as reported on 8/2. For the beginning of August, we now see around 140 cases per day; two weeks later, this increases to 180 per day.

The bottom line is that the "By day of death" graph on Florida's COVID-19 dashboard will never show an accurate picture of the actual trends in recent weeks. It will always understate deaths for the last 2 weeks substantially, and show a decline of deaths in the most recent days. Given the observed reporting delays, the only apparent purpose of the death graph on Florida's COVID-19 dashboard is to mislead.

Even worse, the graph creates an incentive to delay the reporting of COVID-19 deaths. Early in the COVID-19 epidemic, Florida's board of medical examiners published data about COVID-19 deaths directly. However, when the government noticed that the numbers reported by the medical examiners where higher than the numbers reported by the state, the health department stopped the release of the medical examiner's list.  Afterwards, only numbers released by the Florida Department of Health were available, whenever the department chooses to include a deaths. When deaths are added with a 2-week delay, as was typical in the summer, it would help to create the impression that the worst problems were in the past. If a death was added more than 30 days after it happened, it would never show in the death graph on Florida's COVID-19 dashboard.

This created a strong incentive to delay death reports in Florida for anyone who wanted to downplay the severity of the COVID-19 epidemic. As a result, the reporting delays increased substantially since the summer:

But while the delayed reporting was welcome when it reduced the number of reported COVID-19 deaths in the summer, it is now creating a problem: eventually, the death have to be reported!

Killing Two Birds With One Stone: "Investigate All COVID-19 Deaths!"

On October 21, Florida's Surgeon General, who had remained surprisingly quiet during the COVID-19 epidemic up to this point, issued a press release stating that all COVID-19 fatalities reported to the state will be subject to a "thorough review". In addition to criticizing that some reports were more than 30 days late, he focused on 5 cases where more than three months had elapsed between the COVID-19 diagnosis by PCR test and the eventual deaths.
The issue was quickly picked up by governor DeSantis' spokesman Fred Piccolo Jr., who stated:
"What is different about the deaths, is that the health department was finding people who were admitted as positive as far back as March or April and who passed away in August or September or October. Is that a COVID death?”
Looking at the data in the Surgeon General's press release shows that Piccolo is stretching the truth beyond the breaking point. Questioning if someone who was diagnosed in March and died in October really died of COVID-19 seems reasonable, right? But the earliest test date listed by the Surgeon General was from June, not March or April - three months later. The longest elapsed time between test report and death was 111 days. While this is still a long time, it is shorter than times that have been reported for people who recovered from COVID-19, as a quick Google search shows:
  • A patient in North Carolina was released after 137 days in the hospital. Her complications which were directly caused by COVID-19 included a heart attack and kidney and lung failure.
  • Two men in Georgia were in the hospital for COVID-19 for more than 4 months. One of the two was released, the other is still in the hospital. 
  • A 35-year of woman in the UK was treated for 141 days in the hospital, which included 105 days on the ventilator.
The last case is interesting because the treatment happened in a hospital run by UK's National Health Service - a public health system that Republicans typically describe as "socialist".

Those are just some random samples from a quick internet search, and all of the listed patients survived. Scientific studies show that survivors typically spend less time in hospitals than patients who die; other studies report very long hospital stays, for example three patients with more than 50 days in a hospital in one early study from China (as well as two more patients who still were in the hospital after 37 days). Other studies show that hospital stays in the US tend to be longer than in China, and that a significant fraction of patients stay in hospital care for more than 40 days. Some patients get admitted to the hospital for COVID-19 multiple time. In one case in Belgium, DNA sequencing proved that a patient had been infected on two separate occasions from different people; this patient died from the second infection.
These examples show that there is plenty of both anecdotal and  scientific evidence of patients who require hospital treatments for several months, and that a small number of cases with a large time between diagnosis and death is therefore not suspicious. It is very likely that the investigations will come to the same conclusions, although it is extremely unlikely that the Florida government would announce such conclusions.

The Pattern: Create Doubt About COVID-19 Deaths

The Surgeon General's press released discussed above is just one of many examples where Republican politicians in Florida try to create doubt about the true number of COVID-19 deaths. A recent example is a "Florida House report" commissioned by Republican House Speaker Jose Oliva. The report says that "60% of death certificates issued for state residents whose deaths were attributed to COVID-19 had reporting errors and most were filed by medical examiners". It speculates that this "may be inflating the COVID-19 death toll by 10%".

Phased differently, the results could be phrased as "a close investigation looking for problems has found that 90% of the reported death are definitely due to COVID-19, with the remaining 10% possibly being due to COVID-19 or some other cause". But instead, the House Speaker, who has no medical background, talks about "compromised data". 

Note that the reporting about the issue starts with casting doubt on 60% of the death certificates. It is likely that many readers will remember this particular number, and few will remember than in reality, at most 10% of the death certificates are questionable with respect to COVID-19.

Another example of the "cast doubt" strategy is governor DeSantis'  mentioning of the death of a motorcyclist who had tested positive in an accident, and who was initially included on Florida's list of COVID-19 related deaths. However, even before governor DeSantis made the statement in an interview on July 20, this case had already been removed from the reported death counts. Nevertheless, this example is very "sticky", and comes up frequently in conversations with COVID-19 deniers.

 The Reality: Florida Reports Less Than 3 Out Of 4 COVID-19 Deaths

The is a simple number that really determines how deadly the COVID-19 epidemic is: the number of people who die in addition to the number who would die in a typical year without COVID-19. This number, called "excess deaths", can easily be looked up based on death certificate data that all states submit to the CDC, and which the CDC publishes on its web site.

Based on spreadsheets last updated on 10/21/2020, and looking at actually submitted death certificates from the weeks ending between 3/7 and 9/19/2020, we can compare the excess deaths to the number of death certificates that listed COVID-19 as a cause of death:

During these roughly 6 months, the number of excess deaths in Florida was 21,263 (note that this number will go up slightly in the next few months, since some deaths certificates are submitted with delays up to a year). Of these, 14,795 death certificates listed COVID-19 as a cause of death. This is about 69.6% of the excess deaths. The graph above shows that excess deaths and COVID-19 deaths follow the same pattern, which strongly indicates that the vast majority of excess deaths is most likely caused by COVID-19, and not some other cause like violence or suicide.

The data for excess death calculations are readily available. Excess death analyses have been published on many web sites, including the Financial Times and Our World In Data. Several scientific studies have analyzed excess mortality in the US, including a study recently published by the CDC. There is world-wide agreement on using excess mortality analysis to determine the impact of epidemics.

The result of excess death analysis for Florida is clear: the current process fails to correctly identify COVID-19 as a cause of death in 3 out of 10 cases. The COVID-19 reporting problem that Florida has is one of under reporting, not of over reporting. This could be addressed by requiring COVID-19 tests and, if necessary, autopsies for any deaths where COVID-19 cannot be excluded by clear evidence. 

Just don't wait for the governor or state Republicans to suggest that.

Friday, October 23, 2020

New Case Record in the US

The US has set a new record for daily COVID-19 cases today, with 81,210 new cases according to The COVID Tracking Project reports an even higher number of 83,010 cases.

In July, the increase of cases was primarily driven by rapid rises in Texas, Florida, California, and Arizona. These states reacted with measures that partially rolled back the "re-opening", for example bar closures and local mask mandates.

In contrast, the current rise in COVID-19 infections is the result of rising case numbers in the vast majority of US states:

 Source and full table:

A total of 22 states show an increase in average daily cases and report more than 1,000 cases per day. The top 3 states currently account for about 20% of new cases; during the "second peak" in the summer, this number was closer to 50%.

To stop the current growth in new COVID-19 infections, most of these states would have to increase the stringency of restrictions. But whereas several countries in Europe, where COVID-19 has also been rising rapidly, have announced plans for new lockdowns and other severe measures, such actions seem extremely unlikely in most US states, at least in the near future.

Another important trend in COVID-19 infections is that infections have shifted from metropolitan areas to smaller towns and rural areas:


Resistance against anti-COVID measures like mandatory face masks is a lot stronger in most rural areas. At the same time, medical support is often worse, with hospitals mostly located in larger cities, where the frequent sound of ambulances transporting COVID-19 patients alerted every resident about how serious the situation was.

In view of these (and other) factors, it is likely that we will see many more records of COVID-19 infections in the US in the coming weeks and months. Reported COVID-19 deaths have just started to increase from about 700 daily deaths (7-day average) a week ago to more than 800 today. Since reported COVID-19 deaths rise with a delay of at least 2-3 weeks after confirmed case numbers rise, additional increases are inevitable.

Some people in the US will doubtlessly interpret the rising number of COVID-19 cases as a positive sign, hoping that it will help the US to achieve "herd immunity". But we have to look no further than to the rising case numbers in New York, where an estimated 25% to 35% of the population has been infected by COVID-19, to see how far away we are from herd immunity. Close to 9 million confirmed cases in the US may seem like a large number, but still represent less than 3% of the population. Epidemiologists estimate that herd immunity would require at least 60% to 70% of the population to be immune to COVID-19. Even after taking into account that only about one out of 5 COVID-19 infections is reflected in the "confirmed case" numbers, reaching herd immunity through infection would lead to at least one million of additional deaths in the US. Considering what we know about re-infection from other corona viruses, which appears to be common a year or less after the initial infection, it is very questionable if reaching herd immunity "the natural way" is possible at all. But effective vaccines, which could let us reach herd immunity without additional deaths, will not be available in sufficient quantities until the summer of 2021 at the earliest.

Tuesday, October 20, 2020

CDC Reports 299,000 Additional Deaths

Today, the CDC published a study that looked at the excess mortality linked to COVID-19 in the US. As I explained in previous posts, "confirmed cases" and even official COVID-19 death numbers paint a sometimes misleading picture, since such numbers are distorted by many factors, including test availability, the willingness of people to take tests, and test accuracy. But the one number that is not subject to any of these problems is the number of people who have died, compared to previous years. 

Based on the analysis of death certificates submitted to the CDC's "National Vital Statistics System", the CDC reports that 299,000 more people have died this year than in previous years - in other words, the US had almost 300 thousand additional deaths. Only 198,081 of the death certificates listed COVID-19 as a cause of death. I explained possible causes for this discrepancy in a previous post. The predominant cause for additional deaths that do not list COVID-19 as the cause of death are missing positive COVID-19 tests. One clear indicator is that excess deaths are very closely linked to COVID-19 deaths. 

The official COVID-19 death counts include only 2 out of 3 actual deaths linked to COVID-19 in the US. To get a realistic picture of the deaths that COVID-19 has caused in the US, take the official reported numbers, and add 50%. For example, the 220,000 deaths reported yesterday (10/19) by Johns Hopkins University correspond to a total of 330,000 excess deaths due to COVID-19 in the US. Spreadsheets with detailed numbers that are updated weekly are available on the CDC web site.

Multiple countries report low excess death rates

Excess death analysis is also a very useful tool to compare the severity of the COVID-19 pandemic in different countries, which often have very different testing policies, capacities, and COVID-19 reporting rules. A study that was published last week in Nature Medicine looked at the death data from 21 different countries for the first phase of the pandemic, from mid-February to May. Here is a graph from the study that summarizes the results (click on the image for a larger version):

The countries that had the highest excess mortality were Spain and England & Wales, where deaths increased by about 35-40% during the period studied. The next group of countries includes Italy, Scotland, and Belgium, closely followed by Belgium, Sweden and the Netherlands, with roughly 20-25% additional deaths.

There are seven countries that did not show any significant increase in deaths: Bulgaria, New Zealand, Slovakia, Hungary, Czechia, Australia, and Poland. With the exception of Poland, all of these countries actually reported fewer deaths than expected. The study authors mention the reduction of work-related injuries during lockdowns in these countries as one likely reason for the observed reduction in death.

Three countries (Norway, Finland, and Denmark) had excess death rates below 5%; overall, almost half of the countries studied (10 of 21) reported either no excess deaths, or an increase below 5%.

How does  the US compare?

I downloaded the latest data from the CDC web site to calculate comparable excess death numbers for the US, using the weeks ending 2/15/2020 to 5/30/2020. For the entire US, the excess death rate for this period was about 15.3% when using the numbers for reported death certificates only, or 16.3% if using the "weighted" data set that tries to compensate for late submission of death certificates. This number is roughly the same as what France reported.

However, the US is significantly larger than any of the countries in the study above, and closer in size to all of the countries combined. COVID-19 spread in the US in a regional pattern, with the northeastern states reporting the highest numbers from March to May:

The five northeastern states shown (NY, NJ, MA, CT, and RI) had a combined excess death rate of 48.4% - significantly higher than any of the 21 states from the study above.

After the end of May, COVID-19 infections and deaths in most European countries and in New Zealand were at at least 10-fold lower than during the March to May period. In the US, the COVID-19 infections "moved" to southern and western states, which now experienced a large number of additional deaths:

The excess death rates in Arizona and Texas during the summer months were similar to the rates seen in the worst European countries, Spain and England & Wales, in the spring. This is somewhat astonishing, considering that these states had several more months to prepare, and that some improvements in treating COVID-19 had been made in the meantime. Louisiana stands out because it reported excess death rates near 25% both for the spring and the summer periods.

In conclusion, the comparison of excess deaths linked to COVID-19 showed that the affected regions in the US have done as poorly as, or worse than, the European countries that had the highest relative increase in deaths. The primary causes are well known: lack of testing early in the epidemic; false statements by leading politicians about the severity of COVID-19; and an irresponsible push to re-open, ignoring even the minimal re-opening guidelines the administration had released.

In recent weeks, the state of the pandemic has diverged dramatically between the countries. While New Zealand has remained completely free of domestic COVID-19 infections and fully re-opened the economy, many European countries have seen a very rapid rise in COVID-19 infections. Most countries are issuing new restrictions, and the worst-hit areas have initiated a new round of full lockdowns.

In the US, COVID-19 case numbers have increased more slowly, from about 36,000 in the middle of September to almost 61,000 today (7-day averages). Given a weekly growth rate of 17%, the US will set new records for daily COVID-19 cases later this week or next week. If future increases in the US follow the patterns seen in Europe, the increases will likely accelerate further. It is quite possible that the US will see more than 100,000 new confirmed COVID-19 cases per day before election day (November 3). Reported COVID-19 deaths lag behind by about 2-4 weeks, but 7-day averages have started to increase over the last three days, from 704 deaths per day to 753.