Wednesday COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Mid-week:
  • Top story: U.S. tops 21 million COVID-19 cases with record hospitalizations as states ramp up vaccinations (Reuters).
  • Coronavirus vaccine scams are on the rise in Europe and the U.S.; officials are warning the public against fraudsters who swindle customers out of money and personal data with promises of fake vaccines (Daily Mail).
  • COVID-19 tests are in demand and testing has dropped. You can now get an FDA-approved at-home saliva test at Amazon (CNN Business).
  • UC San Diego installs Covid-19 testing vending machines on campus (CNN).
  • Some 86% of people with mild cases of COVID-19 lose their sense of smell and taste but recover it within six months, according to a new study of over 2,500 patients from 18 European hospitals. Loss of smell was more common in younger patients (CNN).
  1. U.S. testing falls to mid-November levels as cases and deaths continue to surge
      Newly reported cases grew 21 percent this week compared to the holiday week adding 1.4 million cases (See Figure A). That itself is not surprising given what we had anticipated. The more concerning signal comes from the state growth-factor chart (Figure B) showing cases rising in every state and the District of Columbia. The largest increases were in Alaska (+76% increase this week compared to the week previous), Arizona (+51%), Hawaii (+55%), Minnesota (+43%), Florida (+44%), Kentucky (+42%), Louisiana (+64%), North Carolina (+46%), and Vermont (+41%). The daily death data shows a similar pattern (Figure C) as Tuesday’s tally was especially disheartening. The weekend slow-down came to an abrupt end as deaths spiked to over 3,400 on Tuesday, the second highest daily total of the outbreak.
     The thing that makes the current surge of particular importance is that daily U.S. testing has been sagging in recent weeks (Figure D). Over 1.6 million tests were recorded today on COVID Tracking Project, which sounds like a lot, but little noticed has been a marked slowing of the progress that had been made earlier in the Fall. Today’s testing totals put us on par with the 7-day average back in Mid-November, but it’s 300,000 tests fewer than the peak achieved in Mid-December. In other words, the fall off in testing masks the severity of the current surge. Another way to put this is that if we were doing 20% more testing like we were in December, the daily case totals would be breaking records every day. Over the next week or two, the effects of Christmas travel will start showing up in the data.
    Bottom line: January is going to be very rough.
Figure A
Figure B
Figure C
Figure D: COVID Tracking Project screen grab January 5, 2021
  1. How does the U.S. pandemic response stack up to other countries? A novel composite national pandemic response score
      On the weekend briefing, I showed you the ranking of countries in terms of COVID-19 deaths per million (reminder, the U.S. was substantially below average). I’ve been working more on this question this week. That’s partly because we can’t trust the daily numbers yet due to the Christmas reporting slow-down and also because the new year seems like a good time to look big picture. Epidemiologists always struggle with proper ways to compare the performance of people, doctors, hospitals, states or countries when those units differ substantially. One standard approach is to compute something called Z-scores. A Z-score is a statistical tool that expresses how far a unit (here country) is from the average relative to a particular distribution of performances. The units are standard deviations, or the average amount a given unit differs from the mean of that parameter. To compute a composite score that summarizes a country’s performance across different outcomes, I used data from WORLDOMETER as of January 1, 2021 for three different outcomes: 1) COVID-19 cases per million, 2) COVID-19 deaths per million, and 3) tests per million. The direction of each is set so that higher numbers reflect better relative performance. As was true over the weekend, I picked all countries meeting three criteria:
    a) at least 5 million population (to exclude smaller nations that lack an essential health infrastructure);
    b) at least 100,000 total cases (to exclude a small set of countries that are probably pretending not to be impacted by the pandemic);
    c) at least 100,000 tests per million people (to exclude countries whose case and death estimates can’t be trusted because of inadequate testing).
     Among the 222 global nations impacted by COVID-19, that results in a subset of 45 countries that should, in theory, be comparable in terms of their pandemic response. The resulting composite national pandemic response score (NPRS) is created by adding three Z-scores, each of which is based on the entire distribution of those 45 countries (See Figure E). This is one new way to use science and data to better understand how this country stacks up on the world stage. The top 3 scores belong to the United Arab Emirates (UAE), Denmark and Malaysia. Because of the way Z-scores work, countries around zero are (by definition) average, or middle-of-the-pack. Countries in this region include Palestine, Jordan, Oman, South Africa, Ukraine, Slovakia and Serbia. Most are middle income nations that have outperformed a number of high-income countries. The bottom three performing nations include the United States, Belgium and the Czech Republic. The U.S. has the third worst performance among these 45 nations, scoring well-below average on all three components. For those who believe the U.S. should not be compared to Kazakhstan (for example), I also show you just the OECD countries that meet the selection criteria (N=23). The U.S. also was third worst among that set of countries, having been outperformed in 2020 by Russia, Canada, Greece, Germany, Turkey, Israel, Portugal, the U.K., Austria, Chile, Poland, France, Columbia, Sweden, Netherlands, Spain, Hungary, Italy, and Switzerland.
     Bottom Line: After summarizing relative performance of comparable nations based on COVID-19 cases, deaths and testing, the U.S. response in 2020 was the third worst.
Figure D
  1. Quirky Qorner: COVID-19 declares video games the entertainment champ in 2020
     My kids will groan to read this but I don’t own a video game console and I don’t play video games (except for solitaire). Thankfully, they don’t read my blog so I am safe. If they did, they might rub it in my face that as movie theaters and music venues have dried up, Americans have turned to video games as their favorite entertainment option. Geez. An article from the Verge today reports on Nielsen 2020 year end review showing that 55 percent of Americans turned to gaming. Interestingly, 1 in 4 used video games as a way to connect to others. I admit I don’t even know what that means.

Weekend COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Saturday/Sunday:
  • Top Story: Anthony “Uncle Tony” Fauci, other experts warn of a post-Christmas “surge upon a surge” as U.S. braces for the worst period of the pandemic (Bloomberg).
  • Los Angeles County is in crisis, reporting a record high 148 new deaths on Thursday. Public Health official Barbara Ferrer told CNN “a person dies every ten minutes in L.A. Country from COVID-19” (CNN).
  • A new study in California shows that from March to August of this year, excess deaths among Hispanics and those without a high school degree or GED tripled. This is important further evidence of how the pandemic has posed the highest risk for low-wage essential workers (JAMA Internal Medicine).
  • Researchers scramble to understand the new variant of SARS-CoV-2 to emerge first in the U.K., now accounting for half of that country’s new cases. Some experts think the current vaccines will work against the new variant but nobody knows that until the studies are done (CIDRAP).
  • More than 1.9 million Americans have now received a COVID-19 vaccine (see Figure A). The Federal government says more than 9.5 million doses have been delivered to the states, but thus far, Illinois is the only state to have vaccinated more than 100,000 persons (New York Times).
Figure A: From https://www.nytimes.com/interactive/2020/us/covid-19-vaccine-doses.html
  1. Christmas chaos in the daily data means we are again flying blind this week. U.S. hospitalizations now double the previous two peaks
     The daily tally of new lab-confirmed COVID-19 cases nose dived after December 23 when 206,000 new cases were logged (See Figure B). I am convinced the data is unreliable as a gauge of transmission intensity due to the reporting slow down associated with the Christmas break. Take note of the big dip in daily cases that occurred around Thanksgiving. It won’t be until the latter part of next week or the week after that we will be able to see where the case numbers are headed. It won’t be until the middle of January that we will see the impact of Christmas and New Years Eve as potential intensifier events. The best evidence that daily cases and deaths are downwardly biased can be seen in the daily hospitalization numbers (Figure C). While not immune to administrative sluggishness in reporting, the hospitalization numbers show no sign of a slow down. In fact, according to the data from COVID Tracking Project, Christmas eve saw a record broken for the highest daily COVID-19 hospitalization totals at over 120,000. That’s a significant number in part because it’s double the previous peak waves of hospitalizations seen in late April and July. The national surge is being driven by a handful of states with COVID-19 hospitalizations of 500 per million population or higher including California (500 per 1 million), Pennsylvania (492), Alabama (517), and Arizona (581). The mortality numbers have also nosedived, indicating a 15% drop in weekly deaths (Figure D). I am inclined to believe that this drop is also nothing but an artifact of the holiday reporting hiatus. Again, note the temporary dip in the death numbers around Thanksgiving.
      Bottom line: The case and death data are telling us the virus’s grip on the country is slackening. The hospitalization numbers contradict this, as does previous experience. In both cases and deaths, the magnitude of the dip is already bigger for Christmas than it was at Thanksgiving so we can hold out hope that the declines may be a hybrid of sluggish reporting and a real flattening of transmission intensity. I won’t be holding my breath.
Figure B
Figure C: From the COVID Tracking Project
Figure D
  1. When will the “third” wave be over? Actually, in the U.S., the first wave is still going strong: comparing and contrasting cumulative cases in linear and log scales
     When the daily numbers get wobbly, I am inclined to go big picture. The figures below show cumulative U.S. lab-confirmed cases on both the linear (Figures E), and the log scales (Figures F). As disease detectives, we know these are different ways to graph and depict the same information. I wanted to highlight this to show how linear and log representations produce an effect on the eye that is like looking at a negative and a photo (the same image but inverted). Figure E shows U.S. cumulative cases and how long it takes to add each million cases on a linear scale. It took 58 days to get to our first million, but starting November 2, things shifted; a million cases were reported a week, further intensifying to a million every 5 days from 14 to 18 million. That is rapid growth to be sure. The story here is that November and December have been the worst two months of the U.S. epidemic. Figure F shows the same data but on the log scale with a focus on doubling times. This almost looks like a reverse image, with clearly exponential growth in March and April (exponential growth looks like a straight rising vertical line in log scale). Here, an inflection point is seen at 1 million total cases and again at 4 million with a slowing of new cases and elongation of doubling rates. What we look for on the log scale is a flattening of growth, which signals a shift from exponential growth to simple linear growth. There was hope we would see that in August. That didn’t happen. Instead, doubling rates shrank from 88 days to 57 days in the jump from 8 to 16 million. That is graphically easier to see in the previous graph. What the log scale graph shows is that the first “wave” never actually ended (cases never completely flatten on the log scale). That’s why you hear me pushing back at any suggestion of a second or third wave. So far in the U.S., we have one continuous wave with three distinct peaks.
    That’s not the case in other countries. The last figure shows the log-log plot best suited to signal the end of a wave (look for a sharp hook where the plot becomes straight vertical for some period of time). Figure G was made using Aatish Bhatia’s super-cool website. I include here a handful of countries where a clear hook can be seen, evidence that the first wave of COVID-19 actually ended. For convenience, I show Spain in highlight. After explosive exponential growth in Spain in the early months, the inflection point happens in April after extensive national lock down. In each of the other countries shown, the telltale hook can be seen. The first “wave” ended in Singapore in Mid-July, in early April in South Korea and France, and in late May in Italy. In the U.S., we see three peaks, but no hook.
    Bottom Line: Unlike most other peer nations, the U.S. has never taken the steps necessary to arrest the spread of coronavirus. This, folks is still the first wave.
Figure E
Figure F
Figure G: From https://aatishb.com/covidtrends/?location=France&location=Italy&location=Singapore&location=South+Korea&location=Spain&location=US
  1. Quirky Qorner: A Texas Boy Scout troop created a hug booth for nursing home residents
      As a former boy scout, and a fan of hugging, I could not help but smile when I saw this story in CNN about a Texas scout troop that made a special contraption that allows for protected “hugs” in a nursing home (See photo below). When the story of COVID-19 is finally written, I suspect that the emotional toll exacted by the virus in terms of loneliness and disconnection will prove to be substantially greater than we now are aware. This story will stick in my mind under the best bright spots heading.
Photo taken by screen grab from https://www.cnn.com/2020/12/27/us/boy-scouts-hug-booth-nursing-home-clear-lake-trnd/index.html

Weekend COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Saturday/Sunday:
  • Top story: FDA authorizes the Pfizer-BioNTech COVID-19 vaccine for emergency use in the U.S. one day after advisory panel recommendation. A second candidate vaccine will be evaluated this week (NPR).
  • “Uncle Tony” Fauci says he will get the COVID-19 vaccine in public (Axios).
  • U.S. reaches record daily toll of 3,309 coronavirus deaths on Friday according to Johns Hopkins. This exceeds by 6% the previous record set Wednesday (Market Watch).
  • The U.S. expects to have 100 million immunized against COVID-19 by the end of March according to the chief advisor to Operation Warp Speed. That may be an overly optimistic estimate coming from the architect of the federal vaccine development effort (Reuters).
  • New genetic study published in Science finds that an international pharmaceutical industry conference held in Boston February 26-27 became a super-spreading event resulting in 205,000-300,000 cases (CBS News).
  • New Time/Harris survey shows that 1-in-4 Americans are planning to travel for Christmas despite COVID-19 being out of control and experts calling on people to stay home. More than twice as many men (27%) as women (15%) say they will travel for New Years (Time).
  • More than 100 million Americans live in places served by hospitals that have no empty ICU beds left (New York Times, See Figure A).
Figure A: From the New York Times
  1. U.S. cases pass 15 million. Last week was the deadliest yet as latest 25,000 fatalities added in shortest interval (12 days)
      On Thursday (December 10) the U.S. passed 15 million lab-confirmed COVID-19 cases, making it the only nation with more than 10 million. Last week, the daily numbers were grim: nearly 1.4 million new cases were reported, an average of just under 200,000 a day and the trend lines continuing to rise (Figure B).
     The numbers were even worse in terms of deaths as Thanksgiving-related illnesses continue to drive daily fatalities to new heights. Last week was brutal with 15,885 COVID-19 deaths, a 12 percent rise over the previous week after four consecutive days of greater than 2,500 deaths (Figure C). Weekly deaths rose in 11 of 12 Northeast states with the biggest gains in Delaware (+76%), and Rhode Island (+43%). Substantial jumps were also seen in the South (Arkansas (+42%) and Virginia (+79%)) and West (Alaska (+50%), California (+50%), and Wyoming (+52%). The Midwest was mixed with 5 states declining in weekly deaths and two states spiking hard: Iowa (+78%) and North Dakota (+58%).
    Is the pace of COVID-19 deaths as bad as it was in the worst weeks of April and May? On a number of fronts, the answer is a clear yes. One way is to check the rate at which deaths are occurring nationally. Figure D is my version, counting how many days it takes to add each 25,000 deaths. We went from 25,000 to 50,000 deaths in 13 days starting April 14; until now that was the fastest interval. The jump from 250,000 to 275,000 took just 12 days. We will get to 300,000 faster than that. More hospitals in more parts of the nation are now filled to capacity compared and more state leaders were taking drastic action to stem the tide than is the case now.
    Bottom line: Daily cases continue to spiral with no end in sight. The vaccine will not stop this surge in transmission intensity and the resulting carnage. This last week was one of the worst weeks in U.S. history with more deaths recorded in one day than on D-Day or 9/11.
Figure B
Figure C
Figure D
Figure E
  1. Maryland update: how to tell if a state is doing better or worse
     A couple of days ago, a good friend asked me a good question: the test positivity rate in our state (Maryland) is up to 8 percent, but it was way higher (23 percent) in March. Are we faring better or worse and why do we need to go back into lock down? It’s a good question for my state but also for how to know if things are better or worse in yours. It also shows that people have gotten more sophisticated as disease detectives. Did anyone even know what test positivity rate was a year ago and why that number is so important? The first response I had was that it is not possible to adequately characterize the state of the pandemic in any place by looking at any single number at any single moment. Even if you could say that test positivity is the best number (it’a a candidate for sure), the how-well-is-it-going question requires looking at several key indicators in concert and in a larger temporal context. It’s a bit like baseball. In judging one pitcher over another, we can’t just look at wins, or pitch velocity or any single stat by itself. We need to look at a package of stats to make valid comparisons and we need to see that player in the context of a particular team and season. Let’s go through the top 5 numbers and how they are trending to see if we can hit a home run answer.
     We can start with the most basic number – trends in daily cases (Figure F) compiled from the same data source I use for everything else. The Maryland Fall surge started October 23 (715 daily cases) and has soared to now over 3,500 a day (a nearly 5-fold increase). Like every other state, we see two earlier peaks in May and July, and we see a big but temporary dip in cases due to the Thanksgiving reporting hiatus. As smart disease detectives, we know that we can’t compare this peak to the early ones because we were in a completely different testing regime then. We’ll get to that, but we can look at the relative slopes across peaks: the rate of rise is clearly faster now than in spring or summer. One point for things being worse. Next, let’s go to the Maryland Department of Health official numbers for testing volume and test positivity (Figure G). On Friday, the state logged the highest volume of testing (over 66,000); that is 10-times higher than the daily testing totals in April, but it’s also just one day. At its peak, the test positivity rate topped out at 26 percent on April 17. Only 3,800 tests were logged that day. Back then the lion’s share of testing resources were being spent in hospitals verifying the infection status of patients who were already very sick. Almost no testing in the community was yet being done. For lots of reasons, those numbers are apples-oranges compared to now. Maryland increased its testing volume dramatically about mid-July and stayed pretty steady until Mid-November. Comparing test positivity while holding total testing constant is much closer to apples-to-apples. During that time, test positivity trended downward steadily from 5 percent to 3 percent until October 22. We were really doing better. Then (as Figure F shows) the Fall surge started in Maryland. Over the next 6 weeks TPR doubled from 3 percent to a peak of 6.7 percent on December 5. Did testing increases explain that? No. TPR doubled, but testing rose only 20 percent. What about hospitalizations (Figure H)? Compared to the Spring, more acute care beds are full but fewer ICU beds are occupied. That’s because improved treatments are keeping more patients out of the ICU. The overall hospital burden though is higher. Another point for worse. How about deaths (Figure I)? Average daily deaths now are about 6.5 per million, middle of the pack in terms of U.S. states. That’s a 5-fold rise from 1.3 on November 5. It is however 30 percent lower than the 9.7 deaths per million on April 30. It’s apples to oranges again though because case fatality rates have dropped sharply since then as doctors have improved therapies and kept more severely ill patients alive. Remember all the stories about how we were running out of ventilators? Had those advances not occurred, the daily deaths would be roughly double what they are now.
    Bottom Line: Are we doing better than the Spring in Maryland? Some yes (lower daily deaths and ICU beds full), some no (cases and test positivity rising faster than the spring, overall hospital beds more occupied, fewer municipalities in lock down). If we add in the bigger context of what is going on in neighboring states, the bottom line is that we are worse off than the Spring, things continue to worsen and the next 4-6 weeks will be the worst yet in Maryland. Comparing the 26 percent TPR in March to where we are now is like comparing a pitcher’s ERA in high school to his numbers in the big leagues. Having said that, if my state’s Republican Governor acted like his colleagues in Iowa and North Dakota, the situation would be MUCH worse. The case for the strongest possible intervention is, for the next month or two, open and shut. It won’t be forever though, the vaccine will bring us the fresh start we crave in late spring and early summer.
Figure F
Figure G: https://coronavirus.maryland.gov, December 12
Figure H
Figure I.
  1. Quirky Qorner: Pandemic weary New Yorkers shell out $100 each for alcohol-soaked hot-tub party in boats on the Hudson river
     The Daily Mail carried a story today that made me just say really? This story may say more about the Daily Mail than it does about the Big Apple. The British news organ has published a dozen stories on the coronavirus-hot-tub nexus from an earlier report about a hot tub party bus in Nashville, to the latest Hollywood craze, hot tubs in tents. Someone’s mind is in the gutter.
https://www.dailymail.co.uk/news/article-9046217/COVID-weary-New-Yorkers-shell-100-hot-tub-parties-boats-Hudson-River.html