Top pick of the day: Sunday

Immunology Is Where Intuition Goes to Die. Which is too bad because we really need to understand how the immune system reacts to the coronavirus.

Health Article by Ed Yong, online at The Atlantic, August 5, 2020.

My kids always remind me how much of a nerd I am. Guilty as charged! This TPOTD is further evidence. Another thoughtful piece by Ed Yong at the Atlantic, this article dives into the mystery of what immunity really means. Spoiler alert: it’s not a black-and-white thing. Like most epidemiologists, immunology seems like a confusing and overly complicated specialty that I wish I understood better. As we inch toward herd immunity and a vaccine, now is a good time to bone up on what that field has to teach us.

Today’s bite-sized, handpicked selection of important news, information or science for all who want to know where this epidemic is going and what we should do.

Daily COVID-19 Briefing: Sunday

A special message and appeal to any who may read this or who has followed my blog:

I began this blog on March 9. Since then, I have made 130 posts, received 20,898 views, 75 likes and 21 comments. I am now very much uncertain about whether to continue this effort. I have tried to bring all my knowledge, experience and skill to bear to make sense of what is happening. I have sought to gather information thoughtfully and critically, to analyze that information responsibly and report the truth as accurately and clearly as I could. I have been proud of this effort. Now, as the the nation seems to be sinking further into confusion, apathy and denial, I worry that my voice is contributing to the collective malaise that seems to be deepening. I am concerned that I have become part of the drone of “experts” counting cases and deaths, expressing alarm and forecasting continued suffering. Is it helping? I am still fascinated by what is transpiring, but I no longer feel that what I am doing is making a difference in a positive way. I get very little feedback and I have no idea whether anyone is still interested.

For these reasons, I am asking you for your input and feedback. Any and all comments would be welcome. Send me a comment through the site or at my personal email ( Please be safe and well.

  1. Do you have questions I could try to answer?
  2. Has my blog been useful?
  3. What has been useful about this site?
  4. What have you not liked?
  5. What could be done better?
  6. Should I continue to publish this blog?

And most of all, to those who have taken the time to read my blog, I thank you sincerely.

Yours truly,
Thomas A. Glass, Ph.D.

Wednesday COVID-19 Briefing

Top news, reports and insights for today:

  1. Daily headline summaries for Wednesday:
  • Russia becomes the first country to approve a coronavirus vaccine, declining to complete a clinical trial to demonstrate that it is safe and effective (New York Times)
  • Anthony Fauci (among others) says he “seriously” doubts Russia’s coronavirus vaccine is safe (Axios)
  • A Stanford University report shows that teens and young adults who use e-cigarettes are five to seven times more likely to test positive for the virus that causes COVID-19 (Wired)
  • A new database created by The Guardian and Kaiser Health News say that over 900 U.S. health workers have died of COVID-19; front-line nurses and people of color are especially hard-hit (Kaiser Health News)
  • University of Florida study (not yet peer-reviewed) isolated live, viable SARS-CoV-2 virus from aerosols collected at a distance of seven to 16 feet from patients hospitalized with Covid-19 adding additional evidence of transmission through the air (New York Times)
  • Confirmed coronavirus cases in U.S. children rose by 90% in about four weeks this summer, bringing the total to over 380,000 (Time, See Figure A)
Figure A: From:
  1. U.S. cases hover at 50,000 a day. Deaths flat at 1,000+
     In the last seven days, the U.S. has added 362,000 new COVID-19 cases, about the same as the week before (See Figure B). If new cases had been falling since late July, that trend appears to have stalled. The 1-week moving average remains above 50,000 daily cases. As I have said before, it is difficult at this point to tell whether these numbers are telling us what is happening with the epidemic or with our testing regime. That’s why we disease detectives need to focus on numbers other than daily case totals (See Point 3 below).
     After the weekend reporting lull, COVID-19 daily deaths jumped to 1,334 on Tuesday, the highest daily death count since July 29 (Figure C). In the last week, deaths rose substantially in Washington (+37%), Arkansas (+23%), Georgia (+20%), Tennessee (+31%), and Pennsylvania (+40%). On a more positive note, weekly deaths declined 9% Florida and in 6 Midwest states.
     Bottom line: Both new cases and deaths continue to hover in place as testing stagnates and uncertainty, fatigue and confusion continue.
Figure B
Figure C
  1. COVID-19 testing is falling in the U.S., test positivity rate (TPR) remains stubbornly high
    To make sense of the falling daily case totals, we must keep our eyes on two really important numbers: a) how many total tests are being done each day and b) what percent of those tests are coming back positive. Figure D is my graph showing the most recent data based on numbers from the COVID-19 Tracking Project. Daily tests peaked at over 900,000 back on July 27. Since then, testing has been falling. It’s not surprising since the commander-in-chief keeps telling people we were testing too much. If the President’s goal was to suppress testing to make the numbers look better, he appears to be succeeding. Over the past two weeks, daily tests have fallen from over 900K to less than 750K. That is a sizable jump. This is partly due to supply shortages, lack of surge capacity in the big testing labs, and long lines in some testing centers. The other number we care about is the test positivity rate or TPR (orange line). If testing were falling, and so was the TPR, we would be in a better position to believe that the real number of cases was dropping as the totals have been suggesting. But we are looking now at a bad combination of factors. Fewer tests are being done. The percentage of tests that are positive is not falling, and if anything is drifting slightly higher. We are still not closer to the 5% target. That tells us that most likely the apparent fall in cases is an artifact of running fewer tests.
    What does it mean: The COVID-19 epidemic continues to surge in the U.S. with no apparent end in sight. Testing problems are stacking up right before schools are suppose to reopen. These challenges are likely to be amplified when cold and flu season hits in a matter of weeks.
Figure D
  1. State variation in TPR remains huge, 11 states are under control, 10 Southern and Western states are “on fire”
     I just told you testing is falling across the U.S. and that the overall test positivity rate is hovering above 8% (which isn’t great). Looking one level deeper, I made the graph in Figure E to look at variation in the TPR across states and regions as of now. First the good news. There are 11 states that are at or below the 5% benchmark. That’s a good indicator that transmission is under control in those states, all other things being equal. Most of those are small-population states not surrounded by high-transmission neighbors like Montana, Vermont and Alaska. Congratulations are deserved however for a few stand outs including Michigan, New Mexico, Oregon and Kentucky that look to be doing a good job. West Virginia is the only Southern state with a favorable TPR. On the other side, 10 states are above 10%, twice the target number, all in the South or West. Arizona continues to have truly baffling numbers. Despite the mind-boggling explosion in cases, they are still testing the smallest fraction of their population resulting in a TPR that is almost 20%.
    The bottom line: Due to the lack of national leadership, resources, standards and planning, we have ended up with states that have TPR rates that differ from low to high by more than a factor of 10. Wow.
Figure E

Sunday COVID-19 Briefing

Top news, reports and insights for today:

  1. Daily headline summaries for Sunday:
  • U.S. tops 5 million confirmed COVID-19 cases as outbreak threatens America’s Midwest (CNBC)
  • Some Mississippi hospitals hit capacity with new COVID-19 patients (NBC News)
  • Testing dropping in half of U.S. states. Harvard Global Health Institute head, and trusted source, Ashish Jha says this shows ‘early cracks’ in a system overwhelmed by demand and not designed for this epidemic (Newsweek)
  • Ex-U.S. chief data scientist says misinformation on social media is killing public trust and is “life or death” (Axios)
  • Study of coronavirus patients isolated in a Korean treatment center shows that asymptomatic patients had levels of virus that were similar to symptomatic patients and for similar durations. This strengthens the evidence that asymptomatic patients can be as contagious as symptomatic patients and makes masks and social distancing even more important (JAMA)
  • Study finds that not all masks/face coverings are equal. In a controlled study, speaking while wearing a fleece neck-wrap was worse than no mask, and a bandana did almost as bad as wearing nothing (Science Advances, see figure below)
Figure A: From ScienceAdvances, August 7. Figure shows measured count of droplets passing through 14 tested masks compared to no mask.
  1. New cases have been steady for 6 days with high intensity in the South. U.S. deaths continue to surge
     U.S. new case totals have been steady this week (See Figure A). In the last 7 days, 365,000 new cases have been reported, a cumulative rise of 8%. That’s about 40,000 fewer weekly cases than were added the August 1. Looking at individual states (Figure B), the picture looks similar to what we saw last week. Eight of 12 Northeast states are under control (<5 new cases per 100K last week). None are over 10. However, the epidemic remains hot in the South where 9 of 13 states are seeing high transmission intensity with 20 or more new daily cases per 100K over the last week. Florida (+31), Georgia (+32) Louisiana (+38) and Mississippi (+33) are seeing especially intense transmission of >30 daily cases. The situation in Louisiana is especially alarming (See main point 3). Midwest states are seeing moderate transmission ranging from Michigan (+6.5) to Kansas (19.4). Western states continue to be inconsistent with heavy transmission intensity in Idaho (+27) and Nevada (+29), while rates are closer to being “in control” in Colorado (+7.5), New Mexico (+9), Oregon (+7.4) and Wyoming (+5).
    Over the last 5 days, the U.S. has seen 1200 or more deaths per day except for Saturday (1,109) (see Figure C). The states where deaths rose more than 20% last week include Illinois (+21%), Minnesota (+20%), Wisconsin (+44%), Arkansas (+30%), Mississippi (+22%), Tennessee (+42%), and Virginia (+86%).
    What it means: New cases appear to have peaked. Slowdowns and delays in testing dampen enthusiasm (see headlines). Deaths are holding steady at well over a thousand a day. The epidemic remains intense in the South and parts of the West.
Figure A
Figure B
  1. COVID-19 rates now highest in the South, Louisiana spiking to unseen highs, 4 states now exceed New York
     Let’s revisit the overall COVID-19 infection rates (or incidence) by state and region (Figure D). As a region, the overall attack rates have been highest in the Northeast until now. The West has an overall rate of 1,802 per 100,000 people, exceeding the northeast by nearly 200. Louisiana, a state that keeps getting hit by big waves of high transmission intensity has surged well past New York and will shortly pass the 3,000 rate barrier. Florida, Arizona, and Mississippi join Louisiana as the 4 states now with greater COVID-19 rates than New York, which in March seemed like the place that would never be matched by the ferocity of the virus’s impact.
    The bottom line: Is anyone else curious why the states in the South appear to have no interest in knowing what New York and New Jersey are doing to keep this virus under control?
Figure D
  1. A neglected consequence of the COVID-19 epidemic: people are not seeking or getting treatment for other serious diseases
     Way back on April 19, the Washington Post ran a story that caught my eye. The headline was “Patients with heart attacks, strokes and even appendicitis vanish from hospitals”. I have been thinking about that story ever since. Many of us have worried that the coronavirus epidemic would draw interest, resources and attention away from other life-threatening medical conditions and that this would lead to trouble down the line. On the other hand, there was a hope that the downturn in health care utilization for the usual things that kill people would be temporary. There was a hope that we would eventually establish a new rhythm and people would resume going to the dentist, seeing their doctor for check-ups, and going to the emergency room with broken bones and chest pain.
     Two important studies have come out recently that suggest things have not gone back to normal, raising further fears that American’s health will suffer later for care not sought now.
     The first study came out June 9 in the Journal of the American College of Cardiology. They looked at how the number of patients coming to 9 high-volume medical centers for treatment of one kind of heart attack changed before and after the pandemic. They found that after the the outbreak, patients coming in for treatment of heart attack fell by 38% (See Figure E). This matches the 40% drop seen in Spain. Given the stress of the epidemic, we might have expected more heart attack patients, not a third less. This raises concerns that people are avoiding seeking appropriate medical care for serious illnesses due to social distancing, fears of getting infected at the hospital, misinformation or a host of other reasons.
     A second study came out August 4 in JAMA Network Open and looked at the number of Americans with newly identified cancer before and after the pandemic. The number of new cancer diagnoses for a given month should be stable over time if patients are seeking care consistently. After COVID-19, the number of weekly patients getting diagnosed with 6 types of cancer fell 46% with big drops in all 6 types. The biggest drop (52%) was seen in breast cancer (See Figure F). Importantly, the drop in new cancer diagnoses leveled off around mid-March and hasn’t gotten worse. But it hasn’t gotten better either.
    Why this matters: We expected a temporary dip in patients seeking and getting care for killer diseases back in the spring when things seemed so crazy and COVID-19 was new. Heart attack is an acute crisis; patients know they are in trouble and need help. It’s possible patients are going to smaller clinics and community hospitals rather than the big medical centers in this study. We also know that when economic activity halts, the number of heart attacks might actually go down. Both could explain the first study. The finding in cancer is more troubling. There is no reason to think fewer people are getting cancer after COVID-19. The fact that we are finding far fewer cases tells us that cancer patients may be diagnosed later in the course of disease, which will lead to higher mortality rates.
    The bottom line: What these studies tell us is that 6 months into the epidemic, American’s are not getting screened, diagnosed and treated for heart disease, and cancer, diseases not directly caused by the virus, but top-killers that when not diagnosed and treated in a timely way, can lead to preventable deaths on a big scale. In the long-run, the possibility exists that SARS-CoV-2 will end up killing as many people because of disruption to our overall health care game than die of the virus itself. That’s a whole different sort of whack-a-mole.
Figure E: From Journal of Am College of Cardiology showing map of 9 high-volume centers and average monthly new activations of heart attack treatment protocols before and after COVID-19
Figure F: From JAMA-open network. Newly Identified Cancers, Baseline Mean and Weekly During the Coronavirus Disease 2019 Pandemic