Weekend COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Wednesday:
  1. Top story: U.S. passes 13 million lab-confirmed cases after a million cases tallied each week in November (NBC News).
  2. A new model from CDC researchers, just accepted for publication, suggests the total number of COVID-19 infections in the U.S. may be 8 times higher than data shows, now reaching 100 million after accounting for the difficulty of counting all cases. Still, the report estimates that “approximately 84% of the U.S. population has not yet been infected and thus most of the country remains at risk” (NPR).
  3. Thanksgiving holiday is skewing the data due to backlogs in testing and reporting that makes it look like cases and deaths have peaked. There is strong evidence that this is an artifact of the holiday impacting the data and not of the pandemic slowing (The Atlantic).
  4. The U.S. Food and Drug Administration has approved the first at-home kit that tests for COVID-19. The device, called the Lucira COVID-19 All-In-One Test Kit, provides results in under 30 minutes by testing a self-collected nasal swab sample, and then a light on the display indicates whether the result is positive or negative (Lonely Planet).
  5. Researchers say COVID-19 immunity can last 6-8 months after infection. While this may be the best answer to this important question we have, the new study will first have to be carefully reviewed and published (Science Alert).
  6. New national poll says 27% of Americans say that the coronavirus pandemic is the biggest issue facing President-elect Joe Biden over the next four years. That’s the top percentage for any issue and shows that Republican claims that COVID-19 would fall off America’s radar screens after the election were incorrect (CNN).
  7. U.S. coronavirus hospitalizations have doubled in the last month, reaching a record high over 91,000 on Saturday. While case and death numbers are now unreliable due to Thanksgiving, the continuing rise in hospitalizations offers a truer picture of where the epidemic is going (Daily Mail, See Figure A).
Figure A from The COVID Tracking Project.
  1. U.S. jumps from 11 to 12 million lab-confirmed COVID-19 cases in record time (six days). Cases and deaths appear to slow due to holiday data disruption
     The rate of new cases continues to be greater than any of the previous peak periods. This in part comes from rising test numbers. Still, as headline 2 indicates, the numbers we see are generally only a rough estimate of the true number of cases, now estimated to be 8 times higher than the official count. The data shows the U.S. added the 12th million cases in just 6 days (See Figure B). In some data aggregators (see headline 1) we have already passed 13 million as I type. Looking at the daily numbers last week, it appears as though cases (Figure C) and deaths (Figure D) may be have reached a new peak. Both 7-day moving average curves appear to have inflected. However, as headline 3 makes clear, the reporting of tests, cases and deaths has turned sluggish due to the weekend and holiday slow downs in data processing. Staffing and supply shortages, heavy data entry backlogs, vacation days, staff sick leave, and Thanksgiving itself have all conspired to paint a picture of a peak that I strongly suspect is not actually there. The primary evidence for that assertion comes from the hospitalization data (Figure A) that shows no sign of the slowing despite the holiday. When other surveillance tools suffer, as they do during a national holiday, smart disease detectives trust the data stream that is most resistant to holiday lapses (hospitalizations).
     Instead of staring at the daily numbers, I spent the afternoon looking more big picture at the overall COVID-19 attack rates (or incidence rates) cumulatively by state. Remember when the incidence rates (lab-confirmed cases per 100,000 population) were 10-times higher in New York compared to any other state and it looked like COVID-19 was going to be a Northeast problem? Have a look at the rates now in Figure E. Now, the Northeast has the lowest overall rate of the 4 U.S. regions. Astonishingly, there are now 34 states with higher attack rates than New York, and four of those have rates that are more than twice as high: Iowa (7,171), North Dakota (10,227), South Dakota (8,344) and Wisconsin (6,541). In fact, all 13 Midwest states, 9 of 13 Southern states and 10 of 13 Western states are all higher than New York.
    Bottom line: The U.S. is essentially flying blind right now due to disruption in the timely and complete flow of information caused by the Thanksgiving break. Don’t trust the apparent peak in cases and deaths. Thanksgiving not only knocked our surveillance off kilter, but also, like Memorial day before, has sewn the seeds of still greater acceleration of transmission intensity that won’t become apparent until, well ehm, Christmas.
Figure B
Figure C.
Figure D.
Figure E.
  1. Original analysis: Did any of our prediction models accurately project where we are now a month ago?
     Does anybody remember back in the spring when we were arguing about which statistical forecasting model we should believe? It seems like most experts and commentators have stopped even paying attention. Not me. It’s a classic case of throwing out the baby with the bathwater. Sure, our projection models weren’t very good in March, but we had very little data to work with and a great many basic questions that were unanswered. The models should have gotten better since then. For a while they were multiplying like bunnies. Since the summer, new models have slowed and a bunch have disappeared. Survival of the fittest perhaps?
    A month ago, I decided to do my own “experiment” by selecting a handful of models that seemed to have been working well this Fall and evaluate them. The idea is simple. Four weeks ago, I graphed the predictions of candidate models for both weekly cases and deaths using the COVID-19 Forecast Hub website created by the Reich Lab at UMASS Amherst. I then took the predictions made by the various models that I had “photographed” a month ago, and overlaid what actually happened as of today (Figure F. for incident cases and Figure G. for incident deaths). Each figure has a purple arrow pointing to where we are now, but the graph itself was made at the end of Week 44 on October 29. The top three predictions are labeled #1 to #3 for both cases and deaths. The last two figures present what those models say will happen four weeks from now (Figure H. for cases, Figure I. for deaths). Below are my summary conclusions based on this analysis. Feel free to comment or send me email.
    Conclusions:
    1. None of these models is a perfect crystal ball (that we would not expect). Although, the 4-week projections are better than they were in the summer.
    2. For both cases and deaths, none of the 17 models tested predicted how bad things got; a month ago, every model under-predicted weekly deaths (-2,700 on average) and cases (-569,000 on average), in many cases drastically.
    3. There was a clear winner for cases and deaths, but it wasn’t the same model (the Discrete Dynamical Systems, Negative binomial dynamical systems model from Rahi Kalantari at University of Texas got, by far closest for cases; for deaths Dean Karlen’s model from the University of Victoria got the closest).
    4. Most of the models compared were crap.
    5. Relatedly, the so-called “ensemble model” that basically “averages” over all these models (Bright pink COVIDhub ensemble in Figures F and G) didn’t perform in the top 5 simply because so many of these models are complete rubbish.
    6. If you believe the 2 best models, 4 weeks from now, we will triple cases from 1.3 million to 3.3 million (DDS-NBDS) while deaths will double from 10,000 to over 22,000. It’s worth noting that just because these two models outperformed the others last month, there is no guarantee they will do so next month.
    7. Taken together, the models that made the most extreme projections were closest to being right, while the average projections came in too low. If that trend continues, the next month will be worse than common sense and most models suggest.
Figure F
Figure G
Figure H. Predicting 4 weeks from now: weekly cases
Figure I. Predicting 4 weeks from now: weekly deaths
  1. Quirky Qorner: Lock down is getting old for one comedian
     I found a funny video on CBS news by comedian Jim Gaffigan who says his Thanksgiving spent, like the rest of the year, with just his wife and kids, would, if set to music be Hotel California by the Eagles. If you are like me, it does feel that you can check out but never leave?

Top pick of the day: Tuesday

You won’t believe how bad coronavirus numbers are about to get in the US

Science Article by Chris Smith published online at BGR.com November 24, 2020.

Things seem pretty bad right now in this country. But, just how bad is it going to get? There is a natural tendency to believe that awful circumstances can only get better. Nature doesn’t always follow that rule. For hints, we turn to our best prediction models, put in all the latest numbers, and project where we think we will be in the future. In my Wednesday briefing, I’ll be looking at what a handful of those models said a month ago and how each one did at predicting where we are now. Spoiler alert: not well. In the meantime, here is an article focusing on what one high-visibility model is predicting for our near future. The bottom line is also not good: cases will double in 2 months despite being at record levels now.


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.

Weekend COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Saturday/Sunday:
  • Top story: Head of Federal “Warp Speed” vaccine effort says U.S. vaccinations for prevention of COVID-19 will “hopefully” start in weeks. Two vaccine makers have applied for FDA approval, a process expected to take about 3 weeks. The first round of vaccines will to go to nursing homes and health workers. Availability for the general public is expected to ramp up in the first half of 2021 (Bloomberg).
  • CDC warns against Thanksgiving travel amid COVID-19 surge (CIDRAP).
  • Dr. Sanjay Gupta, CNN Chief Medical Correspondent (along with many others) says he won’t be visiting family this Thanksgiving and you shouldn’t either (CNN).
  • Over 1 million U.S. travelers flew on Friday, despite calls to avoid holiday travel (Axios).
  • Los Angeles county has the most infections of any in the U.S. since the start of the pandemic. Amid a recent surge in cases, greater Los Angeles added 4,522 new COVID-19 cases on Saturday bringing the area close to the decision point to (once again) lock down restaurants, bars, breweries and other businesses (Bloomberg).
  • Scientists in the U.K. find that tocilizumab (Actemra), a drug used to treat arthritis, showed signs promise in treating severe COVID-19 patients. While not yet definitive, this is important because it illustrates how science is narrowing down effective therapies thanks to our growing understanding of how SARS-CoV-2 works. This drug, like steroids, works by reducing inflammation, the fatal culprit for many seriously ill patients (Imperial College Healthcare News).
  • If states were countries, 16 of the highest rates of new COVID-19 infections in the world this week would be U.S. states (Federation of American Scientists, See Figure A)
Figure A: https://twitter.com/euromaestro/status/1329996608981905408/photo/1
  1. U.S. about to reach 12 million cases, now reporting a million cases a week
      When COVID-19 hit the U.S., it took almost 3 months (58 days) before we hit one million cases (See Figure B). Nine months later, cumulative cases jumped from 10 to 11 million in just one week, and is poised to cross 12 million in even fewer days. Would anyone have believed you in May if you said we would have a million cases a week in November? How did we arrive at a million a week? By recording 150,000 cases or more for 6 of the last 7 days, peaking on Friday at a record high 187,000 (Figure C). As each day passes and each record is broken, this third peak increasingly dwarfs the magnitudes of the first and second peak periods.  If you are looking for a scrap of good news, it might be that weekly cases declined for the first time in both North (-10%) and South Dakota (-23%), as well as in Iowa (-17%) (Figure D). That’s about where the good news ends; cases are increasing weekly in every state in the South, Northeast and West (except Hawaii). Growth factors of +40% or more include previously hard-hit states Arizona (+42%), California (+54%), New Mexico (+71%), Oklahoma (+49%), Florida (+49%), Louisiana (+55%) and Virginia (+54%). No state is below 5 new daily cases per 100,000, a measure of good outbreak control, but 47 are at 20 or more and 32 states are at 40 or higher. Ten states are out of control at 100 or more daily new cases per 100,000 including Montana (116), New Mexico (111), Utah (102), Wyoming (120), Iowa (119), Minnesota (114), North Dakota (163), Nebraska (120), South Dakota (115) and Wisconsin (110).
    Bottom line: The U.S. is now at a million cases a week. New daily cases are highest in the Midwest and West, but numbers are growing more in the South and Midwest. This is a perfect storm, even as hopes for a vaccine rise.
Figure B
Figure C
Figure D.
  1. North and South Dakota have the first and third highest COVID-19 death rates in the world this week, as the third mortality peak rages across the nation
     Total U.S. death toll from COVID-19 passes 240,000 this week as almost 10,000 deaths were reported, a nation-wide increase of 29 percent over the previous week (Figure E). The weekly high daily death toll of 1,956 on Thursday marks the first time since May 6 that 2,000 daily deaths were reported. Figure F shows the three distinct mortality peaks, each with a different state experiencing the worst. During the first (and most severe) peak this spring, deaths per one million peaked at 39 in New York on April 15, with New Jersey, Connecticut and Massachussetts all soaring over 20. As the first peak waned and the Northeast gained control, the epicenter swung to the west leading to a second mortality peak in Arizona at a much lower 11 per one million on July 21; Mississippi also peaking at 11 a week later. As the third mortality peak takes shape, four states have already exceeded the July peak including the Dakotas, Wyoming and Montana. Consider how “resourceful” SARS-CoV-2 has been in this country. The three peaks are remarkably different qualitatively having occurred first in the densely populated, urban, transportation-heavy New York corridor. The third peak, in contrast, is happening in the smallest, most remote and least populace states. This peak is most intense in the Dakotas, two states that have refused to implement coordinated transmission control measures, and where death rates are mid-way between the terrible carnage of the first peak and the worst of the second.
     Just how bad is it in North and South Dakota? Well if those two states, with total populations of just 72,000 and 68,000 respectively, were separate countries, they would have the first and third highest COVID-19 death rates in the world last week according to the Federation of American Scientists (Figure G). Nobody thought that could happen in tiny states with such low density and no big city. More broadly, weekly deaths are rising in all but three states (Figure H) with the most alarming increases in California (+52%), Colorado (+93%), Nevada (+78%), Oregon (+100%), Kansas (+71%), Arkansas (+82%), North Carolina (+65%), New Jersey (+53%), and Pennsylvania (+103%).
    Bottom Line: A third mortality peak is underway, with deaths lagging behind cases by about a month and hospitalizations about 2 weeks (see Wednesday briefing). Right now the third peak is worse than the second but not as bad as the first. Prediction models are too imprecise as of yet to give fool-proof guidance about how bad this peak will get. North Dakota, with the worst death rate in the world and a governor that refuses to take action, remains the control group for the world showing what happens when governments do nothing to stop this virus.
Figure E
Figure F: Three mortality peaks
Figure G: https://twitter.com/euromaestro/status/1328244083308040192/photo/1
Figure H.
  1. Quirky Qorner:This is the way….to mask up
     We should all be wearing masks when we go out, which includes going to Michael’ for Christmas stuff. That’s what a California mom told her 5-year old daughter. According to an article in Buzzfeed.news, mom didn’t expect her daughter to choose the mask she did (See image below posted on twitter). When it comes to masking up, this is the way!
https://www.buzzfeednews.com/article/otilliasteadman/mandalorian-mask-little-girl-viral-tweet