Wednesday COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Wednesday:
  • New study finds since mid-May, U.S. has the highest COVID-19 death rate of any country with a large outbreak. Since June 7, U.S. COVID-19 deaths per 100,000 were more than twice the next highest countries (Israel and Sweden) and 6 times higher than Canada (JAMA, see Figure A below)
  • Sweden’s experiment to avoid shutting down is a “disaster” and should not be a model for the world (Time)
  • For the first time, the U.S. has now hired more than 50,000 contact tracers according to Johns Hopkins data. However, the push to grow a COVID-19 workforce is still less than half way to what experts say we need (NPR)
  • Harvard study finds that patients who survive severe COVID-19 infection retain high antibody levels for up to 4 months. This is as close as we can now come to President Trump’s unsubstantiated claim that he now has lifetime “immunity” to the virus (Daily Mail)
  • A 25-year-old man is now the first in North America to have a documented second infection with SARS-CoV-2. His second infection identified in June was more severe than the first found in April. The true extent of COVID-19 reinfection is not currently known (CBS News)
Figure A: Figure created by me based on https://jamanetwork.com/journals/jama/fullarticle/2771841
  1. U.S. daily cases continue to track upward, surges seen across all regions. Three Midwest states remain white hot and getting hotter
     As we move into a new week, the daily U.S. case data shows a continuing trend toward rising transmission intensity with the 7-day moving average lurching over 45,000 daily cases (Figure B). In the last week 340,470 cases were reported, the first time we have seen more than 300,000 weekly cases since mid-August. At my weekend briefing, cases were rising in all but 8 states. The numbers now look worse (Figure C); all but 5 states are now on the incline. There are numerous states in all regions where cases rose 20% or more week-over-week with the largest number in the Midwest: Iowa (+23%), Illinois (+41%), Indiana (+42%), Kansas (+26%), Michigan (+27%), Minnesota (+21%), North Dakota (+31%), Ohio (+26%), and South Dakota (+33%). The situation in the Dakotas remains especially alarming as things have gone from bad to worse. After weeks of very high transmission, both states saw new cases rise by more than a third. North Dakota added another 3,881 new cases raising its overall incidence rate to 3,706 per 100,000, second only to Louisiana. The largest weekly jumps in new cases actually happened in the West where Colorado (+41%), Montana (+63%), and New Mexico (+55%) are potential new hot spots.
     Switching to the rate of new infections, similar states stand out (Figure D). A week ago, North Dakota had 56 new daily cases per 100,000, now they are at 73. South Dakota, then at 47 is now 62. Montana jumped from 35 to 57 in a week. These are big increases in states that have been hot for some time. All but two Midwest states are now over 20 new daily cases per 100,000 and none are below the 5 benchmark. In the South, only Arkansas, Mississippi and Tennessee remain “hot”. The situation is holding steady in the Northeast although new cases are creeping higher in Rhode Island, now at 22 per day.
     The bottom line: The overall picture is toward rising cases across the board and in all regions. The Dakotas remain the hottest of the hot spots, followed by Wisconsin, and Montana. Thankfully, deaths have not yet started to rise appreciably but it is only a matter of time.
Figure B
Figure C
Figure D
  1. Is the current surge in U.S. cases due to flu? Not yet!
      I want to talk about influenza. There has been a lot of discussion lately about what we should expect given the impending rise of flu cases and what that will mean for the COVID-19 pandemic both in the U.S. and throughout the Northern hemisphere. Some people are suggesting that the kickoff of the flu season may be behind the recent surge in cases.
     I decided to go back and look historically at the time course of influenza in the U.S. in the fall over the last three years. Thankfully, the CDC has a great tool for this called interactive FLUView. It shows trends in influenza-like illness (ILI) across the U.S. by tracking patient visits to doctors with flu-like symptoms each week. Figure E below is my best effort to show you what the U.S. maps look like every two weeks from the middle of October till early January over the last three years. My goal was to answer a very simple question. When does the flu season really start to intensify? If it is late October, it might be true we are already seeing the impact of flu on COVID-19 numbers.
     Have a look at Figure E. There are at least 3 main lessons I take from this picture. First, it is exceptionally unlikely that the surge we are seeing now is the result of early flu activity. Over the last three years, the intensity coming in January through March won’t actually get started until somewhere between late November (last year) and late December (2018-19). The second thing that caught my eye was that flu-like illness intensifies first geographically in the Southeast and works its way north. I don’t know why but it is an interesting epidemiologic puzzle. I will be looking carefully at Louisiana, Texas, Alabama and Georgia as the states most likely to show early flu intensity. Third, last year was a high-intensity flu season months before COVID-19 was on the radar screen.
     The bottom line: It is hoped that with good vaccine uptake, mask wearing and social distancing, this year’s flu season will be less severe. If it is, COVID-19 will be more manageable. If, however, we drop the ball on flu prevention, the co-occurence of influenza and COVID-19 could create a double whammy of tremendous death and suffering.
Figure E
  1. Quirky Qorner: Cyberchondria! Social media and internet browsing are driving COVID-19 fear and anxiety
     I started reading this week about cyberchondria, defined on Wikipedia as the unfounded escalation of concerns about common symptomology based on review of search results and literature online. It’s a very pretty word for a not-so-pretty facet of the COVID-19 pandemic. We all like to believe that having access to more information at our fingertips is a good thing. More and more we are realizing that this is often not true. Researchers find that google search trends can actually predict where outbreaks are heating up. Now, a team from the Netherlands has published a study in the Journal of Anxiety Disorders. The study, based on a survey of 439 adults conducted in March, found that the coronavirus outbreak is causing fear and worry to increase. That’s hardly surprising. The interesting part is that even after controlling for other factors, time spent regularly looking up coronavirus information online, through social media and through regular media increased fear. You would think it is the opposite. Regular intake of social and traditional media heightened people’s fears rather than empowering them. Of course, that can’t apply to my blog. Right? Well in their analysis, looking up information on “professional” websites was not associated with increased fear! Whew!

Wednesday COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Wednesday:
  • Researchers combined information from 32 studies of COVID-19 risk in children, finding that children and adolescents had 44% lower odds of secondary infection with SARS-CoV-2 compared with adults (JAMA Pediatrics)
  • Moderna CEO says its coronavirus vaccine won’t be ready until spring of next year (CBS News)
  • The White House coronavirus task force again this week strongly recommending mask usage in some states like Iowa and Georgia that still do not have statewide mask mandates (CNN Politics)
  • Hospitals feel the squeeze as cases spike in upper Midwest states Wisconsin, North Dakota (ABC News)
  • Facebook removes 38 versions of Trump campaign ads claiming (without evidence) that admitting refugees increases COVID-19 risk (NBC News)
  • Largest study yet of COVID-19 transmission in India published in Science highlights the role of super-spreaders, a small subset responsible for a high percentage of infections. Study also finds that children transmit the disease as easily as adults (Los Angeles Times)
  • Remember how COVID-19 exploded on a cruise ship? The Trump administration has again over-ruled the CDC recommendation to extend the “no-sail” order on cruise ships to next year (ARS Technica)
  1. U.S. passes 7 million lab-confirmed COVID-19 cases. Last million cases added in 26 days
     Let’s start with the big picture today. Over the weekend, based on the Wikipedia data, the U.S. passed 7 million cases (See Figure A). On average, the U.S. has added a half million cases every 12 days. We went from 6.5 to 7 million in exactly 12 days. On average, each million cases has been accruing every 26 days. The jump from 6 to 7 million was just that (26 days). That’s a million cases a month. The more important idea here is that the COVID-19 outbreak is now steady-as-she-goes in terms of the pace of growth. On a big picture basis, the epidemic is locked in to an oddly consistent, even robust degree. Seasonality has been less than expected, surges and falls have been less steep than might have been predicted, and overall, the epidemic curve looks more like an endemic than a pandemic.
    What does this mean: Buckle up for the long hall because SARS-CoV-2 is not going away.
Figure A
  1. U.S. daily cases holding largely steady. Transmission intensity highest in the Midwest, growing fastest in the West
     Figure B shows daily cases; the 7-day average remains just over 40,000 a day. We are now adding cases about twice as fast as the nadir of the epidemic in the first week of June. Today, I wanted to point out how different ways of looking at the same data are needed to address different questions. What questions? First, where are infections being generated most intensively right now? Second, where is the rate of new infections growing the fastest? Sometimes the answers will be the same. But, if a particular state has high sustained transmission intensity for a long time, the rate of growth of new cases will be very low. Conversely, a state with very low transmission intensity might be growing the fastest through regression to the mean in a natural cycle of change.
     Take a look at Figure C showing new daily cases per 100,000 residents by state over the last week. Let’s remind ourselves that the benchmarks we care about are a) less than 5 indicating “low” transmission intensity, and b) greater than 20, or 4-fold higher, indicating “high” transmission intensity. As has been consistently true for weeks, the Northeast is in the best shape with 5 states in the low category and only Delaware is over ten. The South is, thankfully, also relatively quiet with only Arkansas reporting high spread. The region that is clearly most hot is the Midwest with eight of thirteen states in the red zone. Three stand out in particular: North Dakota (54) is 10x higher than the “low” benchmark, while South Dakota (45) and Wisconsin (39) are surging at a white hot pace. Michigan (9.6) and Ohio (7.8) are the only “warm” states below 10. Iowa (29), Kansas (32), Missouri (22), Nebraska (24) and Oklahoma (26) are all hot. In the West, while Arizona remains coolish, Idaho (25), Montana (27) and Utah (32) are all hot.
     So what about the second question? Have a look at Figure D showing 7-day growth factors in cases. The picture is different. Intensity is low in the Northeast, but growth in new cases is strong with five states seeing a week-over-week increase of 10% or more: Delaware, Massachussetts, New Jersey, New York and Pennsylvania. New cases are falling in nine of thirteen states in the South. The region where the most growth is occurring is the West. Cases are rising fastest in New Mexico (+58%), Wyoming (+53%), Nevada (+46%), Washington (+41%), Alaska (+39%), and Montana (+39%) in that order. Whereas transmission intensity is highest in the Midwest, case growth is over 20% in only Michigan (+21%), South Dakota (+28%), and Wisconsin (+23%). Let’s take special notice of the states that pop out of both figures. Montana, South Dakota and Wisconsin, all regionally propinquitous, all have both high intensity and rapid growth.
     Bottom line: Something big and scary is going on in the upper midwest plains states!
Figure B
Figure C
Figure D
  1. Quirky Qorner: Republic of Kazakhstan social influencer Borat tweets praise for U.S. coronavirus handling: “Because of Trump, 350 million Americans still alive”
     If rumors are correct, the long awaited followup to Borat is on its way to Amazon Prime Video sometime soon. According to this piece in Vanity Fair, twitter was shaken by a video appearing just before the first debate, handle @KazakhstanGovt, congratulating “Premier Trump” for his handling of the crisis. Very Nizzzze!

Saturday COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Saturday:
  • Top government infectious disease expert Dr. Anthony “Uncle Tony” Fauci said on Friday he disagreed with President Donald Trump’s assessment the United States has “rounded the corner” on the coronavirus pandemic, saying the statistics are disturbing. (Reuters)
  • National Institutes of Health Director Dr. Francis Collins says the coronavirus vaccines in trials will be held to “the highest standards ever applied” and calls America’s polarization on the pandemic “unfortunate.” (MSNBC)
  • An estimated 41% of U.S. adults say they have delayed or avoided medical care due to COVID-19 including urgent or emergency care (12%) and routine care (32%) according to a new federal study (CDC/MMWR).
  • A classic type of epidemiologic study called a case-control design was just published showing that adults who tested positive for COVID-19 were about twice as likely to have reported dining at a restaurant compared to those who tested negative. This and other studies suggest that dining and drinking establishments may be playing a key role in keeping the epidemic going (CDC/MMWR)
  • Antartica: the last place on earth that is still COVID-19 free? For now (Axios)
  • Dakotas lead the U.S. on COVID-19 case growth as both reject mask rules (ABC News)
  1. After a week of improvement, cases and deaths pop back up as U.S. outbreak see-saws toward Fall. Transmission remains high in 6 Midwest states
     My Wednesday briefing advanced a hopeful tale of falling infection and death numbers. Well, the coronavirus epidemic in the U.S. seems like the weather in [insert your state here] where they say: if you don’t like the weather, wait an hour and it will change. The post-peak epidemic curve in the U.S. is looking more and more like a crazy “dragon tail” (See Figure A). After a hopeful Tuesday, new cases climbed alarmingly on Wednesday (30,000), Thursday (36,000) and Friday (44,000), leaving the 7-day total at 234,000 cases, a number that still represents a declining long-term trend, but not the dramatic plunge the data seemed to portend in the week’s first half. The surge appears to be the result of continued elevated transmission intensity in the Midwest where 6 states remain above the 20 daily cases per 100,000 benchmark (Figure B). Once again, North Dakota stands out as the only state above 30, having reported 1,711 cases last week (see a state spotlight in Point 4 below). Other Midwest states above 20 include Iowa (21 per 100,000 per day), Kansas (27), Missouri (21), Oklahoma (20.2), and South Dakota (25). Thankfully, all other states in the other three regions remain below 20. The pattern is similar in deaths (Figure C) after three consecutive days of more than 1,000 a day. I am sad to report the U.S. just passed 180,000 total deaths among lab-confirmed COVID-19 cases, a number that represents the highest death toll of any nation on earth and roughly 20% of all global deaths.
    The bottom line: after a hopeful start to the week, Midwest flare ups have deflated our balloon of hope leaving a confusing picture about where the epidemic is headed.
Figure A
Figure B
Figure C
  1. What’s happening on U.S. college campuses? We have a brave Kansas teacher to thank for the answer
     Today’s Top-pick-of-the-day from The Atlantic asks the question: what did colleges and universities think was going to happen when they tried to restart in-person classes? Ok, it’s a snarky question for sure, but a fair one. We are marching toward mid-September and colleges and universities are scrambling, scrapping plans to reopen, sending sick students home, and reshuttering programs and facilities as cases flare up. Personally, I had hoped to get in on the lucrative action as a special consultant to universities this summer but somehow, no schools were interested in what I had to say about the prospects of keeping COVID-19 at bay this Fall. Alert readers already know what that was.
    After a summer of hope that reopening would be possible, a series of high-visibility outbreaks on campuses at like the University of North Carolina, Notre Dame and the University of Texas, caused a last minute change of heart as schools were forced to pivot as August turned to September. As the picture grew more chaotic, many were frustrated by the lack of a good, consistent data source to track campus outbreaks.
    One was a Kansas high school teacher named Alisha Morris who decided to do something about it. So, she set up a system on her own and put it on the NEA website. In a short time, we had a solid tool, the NEA School and Campus COVID-19 Reporting Site, that quickly became the go-to place for information on campus COVID. Let’s take a moment to emphasize that while the COVID-19 pandemic has revealed plenty of weaknesses and problems, it has also given us deeply satisfying stories of innovation, bravery and resourcefulness. This is one of them. The data hub is now visible in real time dynamic updates on the New York Times site. The map in Figure D shows the latest numbers across the country since the outbreak began. It shows that outbreaks on campus are by no means isolated or rare. From the northern tip of Maine, to the western edge of Washington state, all the way to the tip of the tail of Florida, cases have been confirmed at more than 1,190 schools. Here are some of the things we know:
    1. At least 88,000 cases and 60 deaths are now linked to colleges and universities since the pandemic began.
    2. More than 150 schools have reported at least 100 cases.
    3. Illinois State University, the University of South Carolina, Auburn University, the University of Alabama and the University of North Carolina at Chapel Hill have all reported more than 1,000 cases.
    4. Many colleges are sending students home in response to outbreaks. “Uncle Tony” Fauci told ABC news this is the “worst thing you could do.” All disease detectives know he is right.
    5. There is growing evidence that outbreaks on college campuses are tied to larger surges in some states.
    6. Despite rules and procedures to the contrary, college kids are partying, gathering, traveling, mixing and exchanging SARS-CoV-19. Who knew?
Figure D. Screen grab from https://www.nytimes.com/interactive/2020/us/covid-college-cases-tracker.html
  1. What’s the story in North Dakota?
     Just because I am a curious disease detective, I decided to look a bit more deeply at the situation in North Dakota, a state that has been running hot for weeks and that leads the nation with the highest rate of new cases over the last week at 32.1 per day per 100,000 people (see Figure B). Why care about North Dakota? We know that population density, linkage to commuter and commercial urban centers, international travel and large public transit systems are all associated with increased spread of infectious diseases. North Dakota has none of these in abundance. High transmission intensity in a sparsely populated state with no major cities and lots of open space is a mystery for the disease detective. What it does have is meat packing plants, large factories, the occasional mass gathering and perhaps a population that believes itself to be safer than it is. North Dakota now tallies 15,151 positive tests and 167 cumulative deaths, according to the official North Dakota government portal. It’s rate of infections (cumulative positive tests per 100,000) stands at 1,927, which is higher than 31 states including California (1,889), Michigan (1,112), Minnesota (1,467), Kentucky (1,119), North Carolina (1,738) and Massachussetts (1,758). Among Midwest states, only Iowa (2,311) and Illinois (2,034) are higher and both have much larger populations. It is also more than double the rate of other remote states like Wyoming (627), Alaska (819), Hawaii (732), Montana (822), Oregon (684) and Maine (340).
     For a deeper look, let’s turn to one of my top sites at rt.live and examine the trends. Figure E shows overall epidemic curve for the state. Between mid-March and the 4th of July, things were fairly stable with about 50 cases a day statewide. Cases doubled over July and then went, well viral in August and September with exponential growth. New cases adjusted for error and testing variations leapt past 400 a day this week. Isn’t it possible that this explosion, now 6 weeks old, is an artifact of a sudden spike in testing? Figure F gives us a clear answer: no. The pink lines tell us the number of positive results (clearly rising after July 4), but the testing volume (gray bars) show inconsistent but stable numbers that if anything likely understate the true transmission intensity. Figure G shows the model-based estimates of the effective reproduction rate or (Rt). North Dakota now is 1.23 and rising, which is top two or three in the nation across many estimates. It’s one of the only states that has been steadily above 1.2 since early August. That number means each infected person is currently expected to transmit the disease to 1.23 other people on average, a number that is more than sufficient for continued high transmission intensity and rapid growth in cases and deaths. So where is all the action happening?
     The final two maps (Figures H and I) show us the raw and adjusted numbers of active cases. I show them both as a reminder for good disease detectives about the dangers of being mislead by the data. Absolute numbers of active cases indicate explosive outbreaks in Burleigh and Kass counties. The story in each of these counties is interesting and complex involving a mix of rising social gatherings, institutional outbreaks, the opening of new testing sites, and plant and businesses restarting. The last graph shows active cases per 10,000 people, which directs our attention to different counties entirely with no doubt a different set of circumstances and stories.
    The bottom line: North Dakota has been and continues to be a hotspot state worth examining. The high transmission intensity is not limited to the past few days or even weeks and is not due to isolated clusters in one community. In theory, the circumstances in this largely rural state should make it hard for coronavirus to propagate. More so than neighboring states, North Dakota persists as a friendly destination for SARS-CoV-2.
Figure E. Epidemic curve for North Dakota as of 9/12/20 From: https://rt.live/us/ND
Figure F. Testing results and volume for North Dakota as of 9/12/20 From: https://rt.live/us/ND
Figure G. Effective Reproduction Rate (Rt) for North Dakota as of 9/12/20 From: https://rt.live/us/ND
Figure H. North Dakota active positive cases as of 9/12/20. Taken from https://www.health.nd.gov/diseases-conditions/coronavirus/north-dakota-coronavirus-cases
Figure I. North Dakota active positive cases per 10,000 population as of 9/12/20. Taken from https://www.health.nd.gov/diseases-conditions/coronavirus/north-dakota-coronavirus-cases
  1. Quirky Qorner: Afraid to visit grandparents during COVID-19? To fight the epidemic of loneliness, try a robot!
    VOX reports on a new option for combatting the epidemic of social isolation and loneliness during this pandemic: robots (Figure J). Even before COVID-19, robots were being introduced in nursing homes and senior centers to provide companionship to residents. This spring, New York’s Association on Aging sent robotic pets to over 1,100 seniors. Socially adept robots have advantages: they don’t get impatient or frustrated, they don’t forget the need for a medication, and they don’t breath virus-laden air. Bioethicists are of mixed mind on whether this trend is a good idea. Who’s a good robot!
Figure J. From VOX.com