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

Wednesday COVID-19 Briefing


Top news, reports and insights for today:

Starting in September, I will be posting my COVID-19 briefings twice a week on Wednesday and Saturday (instead of 3 times a week). Please continue to send me feedback and questions. Thanks for visiting my blog. -Thomas

  1. Curated headline summaries for Wednesday:
  • Pandemic seems to be leveling off in U.S., but numbers remain troublingly high, experts say (Washington Post)
  • Former FDA commissioner and COVID-19 “influencer” Dr. Scott Gottlieb says a safe vaccine for the general population is “unlikely” before January 2021. You should believe him (MSNBC)
  • New audio recordings of interviews with journalist Bob Woodward proves that President Trump deliberately deceived America about the threat posted by coronavirus (Vox)
  • Many patients are avoiding seeking essential health care due to fear of becoming infected in U.S. hospitals. An important new study of a Boston Medical center that cared for more than 9000 patients over 3 months finds only a single confirmed case (and 1 possible) acquired in the hospital. This study suggests that tight infection control procedures mean that the chance of getting COVID-19 in the hospital is very small (JAMA Network Open)
  • Young American’s often believe they are safe from coronavirus and that only old people are at risk. A new study shows that severe COVID-19 poses a larger risk of death in young adults than a heart attack in this age group (JAMA Internal Medicine)
  • Early in the pandemic, there was a belief that an anti-malaria drug (Hydroxychloroquine) along with a broad-spectrum antibiotic (azithromycin) might be an effective treatment. Now, hydroxychloroquine has been completely debunked and rejected. What about the antibiotic? An important study from Brazil shows that azithromycin does not seem to benefit patients with severe disease who are hospitalized (The Lancet)
  • A study of the effectiveness of a promising COVID-19 vaccine was just put on temporary hold to investigate a safety concern in a study participant. Believe it or not, this is good news. It means the slow, painstaking and careful process of testing the vaccine and paying close attention to every detail is working as it should and that the public can trust the process (Vox)
  • Evidence mounts that White House officials are pressuring top Health officials to promote political messages instead of science. The latest: emails from a Senior HHS official demanding “Uncle Toni” Fauci downplay the risk of COVID-19 in children when he appears before the media (Politico)
  1. U.S. daily cases plummet by half since Saturday; 18 states report 0 deaths on Monday, more than since 4th of July
     After spiking to over 50,000 cases on September 4, U.S. cases plummeted this weekend. After the Sunday/Monday slowdown, I wondered if the Tuesday numbers would spike back up. Thankfully, that number was lower than any Tuesday since June 9 (See Figure A). The weekly case total is 255,000, which is half what it had been in mid-August. The trend in deaths is similar with just 354 reported on Tuesday, the lowest numbers for that day since the epidemic started (Figure B). More welcome news: eighteen U.S. states reported zero deaths yesterday.
     So, what is there for a disease detective to worry about next? The answer may be in Figure C showing new case growth factors for the last week (>1 means cases are growing last week compared to the previous 7 days, <1 means new cases are shrinking). Thankfully, all Southern states are seeing slowing transmission intensity (except Arkansas). Risers and fallers are about even in the Midwest; it’s mostly good news in the West where nine of thirteen states are on the decline.
     The worry is in the numbers for the Northeast where six states are reporting rising cases. Two states recorded more than 30% jumps (Delaware and New Hampshire). Cases are up in Maryland (+15%), New Jersey (+5%), New York (7%), and Pennsylvania (+17%).
     What it means: The overall picture looks rosier today than in weeks. My newest worry is that cooler weather, cold season and a new round of coronavirus infections may be on the horizon in the Northeast, a region that has been calm for most of the summer.
Figure A
Figure B
Figure C
  1. Nine states now with higher rates of COVID-19 infection then New York/New Jersey; worrisome jump in new cases in the Northeast
    Figure D3 shows you where we stand in a state-by-state comparison of the cumulative rate of COVID-19 cases (lab-confirmed cases per 100,000 population). I last showed you this graph a month ago when four U.S. states had eclipsed the rate of New York (Figure D2). Why does this matter? In the carousel of images below, look at where things stood on April 16 (Figure D1). Back then, New York didn’t even fit on the graph with an incidence rate of over 1,100 while no state except New Jersey was over 500 and the average was only 202. Now (Figure D3), seven states in the south and two in the West have passed New York. Since April 16, New York’s rate doubled from 1,100 to 2,265. Arizona skyrocketed from 58 to 2,831 cases per 100,000, a rise of 4,781%! Other stratospheric leaps happened in Nevada (+2068%), Alabama (+2,853%), Florida (2,838%), Georgia (+1,650%), Louisiana (+581%), Mississippi (+2,307%), South Carolina (+3,064%) and Tennessee (+2,537%).
    The bottom line: In the four and a half months since Tax day, New York state’s rate of COVID-19 infections doubled. Now, nine states have done what then looked impossible: surpassing New York. Those states saw cases climb an average of more than 25-fold. Politicians and public health authorities have failed the residents of those states.
  1. Quirky Qorner: What sparked the pandemic “legs race”? Peloton! Guess what, they just came out with an even more expensive fake bike for people to see in the background during zoom meetings
     You have seen it right, the peloton bike in the background during the zoom meeting. At nearly $2,000 bucks, they have been flying off the shelfs as home-bound weekend warriors seek to keep up with Joneses. Now, CNBC reports that the folks at Peloton have grabbed the epidemic bull by the handle bars, announcing an even more expensive model. The new “Bike+”, available Wednesday, will cost $2,495. Peloton, whose sales surged 66% after then pandemic started, saw stock prices surge on the news. The CEO told CNBC “We feel like we’re just getting started”.
    The peloton strikes me as the perfect status symbol for a national emergency where we are all worrying so much and working so hard and still seeming to go nowhere.

Saturday COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Saturday:
  • “Uncle Tony” Fauci warns 7 states to take extra precautions over the Labor day holiday to prevent COVID-19 surge (Huffington Post)
  • Up to two-thirds of Americans say they won’t get COVID-19 vaccine when it’s first available, new poll shows (USA Today)
  • After facing criticism for high cases and a go-it-alone strategy, now Sweden has one of the lowest COVID-19 death rates in Europe (CNN)
  • Widespread COVID-19 vaccines not expected till Mid-2021, WHO says (Reuters)
  • A new study (not yet peer reviewed) reports on experiments that show when SARS-CoV-2 was introduced to heart muscle cells, it resulted in “carnage” on the slides, providing clues to explain widespread evidence that COVID-19 does lasting harm to some hearts (STATNews)
  1. U.S. COVID-19 cases spike to 50,000 on Friday, total cases exceeds 6 million. Big spikes seen in the Midwest
    Things were looking good for a slow-down in new cases in the U.S. for about 10 days. I said on Wednesday it appeared the slow-down might be stalling. Like a cold slap in the face, Friday’s numbers leapt to over 50,000 for the first time since August 15 (Figure A). Driving this spike were large rises in several key states increasingly in the epidemic’s cross-hairs (Figure B). Of the nine states with a rate of new case growth of 20 or higher, six are in the Midwest where conditions continue to deteriorate. They include Iowa (+5,851 new weekly cases), Kansas (4,172), Missouri (+9,223), North Dakota (+1,863), Oklahoma (5,780), and South Dakota (2,079). Growth factors in that region showed increasing weekly cases in all states except Michigan and Iowa. The Northeast and West both remain relatively calm although notable surges in cases were reported in Hawaii. Although new cases fell for the week in California, that state still reported over 33,000 new cases in the last 7 days.
    What does it mean: We are still in deep whack-a-mole in the first wave of the U.S. outbreak. We get lulled into a false sense of progress when cases slow in one region, only to see big surges happen in another (in this case the Midwest). Figure C shows the big picture as we eclipse the 6 million case threshold. The most recent 500K cases were added in 12 days (compared to 11 days in the previous half million). The big picture remains largely stable as the U.S. outbreak enters a seventh month.
Figure A
Figure B
Figure C
  1. How is the U.S. doing compared to other nations in the Western hemisphere? Not great.
    As disease detectives, we seek to make apples-to-apples comparison to see how things are changing in different countries. The best way to do that (as I have explained before) is to use Log-log plots showing standardized growth trajectories of cases and deaths setting each country to a time metric indexed by days since a fixed number of cases (as opposed to calendar time). Figure D below does that for cases. The diagonal reference line shows the rate of growth if cases are doubling every week. Countries where cases are growing faster will be above that line, slower nations are below it. The U.S. is the pink line. This figure paints a particularly grim picture. Almost all the nations in our hemisphere saw rapid growth for the first 10,000 cases (on or above the 7-day doubling line). After that, every nation except the U.S. managed to react in a way that slowed the pace of new cases. After about 20,000 cases, every other country managed to get under the 7-day doubling rate. The U.S. didn’t get there until 500,000 cases. This tells us that the first half million cases were especially costly and put us substantially behind the 8-ball. The pace of the US epidemic slowed between 500K and 2 million. Then, things went very badly again: the rate of growth spiked severely between 2 and 4 million. Even compared to Brazil, the U.S. trajectory shows an inability to react early and to maintain epidemic control measures at critical points. While new case growth has been extensive in Argentina, Columbia, Peru and Mexico, none of those nations saw the prolonged unregulated growth seen in the U.S. Canada, which shares exposure to colder weather in the Northern hemisphere, is hidden here among a second cluster of countries that have dramatically better profiles.
    One might argue that the U.S. was testing more than these countries so perhaps cases are the wrong thing to look at. Plus, the U.S. has far more sophisticated health care systems so certainly we won’t see the same pattern for deaths. I’m afraid that picture is equally discouraging (Figure E). Between 100 and 100,000 deaths, even Brazil out-performed the U.S..
    Bottom line: The U.S. has done worse than any other nation (including Brazil) in the Western hemisphere in controlling the speed of the epidemic both in terms of cases and deaths.
Figure D: created by me using COVIDTrends website showing standardized rate of case growth among Western hemisphere nations as of Sept 4.
Figure E: created by me using COVIDTrends website showing standardized rate of growth in reported deaths among Western hemisphere nations as of Sept 4.