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!

Weekend COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Saturday/Sunday:
  • U.S. sees highest number of daily coronavirus cases since August raising fears this may be start of a “dreaded second wave”. (CNN)
  • CDC posts warning about added COVID-19 risk for those who are overweight. With Nearly 40% of American adults obese, this greatly expands the list of high-risk individuals. (Bloomberg)
  • Isolated hot spots have popped up in New York causing Governor Cuomo to close schools, nonessential businesses, banning mass gatherings and limiting houses of worship. Some hot spots are in areas where ultra orthodox Jews reside. On Friday, a U.S. district judge rejected a requested restraining order on the Governor’s restrictions made by Jewish groups (New York Times)
  • Results of a randomized clinical trial from Brazil show that COVID-19 with moderate or severe acute respiratory distress syndrome (ARDS) who were given intravenous steroids (dexamethasone) were less likely to die or need mechanical ventilation. This study adds to our confidence that steroids help reduce the chance of deadly hyper-inflammation linked to poor outcomes in ARDS patients (JAMA)
  • A RAND Corporation survey of U.S. adults found that alcohol use increased in terms of the number of days of drinking but not drinks per month during the pandemic. A key finding was that women (but not men) reported more heavy drinking episodes and more alcohol-related problems. This raises concerns that women may be more vulnerable to pandemic stress (JAMA Open Network)
  • President Trump claims he is “immune” to COVID-19. His doctors won’t say if he has yet had a negative test. Now, twitter has flagged the presidential tweet as misleading. It is. (Axios)
  1. U.S. daily COVID-19 cases spike to mid-August levels. Eleven states record new record high infections.
     On Wednesday, it wasn’t clear which way the trend was headed after a see-saw week. But on Thursday, daily cases shot up again to over 53,000, starting a three day run resulting in 162,506 cases reported (See Figure A). Figure B shows the growth factors for cases; compared to the previous week, new cases are rising in 43 of 51 states and DC. Especially rapid growth in new cases was reported in Alaska (+43%), Montana (+54%), New Mexico (+51%), Missouri (+44%), Tennessee (+50%), Washington DC (+72%), Pennsylvania (+64%), and Vermont (+103%). We have not seen such broad, across-the-board growth in cases since August. More striking, eleven states set new daily high case reports either Friday or Saturday including Alaska (249 daily cases), Montana (722), New Mexico (485), Wyoming (195), Indiana (1,918), Minnesota (1,516), Missouri (5,066), North Dakota (656), Ohio (1,734), Oklahoma (1,533), South Dakota (750) and West Virginia (353). That makes this one of the scariest daily case reports of the entire U.S. outbreak. The surge in cases has not yet translated to a rise in deaths (Figure C), however an upturn can be expected in the coming weeks. Last week we did see big jumps in weekly deaths in Colorado (+160%), Missouri (+139%) Alabama (+72%) and Pennsylvania (+51%).
    What does it mean: The last few days have been rough. Former hot spot states like Minnesota, Ohio and Missouri, along with seven other states reported the most cases of the entire outbreak. Cases are rising broadly in all regions and daily numbers break through the 50,000 ceiling again. This tells me we are at a vulnerable inflection point.
Figure A
Figure B
Figure C
  1. Test positivity rate (TPR): a positively good test for transmission intensity
     Over the past few months, I have gone back and forth between different data streams, each tapping into a different aspect of the epidemic. This reminds me of the parable of the blind men examining an elephant. Each has his hands on a different part of the same beast. Thus far, we have emphasized daily cases and deaths, and hospitalizations, graphed by state and region. Let’s zoom in on test positivity rate. TPR is a fairly simple statistic, although getting good data to measure it is anything but easy. Here we are again grateful to the COVID Tracking Project for the best available data. It is the percentage of all tests (with a definitive result) that are positive for COVID-19 infection. Most agree that we want this number to be 5% or lower, indicating that our testing regime is sufficient to identify a healthy fraction of all the cases, while 95% negative results tells us that the barriers to testing are low enough that testing is happening broadly and at sufficient capacity. In the early days, TPR was 40% and higher largely because we were only testing those hospitalized with COVID-19 symptoms and tests were in short supply. We have come a long way and our testing strategies and capacity have evolved.
     I set out to find a data source that would tell me the TPR just for the past two weeks, rather than the entire duration of the outbreak. This is, in my view, a better number for tracking change in transmission intensity. In states where the 2-week TPR is drifting higher, the virus is outstripping capacity, and causing surveillance efforts to fall further behind the eight-ball. I created Figure D below as a new tool to examine state-level variation in TPR in the last two weeks. Not surprisingly, the variation across states is huge. First the good news: out West, six states are keeping up nicely including Alaska, California, Colorado, Hawaii, New Mexico and Washington. To illustrate the value of this data stream, compare the findings in Point 2 above, where Alaska and New Mexico are seeing sharp rises in cases, however their TPRs remain low. Combining the two data streams, we look for states with the deadly combination of rising cases/deaths and high TPR. In the Midwest, Illinois, Michigan, Minnesota and Ohio are in good shape. In the South, that distinction is shared by only Louisiana and West Virginia. All but three Northeast states are in the green zone and none is over 8%.
     Now for the bad news: there are six states, two out West and four in the Midwest where TPRs have shot up past fifteen percent, or three times greater than the quality benchmark. Idaho (23%), South Dakota (23%) and Wisconsin (21%) are extreme with more than 1 in 5 tests coming in positive. All three states are reporting in excess of 30 daily cases per 100,000 population. They also vary in how much testing they are doing. Idaho, for example, is testing only 1.3 per 1,000, among the lowest in the nation and less than half the rate of Colorado (3.0 per 1,000). South Dakota is also at 3 tests per 1,000 residents but their TPR remains high due to explosive epidemic growth (as covered on Wednesday). Wisconsin, also white hot right now, is testing in the middle (2.2 per 1,000) and most likely continuing to fall behind. The maps of these three states show somewhat similar patterns (Figure E, from the Johns Hopkins Coronavirus Resource Center). Each state is a checkerboard of rural counties with very low case totals and a handful of counties in and near cities and towns with extremely high numbers. Tomorrow I will explore how many of these counties have colleges and universities in them.
     The bottom line: While the U.S. overall continues to hover around 5-6% test positivity rate (TPR), this hides tremendous state-level variation. There are now six hot spot states where greater than 15% of tests are positive indicating a mix of inadequate testing and high transmission intensity.
Figure D
  1. Quirky Qorner: 10,000 minks die of COVID-19 in Utah, foreshadowing coming shortage of luxury coats
     The Guardian is reporting on an outbreak of COVID-19 among mink in Utah where almost 10,000 have died prompting quarantines conditions among the state’s mink farms. The first U.S. case of COVID-19 in mink was found in Utah in August. COVID-19 has also been seen in mink populations in Wisconsin and Michigan. How many mink farms are there out there? All this apparently started when it was found that mink in Europe were infected by SARS-CoV-2 by their human handlers back in the Spring. In May, the first examples of animal-to-human transmission of COVID-19 outside of China was found when 2 people in the Netherlands were found to have contracted the disease from mink. Agricultural authorities in Utah are saying that mink-to-human transmission is “unlikely” and are trying to control the outbreak with quarantine measures. Meanwhile, a million mink have been euthanized in Netherlands and Spain. That’s what countries do who place public health above short-term economic gain.

Wednesday COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Wednesday:
  • Half of U.S. states are reporting increased COVID-19 cases as some leaders are pushing for new control measures (CNN)
  • Top federal immunologist and whistleblower Dr. Rick Bright, fired in April as head of vaccine development program for opposing political pressure on health policy, has just resigned from the NIH saying “…he can no longer sit idly by and work for an administration that ignores scientific expertise, overrules public health guidance and disrespects career scientists, resulting the [sic.] in the sickness and death of hundreds of thousands of Americans,” (Politico)
  • Six U.S. states report record high COVID-19 hospitalizations. Wisconsin Governor Tony Evers said in a statement: “We’re in a crisis right now and need to immediately change our behavior to save lives. …. We are continuing to experience a surge in cases and many of our hospitals are overwhelmed…” (Reuters)
  • Skepticism toward science fell globally during the COVID-19 pandemic, according to a new survey following a 3-year trend of rising mistrust (Axios)
  • President Trump again tweeted that COVID-19 is “far lass lethal” than influenza. The truth: in just 8 months, SARS-CoV-2 has killed more than the past 5 seasons of flu combined and is much more contagious (CNN)
  1. Trend toward rising daily cases continues in the U.S. Deaths are steady at 700 a day. New infections continue to surge in the Midwest
     Average daily U.S. COVID-19 cases remain over 40,000 after the weekend reporting slow down. The Tuesday numbers were, like last Tuesday, encouraging but may be followed by a rebound on Wednesday. As data systems mature and routinized, I suspect we will see the weekend lull extended to Tuesday in the foreseeable future. At the state level (Figure B), the picture is similar to recent briefings: 8 Midwest states currently have new daily cases per 100,000 residents of 20 or more, making this region the ongoing national hot spot. Three states stand out in particular: North Dakota (56 daily cases per 100,000), South Dakota (47) and Wisconsin (40). Of these, North Dakota is the only one that is higher than October 3, suggesting that transmission intensity continues to increase in that state. Two Western states are above 30: Montana (35) and Utah (33), while thankfully, only Arkansas (25) and Tennessee (23) are above 20 in the South. While overall new case reporting is low in the Northeast, the growth factors show the biggest week-over-week gains are happening there, with new cases doubling last week in New Hampshire, Rhode Island and Vermont. On Tuesday, an additional 626 COVID-19 deaths were reported (Figure C) continuing a slight decline in deaths over the last week. Consistent with the lag in how the data proceeds from testing to hospitalizations to deaths, we are now seeing elevated growth factors for weekly deaths in Iowa (+88%), Kansas (+86%), Minnesota (+63%), Nebraska (+7%) and Wisconsin (+102%).
    What it means: The U.S. remains in a precarious position in terms of COVID-19 as daily cases continue to edge higher since the Mid-September trough. The Midwest remains the region of greatest concern while signals continue to foreshadow a coming surge in the Northeast.
Figure A
Figure B
Figure C
  1. Update on hospitalizations: Upper Midwest states under significant hospital stress, Wisconsin and South Dakota are ‘white hot’
     If you read the headline summary from Reuters on hospitalizations you know already that a number of upper Midwest states are right now seeing hospital beds fill to capacity with COVID-19 patients amidst the surge in cases. If you have read this blog for a while, you know that I am keen to pay close attention to hospitalization rates because they provide a concentrated surveillance signal for the epidemiologist. Because the barriers to being identified accurately and reliably as a case differ for testing, death and hospitalization, each offers a different window into the workings of the underlying transmission dynamics. None is free of bias and distortion, but hospitalizations may be especially “clean” from a data quality point of view. Let’s start with a look at current hospitalizations by region over the last month (Figure D). These data come from our good friends at the COVID Tracking Project. These data show rising hospitalizations in all regions in the last week, except the Midwest. That suggests a general trend toward increasing transmission intensity that is not specific to the particularities of one place. These data tell us that on an absolute basis, there are more people hospitalized in the south than in the other three regions combined. The South and West have seen a net decrease in overall hospitalizations since a month ago, while the trend is rising in the Northeast and Midwest. Let’s look more closely at the situation in the Midwest in the states we highlighted in the case report above.
     Figures E and F, also from the COVID Tracking Project, show daily cases and hospitalizations for 5 Midwest states with the largest new daily cases per 100,000 now: Wisconsin, Iowa, Kansas, North Dakota and South Dakota. There are two views of the data here, one is absolute numbers (Figure E) and the other is rates per million (Figure F). This is vitally important for an apples-to-apples comparison between a populated state like Wisconsin (5.8 million) and South Dakota, which has no major cities and far few people (885,000). Both figures show just how intensely the epidemic is crushing Wisconsin right now. Since their previous peak of 944 cases a day on July 27, Wisconsin has tripled to 2,500 a day. North and South Dakota were at fewer than 100 day till mid-summer, now both are averaging over 400 a day. Hospitalization numbers are chilling. Wisconsin now has 853 hospitalized having not previously exceeded 443, with 261 currently in ICU beds. Iowa and Kansas have surging cases but hospitalizations have not exceeded previous peak levels. Like Wisconsin, the Dakotas have seen exponential and explosive growth in hospitalizations in recent weeks. Shifting to Figure F showing rates, the situation looks especially challenging in South Dakota. On a per capita basis, both cases and hospitalizations in that state are off-the-charts at 2.5 times higher than any of the other states. I can’t find any case where COVID-19 hospitalization exceeded 200 per 1 million since the pandemic began. Is this perhaps a ballooning in testing? Figure G says no. Testing has risen about 75% since July but remains lower than the peak in June. Every metric in South Dakota is showing exponential and explosive increases except testing.
     The bottom line: COVID-19 hospitalization data confirms what we see in the data stream for cases and deaths: a handful of upper Midwest states are ‘white hot’ with extreme transmission intensity. Hospitalization data offers a third leg in the information stool.
Figure D. Total COVID-19 hospitalizations by region for 9/2/20 – 10/6/20 from the COVID Tracking Project
Figure E: Daily COVID-19 cases and hospitalizations, absolute numbers for 5 Midwest states from the COVID Tracking Project
Figure F: Daily COVID-19 cases and hospitalizations, rates per million for 5 Midwest states from the COVID Tracking Project
Figure G: Key metrics from South Dakota, October 6
  1. Quirky Qorner: COVID-19 is infecting our dreams
     I read a fascinating article in Scientific American over the weekend about how COVID-19 is impacting our dreams. It came from a Montreal Psychiatrist, Tore Nielsen, who is the director of the Dream and Nightmare Laboratory. Fun place I bet. The article was banging around in my head for a couple of days when I woke up yesterday morning in the middle of, you guessed it, a COVID-19 dream. Has this happened to you? In the article, they describe several ongoing research efforts that point to a surge in dreaming as so many of us adapt to more time at home, more time in the sack, and altered sleep patterns. Qualitative content analysis also suggests the content of our dreams is being impacted as a growing fraction of dreams include themes of loneliness, isolation, loss of control, anxiety, insufficiently completed tasks, contamination and cleanliness.
    The bottom line: Studies show we are taking COVID-19 to bed with us.