Weekend COVID-19 Briefing

Top news, reports and insights for today:

  1. Curated headline summaries for Saturday/Sunday:
  • Epidemiologists issue stark warnings and predictions about where the U.S. COVID-19 outbreak is headed over the holiday period. Is anyone listening (CNN)?
  • With COVID-19 cases at record levels topping 180,000 on Friday, states including New Mexico, North Dakota and Oregon are rolling out new restrictions (VOX).
  • Student athletes who contracted COVID-19 had their hearts imaged in a recent study. Over a third had heart abnormalities that could later cause serious problems. Most in the study had few or no symptoms. The American College of Cardiology says student athletes should be followed. This is one more example of how SARS-CoV-2 effects everyone (INVERSE).
  • As COVID-19 surges, a vaccine looms and ‘lockdown fatigue’ deepens, a new Ohio State University national survey shows that 38% of Americans plan to attend a Thanksgiving gathering of 10 or more and a third would not ask others to wear masks at holiday gatherings (VOX).
  • This week an outbreak of COVID-19 occurred in the Minnesota State Senate, linked to a Republican senator who tested positive after attending a recent party caucus. As a measure of how deeply politicized the pandemic has become, State Republican leaders urgently warned Republican colleagues about the outbreak. State Democrats, who shared the same spaces, were not told anything (Huffington Post).
  • As concerns rise about the start of flu season, the U.S. Surgeon General Dr. Jerome Adams told NPR there is one sure sign you have COVID-19 rather than influenza: loss or alteration of taste (ageusia/dysgeusia) and/or loss of smell (anosmia) (Eat This, Not That).
  • Grocery stores nationwide re-impose purchase limits on toilet paper, soap and other essentials in response to fears that consumers will overstock as cases surge (Newsweek).
  • A small study of patients hospitalized with COVID-19 between March and July suggests that aspirin may lower risk of being put on a ventilator, admitted to the ICU and in-hospital mortality. Combined with growing understanding of the importance of inflammation and blood clots, this study shows aspirin should be further investigated (Anesthesia & Analgesia).
  1. U.S. cases shoot through the roof. Every Midwest state now white hot
    Friday set a new record as more than 166,000 U.S. COVID-19 were reported (See Figure A). Is it all about rising testing? The answer is a qualified no. Figure B shows that since the trough on September 11, daily testing has doubled from 774,000 a day to over 1.4 million a day (blue line). At the same time, cases jumped 4-fold from 34,000 a day to over 141,000 averaged over a week (red line). It’s not just cases that are through the roof. Figure C shows the U.S. figures for currently hospitalized (light blue) and daily deaths (black). The three peak periods of the U.S. outbreak are clearly visible in Figures B and C. Hospitalizations are now higher than either the April or July peaks, while deaths are now higher than July but lower than April. How long will that last depends on what happens in the next month.
     The overall U.S. situation is rough just about everywhere. COVID Act Now classifies all but 10 states as critical (uncontrolled spread). My analysis suggests it is currently substantially worse in the Midwest region (Figure D). Transmission rates (new daily cases per 100,000 people last week) are above 40 in all 13 Midwest states and over 80 in Iowa (144), Illinois (96), Indiana (83), Kansas (88), Minnesota (101), North Dakota (181), Nebraska (107), South Dakota (150) and Wisconsin (106). No states in the South or Northeast are currently above 80; three Western states are: Montana (93), Utah (93) and Wyoming (116). I continue to believe that cold temperatures accelerate transmission increases based on these numbers.
    Bottom line: Overall, the U.S. outbreak continues to break previous records. While testing doubled in the last 6 weeks, cases have risen 4-fold, a signal that this surge is very real. Deaths are now rising with daily mortality now above the July peak but not yet as high as the nightmare we experienced in April. Hospitalizations are now higher than either of the previous peaks with no end in sight. While a few states have started to take action, I believe there is little reason to think that deaths, hospitalizations and cases will do anything but continue to explode unimpeded.
Figure A
Figure B. From COVID Tracking Project
Figure C. COVID Tracking Project
Figure D.
  1. The BIG picture: New U.S. cases pass 10 million, rate of increase doubles this month. The U.S. is the only developed wealthy nation that still has not stopped the first wave and now has the worst COVID-19 trajectory on the planet
     You have seen the headlines. Cases are still exploding in the U.S. as well as other nations. Let’s step back and see the bigger picture. It took 2 weeks to go from 8 million cumulative cases on October 19 to 9 million on November 2. Since then, the rate of new cases has doubled, rising to 10 million in just 8 days (See Figure E). The word doubling is the key. Obviously the total number of cases didn’t double in a week, but the rate at which cases are rising doubled. The result is we have seen the shortest interval between each million cases by far. We are back to the exponential rate of increase not seen since June.
     The headlines also tell us we are not the only country facing a fall surge. Cases are also spiking in Brazil, Italy, Germany, the U.K., Poland, Russia and Spain (among others). Almost way you compare countries though, the U.S. stands out as the worst. Here are two cases in point. Figure F shows new daily cases from the 10 most impacted nations using Johns Hopkins data. Multiple nations are seeing cases rise, but none has the consistency and rate of climb seen here. The last figure is really big picture – based on log-log plots of the overall trajectories of the entire outbreak in the 15 countries with the highest cumulative cases in the world. I’ll make three points about Figure G, which I made using Aatish Bhatia’s fantastic site. First, the straight dotted reference line shows what we would see in a country doubling cases every 7 days. That’s uncontrolled exponential growth. The U.S. trajectory is the closest overall to that reference line meaning that overall, COVID-19 is growing fastest in this country. Secondly, until April 7, we are the only country that actually saw the outbreak grow even faster than 7-day doubling. Thirdly, the 3 big peaks of the epidemic are clearly visible as humps in the red U.S. trajectory. It is however a mistake (made by many) to call these three separate waves. It is one continuous wave with three peaks. As I have said before, an epidemic transmission wave is over when the log-log plot shows a nose dive resulting in a period of vertical decline signalling a cessation in exponential growth and a shift to additive growth. Of the 15 hardest-hit countries, the first wave ended (if only briefly) in France, Germany, Italy, Spain, the U.K., South Africa, and Peru. In the rest (Mexico, Russia, Brazil, Iran, Columbia, Argentina, and the U.S.) the end of the first wave never happened. That means the U.S. (although one could argue also Russia) is the only highly developed nation that has not been able to control the outbreak sufficient to end the first wave.
    Bottom Line: Things are bad in several countries, but none worse than the U.S. A third peak is in full swing in the never-ending first wave of the U.S. coronavirus outbreak. Meanwhile, the President and the White house have completely dropped out of the game now that the election is “over”. The nation and its leaders waits for a vaccine to save the day, even though that is months from making a difference. Add to this colder weather more favorable to the virus, American’s shifting indoors, the approach of Thanksgiving, and a nation sick and tired of locking down and masking up. The perfect storm gathers.
Figure E
Figure F. Source: https://coronavirus.jhu.edu/data/new-cases, Captured November 14
Figure G: Source: https://aatishb.com/covidtrends/?doublingtime=7&location=Argentina&location=Brazil&location=Colombia&location=France&location=Germany&location=Iran&location=Italy&location=Mexico&location=Peru&location=Russia&location=South+Africa&location=Spain&location=US&location=United+Kingdom


Daily COVID-19 Briefing: Thursday

Top news, reports and insights for today:

  1. Daily deadline summaries for Thursday*:
  • Scientists at University of Oxford say that an inexpensive and widely available steroid medication, dexamethasone, reduced deaths in patients with severe COVID-19, highlighting the dangers of inflammation and offering an unexpected glimmer of hope (New York Times)
  • Coronavirus cases rise sharply in prisons even as they flatten elsewhere. The number of prison inmates infected has doubled during the past month to 68,000; deaths have also risen by 73% since mid-May (New York Time)
  • New Chinese study of the immune response over time to SARS-CoV-2 virus suggests it is possible that immunity may only last for 2-3 months. Also, asymptomatic patients had a weaker immune response and had a quicker reduction in the key virus-fighting antibodies. This raises the possibility that people who were infected but didn’t have symptoms may be at risk for re-infection more quickly than previous coronavirus (NatureMedicine)
  • The next U.S. hot spots look to be these 7 states: Arizona, Arkansas, Florida, North Carolina, South Carolina and Texas (VOX)

*For anyone who wonders, I was away for a few days this week and will restart blogging every day or every other day.

  1. U.S. cases are now clearly on the rise, deaths remain on a declining trend but may be ticking up in the last 3 days
    Last week the U.S. reported 158,164 new COVID-19 cases, a rise of 8% in the cumulative total, with daily increases above 23,000 on Tuesday and Wednesday. The 7-day moving averages are clearly now on the rise since June 9, demonstrating a rate of increase not seen since the first week of April. The second figure shows daily deaths, revealing a slowing in the rate of decline over the last couple of weeks. As usual, we see the weekend lag in reporting of deaths on Sunday and Monday, with over 700 daily deaths reported Tuesday and Wednesday, which could signal that deaths will plateau and potentially begin to follow cases and rise. Last week, 4,520 Americans lost their lives to this virus, a weekly increase of 4.3%. The U.S. continues to have the largest number of cases and deaths on the planet, with Brazil now in second place in both.
    The bottom figure shows what’s going in states, focusing here on new daily cases per 100,000 population. Arizona continues to be the most extreme and worrisome with 22 new cases per 100K per day last week, more than 4-times higher than the 5 per day per 100K benchmark. The 1-week growth factor there is 1.45 showing that while new case growth has been high for a while, it is still 45% higher last week compared to the week before. Other states of considerable concern include Oklahoma, a state that doubled its cases last week. In the south, Alabama, Arkansas, Florida, Louisiana, Mississippi, North Carolina, and South Carolina, all reported more than 10 new daily cases per 100K last week, indicating strong resurgence of cases in these states. Only Utah and Arizona had high transmission intensity outside the South.
    What it means: Arizona, Utah and 8 southern states are now experiencing dramatic intensification of the epidemic, which has been sufficient to tip the balance in the U.S. toward rising cases at levels not seen since the first of April. The first wave is far from over.

Daily COVID-19 Briefing: Sunday

Top news, reports and insights for today:

  1. Daily headline summaries for Sunday:
  • New study from the South Korean CDC finds no evidence that “re-infection” cases resulted in a new secondary case. Crucially, they also did viral cell culturing in 108 such cases finding that all were negative. Taken together, this is the strongest evidence yet that getting infected a second time is not happening and that those who re-test positive are not passing the disease to others. The vast majority of these cases are test errors or a period of prolonged recycling of viral waste that cause a positive test result, not a true second infection in the same person (KCDC)
  • Social distancing measures aimed at COVID-19 have stopped influenza in its tracks 6 weeks early (Nature)
  • New study from China (not yet peer reviewed) examined 319 outbreaks in detail finding most occurred at home and on transportation. Importantly, they find evidence of only 1 outbreak that occurred outdoors. Study may provide important evidence of substantially lower risk of transmission outside (medRxiv)
  • CBS News and others have reported that CDC guidance has been updated to say that COVID-19 is “…not caught easily” from touching surfaces and that “…40% of transmission occurs before people feel sick”. I can’t find either of those statements on the CDC website (CBS News)
  1. Map check, 4 weeks later: the epidemic has shifted to places nobody notices or wants to talk about
    I am a map fanatic. I enjoy staring at them. It actually is a pretty useful fetish if you are a disease detective because the spatial patterning of disease is often among our most vital clues. I last showed you a U.S. map of incidence (confirmed COVID-19 cases per 100,000 residents) back on April 30, just under 4 weeks ago. I grabbed a picture from a similar map today from my colleagues at coronashutdown. Comparing the 2 maps tells us where we have been in recent weeks. Here are my take-home messages from this comparison:
    1. The epidemic has shifted from the east coast to the midwest, south and southwest.
    2. Epidemic radiation from last month’s hotspots can be seen from southwest Georgia all the way to Eastern Texas and Northern Florida, Southern New Jersey into Delaware and eastern Maryland, southern Utah and western New Mexico, the Texas panhandle, and Ford county in southern Kansas.
    3. New hotspot counties include (marked on map) Franklin Parish in Louisiana (1433), Liberty County Florida (2442), Duplin County North Carolina (927), Buckingham Co. Virginia (2560).
    4. Continuous corridors of higher infection can be seen along major transportation routes. Compare for example the area from New Orleans all the way to Chicago. Or note the increasing connection of high incidence counties going west from Chicago into parts Illinois, Wisconsin, Iowa, Minnesota and South Dakota.
    5. Ford County Kansas was a hotspot on April 30 at 2,088 per 100,000. That county has now more than doubled to 4,634, which is twice the rate of infection in the county containing part of New York City. The rates have gone to more than 1,000 in 5 surrounding counties.
    6. The bottom line: while many congratulate themselves on winning the battle against COVID-19, these maps tell us that what has really happened is that the epidemic has shifted to places nobody notices or wants to talk about.
  1. Severe illness similar to Kawasaki disease impacting children
    Recent articles in Science, the Lancet, and Nature have drawn attention to a rare and severe post-infection syndrome associated with coronavirus that is occurring in children. While children are at lower risk of severe illness during the pandemic, it now appears that a small number are becoming very sick with a condition that looks similar to Kawasaki disease – a rare condition affecting about 1 in 10,000 children in Western countries, characterized by a hyperactive immune response to viral infection leading to rash, fever, and dangerous inflammation in blood vessels (also called vasculitis). The disease named after a Japanese physician who was the first to describe it is associated with dangerous heart complications, most notably aneurisms. Hot spots for this newly recognized Kawasaki-like illness have been noted in Bergamo Italy and New York city. A study in the Lancet found a 30-fold increase in the incidence of Kawasaki-like illness in one region of Italy. New York state is investigating about 157 cases. Outbreaks have also been noted in the UK (where it was first noticed) and Los Angeles. Kawasaki disease is not new. It is generally assumed to be a post-viral syndrome involving an immune system “overshoot”. Currently, experts are not certain whether the outbreak of cases is Kawasaki disease or something similar. In Europe they are using the term paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS), or multisystem inflammatory syndrome (MIS-C) at the CDC. So far, children treated for MIS-C have had good survival, but when it occurs, it requires urgent and comprehensive medical intervention. The condition has been seen mostly in children under age 18 but is increasingly appearing in somewhat older ages. There is no certain diagnostic test for Kawasaki or MIS-C and more will be learned in the coming weeks.
    What this means? While it’s scary to think that we have to add very sick kids to the list of things to worry about, the disease detective in me believes at this point that the emergence of super-rare autoimmune reactions to a novel virus is an inevitable development in a disease impacting almost 5.5 million people. At this time, I do not believe this is cause for concern. Having said that, it is urgent that experts determine whether children and young adults with a previous history of Kawasaki disease should be considered at elevated risk for MIS-C.