COVID-19 Top pick of the day: Thursday

It’s Time to Hunker Down

Health Article by Zeynep Tufekci published online at The Atlantic November 14, 2020.

This is the article you don’t want to read but know you should. Of course the news is not good but consider this: there are right now, hundreds if not thousands of American citizens who will soon be dead because they celebrate Thanksgiving indoors in groups instead of taking this advice.

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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.

Wednesday COVID-19 Briefing

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Top news, reports and insights for today:

1. Curated headline summaries for Wednesday:

• At least 1,707 new COVID-19 deaths were reported Tuesday, the highest daily death toll since May 14 (CNN)
• The vaccine being developed by Pfizer and German biotechnology firm BioNTech is 95 percent effective at preventing disease, according to an analysis after the trial reached its endpoint. The vaccine trial also reached a safety milestone, with two months of follow-up on half of the participants, and Pfizer will submit an application for emergency authorization “within days,” according to a news release (Washington Post).
• Moderna’s vaccine also found to be 95 percent effective in trial involving 30,000. The company will apply to regulators in the coming weeks, expects to have 20 million doses available. Unlike the Pfizer vaccine, this one does not require ultra-cold storage (BBC, See Figure A).
• U.S. hospitals report record high COVID-19 patient load over 73,000. City and state leaders scramble to institute new restrictions to curb the virus (CBS News)
• As hospitals fill up, now 22 percent don’t have enough staff according to new data just released by the Department of Health and Human Services (The Atlantic)
• Despite higher risk among American Indian and Alaskan Native populations, the Navajo Nation in Oklahoma has been a hidden success story. How did they do it? They followed the science, instituting a mask mandate in the Spring, free drive-through testing, hospitals well-stocked with PPE and intensive contact tracing using an army of public health officers fully supported by tribal leadership (STATNews).
• Dr. Anthony Fauci is urging Americans to “think twice” about traveling and having indoor gatherings for the holidays (USA Today).

Figure A: https://www.bbc.com/news/health-54902908

2. Attention shifts to rising deaths
    U.S. COVID-19 cases continue to soar higher as daily cases cross 150,000 on the 7-day average (red) curve (See Figure B). Average daily cases have more than doubled since the previous peak in mid-July. Meanwhile, a record high 76,830 hospitalizations were reported yesterday by the COVID Tracking Project (Figure C). That is not double the previous peak but the expectations are that hospitalization rates will continue to climb for several weeks despite growing signs that hospitals are reaching capacity and short on staff.
    While the rise in cases and hospitalizations is alarming, the big story today is the spike in daily COVID-19 deaths (Figure D). The trend toward rising deaths began a month ago when daily deaths were averaging about 685. In main point 3 below, I have a look at the lag between cases and deaths. Yesterday, 1,510 deaths were reported, a higher death toll than at any point during the summer peak and one not matched since May 20th.
   Where are deaths spiking? See Figure E for that. As always, states with small numbers of deaths have gridded bars to indicate unstable estimates of growth factors (the ratio of deaths this week to the week before). For the first time since spring, weekly deaths doubled or more in seven states, three out West (Alaska, Hawaii and Wyoming), Nebraska in the Midwest, Virginia in the South and Delaware and Maine in the Northeast. Increases of 50% or more were seen in Michigan (+75%), Minnesota (+50%), Missouri (+77%), West Virginia (+60%), Maryland (+77%), New Hampshire (unstable), and New Jersey (+79%). Thankfully, weekly deaths were trending down 10% or more in California, Nevada, Kansas, Oklahoma, Arkansas, North Carolina and Washington DC. Some states where deaths are spiking still have significant hospital bed and ICU capacity. For example, in my home state of Maryland, deaths rose 77% from 52 to 74 last week while the state retains three-quarters of its available ICU bed capacity. Nebraska, on the other hand, jumped 94% but are now using 72% of their ICU beds. Several states, including Montana, Oklahoma and South Dakota, are reporting that all ICU beds are full.
    Bottom line: U.S. cases continue to rise at a rapid pace. We will have to wait for the rest of the week’s data to see if there is any sign of a slow-down. Meanwhile, the attention shifts to a sharp spike in deaths yesterday. As hospitals and ICU beds fill up, and staffing shortages mount, we will have to monitor things closely for signs that health care systems are not keeping up. Remember that overall death rates have come way down since the spring peak thanks to the work being done in the health care sector. As hospitals become overwhelmed, deaths will skyrocket and those gains will be erased.

Figure B

Figure C

Figure D

Figure E.

3. Lag analysis: how long after cases and hospitalizations rise to deaths surge?
    I want to talk about lags. Lag is the time gap between different features of an epidemic. Understanding the dynamics of any outbreak is all about these lags. There is the lag between exposure to the virus and infection (that we call the incubation period). Then there is the lag between infection and symptoms, the lag between symptoms and seeing a doctor, the lag till seeking a test, the lag in receiving test results, and the lag till hospitalization and ultimately to recovery of full health. Another critical lag is the time between inflection points in test results (our proxy measure of cases), hospitalizations and deaths. I decided to go back into the data and look carefully at two such lags. There are lots of details here, and my analysis is not perfect, but I’ll cut to the chase and show you 5 graphs in Figure F that explain what I found. The first 4 represent the lag (days) between the inflection point in cases (when cases bottom out and shift upward) in the second and third peak for the whole country and for 3 regions. For the entire country, the lag between cases rising and deaths rising was 26 days for the second peak and 34 days for the third (Figure F1). In the South, there was no second peak inflection point, but the 3rd peak lag was 33 days (Figure F2). In the Midwest, the 2nd peak lag was 29 days (Figure F3), while the lags were longest in the West at 46 and 31 days respectively (Figure F4). We would expect the lag between hospitalizations and deaths to be shorter; they are at 16 and 14 days (Figure F5).
    Bottom Line: Looking at lag times is useful for lots of reasons. In the U.S., the pattern is pretty clear and consistent. Once cases bottom out between peaks and start to rise again, then deaths will start to rise about a month later (median of 6 observed lags was 32 days). The lag between rising hospital admissions and deaths is about half as long or two weeks. Next week I will look instead at the lag between the peak of cases and the peak of deaths.

Figure F: Lag analysis

4. Quirky Qorner: COVID-19 denier Elon Musk has apparently contracted the virus. That was enough to get him banned from the launch of the Crew Dragon spacecraft. Musk is not happy.
    Elon Musk, the controversial head and founder of SpaceX announced on Twitter that at least one of the COVID-19 tests he took was positive. How inconvenient for the billionaire mogul who has been a skeptic of the disease for months. According to a story in Fatherly, Musk has only cold-like symptoms but the timing could not have been worse. NASA and SpaceX were scheduled to launch their jointly developed rocket ship to the international space station on Monday (which they did) and Musk had intended to attend. Apparently he wasn’t happy when NASA administrators blocked him from doing so for obvious reasons (see photo below).

From: https://www.fatherly.com/news/nasa-elon-musk-spacex-covid-launch/

Weekend COVID-19 Briefing

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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).

2. 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.

3. 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