Wednesday COVID-19 Briefing


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
  1. 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.
  1. 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.
  1. 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


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

Wednesday COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Wednesday:
  • Pfizer announces early results showing its leading vaccine is more than 90% effective at preventing COVID-19. Details are sparse and not yet published, but the company says their new vaccine is working better than expected with “no serious safety concerns”. While promising, we have a long way to go before this translates to an available solution (New York Times)
  • Big urban medical centers are rushing to buy ultra-cold freezers that will be needed to store the leading vaccine. Rural hospitals can’t afford them (STATNews)
  • COVID-19 in nursing homes grew by 40% between mid-September and late October, erasing several months of progress. Experts say it is impossible to keep the disease out when uncontrolled transmission is occurring in the community. President-elect Biden has promised special emphasis on managing the pandemic in nursing homes. Rising infections will translate into a surge in deaths (Politico)
  • Experts emphasize that wearing masks is important for ‘source control’ (preventing the wearer from transmitting the virus to others). New CDC guidance has been issued after studies increasingly show that masks also protect the person who wears them (CDC Scientific Brief)
  • After months of refusing to require masks, Utah’s governor declares a state of emergency, joins 34 other states in issuing a statewide mask mandate (Washington Post)
  • First people refused masks. Now, reports are growing that more people are refusing to be tested for COVID-19. This has led to big variation in rates of testing (JAMA Network)
  • According to the COVID Tracking Project, today, more than 61,000 hospitalized COVID-19 patients were recorded, breaking the record highs from the two previous peaks (COVID Tracking Project, See Figure A)
Figure A. Current hospitalizations across the U.S. by day
  1. U.S. poised to pass 10 million cases. New weekly cases on the rise in every state and DC. Twenty-nine states now with higher infection rates than New York
     The explosive growth in U.S. daily cases continues despite the weekend reporting slow down as over 821,000 cases reported last week (See Figure B). The website COVID Exit strategy now classifies all but 2 U.S. states as “uncontrolled spread”. For the first time since I have been blogging, weekly cases are now rising in all 50 U.S. states and the District of Columbia (Figure C). While every case growth factor is greater than 1.0 (last week’s cases were higher than the week before), the picture is more dramatic in the Northeast, West and Midwest. Fifteen states saw weekly cases rise by 50 percent or more including Nevada (+52%), Washington (+67%), Wyoming (+71%), Iowa (+79%), Illinois (+73%), Minnesota (+66%), Nebraska (+57%), Ohio (+52%), Oklahoma (+71%), Tennessee (+60%), Massachussetts (+59%), Maine (+90%), New Hampshire (+60%), New Jersey (+53%) and Vermont (+81%). Astonishingly, we see no regression-to-the-mean as North (+14%) and South Dakota (+4%) both continue to rise despite being white hot for weeks.
     Remember when New York had the highest infection rate in the nation and the Northeast was THE hot spot region with rates that would never be matched? All good disease detectives watch Figure D closely during an outbreak (state level variation in COVID-19 infection rates – aka incidence). What does it show? First, New York (2,756 cases per 100,000 population) is actually now below the national average (3,026). Second, there are now 29 states with incidence rates greater than New York. Finally, both North and South Dakota now have rates that are more than double New York at 7,393 and 6,161 respectively. The North Dakota attack rate is now the highest in the world and it’s hospitals are now 100 percent full. Governor Burgum’s response? He says it’s ok for nurses who have been infected to stay at work as long as they don’t have symptoms. WTF!
    Bottom line: The explosive growth in U.S. COVID-19 cases shows no signs of slowing as the 10 million case benchmark will pass today. Cases are growing everywhere. New York has outperformed 29 states. The explosive growth continues to escalate where cold air is descending.
Figure B
Figure C
Figure D
  1. The surge in daily deaths we had feared has arrived
     U.S. daily deaths spiked to 1,366 on Tuesday, surpassing 1,300 for the first time since August 19 (Figure E). Last week, 6,800 deaths were reported, a weekly total also not seen since August. As we have watched cases explode and hospitals fill up, the start of a rising death trajectory was inevitable. For the last couple of months, the Wednesday death numbers have been the highest of the week, so I worry today’s numbers will be a further shock. Where are deaths booming? The Northeast and Midwest stand out (Figure F). Weekly deaths jumped by 40 percent or more in Connecticut, New York and Pennsylvania in the Northeast, Kansas, Michigan, Minnesota, North Dakota and Nebraska in the Midwest. Weekly deaths actually doubled in Wyoming and West Virginia. If you read my blog over the weekend, you may note that Kansas, Michigan, Tennessee and Pennsylvania were all identified as states with hospital systems under stress with 80% or more of ICU beds occupied.
    Bottom Line: Federal and state leaders continue to wait for the vaccine to ride to the rescue. Thus far, flat death numbers have made it more politically feasible to do nothing. What social and political consequences will there be when daily deaths double or more in the coming weeks?
Figure E
Figure F
  1. Quirky Qorner:What sport is exploding due to coronavirus? Golf!
     I have a love-hate relationship with golf. I used to play a lot but it drove me crazy. Recently, I find myself gravitating back to my old clubs with a peculiar renewed fascination. Funny thing, since dusting off my clubs, I find all the courses and driving ranges around me are packed. What gives? Along comes a story from Axios by Jeff Tracy that drives the ball in the right direction. My local situation is not unusual. The number of rounds of golf played in September grew 25.2% compared to last year, the fifth straight month of increases. Golf equipment sales are up 42 percent year-over-year as well. In June the professional golf tour was one of the first professional sports to resume. According to the author, “Golf was a physical and mental safe haven for millions of Americans with cabin fever this year”. Epidemiologically, this makes sense given what we know about how much less likely transmission is when everyone stays outside in the open. Four!