Weekend COVID-19 Briefing

Top news, reports and insights for today:

  1. Curated headline summaries for Saturday/Sunday:
  • The U.S. Centers for Disease Control and Prevention (CDC) on Saturday reported more than 8 million confirmed COVID-19 cases and 217,918 deaths (Reuters)
  • A small randomized trial shows that the Chinese coronavirus vaccine is safe and does elicit an antibody response. This is a key preliminary stepping stone to showing that the vaccine prevents COVID-19 in the population (Lancet)
  • Ukrainian fitness guru, Instagram influencer, who thought COVID-19 was a hoax, dies of the virus (Daily Mail)
  • In an open letter, more than 1,000 current and former CDC officers criticize U.S. COVID-19 response, decried political interference and called for the CDC to have a larger role (Wall Street Journal)
  • CNN anchor Jake Tapper says the White House refused his invitation to allow coronavirus experts including Anthony Fauci and Robert Redfield to appear on his show (Axios)
  • Rural Midwest hospitals struggling to handle COVID-19 surge (ABC news)
  • Pharmaceutical giant Pfizer delivers “final blow” to President Trump’s hope for a pre-election vaccine. The company, considered a frontrunner in the vaccine race, says it won’t seek an emergency use authorization (EUA) for it’s candidate vaccine before late November (Politico)
  1. U.S. daily COVID-19 cases return to near explosive growth. Deaths stay steady
     The end of this week saw a continuation of a trend toward sharp escalation in daily U.S. COVID-19 cases. Thursday and Friday numbers spiked over 66,000, a number not seen since the end of July (Figure A). The rate of increase is not as steep as the explosive growth seen from June 22 to July 15, but it is steeper than it has been since then. Record high daily case totals were broken on Thursday in Montana (723), Michigan (2,030) and Ohio (2,069) as well as on Friday in Idaho (1,094), New Mexico (812), Wyoming (248), Indiana (2,283), Minnesota (2,280), North Dakota (864), Nebraska (1,286), Wisconsin (3,861) and West Virginia (358). In just 2 days, 12 states recorded more cases than any other day in the outbreak making this one of the most disconcerting days thus far. That brings the total number of states with 100,000 lab-confirmed cases to 26, half of all states. Of those, six states now have at least a quarter of a million cases and three, California (864,000+), Florida (751,000+) and Texas (822,000+) now exceed a three quarters of a million. To put this in perspective, California and Texas would now rank in the top ten most impacted countries with more cases than the entire United Kingdom and about as many cases as Peru, Mexico and France.
     Thankfully, there is little indication yet that the trend in cases over the last month is matched by a trend toward rising deaths (Figure B). The 7-day moving average has been steady between 600-800 a week since September. Based on what we know about the time lag between cases and deaths, most experts expect deaths to begin to rise in the coming days or weeks. In my opinion, that expectation may be tempered by continual improvement in medical management strategies that have gradually lowered the lethality of the disease. However, a major caveat is that there will be an inflection point as the cases rise where the capacity of the hospital system to maintain the highest standard of care will be jeopardized. We are already seeing signs of that in states like South Dakota and Wisconsin (see headline 6). Death rates will soar if thresholds are exceeded in the coming months as most experts now predict.
     The bottom line: Daily cases are now spiking at a rate not seen since the summer crush. The U.S. has now passed 8 million cases, the most of any nation and more than a quarter of the 40 million cases world-wide. The incidence of COVID-19 is now 5 times higher in this country (25,171 cases per 1 million population) than for the entire planet. In my view, this is not a second wave and not a third wave, but another wavelet within the tidal undulation of the first epidemic wave of COVID-19 in the United States. The prognosis is not good heading into colder temperatures, lowered humidity, more time spent indoors and continuing social and economic pressure to return to “normal”. The march of suffering and death continues apace and the U.S. still refuses to do what must be done to quell this viral firestorm.
Figure A
Figure B
  1. Why do U.S. COVID-19 death totals differ wildly across sites tracking the pandemic? The disease detective goes to work.
      Above I reported the daily epidemiologic curves for U.S. cases and deaths as I always do using data compiled by Wikipedia. No data source is perfect. There is, I have argued, a big advantage to sticking with the same data source over time despite its limitations if the primary purpose of surveillance is to track patterns of change over time. That having been said, I am increasingly uncomfortable with my choice to stick with Wikipedia in light of growing discrepancies between this source and most of the high-visibility alternatives. Figure C shows you the current total U.S. COVID-19 deaths from my source (Wikipedia, medical cases) and 7 others. I won’t call these independent data sources because they are all tapping into the same underlying data streams coming from official state reporting agencies. I’ll call them data compilers instead. In theory, given the common data sources, you would think the grand totals should very similar. The first thing to say about Figure C is that no two of these compilers arrive at the same total as of October 16. The highest is from WORLDOMETER and the lowest is from Wikipedia. The average (median in this case) is just over 218,200 as of today (red line). Worldometer is reporting 17,952 more U.S. deaths than Wikipedia. That’s a big difference. As disease (and data) detectives, let’s dig into these numbers and see if we can figure out why.
     What we know based on detailed analysis of excess all-cause mortality is that about 68% of the actual COVID-19 deaths are being correctly attributed to the coronavirus. Based on that, one could assume that the compiler with the largest number is likely to be closest to correct since it’s much less likely that deaths are being incorrectly attributed to COVID-19 than they are being missed. So for this exercise, we will focus on the high vs. low estimate.
     After digging into the details, I learned that the Worldometer (WO after) is highest in part because they don’t rely just on numbers compiled from state agencies, but include also deaths among “U.S. military” abroad (100), and a category labeled “Veterans affairs” (3,711), Federal prisons (128) and Navajo Nation (571) along with three deaths from the Grand Princess ship. That accounts for about 4,000 of the deaths not reported in Wikipedia.
     Next, what states are responsible for the discrepancy? Figure D is my picture after a careful comparison between these two compiler. Aha! We now know that the two sites are in perfect agreement in about one third of states (N=15). About half of states are plus or minus five (N=27). The bigger discrepancies come mostly from a few select states. Wikipedia has more deaths in ten states (only 2 are more than 10 more), and most of these are because the Wikipedia numbers include the deaths from Saturday. Of the 23 states where the WO count is higher, 13 of them are more than 100 apart. The real story is the two numbers that really pop out: New Jersey (+1,917) and New York (+7,814). Three quarters of the “excess” COVID-19 deaths in the WO data are in these two states with 62 percent just from New York. Why are there almost 8 thousand deaths in WO that aren’t in Wikipedia? The difference arises from where the compiler gets the information. Wikipedia uses numbers from the New York State Department of Health COVID19 tracker while WO uses Johns Hopkins numbers. The Hopkins dashboard says they get their New York numbers from the Governor’s coronavirus newsroom. There is no hint there as to why the two data sources differ so markedly. This disease detective found an important clue on the WO’s page describing the data where there is a very helpful and instructive footnote about U.S. data. This footnote announces a change in the death definition on April 14 to include “probable deaths” following updated CDC guidelines. Have a look at Figure E which is a screen capture of the part of that memo that relates to reporting in New York. The plot thickens!!! It tells us that the New York Department of Health has, for unknown reasons, not yet folded in “probable deaths”, but WO has combined them. A good chunk of the data gap arises from “probable” deaths, mostly in New York City that occurred during the high-mortality period in March and April. It looks like the New York state DOH numbers never included those that could never be directly linked to a positive test. The Hopkins dashboard, along with WO, have included those since mid-April.
     What have we learned: There are big differences in mortality numbers across data compiler sites. Wikipedia and the COVID Tracking Project are below average due, because they are more “conservative” and do not count all the “probable” deaths, relying more tightly on official state departments of health. WORLDOMETER reports the highest death totals for 2 reasons: 1) they channel the higher Johns Hopkins numbers that include more “probable” deaths, and b) they include deaths counted outside official state agencies (e.g., military, and Navajo nation). It is very hard to get to the bottom of these differences. Each data compiler should provide a clear and organized statement about their reporting policies, where the source data comes from. The lion’s share of the discrepancy comes from accounting differences in New York and New Jersey. Even the highest estimated deaths from the WO site represent about 70% of the true death toll from this disease.
Figure C
Figure D
Figure E: Screen grab from: https://www.worldometers.info/coronavirus/us-data/
  1. Quirky Qorner: The ‘coronavirus crush’ is a thing. Why a pandemic is the perfect moment for our infatuation with the unattainable
     What is being cooped up doing to us? Lots we all suspect. Some effects are obvious and others are more subtle and nuanced. I have been reading stories lately about the ‘coronavirus crush’. Apparently, being cooped up all day with just our cats and our thoughts has led many of us to become infatuated with someone not in our bubble. Once again, Vox comes to the rescue with this juicy piece by Terry Nguyen from October 16. Here are some highlights that struck my fancy:
    1. 2020 has been a “big year for yearning” that has translated into a deep, unattainable longing for all sorts of people, places and experiences. I hear that!
    2. Pandemic conditions make crushes lower risk for those already in committed relationships.
    3. Romantic yearning is a convenient and pleasant form of escapism and distraction.
    4. Most of us are craving the pleasant surge of oxytocin and dopamine that a crush can bring forth.
    5. Being on zoom all the time can make us feel like high school kids.
    6. With real relationships now off-line and verboten, our erotic energies are free to play in the realm of fantasy.

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.

Daily COVID-19 Briefing: Saturday

Top news, reports and insights for today:

  1. Daily headline summaries for Saturday:
  • Nineteen states this week set new highs for coronavirus infections recorded in a single day (Axios)
  • White House has blocked CDC Director Redfield and other officials from testifying on school reopenings (USA Today)
  • FDA approves pooled testing for coronavirus, promising to increase testing efficiency and reduce backlogs (Axios)
  • 85 children under age 2 tested positive for coronavirus in 1 Texas county (NBC News)
  • Studies in both the U.S. and U.K. show evidence that several candidate vaccines show early signs in Phase II studies showing they produce an immune response. Still, the highest hurdle remains as drug makers move to initiate Phase 3 trials in coming weeks (BBC News)
  1. New daily high case records set Thursday and Friday. Deaths rising. Increasing transmission seen in all but 5 states
    New record high daily case totals were established on Thursday and Friday, with more than 145,000 cases reported in two days (Figure A). This brings total U.S. cases to over 3.5 million. A half million cases were added in just 8 days, faster than any previous period (Figure B). At the state level, while the nation has been watching a Arizona and Florida, community transmission this week is increasing across the board. Figure C shows one week growth factors (ratio of cases in last 7 days to the previous week) by state. All but 5 (46 of 51) states are increasing. Unlike last week, cases are rising again in the Northeast, where new cases rose by 20% or more in Washington DC (+21%), Maryland (+51%), New Hampshire (+30%), and Rhode Island (+50%). All states in the South saw cases rise by 10% or more, lead by Alabama (+43%) and Virginia (+46%). Transmission increased in all Midwest states except South Dakota. The largest 1-week rise was in the West, lead by Colorado (+96%), Alaska (+58%), Montana (+66%) and Nevada (+42%). Thankfully, new cases finally went down in Arizona by 2%. The trend toward rising deaths continued as 936 deaths were reported Friday (Figure D). Still, the number of deaths remains far lower than the peak period in April and May despite twice the number of cases.
    What does it mean: Instead of summer suppression, we see summer surge. Deaths, thankfully remain lower than cases would suggest. This tells us that we are capturing a larger percentage of the true cases in our testing. Instead of isolated state hot spots, transmission is intensifying more broadly across all states and regions than at any time in the past.
Figure A
Figure B
Figure C
Figure D
  1. The summer story: The rest of the nation catches up with New York and New Jersey
    Over the last few months, I have been repeatedly checking the overall rates of confirmed COVID-19 infections per 100,000 population by state to see how the epidemic’s distribution has shifted. Disease detectives look most closely at rates (rather than raw numbers) when comparing different places. The graphs below show state rates at 4 different time points. Three short months ago (Graph A), New York and New Jersey were “off the charts” at 1,143 and 848 cases per 100K. No other state was above 500, the national average was 202 and it seemed that New York would never be exceeded. By memorial day (Graph 2), New Jersey doubled and New York neared 2,000, while the national average rose to 541. Rates were still 4 times higher in the Northeast compared to the West. One month ago, it was clear other states were catching up (Graph C). New York and New Jersey saw new cases finally subside, just as the surge erupted in the Midwest and South. The Northeast was still 3-fold higher than the West, but there were now 8 other states over 1,000 and two were outside the Northeast (Illinois and Louisiana). With this context in mind, the picture has changed dramatically over the last month (Graph D). Infection rates in the Northeast are now only 2/3 higher than the west. Arizona had just 58 confirmed COVID-19 cases per 100,000 on April 16. Yesterday, they had all but matched New Jersey at 1,903. The average infection rates in the South were 1/10th of those in the Northeast in April and will soon be about the same (1,165 vs. 1,513).
    What does it mean? Three months ago, many were convinced the epidemic was a crisis of the greater New York region. We waited for the summer to deflate the epidemic so we could get back to normal. That has not been the story. Instead, the success of the Northeast in curtailing the epidemic and flattening the curve has been more than matched by the inability and unwillingness of other states to halt transmission. While it was unthinkable 3 months ago, the rest of the nation has rapidly caught up. There is no evidence that the new hot spot states have learned from the successes of New York and New Jersey.