Weekend COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Saturday/Sunday:
  • Top Story: Anthony “Uncle Tony” Fauci, other experts warn of a post-Christmas “surge upon a surge” as U.S. braces for the worst period of the pandemic (Bloomberg).
  • Los Angeles County is in crisis, reporting a record high 148 new deaths on Thursday. Public Health official Barbara Ferrer told CNN “a person dies every ten minutes in L.A. Country from COVID-19” (CNN).
  • A new study in California shows that from March to August of this year, excess deaths among Hispanics and those without a high school degree or GED tripled. This is important further evidence of how the pandemic has posed the highest risk for low-wage essential workers (JAMA Internal Medicine).
  • Researchers scramble to understand the new variant of SARS-CoV-2 to emerge first in the U.K., now accounting for half of that country’s new cases. Some experts think the current vaccines will work against the new variant but nobody knows that until the studies are done (CIDRAP).
  • More than 1.9 million Americans have now received a COVID-19 vaccine (see Figure A). The Federal government says more than 9.5 million doses have been delivered to the states, but thus far, Illinois is the only state to have vaccinated more than 100,000 persons (New York Times).
Figure A: From https://www.nytimes.com/interactive/2020/us/covid-19-vaccine-doses.html
  1. Christmas chaos in the daily data means we are again flying blind this week. U.S. hospitalizations now double the previous two peaks
     The daily tally of new lab-confirmed COVID-19 cases nose dived after December 23 when 206,000 new cases were logged (See Figure B). I am convinced the data is unreliable as a gauge of transmission intensity due to the reporting slow down associated with the Christmas break. Take note of the big dip in daily cases that occurred around Thanksgiving. It won’t be until the latter part of next week or the week after that we will be able to see where the case numbers are headed. It won’t be until the middle of January that we will see the impact of Christmas and New Years Eve as potential intensifier events. The best evidence that daily cases and deaths are downwardly biased can be seen in the daily hospitalization numbers (Figure C). While not immune to administrative sluggishness in reporting, the hospitalization numbers show no sign of a slow down. In fact, according to the data from COVID Tracking Project, Christmas eve saw a record broken for the highest daily COVID-19 hospitalization totals at over 120,000. That’s a significant number in part because it’s double the previous peak waves of hospitalizations seen in late April and July. The national surge is being driven by a handful of states with COVID-19 hospitalizations of 500 per million population or higher including California (500 per 1 million), Pennsylvania (492), Alabama (517), and Arizona (581). The mortality numbers have also nosedived, indicating a 15% drop in weekly deaths (Figure D). I am inclined to believe that this drop is also nothing but an artifact of the holiday reporting hiatus. Again, note the temporary dip in the death numbers around Thanksgiving.
      Bottom line: The case and death data are telling us the virus’s grip on the country is slackening. The hospitalization numbers contradict this, as does previous experience. In both cases and deaths, the magnitude of the dip is already bigger for Christmas than it was at Thanksgiving so we can hold out hope that the declines may be a hybrid of sluggish reporting and a real flattening of transmission intensity. I won’t be holding my breath.
Figure B
Figure C: From the COVID Tracking Project
Figure D
  1. When will the “third” wave be over? Actually, in the U.S., the first wave is still going strong: comparing and contrasting cumulative cases in linear and log scales
     When the daily numbers get wobbly, I am inclined to go big picture. The figures below show cumulative U.S. lab-confirmed cases on both the linear (Figures E), and the log scales (Figures F). As disease detectives, we know these are different ways to graph and depict the same information. I wanted to highlight this to show how linear and log representations produce an effect on the eye that is like looking at a negative and a photo (the same image but inverted). Figure E shows U.S. cumulative cases and how long it takes to add each million cases on a linear scale. It took 58 days to get to our first million, but starting November 2, things shifted; a million cases were reported a week, further intensifying to a million every 5 days from 14 to 18 million. That is rapid growth to be sure. The story here is that November and December have been the worst two months of the U.S. epidemic. Figure F shows the same data but on the log scale with a focus on doubling times. This almost looks like a reverse image, with clearly exponential growth in March and April (exponential growth looks like a straight rising vertical line in log scale). Here, an inflection point is seen at 1 million total cases and again at 4 million with a slowing of new cases and elongation of doubling rates. What we look for on the log scale is a flattening of growth, which signals a shift from exponential growth to simple linear growth. There was hope we would see that in August. That didn’t happen. Instead, doubling rates shrank from 88 days to 57 days in the jump from 8 to 16 million. That is graphically easier to see in the previous graph. What the log scale graph shows is that the first “wave” never actually ended (cases never completely flatten on the log scale). That’s why you hear me pushing back at any suggestion of a second or third wave. So far in the U.S., we have one continuous wave with three distinct peaks.
    That’s not the case in other countries. The last figure shows the log-log plot best suited to signal the end of a wave (look for a sharp hook where the plot becomes straight vertical for some period of time). Figure G was made using Aatish Bhatia’s super-cool website. I include here a handful of countries where a clear hook can be seen, evidence that the first wave of COVID-19 actually ended. For convenience, I show Spain in highlight. After explosive exponential growth in Spain in the early months, the inflection point happens in April after extensive national lock down. In each of the other countries shown, the telltale hook can be seen. The first “wave” ended in Singapore in Mid-July, in early April in South Korea and France, and in late May in Italy. In the U.S., we see three peaks, but no hook.
    Bottom Line: Unlike most other peer nations, the U.S. has never taken the steps necessary to arrest the spread of coronavirus. This, folks is still the first wave.
Figure E
Figure F
Figure G: From https://aatishb.com/covidtrends/?location=France&location=Italy&location=Singapore&location=South+Korea&location=Spain&location=US
  1. Quirky Qorner: A Texas Boy Scout troop created a hug booth for nursing home residents
      As a former boy scout, and a fan of hugging, I could not help but smile when I saw this story in CNN about a Texas scout troop that made a special contraption that allows for protected “hugs” in a nursing home (See photo below). When the story of COVID-19 is finally written, I suspect that the emotional toll exacted by the virus in terms of loneliness and disconnection will prove to be substantially greater than we now are aware. This story will stick in my mind under the best bright spots heading.
Photo taken by screen grab from https://www.cnn.com/2020/12/27/us/boy-scouts-hug-booth-nursing-home-clear-lake-trnd/index.html

Top pick of the day: Wednesday

The looming questions scientists need to answer about the new variant of the coronavirus

Article by Andrew Joseph published online at statnews.com December 21, 2020.

Have you heard there is a new “strain” of the virus that causes COVID-19? Several people have sent me questions about this. Scientists are referring to it not as a new strain but as a novel variant of the coronavirus, first spotted in the United Kingdom where it is now the dominant version of the virus in many areas. The new variant, referred to as B.1.1.7 or VUI-202012/01, contains between 17 and 60 genetic mutations. This has led to stricter lockdowns in England and travel bans for UK residents. Scientists are working hard to determine whether it functions differently than previous variants in 3 key ways: A) does it spread more easily, B) does it cause more or less severe disease and C) can it evade our vaccines or our hard-fought natural immunity? So far, it looks like the answer to A) may be yes (the jury is still out). There is, so far, no solid evidence the answers to B and C are yes. This article by Andrew Joseph lays out what we now know and don’t about this development, striking the right balance between caution and concern. I am following developments about this as well as another variant being tracked in South Africa and will keep you updated as the science evolves.


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.

Weekend COVID-19 Briefing


Top news, reports and insights for today:

  1. Curated headline summaries for Saturday/Sunday:
  • Top story: The U.S. FDA authorized a second vaccine (made by Moderna) under an Emergency Use Authorization (EUA). The company has begun distributing its vaccine to 3,700 locations as the U.S. vaccine distribution program begins to take shape (Reuters).
  • Twitter announced Wednesday that it would moderate, label and in some cases remove harmful misinformation about COVID-19 vaccines starting next week (CNBC).
  • Thousands of leaked directives show how China paid an army of internet trolls to make the coronavirus look less dangerous and its own response more competent than was true (ProPublica).
  • The WHO and the UK are working closely to monitor the emergence of a new variant of SARS-CoV-2 that might be spreading more efficiently. The new variant has been seen in the Netherlands, Denmark and Australia. Numerous countries are banning flights from the UK in response. There is no evidence yet that the new variant causes more severe disease or will respond differently to the vaccine. This story highlights what has been lost by the Trump administration’s ill-advised decision to withdraw from the WHO and why global coordination is so crucial going forward (BBC News).
  • The U.S. Equal Employment Opportunity Commission has determined that employers will be allowed to require employees to get a COVID-19 vaccine and block them from entering the workplace if they refuse (Huffington Post).
  • While older people make up 80 percent of COVID-19 deaths, many people falsely believe the virus is not impacting younger adults. A new study published in JAMA shows that from March to the end of July, U.S. adults aged 25-44 experienced almost 12,000 more deaths than were expected based on historical norms. Only a third of these excess deaths were officially attributed to COVID-19, suggesting that limitations in testing led to a severe undercounting of virus-related fatalities in younger adults. The chances of dying were more than double among young people in New York and New Jersey in this period (New York Times).
  • New study from Dallas TX adds to growing evidence that SARS-CoV-2 infection in pregnancy is not associated with adverse pregnancy outcomes (JAMA Open Network).
  • Newly released data shows nearly 900 out of 938 metropolitan areas and more than 2,000 out of 3,270 counties qualify as “sustained hotspots,” meaning they have “potentially higher risk for experiencing healthcare resource limitations.” (NPR, See Figure A).  
Figure A: From NPR (see above link), created from data released at https://healthdata.gov/blog/covid-19-open-data-–-our-data-your-data
  1. U.S. daily cases may be leveling but new transmission remains high in all but 9 states. Tennessee has gone ballistic. Hospitalizations have peaked in the Midwest but soar in 3 other regions.
      Friday broke the all-time daily record for most cases with 225,000 capping a 4-day stretch of over 190,000 cases a day (See Figure B). The 7-day moving average is hinting at a leveling trend, but as clever disease detectives, we wonder if this is a peak in cases or testing capacity. This week saw weekly new cases continue to fall in the Midwest, however the force of transmission intensity in that and all other regions remains exceptionally high as all but 9 states have new daily cases per 100,000 population of over 40 (Figure C). The benchmark for a state to have transmission intensity is just 5 (only Hawaii and Vermont are even close). A handful of states are again ‘white hot’ with transmission intensity over 75 including Arizona (90 cases per day per 100,000), California (104), Nevada (83), Utah (76), Indiana (81), Oklahoma (81), Arkansas (75), Delaware (77) and Rhode Island (94). Then there is Tennessee, which has gone ballistic this week, spiking to over 140 per 100,000, rising 48 percent week-over-week. That state this week became the 9th to record half a million cases after racking up 67,000+ in previous seven days.
     Reports continue to pour in about hospitals under stress and ICU beds and staff running short. The COVIDACTNOW site now lists more than 100 metropolitan counties and 88 non-metro counties where the ICU beds are 100% full. Figure D below from the COVID Tracking Project shows the moving average daily hospitalizations for four U.S. regions. In all but the Northeast, hospitalizations are now higher than they have been at any point during the pandemic. Nationally, we have about 110,000 people in hospitals compared to 60,000 during the two previous peaks. The only “good news” in this figure is that hospitalizations appear to have peaked in the Midwest, falling from a max of 29,000 on December 1, to 23,300 yesterday. The rate of increase in the three remaining regions is staggering.
    Bottom line: There may be signs that overall daily cases may be leveling, but transmission remains high in all regions and in all but 9 states. The situation continues to worsen in California, Arizona, Tennessee and Rhode Island. Hospitalizations are exploding at unprecedented levels in three regions, a warning sign that deaths will continue to soar for the next few weeks at least.
Figure B
Figure C.
Figure D
  1. Daily U.S. COVID-19 deaths pass 2,500 a day. Cumulative deaths to eclipse 300,000 tomorrow. Let’s compare state totals and rates
     On Wednesday, a new record for deaths was set in the U.S. with COVID-19 claiming the lives of 3,331 American citizens (Figure E). The daily trend continues to rise, passing 2,500 a day this week. Daily deaths have doubled since November 30 and, given the hospitalization data, are expected to continue to climb. If we look at total deaths by state (Figure F), the carnage looks especially lopsided, with just 9 states reporting 10,000 or more cumulative lab-confirmed COVID-19 deaths, including one out West (California), two in the Midwest (Illinois and Michigan), two in the South (Florida and Texas), and four in the Northeast (Massachussetts, New Jersey, New York and Pennsylvania). It’s a very basic tenet of epidemiology that we can’t compare states using the total numbers to determine which are doing better or worse at keeping citizens alive. COVID mortality is no exception; rather it is a rather apt illustration. We calculate COVID-19 death rates as total deaths divided by total population times 100,000 (Figure G). This picture looks completely different. California and Texas are ranked 2 and 3 in total deaths but have rates that are below the national average, shown here as the red dashed line. North and South Dakota have COVID-19 death rates over 150, the highest in the Midwest; that is triple the rates in California. In the South, Louisiana and Mississippi have rates above 140 per 100,000 but neither state has more than 6,700 total deaths. A handful of states have done dramatically better than average, keeping their death rates below 40, less than half the national average including Alaska (25), Hawaii (20), Oregon (32), Utah (36), Washington (40), Maine (22), and Vermont (18).
      Bottom Line: As 2020 comes to a close, we remain astonished at the wide range of COVID-19 death rates. The best and worst death rates vary by a factor of ten from Vermont (17.5) to New York (183.1). These disparities are further evidence of what happens in the absence of national leadership during a pandemic. The U.S. will pass 300,000 COVID-19 deaths today or tomorrow. That is the most of any nation by far and 19 percent of the world’s grand total death toll. We remain the world’s control group, showing what happens when the Federal government offer’s its people sugar pills, instead of real medicine.
Figure E
Figure F
Figure G