Daily COVID-19 Briefing: Friday

Top news, reports and insights for today:

  1. Daily deadline summaries for Friday:
  • Florida just reported nearly 9,000 new daily cases, a record high, bringing the state’s total to 122,960. This is almost 4,000 more cases than the 5,004 reported yesterday (CNN)
  • Both Florida and Texas moved to close bars on Friday after cases exploded in those states. Florida’s Governor left it to the Secretary of Department of Business and Professional Regulation to tweet the announcement. The Texas governor followed suit reinstating some restrictions on dine-in restaurants (NBC News)
  • Top doc “Uncle Tony” Anthony Fauci said today that the White House coronavirus task force is considering the need for a new testing strategy, admitting that the current approach is not working (CNN)
  • It’s more clear than ever that medical workers should be using N95 respirators, not just regular masks. While production has ramped up, shortages remain. N95 masks were designed to be single use. Researchers have now shown an effective method of decontaminating N95 masks using steam and a microwave in just 3 minutes (FastCompany)
  1. Zooming in on weekly growth-factors: key trends in deaths and cases by state
    Every detective has to decide which clues to pay attention to and which to ignore. A good detective will often pay attention to details others miss. This is just as true for disease detectives. While most people are watching case and death totals by day, I watch 1-week growth factors. If you have read my blog you may recall that these are important metrics to gauge recent trends. They tell us how fast the epidemic is moving in a state right now. Below are 7-day growth factors for cases and deaths by state, showing the ratio of cases/deaths in the last seven days and the 7 days before that. For example, 1.5 means there were 50% more cases/deaths last week compared to the week before. In contrast, 0.6 means there were 40% fewer cases/deaths last week. We know that deaths keep falling even as cases are surging. That’s a mystery. What do these growth-factors tell us?
    For cases, outbreaks have slowed in all Northeast states except Delaware (1.22) and Pennsylvania (1.21) where cases are rising. Numbers are too small in Vermont. That, by the way was the only state in the U.S. with fewer than 50 new cases last week. In contrast, growth factors are >1 (cases are rising week-over-week) in all western states, all southern states except Alabama and 9 of 13 mid-west states. While everyone is watching headline states like Arizona, Florida and Texas, the bigger picture is that cases rose by 10% or more in an astonishing 32 states. Idaho spiked the most with 1,122 new cases last week, up from 441 the week before. Arizona (+19,587), California (+34,472), Montana (+148), Nevada (+2,783), Michigan (+1,688), Missouri (+2,518), Florida (+28,092), Georgia (+10,183), Mississippi (+3,875), and Texas (+32,066) all saw weekly cases jump 50% or more.
    Deaths were more volatile despite the overall falling trend. Delaware stands out after reporting 43 deaths last week, more than triple the previous 7 days. Arizona (+219), Kansas (+14), Alabama (+79), and South Carolina (+70) all saw deaths rise by 50% or more last week. Falling deaths in states where cases are surging still begs for an explanation.
    Bottom line: The virus is spreading fast in 32 states, not just the few in the headlines, with trends indicating a return to exponential growth in some. Deaths remain a mystery. It may be the calm before the storm. Few expected the U.S. to be back to the April peak as we head into the heart of summer.
  1. Dark times in the sunshine state: a deep dive in Florida
    Florida is a bellwether state, worthy of close attention for many reasons. It has played a key role in the national epidemic as a hub of early transmission and a touch-off point for national spread after spring break. It is a state that has been under scrutiny for it’s slow actions, confusing messages and challenges in data collection and reporting. Perhaps of biggest concern is that Florida is home to a high concentration of the most vulnerable of our citizens: older people. One fifth of it’s population is over 65 and there are about 700 nursing homes with more than 80,000 beds. It is a treasure trove of America’s grandparents. What happens in Florida will disproportionately contribute to the overall burden of death and suffering in America’s outbreak.
     Florida is our patient, and the patient is sick. As numerous news outlets like CNN are now reporting, Florida is a top candidate for the next hot spot or epicenter as numerous sun-belt states battle the front edge of the U.S. outbreak. New record cases are being set almost daily with no apparent end in sight. In desperation, the governor closed bars this evening. Let’s order a battery of tests and have a look at what’s going on. The gallery below contains 8 figures that represent those test results. What do we learn:
    1. Graph 1: This is the overall epidemic curve for Florida (from STATNews COVID-19 Tracker) showing daily cases. It shows what all the fuss is about. Around June 6, the curve switches from linear growth to exponential growth in cases. There were 60,000 state-wide cases then, that has doubled in 20 days. Today, a record high 8,942 new cases were reported, a rise of 79% over the previous day. The first case was reported 109 days ago.
    2. Graph 2: In states like Minnesota and Arizona, big surges can be blamed on a small number of counties that become white hot for a period. Lets see how wide-spread the problem is. First, we see Miami-Dade County, home of the highest number of cases in the state (28,664 cases and 935 deaths). We see the previous spike there around April 9 that eventually lead the state to shut things down. The shut-down worked and cases fell until Memorial day. Then the old peak was surpassed in just 7 days, and now the county is seeing more than 600 a day, with a 50% rise in the last week.
    3. Graph 3: Maybe the problem is just in the urban south. How about the other end of the state, way up in Nassau county, a suburban area north of Jacksonville. Looks like a carbon copy. First peak is clear in early April, general decline till end of May and then an even more severe spike starting June 10. Here the new peak is twice as large as the April peak. It is the same pattern in a less populous county in the north. While there are only 136 total cases, the weekly new case total jumped 167%.
    4. Graph 4: Ok, what about the Northwest of the state? Leon County is home to the state capital. That part of the state hasn’t been on the radar yet. Now at 642 cases, the picture is fairly similar. First peak occurred later in mid-April at 15 daily cases. Here there was a smaller aftershock in the last two weeks of May, and then around June 15, the firestorm started, surging to the previous peak and then 70% higher in a bit over a week. In the state capital, average new cases have risen 280% week-over-week.
    5. Graph 5: What about the sleepy middle of the state? Perhaps lower density communities in smaller towns and big farms offers some insulation. Polk County covers a large area right in the center of Florida, home to just 603,000, it’s largest city is Lakeland; universities, farming, mining and the headquarters of Publix are key features. The story here is different and the same. Polk county was spared the first peak, never rising above 20 cases a day in April. But even in this low-population, largely agricultural county, a firestorm took off around June 9, with cases surging from 20 a day to over 130. Last week averaged 117 a day, compared to 50 the week before, a rise of 137%. There are some counties in Florida where surge hasn’t happened. The main point is that the surge is occurring all over the state, north to south, urban to suburban, with a similar pattern of exponential growth in June.
    6. Graph 6: Maybe this surge is all about more testing. This graph from rt.live shows positive daily tests and total testing volume for the state. Testing doubled from 20K per day to 40K around May 20. Since then, it’s been up and down but the overall trend has been steady. There is nothing in these numbers that would convince me that the June surge comes from testing increases. The curves for testing and cases are not the same shape. What is evident is that the surge in cases started a month after shelter-in-place orders were lifted.
    7. Graph 7: The effective Reproduction rate (or Rt) is an important test result. We now have pretty compelling models that allow us to see how the R-value changes over time. This graph also comes from rt.live, a model I and others have come to trust. A reminder, the Rt is the time-specific estimate of how many additional people each infected person subsequently sickens. Currently, Florida is estimated to be 1.4, which is the 5th highest in the country. The model shows that Rt was below 1.0 during the SAH phase, then started rising above 1, where it has been flat since Memorial day. A sustained Rt of 1.4 means each infected person passes the illness to 1.4 others. That is sufficient to drive nearly exponential growth. Without any epidemic control measures, Florida experienced an initial Rt of about 3.0. The control measures put in place knocked this down to below 1, where the virus might have then failed to thrive. Reopening the state however has brought the state back to a place where the virus is spreading half as fast as when nothing was being done.
    8. Graph 8: Models like this can be used to predict the near and intermediate term future. My current favorite model uses machine learning and combines many models and various data sources from COVID-19 Projections. This graph tells us where Florida is now, taking account not only of those testing positive, but also for asymptomatic infections that are never tested. This tells us that currently about 3% of Florida’s residents have been infected. That is light years away from the 55-70% attack rate needed for herd immunity to halt the epidemic. It estimates Florida is now actually acquiring around 11,000 true infections every day. Based on these parameters, the model predicts cases will peak again in Florida, but not until July 26, one month from now, at which point there will be an estimated 13,716 infections each day. Given the uncertainty in the model, that could be as high as 24,000 or as low as 4,700. Estimated current infections will rise from 150,000 to over 200,000 before this peak occurs.

Daily COVID-19 Briefing: Thursday

Top news, reports and insights for today:

  1. Daily deadline summaries for Thursday:
  • President Trump’s administration is ending support for 13 coronavirus testing sites including 7 in Texas just as that state reports an all-time daily high in cases (The Hill)
  • California sets record daily high of more than 6,600 cases sparking fears the epidemic is out of control in that state (Los Angeles Times)
  • Alarming resurgence of COVID-19 cases seen in Europe across 11 countries as countries reopen, mirroring trend in the U.S. (BBC News)
  • The national weekly average daily incidence of new cases is now nearly as high as it was at the initial peak on April 10 (STAT News, see graph below)
  1. U.S. cases explode, new record daily high reported. Things are really crazy in Arizona
    On Wednesday, a record high 37,915 new COVID-19 U.S. cases were reported eclipsing the previous daily high set April 24. This further clarifies two important facts: 1) reopening has led to wide-spread transmission intensification; 2) the “first wave” is still in progress (see today’s Top Pick). The surge in cases nationally is the result of significant increases in new cases in 17 states throughout the south, midwest and west. The lower chart shows where the new case growth is most intensive. As has been true over the past 10 days, Arizona is “off the charts” now reporting more than 37 new daily cases per 100,000 population, a number in excess of what has been seen in any state since April 1. Arizona’s total increased by almost 20,000 last week, a 47% surge, indicating cases are doubling every 2 weeks. The incidence rate has risen almost 900% in the last 2 months. COVID-19 hospitalizations and patients in the ICU have both doubled there since April 24. Big rises in new cases (>8 daily cases per 100,000) are also being reported in California, Idaho, Nevada, Utah, Iowa, Oklahoma and 10 of 13 states in the South, where only Kentucky and West Virginia are below the 5 cases benchmark. Alabama, Arkansas, Florida, Georgia, Louisiana, Mississippi, North Carolina, South Carolina, Tennessee, and Texas are all higher than 10 new cases per 100,000. The surge in cases in the warmest states clarifies that the epidemic is not curtailed by heat and humidity.
  1. The big mystery of the moment: Why are deaths not rising
    Disease detectives are driven by the prospect of solving puzzles and unraveling mysteries. A big mystery is coming into clearer focus. Have a look at this graph showing daily deaths. Cases have clearly been on the rise since June 10. The trend in deaths however is quite different. The 7-day average continues to trend downward. While new daily cases are now back to where they were at peak, deaths are at 600 a day, a third of what they were at peak over 2,000 on April 24. This is a big mystery. Why have deaths not surged as cases have? There are many possible explanations, but the 4 most likely are listed below. In coming blog posts, I will try to unravel this mystery.
    1. Cases have risen as a function of more testing, that has not translated to deaths. I will comment on this in Point 4 below.
    2. The time lag between infection, symptoms, a positive test and death is longer than we thought. Deaths will rise soon.
    3. COVID-19 deaths are being hidden for political reasons.
    4. COVID-19 is becoming more infectious (especially among younger people), less lethal or both.
  1. Increased testing does not explain the spike in cases
    President Trump believes testing is a bad thing because it finds too many cases. Don’t get me started. Some governors have blamed surging case numbers on increases in testing. Let’s look at some data. The first thing I went to is the overall shape of the epidemic curve in testing. Like the daily case and death totals we saw above, we can learn important things by looking at the overall shape of global testing intensity. Using data from the invaluable COVID Tracking Project, the graph below shows what the pattern in global testing looks like since March 15. The blue area describes the steady rise in daily testing over the course of the U.S. outbreak. It shows, in my opinion, four phases. First, there was rapid acceleration of daily testing from mid-March till the end of April. Next, we saw linear growth that stalled out by April 20. This was followed by steady linear increase until the end of May (Memorial day). Since June 1, the increase has been slower that the previous period. Daily testing, now at about half a million a day, has doubled since the beginning of May. However, the period of greatest interest, when U.S. daily cases changed direction and began a steady rise, starts around June 9. During that period, testing rose modestly from about 425,000 a day to just over 500,000. Similarly, the test positivity rate, has been declining steadily, dropping by half since April 22. Strikingly, that decline has stalled at around 7% over the last week.
    What this means: If the surge in cases has been caused by a rise of testing, we would expect to see something different than we do. Testing rose more rapidly before Memorial day, when cases were falling. There is no visible bounce in testing that would explain the June surge. If anything, the absence of any big shift in the TPR tells us that the overall testing regime has been business as usual for most of May and June. I believe this chart provides solid evidence that the surge in cases is being driven by the virus, and not by increased testing.

Top pick of the day: Sunday

What a Negative COVID-19 Test Really Means

Science article by Sarah Zhang published online at The Atlantic, June 21, 2020.

We know that the current tests for the SARS-CoV-2 virus are not perfect. The sensitivity of the test is concerningly low, resulting in a significant number of false negative results (when the test says the person is not infected when they actually are). We also know that up to 40% of cases are transmitted by persons who are asymptomatic or presymptomatic. This article covers the overlap, addressing what it means that false negatives may be even more common in people without symptoms and what this means in practical terms.

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.