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: 5/2/20

Top news, reports and insights for today:

  1. Daily COVID-19 headlines for Saturday:
  • White House blocks Dr. Fauci scheduled testimony calling it “counterproductive” for the nation’s top infectious disease expert to speak to congress (The Guardian)
  • University of Pennsylvania says Dogs may be able to detect coronavirus (Washington Post)
  • Number 2 official at the CDC issues report saying U.S. was too slow in testing and travel restrictions (Forbes)
  1. U.S. deaths fall, cases rise as states reopen
  1. Epidemic control measures worked in China, a look at R0
    Dr. Thomas Inglesby wrote a very informative paper in JAMA today reminding us of a recent study that showed dramatic changes over time in the value of R0 in China.
    First a quick review. You have probably heard people talk about R0, also known as the basic rate of reproduction. This is a measure of how infectious a pathogen is. It’s a really important number if you want to understand and stop an outbreak. R0 is the expected number of secondary infectious cases produced by a primary infectious case. Knowing how many other people will be sickened by each infected person tells us a great deal about how far and fast an outbreak can spread. As a rule of thumb, an outbreak with an R0 greater than 1 will continue to propagate via ongoing cycles of transmission. How far above 1 tells us how far and fast it will spread. R0 of 2 or more means exponential growth of new cases. The goal of epidemic control is to lower this number to below 1.0 so the outbreak will burn out. That means the actual value of R0 will be high initially before the outbreak is identified, and control measures like social distancing and testing are put into place. As those measures come on line, we expect this number to fall. How far and fast it falls is a good measure of how well you are doing at addressing the epidemic. So, during an outbreak, it is important to measure the rate of reproduction and how it changes over time. That number we call the effective reproduction number, or Rt (read: R-Sub-T).
    Pan and colleagues published this very compelling figure in their April 10 paper showing just how potent the outbreak control measures were in China. In the first 3 weeks of January, before control measures were initiated, the Rt in Wuhan ranged from 2.5 to 4; the epidemic had exploded in Hubei Province. Then, after lockdowns, traffic suspension, and home quarantine, the Rt plummeted to below 1 by early February. Additional control measures have kept the disease in check since then.
    What this means? The big take-home message is that outbreak control measures work. China effectively suppressed an outbreak in a matter of weeks, driving the Rt down below 1 using potent measures, many of which seem draconian to us in the West. China, a nation of 1.44 billion people, now reports 3 deaths and 58 cases per 1 million population (compared to over 200 deaths and 3,500 cases per million in the U.S.). We can not and should not do everything that China has done, but the story in China is a warning to the U.S. about what might lie ahead as we now move to suspend those control measures that have mitigated the pandemic in the U.S. to this point.
  1. New Zealand is stopping COVID-19 with strict control measures, offering a model to the world
    The National Geographic has a story today about the success story in the island nation of New Zealand, home to 4.8 million people. We haven’t heard much about New Zealand since the early days of the pandemic. That’s because they have done an amazing job of arresting the spread of the disease. They now rank 53rd among nations in cases per million population. They have reported less than 1,500 cases in total and 20 deaths (according to Worldometer). They have tested more than 30,000 per 1 million, 30% more than the U.S.. I used Aatish Bhatia’s site to generate the figure below. What’s really impressive is that things looked pretty bad for New Zealand in the beginning. Then, at around 900 total cases, we see the telltale downward hook that shows an abrupt end of exponential growth. We see this in other Southeast Asian nations, especially China, but New Zealand and South Korea are developed, democratic open societies, where the harsh measures employed by China and Hong Kong were not implementable. That doesn’t mean they weren’t strict. New Zealand locked it’s borders tight and instituted mandatory quarantine for all visitors. Then came a complete nationwide lockdown with domestic travel moratorium, restricted vehicle traffic and some of the strictest measures of any country. They did this when they had a handful of cases. The prime minister, Jacinda Ardern, makes regular statements to the nation, explaining her policies and why they are being taken. She relies of a team of scientists and public health experts in crafting the response. Now, they are seeing 20 new cases per week. The U.S. has 200,000. If only we could all be Kiwis.

Top Pick of the Day

Fauci says coronavirus-like outbreak is ‘what keeps me up at night’

NBC News online story by Adam Edelman, Posted April 28, 2020 at 12:38 PM EDT


Uncle Tony tells us what’s on his mind: implications of a novel pathogen, timeline for vaccine, everyone is at risk, likely resurgence in the fall/winter.

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.