Weekend COVID-19 Briefing

Top news, reports and insights for today:

  1. Curated headline summaries for Saturday/Sunday:
  • U.S. sees highest number of daily coronavirus cases since August raising fears this may be start of a “dreaded second wave”. (CNN)
  • CDC posts warning about added COVID-19 risk for those who are overweight. With Nearly 40% of American adults obese, this greatly expands the list of high-risk individuals. (Bloomberg)
  • Isolated hot spots have popped up in New York causing Governor Cuomo to close schools, nonessential businesses, banning mass gatherings and limiting houses of worship. Some hot spots are in areas where ultra orthodox Jews reside. On Friday, a U.S. district judge rejected a requested restraining order on the Governor’s restrictions made by Jewish groups (New York Times)
  • Results of a randomized clinical trial from Brazil show that COVID-19 with moderate or severe acute respiratory distress syndrome (ARDS) who were given intravenous steroids (dexamethasone) were less likely to die or need mechanical ventilation. This study adds to our confidence that steroids help reduce the chance of deadly hyper-inflammation linked to poor outcomes in ARDS patients (JAMA)
  • A RAND Corporation survey of U.S. adults found that alcohol use increased in terms of the number of days of drinking but not drinks per month during the pandemic. A key finding was that women (but not men) reported more heavy drinking episodes and more alcohol-related problems. This raises concerns that women may be more vulnerable to pandemic stress (JAMA Open Network)
  • President Trump claims he is “immune” to COVID-19. His doctors won’t say if he has yet had a negative test. Now, twitter has flagged the presidential tweet as misleading. It is. (Axios)
  1. U.S. daily COVID-19 cases spike to mid-August levels. Eleven states record new record high infections.
     On Wednesday, it wasn’t clear which way the trend was headed after a see-saw week. But on Thursday, daily cases shot up again to over 53,000, starting a three day run resulting in 162,506 cases reported (See Figure A). Figure B shows the growth factors for cases; compared to the previous week, new cases are rising in 43 of 51 states and DC. Especially rapid growth in new cases was reported in Alaska (+43%), Montana (+54%), New Mexico (+51%), Missouri (+44%), Tennessee (+50%), Washington DC (+72%), Pennsylvania (+64%), and Vermont (+103%). We have not seen such broad, across-the-board growth in cases since August. More striking, eleven states set new daily high case reports either Friday or Saturday including Alaska (249 daily cases), Montana (722), New Mexico (485), Wyoming (195), Indiana (1,918), Minnesota (1,516), Missouri (5,066), North Dakota (656), Ohio (1,734), Oklahoma (1,533), South Dakota (750) and West Virginia (353). That makes this one of the scariest daily case reports of the entire U.S. outbreak. The surge in cases has not yet translated to a rise in deaths (Figure C), however an upturn can be expected in the coming weeks. Last week we did see big jumps in weekly deaths in Colorado (+160%), Missouri (+139%) Alabama (+72%) and Pennsylvania (+51%).
    What does it mean: The last few days have been rough. Former hot spot states like Minnesota, Ohio and Missouri, along with seven other states reported the most cases of the entire outbreak. Cases are rising broadly in all regions and daily numbers break through the 50,000 ceiling again. This tells me we are at a vulnerable inflection point.
Figure A
Figure B
Figure C
  1. Test positivity rate (TPR): a positively good test for transmission intensity
     Over the past few months, I have gone back and forth between different data streams, each tapping into a different aspect of the epidemic. This reminds me of the parable of the blind men examining an elephant. Each has his hands on a different part of the same beast. Thus far, we have emphasized daily cases and deaths, and hospitalizations, graphed by state and region. Let’s zoom in on test positivity rate. TPR is a fairly simple statistic, although getting good data to measure it is anything but easy. Here we are again grateful to the COVID Tracking Project for the best available data. It is the percentage of all tests (with a definitive result) that are positive for COVID-19 infection. Most agree that we want this number to be 5% or lower, indicating that our testing regime is sufficient to identify a healthy fraction of all the cases, while 95% negative results tells us that the barriers to testing are low enough that testing is happening broadly and at sufficient capacity. In the early days, TPR was 40% and higher largely because we were only testing those hospitalized with COVID-19 symptoms and tests were in short supply. We have come a long way and our testing strategies and capacity have evolved.
     I set out to find a data source that would tell me the TPR just for the past two weeks, rather than the entire duration of the outbreak. This is, in my view, a better number for tracking change in transmission intensity. In states where the 2-week TPR is drifting higher, the virus is outstripping capacity, and causing surveillance efforts to fall further behind the eight-ball. I created Figure D below as a new tool to examine state-level variation in TPR in the last two weeks. Not surprisingly, the variation across states is huge. First the good news: out West, six states are keeping up nicely including Alaska, California, Colorado, Hawaii, New Mexico and Washington. To illustrate the value of this data stream, compare the findings in Point 2 above, where Alaska and New Mexico are seeing sharp rises in cases, however their TPRs remain low. Combining the two data streams, we look for states with the deadly combination of rising cases/deaths and high TPR. In the Midwest, Illinois, Michigan, Minnesota and Ohio are in good shape. In the South, that distinction is shared by only Louisiana and West Virginia. All but three Northeast states are in the green zone and none is over 8%.
     Now for the bad news: there are six states, two out West and four in the Midwest where TPRs have shot up past fifteen percent, or three times greater than the quality benchmark. Idaho (23%), South Dakota (23%) and Wisconsin (21%) are extreme with more than 1 in 5 tests coming in positive. All three states are reporting in excess of 30 daily cases per 100,000 population. They also vary in how much testing they are doing. Idaho, for example, is testing only 1.3 per 1,000, among the lowest in the nation and less than half the rate of Colorado (3.0 per 1,000). South Dakota is also at 3 tests per 1,000 residents but their TPR remains high due to explosive epidemic growth (as covered on Wednesday). Wisconsin, also white hot right now, is testing in the middle (2.2 per 1,000) and most likely continuing to fall behind. The maps of these three states show somewhat similar patterns (Figure E, from the Johns Hopkins Coronavirus Resource Center). Each state is a checkerboard of rural counties with very low case totals and a handful of counties in and near cities and towns with extremely high numbers. Tomorrow I will explore how many of these counties have colleges and universities in them.
     The bottom line: While the U.S. overall continues to hover around 5-6% test positivity rate (TPR), this hides tremendous state-level variation. There are now six hot spot states where greater than 15% of tests are positive indicating a mix of inadequate testing and high transmission intensity.
Figure D
  1. Quirky Qorner: 10,000 minks die of COVID-19 in Utah, foreshadowing coming shortage of luxury coats
     The Guardian is reporting on an outbreak of COVID-19 among mink in Utah where almost 10,000 have died prompting quarantines conditions among the state’s mink farms. The first U.S. case of COVID-19 in mink was found in Utah in August. COVID-19 has also been seen in mink populations in Wisconsin and Michigan. How many mink farms are there out there? All this apparently started when it was found that mink in Europe were infected by SARS-CoV-2 by their human handlers back in the Spring. In May, the first examples of animal-to-human transmission of COVID-19 outside of China was found when 2 people in the Netherlands were found to have contracted the disease from mink. Agricultural authorities in Utah are saying that mink-to-human transmission is “unlikely” and are trying to control the outbreak with quarantine measures. Meanwhile, a million mink have been euthanized in Netherlands and Spain. That’s what countries do who place public health above short-term economic gain.

Daily COVID-19 Briefing: Tuesday

Top news, reports and insights for today:

I wish to thank those who reached out to me in the past few days with encouragement and feedback. I needed to hear that my efforts in this blog are making a difference. My plan is to continue with regular briefings at least 3 times a week (tentatively Tuesday, Friday and Sunday). I will add supplemental posts when timely and important events arise. I plan to add a new feature: reader comments and questions. I will add an option on the blog for visitors to post specific questions of interest. I will try to address those questions as best I can and share the back and forth in this space. Thanks again for continuing to read this blog and I look forward to continuing to bring you fair, balanced and scientifically-oriented news, insights and analysis. Please keep the feedback coming!

  1. Daily headline summaries for Tuesday:
  • U.S. coronavirus deaths top 150,000 (NBC News)
  • It’s not just the U.S. that is experiencing coronavirus fatigue as several European nations are seeing recent spikes in new cases as control measures become more lax (Washington Post)
  • At least a dozen states are running out of doctors and nurses as COVID-19 cases surge. Shortages are especially acute in intensive care units. Military units stepping in to assist in California (ARS TECHNICA)
  • Opinion from 19 doctors and a nurse: Trump administration issued a new rule this month requiring hospitals to report COVID-19 data directly to the Trump administration instead of the CDC. “This sudden and radical decision to change hospital reporting from the CDC to a private third party within the Department of Health and Human Services will disrupt established lines of communication and has grave potential to hobble our ability to respond to the pandemic….” (USA Today)
  1. U.S. daily cases have leveled out; the latest half million cases added in just 7 days
     From Mid-June till Mid-July, we have seen daily cases rapidly and steadily rise in the U.S. as a result of widespread transmission intensity across multiple states and regions. In the last week, that trend has finally shifted and new COVID-19 cases have plateaued. That is welcome news. As was the case in the first apparent peak in late April, it is not clear if the flattening is driven by the epidemic itself or by a new ceiling in testing capacity. There is evidence that both are at play (see main point 3). The U.S. now has over 4.2 million total lab-confirmed COVID-19 cases, which is over 1/4 of the world’s cases (27%). The cumulative total rose from 3.5 to 4 million in just 7 days, the shortest interval thus far that half a million cases were added (See Figure B).
     At the state level, transmission intensity remains high in many states. Two states now exceed the overall rates of infection per 100,000 in New York (now at 2,120 per 100,000): Arizona (2,251) and Louisiana (2,394). New daily cases over the last week per 100,000 is shown in Figure C. Fourteen states added 25 or more new cases per day last week including Arizona (+37), California (+25), Idaho (+27), Nevada (+33), Oklahoma (+26), Alabama (+33), Arkansas (+26), Florida (+48), Georgia (+34), Louisiana (+46), Mississippi (+44), South Carolina (+30), Tennessee (+35), and Texas (+26). Transmission continues to be well controlled in much of the Northeast where Connecticut, Massachussetts, Maryland, Maine, New Hampshire, New York, New Jersey and Vermont remain below the benchmark value of 5 new cases per day per 100,000.
    The bottom line: The overall trend is flattening of new cases. It is possible we have simply maxed out on testing capacity. The virus continues to spread extensively in 14 states. Conditions in Arizona, Nevada, Alabama, Florida Georgia, Louisiana, Mississippi and Texas remain especially alarming.
Figure A
Figure B
Figure C
  1. What’s going on with testing in the U.S.?
     Across the nation, testing is under the microscope. Viral twitter posts have planted the idea that the U.S. only thinks it’s in bad shape because we are testing too many people. More tests make more cases, so the logic goes. Some national leaders have suggested a slow down in testing. The Trump administration has sent mixed signals. This week, “Uncle Toni” Fauci, the nation’s top infectious disease doctor told government panels two key things: 1) more testing does not lead to more cases by itself, and 2) he has never been told by the White House to slow down testing. But the question remains in a lot of minds: is the recent surge in cases just about more testing?
     To begin tackling this, let’s consider some basic facts. First, it is true that relative to the true underlying rate of a disease, the more testing that is done, the higher will be the number of cases identified. That’s why we have to look beyond total numbers of positive tests. Second, just as with cases, we can be easily mislead by looking at the raw number of tests. We have to look at rates. There are two that matter. The first is tests per million people. There are now 78 countries with 10,000 or more cases. Among those nations, the U.S. currently ranks 1st in total cases and 9th in testing per 1 million. That’s an improvement since the U.S. ranked 17th 2 months ago. The top graph below is from OurWorldInData.org and shows the current place of the U.S. in testing rate compared to some other key nations. It shows we are in the middle of the pack. It also shows that while testing rates have climbed steadily, there is no big jump that would explain the June surge in cases.
     The other key rate is the test positivity rate (TPR). In many ways, the TPR can be a better measure of viral transmission intensity than the number of positive tests. Ideally, we would like the TPR to be at or below 5%, which tells us we are testing broadly in the population and that 95% of people are testing negative. In the early phase of the epidemic, we are only testing selectively: mostly those we already know to be sick. For that reason, the TPR was over 30% in the initial weeks of the pandemic. Let’s look now at the lower graph I made using data from the COVID Tracking Project, showing total tests per day in the U.S. and TPR since May 1. This graph shows two really important things. The blue bars are how many tests we are doing a day. That number has been steadily climbing since May 1. But, and here is the important point, it appears the growth in testing has flattened in the last week and may be declining. That is important when we put the numbers of daily positive tests in perspective. It is possible that the flattening of new cases is partly due to a flattening in the growth of new tests. To help clarify, we look at the orange line, which shows the TPR. That number fell from 17% on May 1 to around 8% in late June. Total tests continued to rise, but TPR did not fall. That’s important. If it had, we would be able to say that our testing is coming into better alignment with the true magnitude of the outbreak. That didn’t happen. The TPR has been consistent since Mid-June. That’s a sign that the surge in cases is mostly about the epidemic, and not “excess testing” whatever that might mean.
     The bottom line: We still aren’t testing enough. The surge in cases is mostly the spread of disease, not the rise in testing. Our capacity to test may have maxed out, suggesting we should be cautious in celebrating the apparent plateau in cases.
From: https://ourworldindata.org/coronavirus

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.