Daily COVID-19 Briefing: Tuesday

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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)

2. 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

3. 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

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Daily COVID-19 Briefing: Saturday

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Top news, reports and insights for today:

1. Daily headlines summaries for Saturday:

• U.S. posts largest single-day jump in new COVID-19 cases. Downward trend seen in only 2 states (CIDRAP News)
• Huge daily jump pushes global COVID-19 total past 10.5 million (CIDRAP News)
• In contrast to recent messages from the White House, CDC Deputy Director says coronavirus is spreading too quickly to contain, calling for an end to wishful thinking (Axios)
• White house drug policy office analysis shows an 11.4% year-over-year increase in drug-related fatalities in the first 4 months of 2020 as lockdown, anxiety, economic uncertainty and stress combine to amplify the challenges faced by those battling addiction (Politico)
• Texas Medical Center hospitals go into phase 2 surge plans as patients requiring intensive-care beds now exceeds 100 percent of capacity (Houston Chronicle)

2. Cases rose last week in all but 3 states; new daily highs set three days in a row
   Another day, another record high reported new cases in the U.S. as a staggering 57,000 infections were added to the total. Friday caps a three day run of new records each day. The bottom graph shows just how widespread the surge has been across the nation. It shows that the growth factors (ratio of last week’s cases to the week before) are >1.0 for 48 of 50 states and the nation’s capital. Only Arkansas, New York and Vermont had steady of falling cases. An astonishing 7 states saw cases rise by 10,000 or more in 7 days: Arizona (+25,400), California (+47,774), Florida (55,634), Georgia (+17,498), North Carolina (+11,423), South Carolina (+11,150), and Texas (+45,908). Ten states saw weekly cases rise 50% or more compared to the week before.
   What it means: The epidemic is raging across the country. We are returning to a period of near exponential growth. This is a critical moment in the pandemic in the U.S. where a clear strategy is needed and hard choices must be made.

3. Double deja vu: Arizona and Florida are repeating the rate of growth seen in New York during the first peak
    Remember back when it looked like coronavirus was going to be a big deal in New York, but not elsewhere? That was about 100 days ago. Many Americans believed that the epidemic was a coastal thing, having first hit the left edge, then hammering the right. The nation shook its head watching cases skyrocket in New York city and state. Good thing we aren’t there, said many. Must be all the immigrants, the subway, or high population density. Of course it was those things, but it was only the first inning of a long baseball game. We collectively breathed a sigh of relief when the wave of cases in New York finally started to fall, and for a time, it looked like the first was over. The disease detectives weren’t convinced, but the nation wanted to believe that the worst was over. It was time to start getting back to normal. A hurricane had come through, damaging the northeast extensively, but the skies seemed to be clearing.
    Over the last week. I keep having the same conversation with different people. It goes something like this: you know Tom I heard what you were saying, that this is a marathon and not a sprint, that cases would surge again when we stopped social distancing, and that we were in this for the long haul. But, I just didn’t want to believe it. I just hoped that you were wrong. I really wanted the things we did to work and for all this to just go away. I get it. I really do. It’s not been fun to be the bearer of unwanted news and information.
    As I reflect, it seems that America has always been a can-do nation, able with enough resolve and our boundless innovative capacity, to handle any problem. Mother nature, we seem to believe down deep, won’t get the better of Uncle Sam. The forces of nature at play are certainly no match for the indomitable spirit of American resourcefulness! Call it wishful thinking, call it can-do spirit, call it mass denial, the truth is that nature is winning and we are falling further behind by the day.
    On this particular 4th of July, there are reasons for hope. That American spirit is alive and well and capable of great things. Deaths are low right now, partly because we have learned how to keep the sick alive. We are making progress toward a potentially effective vaccine at record pace. States and cities are experimenting, pivoting and reassessing. But on the nation’s birthday, my message is simple. We need to wake up and realize the reality of this situation. The virus is winning in the U.S. and we must face the reality that this will be a long and continuous battle until we get to herd immunity, which remains a long way off. If you still think this is extreme, alarmist thinking, please look at the graph below. This visualization is from 91-DIVOC and shows daily cases per 1 million population by U.S. States on a common time scale. The orange line is New York. The blue and green show that what we are seeing now in Florida and Arizona looks like a repeat of the story seen in New York 100 days ago. Double deja vu. Whack-a-mole strikes again.

Screen grab from 91-DIVOC: http://91-divoc.com/pages/covid-visualization/

Daily COVID-19 Briefing: Tuesday

Top news, reports and insights for today:

1. Daily headline summaries for Monday:

• As Americans celebrate Memorial day, new cases continue to rise in 17 states, stay flat in 13 and are going down in 20 (CNN)
• All eyes remain on Georgia where cases have declined slightly since reopening began with a slight uptick since May 12. So far there has been no spike of cases and test positivity rate are falling and daily tests are rising (CNN)
• Largest study yet published in Lancet of impact of antimalarial drugs hydroxychloroquine and chloroquine in COVID-19 found the drugs had no benefit and were associated with higher risk of death in hospital patients (CIDRAP)
• Recent study shows that state-level stay-at-home orders were consistently followed by reductions in daily infection rates in 42 states and DC studied (American Journal of Infection Control)

2. U.S. cases remain flat, deaths continue to trend downward, midwestern and southern hotspots remain
    Over the last week, U.S. cases (top graph) show a generally flat trajectory adding more than 152,000 infections, a rise in cumulative cases of 10%. The U.S. now has a third of all cases on the planet, more than 1.3 million more cases than Brazil, now at #2. Among nations with more than 100,000 cases, the U.S. now ranks second in cases per 1 million population at 5,098 behind Spain (6,050) and ahead of the UK at 3,825.
    As always, we pivot from the overall national numbers to what is happening in states. The middle graph shows 7-day change in cases by state and region. Seven northeast states had less than 10% case increases and none had more than 25% increases. Similarly, 7 of 13 western states saw slow case growth and none rose more than 20%. As was true last week, the epidemic has shifted to the midwest and south. Among the states that saw cases grow more than 25% (a rate of doubling in 4 weeks), 2 were in the midwest (Minnesota and North Dakota) and two were in the South (Arkansas and North Carolina). Kentucky, Michigan and Louisiana were the only states in these two regions with less than 10% growth in cases (although Kentucky hasn’t reported new cases since Saturday).
    The bottom figure shows the overall trend in COVID-19 deaths by day. In contrast to the steady continued rise in cumulative cases, the trend in deaths is more clearly toward decline in daily deaths as evidence by the 7-day moving average line. Sunday and Monday again saw new deaths below 1,000, although in the past 3 weeks, similarly low numbers were followed by substantial jumps on Tuesday as the weekend lag ends and state authorities catch up.
    What this means: Despite warming weather, the epidemic continues to yield rising cases, especially in the midwest and south, even as deaths drop. Minnesota, North Dakota, Arkansas and North Carolina continue to be the U.S. hotspots. Experts brace for new surges in cases and deaths.
   

3. The new front line of the coronavirus epidemic is in rural America: a deadly ‘checkerboard’
   A recent article in the Washington Post by Reis Thebault and Abigail Hauslohner highlights a theme that I have stressed over the last week. Two months ago, many were convinced that COVID-19 was a crisis for big coastal cities in densely populated places like Los Angeles and New York. In the whack-a-mole story of this epidemic, a very different picture emerges as May comes to a close with the U.S. poised to pass 100,000 deaths and 2 million cases in the next few days. We are reminded that viral outbreaks spread like water from area to area, seeking a favorable ecology for transmission even as barriers to transmission succeed in the places initially attacked. The top graphic, taken from the Washington Post article shows the whack-a-mole effect. Until the middle of April, the majority of cases were in the 14 counties that were initially impacted, while the fraction of new cases over the last 6 weeks are in the rest of the country. As of this week, there are now twice as many cases elsewhere than in New York, Washington, Detroit and New Orleans. The bottom graphic from the same article shows that while death rates have dropped substantially in large cities and their suburbs, those rates are largely flat in small cities, towns and rural counties. The shift to small towns and rural communities is fueled by a variety of factors very few thought of in the epidemic’s earlier days. Of the 25 rural counties with the highest per capita case rates, 20 have a meatpacking plant or prison where the virus took hold and spread rapidly, then jumped to the surrounding community when workers took it home. Like all other health scourges, the coronavirus has capitalized on the spatial patterning of poverty, racism and inequality to find cracks in our epidemic control measures. Take for example Texas County, Oklahoma, where predominantly Hispanic workers from a local pork processing plant started filling the local hospital with symptoms. Two weeks ago, state health officials finally tested everybody at the plant and found 350 positive cases among the 1,600 asymptomatic plant workers, roughly 4-times more cases than had been known.
   What it means: Lack of adequate health care resources, language and cultural barriers, poverty, lack of testing, low adherence to social distancing measures have all conspired to create the conditions for the coronavirus epidemic to seep into high-severity pockets across rural America. At the same time, there are still 180 counties across 25 states that report no positive cases. This has made middle-America look like a checkerboard of risk.