Friday COVID-19 Briefing

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Top news, reports and insights for today:

1. Daily headline summaries for Friday:

• Data shows signs the epicenter of the coronavirus epidemic may be shifting to the Midwest on Thursday while Sunbelt states saw new infections begin to decline while cases rise in Ohio, Kentucky, Tennessee, Missouri, Kansas and Nebraska (Reuters)
• The Trump administration abruptly required hospitals to stop reporting COVID-19 data to CDC and use a new reporting system set up by a contractor. That system remains plagued with delays and inaccuracies. Hearings and investigations now underway (NPR)
• Scammers are making millions selling bogus dietary supplements to treat and prevent COVID-19. NPR found over 100 supplements listed for sale on Amazon that make unsubstantiated and potentially illegal claims that they fight viruses. These include products sold by a company recently sued by the Department of Justice over fraud allegations related to COVID-19 (NPR)
• African-Americans are known to suffer disproportionately from COVID-19 in many ways. A recent study in 5 hospitals in Baltimore/Washington from March to May shows that Latinos had test positivity rates 5-times higher than whites and double that of blacks. The Latino community needs greater attention (JAMA)

2. New daily cases remain flat but “bouncy”, 3 states pass New York for cumulative rates of COVID-19; new case growth pops up in Northeast and Mid-west
    On Tuesday I noted that new daily cases seemed to have flattened. That trend has largely continued this week, although numbers have fluctuated substantially (See Figure A). The U.S. added 442,658 new cases last week, a rise of 11% in total. Over the last 3 days, new record high daily cases were set in Hawaii (124), Missouri (2,084) and Mississippi (1,775). Figure B shows the 1-week growth factors for each state indicating the ratio of new cases this week to the week before. They show something important and unexpected. Our attention has been on the Sunbelt states where the epidemic has been surging. For the first time in weeks, we see bigger hikes in new cases in the Northeast and Mid-west while cases declined in 6 Southern states. Connecticut added a startling 1,438 cases, tripling the previous week’s total. New Jersey also saw new cases more than double, prompting Governor Murphy to update quarantine advisories issued for travelers from 3 new states, Puerto Rico and Washington DC. CBS News in New York is reporting that New Jersey hospitals are bracing for a surge of new cases. New cases also rose by 20% or more in Massachussetts (+22%), Maryland (+23%), New Hampshire (+26%), and Rhode Island (+84). In the Midwest, Missouri (+53%) and Oklahoma (+72%) saw the largest spikes. Michigan (+20%), Minnesota (+14%), Nebraska (+16%) and South Dakota (+21%) all saw new cases rising. In the West, big increases were seen in small states as new cases surged in Alaska (+37%), Hawaii (+280%) and Montana (+33%).
    Figure C updates us on the overall rates of COVID-19 cases at least for that subset captured in our testing. A couple of months ago, it looked like no state could possibly catch up to New York. Now three states have a higher overall rate of cases per 100,000: Louisiana now has the highest (2,463), followed by Arizona (2,347) and Florida (2,148). As a region, the South now nearly matches the Northeast at 1,560 per 100,000 (compared to 1,582). In the South, only Kentucky and West Virginia have kept rates below 1,000 per 100,000, a feat also matched by 7 of 13 Western states and 10 of 13 Midwest states.
    The bottom line: While the flattening of new cases is good news, the whack-a-mole continues as falling new cases are offset by brush fires of transmission intensity breaking out in previous hot spots. Key factors appear to be lax social distancing associated with vacation travel and people staying indoors to avoid the heat.

Figure A

Figure B

Figure C

3. U.S. COVID-19 deaths pass 140,000; daily totals continue to rise
    On Thursday, 1,231 Americans were reported dead from the SARS-CoV-2 virus. This caps a four-day run of more than 1,000 daily deaths and continues a trend of rising mortality that started around the 4th of July (see Figure D). The U.S. reported over 7,500 deaths last week, a cumulative rise of 6%, which is double the 3% rise seen the week prior to July 26. In all major data tracking sites, the U.S. has now exceeded 140,000 deaths. The U.S. remains the nation with the largest death total with more than twice that of the next two highest countries (Brazil and the UK) combined. Figure E shows the states that rose the most last week compared to the week before. As always, states with fewer than 25 weekly deaths are shown with a patterned bar since the ratios of two small numbers tend to be unstable. As expected, the most consistent region is the South, where despite an apparent peak in cases, deaths continue to surge. Weekly deaths rose by 20% or more in Arkansas (+24%), Florida (+27%), Georgia (+21%), Kentucky (+38%), Mississippi (+37%), North Carolina (+28%), South Carolina (+27%), Texas (+183%) and Virginia (+175%). Deaths spiked particularly in Kansas (+456%) and Delaware (+500%) although the absolute numbers are smaller. Deaths were on the rise significantly in Ohio (+22%) and Oklahoma (+51%) but fell in Illinois, Michigan, Missouri, Minnesota and Wisconsin. In the West, deaths rose in California (+29%), Idaho (+63%), Oregon (+79% and Washington (+49%) while holding steady in Arizona for the first time in several weeks.
    The bottom line: Consistent with the lag between infections, testing, and mortality, the summer surge in cases is now resulting in a rise of COVID-19 deaths. Importantly, we are still significantly below the peak of 2500+ deaths a day seen in April in May despite vastly more cases. This is because of the doubling of testing. While we were capturing approximately 10% of the total number of actual infections occurring in the population in May, we have now roughly doubled the number of daily tests from 40,000 a day to around 80,000 (see Tuesday’s blog). This expansion of testing as lowered the TPR from 10% to 8% allowing us to capture closer to 20+% of true infections. All this suggests that the overall mortality rate is likely fairly stable. The reality is that we had far more cases of active infection occurring in April and May than we knew – like 10-times more. The best performing model by Youyang Gu and colleagues, suggests that new infections in the U.S. peaked around July 16 and that deaths are projected to peak at just over 1,100 a day around August 13. We will see.

Figure D

Figure E

4. Two timely and important studies released about the role of schools: reopening this fall carries unavoidable risks
    Here we are in the middle of the strangest summer of our lives. Now is the time people are thinking about the Fall and what it will mean for schools. Should they reopen? Should they stay closed? Is online training even worth it? Why not let the kids go back to school given that they don’t seem to be getting very sick. I want to make you aware of two important and timely studies that have come out that bear on this issue and should be kept in mind as we lurch toward the Fall.
    The first study was published July 29 in JAMA by Katherine Auger and colleagues from Cincinnati. They looked at whether there was a relationship between the timing of state-wide school closures and COVID-19 infection and death rates across all 50 states in the period from March 9 to May 7. The analysis they did was a bit complicated but their approach was very solid. They found that state-wide school closures were associated with a 62% reduction in weekly cases and a 58% lower weekly rate of deaths. This doesn’t prove causation, but it suggests that despite the fact that school-age children are not the ones at highest risk of sickness and death, shutting down schools may have a substantial impact on the overall risk in the community. Children can be conveyors of disease directly by transmitting to more at risk groups. In addition, through the patterns of interaction and mixing that school requires, transmission intensity can increase among all age groups because of the increase in overall interactions in and out of school.
    The second relevant study came out in Eurosurveillance on July 21 and was done by researchers affiliated with the Jerusalem District Health Office in Israel. (Note: I apologize if either of these links are behind a firewall. I can’t tell. Let me know if they are and I can post the article). This study looked at what happened when schools were reopened on May 17 after being closed across the country in Mid-March. Considerable planning went in to the reopening plan; daily health reports, hygiene procedures, facemarks, social distancing and minimal interactions were all required and put into place. Disease detectives were put on stand-bye to monitor the situation. Despite these efforts, ten days later, the first significant outbreak occurred in an Israeli High School. After an official outbreak declaration, mass testing and contact tracing was undertaken. Overall, 153 students and 25 staff members were confirmed to be COVID-19 positive, yielding an attack rate of 13% in students and 17% in staff. This outbreak appears to have started from 2 initial index cases not related to each other that sparked the larger outbreak.
    What do these studies mean? In thinking about what we should do as a nation, these studies suggest two tentative conclusions, recognizing that we are only looking at 2 imperfect studies when we would like to have 200. The first is that open schools can increase the risk for entire communities, not just the students in those schools. We have good evidence that school closures were a vital tool for controlling the spread of influenza in 1918-1919. Cities that reopened schools suffered a worse fate than those that closed schools early and kept them closed. But coronavirus is not influenza and we are tempted by the fact that children seem to be at lower risk. But the JAMA study tells us that what happens in schools, doesn’t stay in schools. Returning to classrooms invites greater chance of community-wide transmission, leading potentially to higher rates of hospitalization and death. The second study warns us that even with the right planning and the best available epidemic control measures in place, outbreaks can happen in school settings and happen fast. Testing, monitoring and social distancing do matter and they do help, but the school environment is to some extent an unavoidable petri dish for infectious disease transmission.

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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

Daily COVID-19 Briefing: Monday

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Top news, reports and insights for today:

1. Daily headline summaries for Monday:

• Florida breaks state, and U.S. all-time record for highest daily cases with 15,300. The state-wide total including non-residents is 269,811 (Orlando Sentinel, see graph below)
• At least 26 members of Mississippi’s legislature have tested positive for the COVID-19 after weeks of working at the Capital, often absent face masks and social distancing (NPR)
• MIT has developed a robot that uses UV light to kill coronavirus in stores and warehouses (Yahoo/Finance)
• White House seeks to discredit Dr. Fauci as cases surge (The Guardian)

2. U.S. COVID-19 daily cases doubling previous peak daily cases. 13 States adding 20 or more new daily cases per 100,000
   The U.S. crossed the 3 million case threshold this weekend, adding more than 60,000 new cases in three of the last 4 days. We continue to set new daily records at an alarming pace. The most recent daily record of 66,660 came on July 10. That number is almost double the number of daily high cases set during the first peak on April 24. The middle graph below shows the number of days it took to reach each 500,000 new cumulative cases. We went from 2.5 to 3 million cases in a record 10 days, a week faster than the previous fastest interval and half the time it took to add 500,000 cases any previous period. The bottom graph shows what is happening in states. It shows new daily cases per 100,000 population. In the West, Midwest and South, the only 2 state with its epidemic under control (<5 new daily cases per 100K) were Wyoming and Hawaii. Thirteen states added more than 20 (4-times the benchmark) daily cases per 100,000; four in the West (Arizona, California, Idaho and Nevada) and 9 in the South (Alabama, Arkansas, Florida, Georgia, Louisiana, Mississippi, Tennessee, South Carolina and Texas). The Northeast, which was the sole focus of national attention for most of this spring, remained quiet with low growth in cases in all states except Delaware. Arizona (+50), Florida (+43), and Louisiana (+42) remain “off the charts”.
   The Bottom Line: Uncontrolled community transmission is widespread throughout the South despite very hot and humid conditions. The South and West are losing ground as the epidemic surges across many states. More than a dozen states slow or reverse reopening as we enter a period of uncertainty and stagnation. There is no national leadership visible on the horizon.

3. We were waiting to see if deaths would start rising. They just did
   The post-reopening surge in cases took longer to arrive than we thought. But it came. As cases surged beyond the previous peak, we waited to see what would happen with hospitalizations. It took a bit longer than we thought, but the surge in sick patients came. Then we waited to see the numbers rise for deaths. For a moment, it seemed that something had changed, that the gap between cases and deaths was peculiarly large. This week, as the graphs below show, that has now shifted. Eric Topol called it on Twitter on July 13. In the last week, the 7-day moving average for daily reported COVID-19 deaths inflected upward (top graph). According to CNN, counties in Texas are running out of morgue space and asking FEMA for refrigerated trucks to hold the dead. The lower graph shows the story at the state level. Compared to 2 weeks ago, deaths last week rose in all Western states, all Midwest states except Minnesota and all Southern states except Virginia. While numbers were two small for stable estimates in several states (patterned bars), the trend in the south especially is clear where weekly deaths rose from a low of 19% in Alabama to more than doubling (208%) in Texas. Weekly deaths rose by 50% or more in Arizona, Nevada, Washington, Iowa, Florida, Georgia, Mississippi and Tennessee.
   What it means: The much-anticipated rise in daily deaths has begun and its not limited to a few high-profile states. Deaths are rising fast in 8 states. This trend should continue and accelerate. If hospital capacity is dramatically exceeded, deaths may spiral.