Tag Growth Factors

Daily COVID-19 Briefing: Saturday

Thomas A. Glass Leave a comment

Top news, reports and insights for today:

  1. Daily headline summaries for Saturday:
  • Nineteen states this week set new highs for coronavirus infections recorded in a single day (Axios)
  • White House has blocked CDC Director Redfield and other officials from testifying on school reopenings (USA Today)
  • FDA approves pooled testing for coronavirus, promising to increase testing efficiency and reduce backlogs (Axios)
  • 85 children under age 2 tested positive for coronavirus in 1 Texas county (NBC News)
  • Studies in both the U.S. and U.K. show evidence that several candidate vaccines show early signs in Phase II studies showing they produce an immune response. Still, the highest hurdle remains as drug makers move to initiate Phase 3 trials in coming weeks (BBC News)
  1. New daily high case records set Thursday and Friday. Deaths rising. Increasing transmission seen in all but 5 states
    New record high daily case totals were established on Thursday and Friday, with more than 145,000 cases reported in two days (Figure A). This brings total U.S. cases to over 3.5 million. A half million cases were added in just 8 days, faster than any previous period (Figure B). At the state level, while the nation has been watching a Arizona and Florida, community transmission this week is increasing across the board. Figure C shows one week growth factors (ratio of cases in last 7 days to the previous week) by state. All but 5 (46 of 51) states are increasing. Unlike last week, cases are rising again in the Northeast, where new cases rose by 20% or more in Washington DC (+21%), Maryland (+51%), New Hampshire (+30%), and Rhode Island (+50%). All states in the South saw cases rise by 10% or more, lead by Alabama (+43%) and Virginia (+46%). Transmission increased in all Midwest states except South Dakota. The largest 1-week rise was in the West, lead by Colorado (+96%), Alaska (+58%), Montana (+66%) and Nevada (+42%). Thankfully, new cases finally went down in Arizona by 2%. The trend toward rising deaths continued as 936 deaths were reported Friday (Figure D). Still, the number of deaths remains far lower than the peak period in April and May despite twice the number of cases.
    What does it mean: Instead of summer suppression, we see summer surge. Deaths, thankfully remain lower than cases would suggest. This tells us that we are capturing a larger percentage of the true cases in our testing. Instead of isolated state hot spots, transmission is intensifying more broadly across all states and regions than at any time in the past.
Figure A
Figure B
Figure C
Figure D
  1. The summer story: The rest of the nation catches up with New York and New Jersey
    Over the last few months, I have been repeatedly checking the overall rates of confirmed COVID-19 infections per 100,000 population by state to see how the epidemic’s distribution has shifted. Disease detectives look most closely at rates (rather than raw numbers) when comparing different places. The graphs below show state rates at 4 different time points. Three short months ago (Graph A), New York and New Jersey were “off the charts” at 1,143 and 848 cases per 100K. No other state was above 500, the national average was 202 and it seemed that New York would never be exceeded. By memorial day (Graph 2), New Jersey doubled and New York neared 2,000, while the national average rose to 541. Rates were still 4 times higher in the Northeast compared to the West. One month ago, it was clear other states were catching up (Graph C). New York and New Jersey saw new cases finally subside, just as the surge erupted in the Midwest and South. The Northeast was still 3-fold higher than the West, but there were now 8 other states over 1,000 and two were outside the Northeast (Illinois and Louisiana). With this context in mind, the picture has changed dramatically over the last month (Graph D). Infection rates in the Northeast are now only 2/3 higher than the west. Arizona had just 58 confirmed COVID-19 cases per 100,000 on April 16. Yesterday, they had all but matched New Jersey at 1,903. The average infection rates in the South were 1/10th of those in the Northeast in April and will soon be about the same (1,165 vs. 1,513).
    What does it mean? Three months ago, many were convinced the epidemic was a crisis of the greater New York region. We waited for the summer to deflate the epidemic so we could get back to normal. That has not been the story. Instead, the success of the Northeast in curtailing the epidemic and flattening the curve has been more than matched by the inability and unwillingness of other states to halt transmission. While it was unthinkable 3 months ago, the rest of the nation has rapidly caught up. There is no evidence that the new hot spot states have learned from the successes of New York and New Jersey.
  • Graph B: May 31
  • Graph A: April 16
  • Graph C: June 16
  • Graph D: July 17
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Daily COVID-19 Briefing: Thursday

Thomas A. Glass Leave a comment

Top news, reports and insights for today:

  1. Daily deadline summaries for Thursday:
  • U.S. daily coronavirus case count crosses 50,000 setting a single day record as some states reverse course on reopening and hospitals were hit by a surge of patients (Wall Street Journal)
  • Experts suggest a plastic face shield, if properly fitted and warn, has advantages over cloth masks for use by the public and should be used more widely (JAMA)
  • The American Academy of Pediatrics issues guidance in favor of reopening schools in the fall. Guidance stresses that children do not appear to be driving the epidemic, are less likely to be infected than other respiratory illnesses and that in-person education is better than online teaching (American Academy of Pediatrics)
  • Italian researchers studied nearly all residents of one town before and after lock-down. Main results were that 40% of those infected never developed symptoms. None of the children in the study became infected. Those with and without symptoms did not differ on viral load. Half of those infected had cleared the virus 2 weeks later. The lockdown was very effective at halting transmission (Ars Technica)
  1. U.S. enters new dangerous phase, smashing previous daily high record new cases, decline in deaths stops
     I have said for months that a return of widespread community transmission with Rt>1 was inevitable by July 1 given that states reopened recklessly. However, the ferocity of the resurgence in cases has caught me and many experts off guard. I apologize for showing you 4 different graphs for today’s briefing, but the story they tell is chilling. The first graph is our usual epidemic curve of new reported lab-confirmed COVID-19 cases by day. A record high 52,554 new cases were reported yesterday, the first day with more than 45,000 cases and 16,000 more than the peak set in late April. For the first time since the epidemic, the U.S. reported more than 300,000 new cases in one week. In just 7 days, the U.S. reported more infections than were accumulated from the start of the epidemic until April 4. The U.S. now has more than 2.6 million reported cases, 26% of all cases on the planet and twice as many as Brazil, still ranked second.
     Deaths flatten: The second graph shows daily deaths. This remains a mystery. The 7-day moving average has been falling since Memorial day. In the last few days, that decline looks to have stopped. Yesterday, Arizona, a state on the front edge of the case surge, reported a spike in deaths with 88, a rise of 100% from the previous day. Arizona, Iowa, Oklahoma, South Dakota, Kentucky, Texas, Virginia, and Rhode Island, all have seen deaths rise by 20% or more in the last week. I believe we will see deaths rising sharply in the states where cases first started surging.
     Cases increased last week in all but 3 U.S. states: The next graph shows the weekly growth factors by state. Nationally, the U.S. had it’s first week with 300,000 new cases. Astonishingly, the growth factors for last week compared to the week before are >1 in all U.S. states except Rhode Island, New Jersey and the nation’s capital. Weekly cases rose by 50% or more in Alaska, Idaho, Montana, Kansas, Florida, Georgia, Louisiana, Mississippi, and Tennessee.
     13 States reported more than 15 new daily cases per 100,000 population last week. The last graph shows the rate of new daily cases last week. Arizona continues to be the most extreme, now reporting more than 47 new cases per 100,000 every day. That is the highest rate we have seen anywhere at any point. In the South, 9 of 13 states are above this mark, which is 3-times higher than the 5 cases per day per 100,000 benchmark for low transmission. Florida, Georgia, Louisiana, Mississippi, South Carolina and Texas are all over 20. Only 1 Northeastern state is over 5.
     The bottom line: The U.S. epidemic is out of control with no end in sight.
  1. U.S. capturing about 2/3 of the true number of COVID-19 deaths
    We already know that deaths from COVID-19 are undercounted for a variety of reasons. We also know that an accurate tally of the death toll is very important. As I have emphasized here before, our best tool for understanding the true mortality picture is to examine deaths from all causes using the best available data and comparing the numbers from 2020 to previous yearly averages. This allows us to capture excess deaths above what is expected in a “normal” month taking seasonal variation into account. It’s not perfect, but it is closer to the truth than our current count. Previous studies using similar methods have found that the ascertainment rate (% of true COVID-19 deaths that are counted) is about 50%. Over time, we hope that will improve. Yesterday, a new study was published by my former colleague and friend demographer Steven Woolf and in JAMA that adds important new information. They used a state-of-the art model to estimate total excess deaths that are probably COVID-19 related. This includes cases where COVID-19 is mentioned on the death certificate, but also more indirect causes. They specifically examine rises in deaths above temporal trends in past years that may reflect those who died because they didn’t seek care for existing problems, had exacerbations of chronic diseases, or may have succumbed to secondary distress (e.g., drug overdoses). Their main finding is that in the 8-week period from March 1 through April 25, about 65% of the excess deaths likely related to COVID-19 were actually counted as such. That means, the remaining 35% of deaths were not counted. The 5 states with the most COVID-19 deaths experienced large proportional increases in deaths from non-respiratory underlying causes including diabetes (96% increase), heart disease (89%), Alzheimer disease (64%) and cerebrovascular disease (35%). New York City, which reported the highest number of COVID-19 deaths, saw a 398% rise in the number of heart disease deaths. The graph below, taken from the paper, shows that in the 5 hardest hit states, a significant jump in deaths can be seen in March and April of this year for heart disease, diabetes. Smaller but still substantial increases happened for stroke and Alzheimer disease as well. Diabetes deaths rose from 40% to more than doubling depending on the state.
    The bottom line: The true number of COVID-19 deaths is probably about 1/3 higher than our current numbers suggest. If true, the U.S. now has an estimated 177,000 deaths rather than the official count of 131,000. Significant numbers of people are dying of non-respiratory manifestations of SARS-CoV-2 and are not being counted. States vary widely in the accuracy of their counts.
From Woolf et al, JAMA Published online July 1, 2020. doi:10.1001/jama.2020.11787

Daily COVID-19 Briefing: Friday

Thomas A. Glass Leave a comment

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.
  • Graph 1: Epidemic curve for Florida
  • Graph 2: Miami-Dade Co.
  • Graph 3: Nassau Co.
  • Graph 4: Leon Co.
  • Graph 5: Polk Co.
  • Graph 6: Testing
  • Graph 7: R(t) for Florida
  • Screen grab from rt.live.com on 6/26/20: https://rt.live/us/FL