Quantitative analyses on the global coronavirus pandemic

Month: August 2020

COVID-19 Cases and Deaths are Falling in the USA

COVID-19 cases that began to surge in the USA in June, peaked in July, and have continued to ease leading to lower hospitalizations and deaths (see figure below).  While infections continue to erupt in certain parts of the USA, the largest outbreaks in California, Texas, Florida, Georgia, and Arizona have all topped out leading to improving trends for the USA as a whole.  The 7-day rolling average of daily cases has fallen from a high near 70,000 in early August to near 40,000 recently.  The US can continue on this virtuous path if the President stops waffling about masks and tests. 

It is far too early to declare victory because part of the decline in newly confirmed cases is due to a significant reduction in testing (see figure below).  The 7-day rolling average of daily tests peaked 4 weeks ago near 810,000 and has since declined 16% to near 680,000.  It is unclear whether this is being driven by a President that continues to be ambivalent about doing too much testing and/or a CDC that has recently eased its guidance on testing.  Delays in getting test results continue to plague the country.  While the positivity rate has improved from a high near 9% to 6%, it is still higher than the near 4% low reached in early June.  Moreover, since deaths lag daily new cases by 3 to 4 weeks, death counts have just recently topped out near 1,100 per day in early August.  Due to the high number of cases in the pipeline, 21,000 more Americans will almost certainly die over the next 4 weeks

This summer outbreak differs from the spring outbreak in two very important ways.  One is that the case fatality rate (CFR = deaths/cases) is much lower the second time around as more testing produced more asymptomatic and mildly symptomatic cases that do not require hospitalizations.  Thus the CFR for the country as a whole that was 5.2% for cases that resulted in deaths this past winter and spring (to 6/20/20) improved to 1.7% for deaths reported and projected for the period 6/20 to 9/22.  (Note that the CFR for an active pandemic will necessarily be only a rough estimate as many factors that affect the calculation are dynamic.) 

COVID-19US casesUS deathsUS CFRFL cases FL deathsFL CFR

 But one interesting question that it raises is whether any of the improvement in CFR is associated with any improvement in techniques or therapeutics used to treat COVID-19 patients.  Careful clinical studies will be required but the early answer seems to be no.  The US numbers are influenced by too many different factors but cases in Florida were less disparate and if we look at the number of hospitalizations compared with deaths it should show how successfully the hospitals were able to cure their patients.  The strong correlation between deaths and hospitalizations in FL is there even after we smooth out the strong weekly reporting cycle by comparing 7-day rolling averages.  The slope of the best fit straight line indicates that 32% of those going to hospitals for COVID-19 end up dying with the summer showing worse above-trend behavior.  (The percentage may be lower due to those who die outside of hospitals.)  We expect that wider availability of Remdesivir, steroids (dexamethasone), convalescent plasma and improved technique may eventually drive this number down.  Until then, vulnerable adults are still well-advised to avoid getting infected and hospitalized.  

 The other important difference is that so far the summer outbreak has avoided general lockdowns that were imposed by scores of countries and 43 US states in the spring and that came with enormous economic and social costs.  As a result of the resurgence, certain states have rolled back some of their more aggressive reopening steps taken in May by restricting select businesses such as bars, indoor dining, gyms, theatres, and other crowded venues.  Some states and numerous cities and counties have mandated mask-wearing in public and closed spaces.  In early August when few of these measures were working, some observers such as Osterholm and Kashkari and the NY Times Editorial Board called for a general lockdown to crush the pandemic.  Many observers now suggest that selective business closures combined with masking, social distancing, and diligent personal hygiene can help to flatten the curve without general lockdowns.  These cost-effective steps have been widely recommended by health organizations such as the WHO and CDC, and business organizations such as the German Institute of Labor Economics and Goldman Sachs Group.  Along with more accurate and timely testing, contact tracing, and selective quarantines, this low-cost approach might convince more businesses, institutions, and individuals that it is possible to reopen the economy safely.  However, this approach does require that the President stop his waffling and mandate mask-wearing and push for accurate and timely testing.  These should have never been politicized in the first place. 

The Villages in Florida Playing with COVID-19 Fire

The Villages is comprised of 17 special purpose Community Development Districts (CDD) for mostly retirees located in Sumter County, 45 miles northwest of Orlando, Florida.  It has consistently ranked as one of the fastest-growing areas in the USA with a current population estimated at 132,420.  The Villages dominate Sumter County which is considered part of The Villages Metropolitan Statistical Area (MSA).  It was largely spared the full force of the pandemic earlier this year, suffering only 363 cases and 17 deaths to July 1st.  Since then the number of cases has quadrupled to 1475 and the number of deaths has increased to 44.  

These growth rates are consistent with the state of Florida (FL) as a whole and slightly better per capita-wise than FL averages.  For example 2.69% of Floridians have contracted the virus while only 1.16% of Sumter County residents have.  Death count per million is 440 for FL and 330 for Sumter County.  It is this latter number that is worrisome because Sumter County has the oldest population in the USA: the median age is 63 yrs compared to 42 yrs for FL.  Just this age difference would make the case fatality rate (CFR=deaths/cases) 9 times higher than for Florida as a whole.  

That means that the CFR for Sumter County could be 5%-10%.  Given the number of cases that have gone to hospitalization – over 100 in the last 4 weeks – the death count could easily double over the next 4 weeks.  What is equally alarming is that Sumter County along with Marion County (which contains some portion of The Villages and is even more infected) residents and officials do not seem to care and carelessly flaunt masking and social distancing rules.  This makes it very likely the virus will continue to thrive in this NW region of central Florida and kill hundreds of seniors unnecessarily. 

Progression of Novel Coronavirus Infections to COVID-19 Deaths or Recoveries

How does someone who gets infected by the novel coronavirus progress to symptoms to diagnosis to hospital and then to death or recovery?  Much about how the virus attacks the human body remains a mystery but we can get some idea of how the typical case progresses by looking at the data that has been collected about the 18 million people that have been diagnosed with COVID-19 around the world. A significant portion of the world’s population, 100+ million, may have already been infected but never developed symptoms strong enough to warrant a diagnosis or treatment.  In the USA, this number may be as high as 20 million with 4.8 million diagnosed cases.  When a person is diagnosed, it may take 3-12 days before symptoms develop if they develop at all. When they do develop symptoms they may ask for a test which can take a few days to return with a result.  If positive they may be asked to quarantine in place at home for 14 days or be admitted to a hospital if the symptoms are severe enough.  The latter are treated in a hospital and if severe enough may progress to ICU and ventilator.  All along this journey some may recover and be discharged from the pool of active patients or they may die.  In the USA, 157 thousand have died while 2.4 million have recovered.  The census of recoveries is clearly undercounted since the number of known active cases in the USA is probably less than 1 million.  The more information we have about the structure of this pipeline the better we can model and forecast the progression of this disease and subsequent outbreaks. 

Once a case is identified we can begin to track its progress through the pipeline.  Single-day counts have a lot of noise and are dominated by the 7-day weekly cycle so we use 7-day rolling averages for all the Florida (FL) data analyzed below.  The figure below shows the correlation between hospitalizations and cases identified 13 days earlier.  Most patients are tested and sent home to quarantine and wait for test results.  If and when their symptoms worsen they are then hospitalized with an average lag time of 13 days.  As many as 25% (=150/600) of the early cases led to hospitalizations when testing was limited to the most severe cases (the cluster at the lower left).  As testing widened a decreasing percentage went to hospitalization in July (brown squares at the upper right) and fell below the average hospitalization rate of 4.7% represented by the best-fit slope.  

Most of the confirmed COVID-19 deaths occur in hospitals so we would expect deaths to correlate well with hospitalizations with a lag.  The best-fit lag is 6 days.  The best-fit slope indicates that 30% of all Floridians who require hospitalization will ultimately die.  This lag time and correlation have not changed much from spring to summer so there seems to be little improvement in therapeutics to improve outcomes.  In fact, July data shows that when the hospitalization rate got high and facilities and resources in counties such as Miami-Dade may have been stretched, death rates increased above trend.    

Deaths also correlate with cases.  Deaths lag case diagnosis by 19 days.  This is now much longer than the average of 9 days that were typically seen at the early stage of infection when tests were only given to those with serious symptoms or who were most likely infected.  With more testing, mild and asymptomatic cases are now identified and symptomatic cases are identified earlier before they need to go to hospitals.  The best-fit slope is the case fatality rate (CFR=deaths/cases) of 1.65%, much better than the roughly 6% (36/600 = cluster of data at the lower left above the trend line) seen at the beginning of the spring outbreak in FL.   

Given this strong correlation, we can then use the daily case counts to forecast the daily death counts that are sure to follow 19 days later.  If we had good age, gender, and comorbidities data we could refine our prediction for the number of patients that will need hospitalization 13 days after diagnosis and the death rate to follow 6 days later.  This is how we forecast the death count over the next 3 weeks for the USA and every state and county in the USA.

The case counts in Florida peaked on 7/17 and we would expect the death count to peak on 8/4.  A plot of new daily hospitalizations peaked on 7/30 and confirms the 8/4 date for the death count peak.     

This is good news for Florida and some of the other Sunbelt states such as Texas, California, and Arizona, but because these peak rates are very high there is little reason to celebrate yet.  In fact, given that some schools are reopening around the country this month at the urging of the President, we need to remain ever vigilant to avoid a fall resurgence of the spring and summer surges.  A fall resurgence could be more problematic as it will overlap with seasonal flu cases that usually begin in October. 

Are Children immune? – Age Dependence of COVID-19

Recent debates about how and when it might be safe to reopen schools for the coming academic year has put the spotlight on whether young adults get infected by the novel coronavirus and how many subsequently die of COVID-19?   We had noted early on in the pandemic that the case fatality rate (CFR=deaths/cases) for COVID-19 is highly skewed against older males.  The average 85+ years old male has >30% chance of dying once they are infected which is 1000 times worse than the <0.03% measured for 17- years old young females (see figure below).  While you hear about the occasional death of a teenager this is out of more than hundreds of thousands of teenagers who have been infected in the USA.  Of course, no one knows the long term damage that could be caused by this pernicious and poorly understood virus so young adults are still cautioned against behaving irresponsibly and tempting fate. 

Moreover, it is important to note that there is no evidence that young adults are not as susceptible to getting infected by the novel coronavirus and spreading the disease to older adults.  Early data seemed to show that a lower percentage of young adults got infected primarily because many of them got mild and asymptomatic cases and testing was limited by supply constraints to older and more vulnerable people.  In the early days, California and the rest of the USA behaved like Spain who seemed to show that kids and young adults were 100 times less likely to get infected than older adults.  After the USA expanded its testing capacity it became clear that young adults are just as likely to get infected.  The modestly lower infection rate that is measured for children is probably due to more asymptomatic young adults who don’t even bother to get tested.  However, scientific studies have shown that asymptomatic and pre-symptomatic infectees can still infect others. 

This why the June resurgence that started out with young adults partying on beaches and in bars was initially viewed optimistically by some governors as the young behaving irresponsibly with little impact on the rest of the country laser-focused on reopening the economy as soon as possible.  They downplayed the possibility that young adults will interact with older adults and inevitably spread it to them with disastrous consequences.  The following graph shows that the median age of new cases in Florida cases dropped from 47 years to 33 years in late June but has since then crept up above the median age of all people in Florida at 42.2 years.  Now Florida and many other states are announcing record-high death rates every day. 

This bodes ill for reopening schools too quickly when the infection in many parts of the country is still raging hot.  For those counties that have active virulent outbreaks such as Miami-Dade, the fifth-largest school system in the USA, the prudent thing to do for students, teachers, and parents is to reopen with virtual classrooms.  Children are not immune to COVID-19, nor are their teachers and parents.  Assuming the current outbreak tops out, do we really want to repeat the June resurgence in September?

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