Quantitative analyses on the global coronavirus pandemic

Month: July 2021

COVID-19 Pandemic in Florida – Wave #5

Florida just reported 110k new COVID-19 cases for the past week – nearly equal to the all-time high we had predicted Florida (FL) will set by early August.  Florida continues to lead the USA higher in COVID-19 cases although Texas Governor Abbot is trying very hard to catch up by banning mask and vaccine mandates.  The Delta variant is so ferocious even CA and NY are seeing exponential growth as are nearly all 50 states in the USA.  But Florida continues to lead and may be a harbinger for what will happen to the USA in August.

There are several reasons why Florida is doing so well in this race to the bottom:

1.     FL has been very welcoming to all variants since Governor DeSantis removed all local COVID-19 mitigations on May 3.

2.     FL stopped daily reporting and possibly tracking of COVID-19 cases on June 3 – suggesting the pandemic is over.

3.     The Governor stopped responding to the COVID-19 crises even as cases began to rise 7 weeks ago and shifted his focus to his potential presidential run

This has left Florida wide open and blind to the COVID-19 Delta variant just as it began to take over the USA 2 months ago.  Reporters, scientists, and citizens clamored for more information but the Governor just seem to double down on his obstruction efforts.  His latest attempt to help the SARS-CoV-2 virus is to declare war on municipalities that want to restore mask mandates for schools.  In the meantime, he continues to turn a blind eye to the burgeoning crisis as exemplified by the weekly FL DOH (Department of Health) COVID-19 reports.  These weekly reports are totally inadequate and obscure the real picture of the fast-developing crisis in FL. 

As a small but indicative example of misleading the public, we look at the summary data from these weekly DOH reports.

report dateCum casecalc diffpre wk casecum deathcalc diffpre wk deaths
30-Jul       2,590,699       110,724       110,477       39,079        409        108
23-Jul       2,479,975         73,166         73,199       38,670        282          78
16-Jul       2,406,809         45,449         45,604       38,388        231          59
9-Jul       2,361,360         23,747         23,697       38,157        172          32
2-Jul       2,337,613         15,684         15,978       37,985        213          48
25-Jun       2,321,929         11,048         11,873       37,772        217          44
18-Jun       2,310,881         10,095         10,629       37,555        290          43
11-Jun       2,300,786         12,157       37,265          40

The weekly cumulative cases and per week cases data make sense (cols 2-4 in the table above).  Subtracting the current week’s cases from the previous week’s cases yield the increment for the week (roughly as the data is sometimes corrected/updated).  This number increased by a factor of 11.1 over the last 6 weeks and should scare everyone including the Governor.  Subtracting the cumulative death numbers each week from the prior also yields a rising trend over the last 3 weeks – lagging the rise in cases by 2-4 weeks as it always has.  But the last column seems to try to understate the problem.  For example DOH reports 108 deaths for the previous week when 409 was the more indicative number of deaths.  The reason for this difference (unexplained) is that the DOH 108 number reflects only deaths that occurred AND were reported for that week.  Since deaths lag by as many as 10 weeks in FL, the initial report of this number is always too small and not very meaningful until the full number emerges 10 weeks later which may be 400-500.  The DOH used to explain this more clearly in their daily reporting but not in these truncated and censored weekly reports.  Thus a misleading impression is left to the reporters and other readers of this report.  This faux pas has potentially significant consequences because many doctors and hospitals are finally seeing a resurgence of vaccinations over the last few days as people see rising deaths.  Reporting the true death count trend could have scared more fence-sitters into action sooner and end this pandemic sooner.

Our prognosis for FL is generally optimistic.  Because the Delta variant spreads so quickly and ferociously we expect the current surge to top out within two weeks.  The recent CDC recommendation to reinstate indoor masking will help.  The recent decision by POTUS, Disney, and other major companies to mandate vaccinations for their employees or be subjected to more testing is another step in the right direction.  More people scared into vaccinations buttress this optimistic view.  Countering this is our fear that the Governor by fighting schools, cruise liners, and other companies will provide more kindling for the FL COVID-19 fire and prolong this current surge – infecting hundreds of thousands of unvaccinated kids as FL schools start to reopen in 10 days.  Few of these kids will die but a large number may succumb to MIS-C and long COVID symptoms.  This is an extremely scary scenario that may play out if the Governor is successful in his efforts to stymie and confuse schools, parents, and other Floridians.  

COVID-19 Breakthrough Cases

The CDC in the USA continues to lag the best-in-class by requiring minimal genetic testing and tracking of COVID-19 cases compared to the UK or Israel.  This has led to slower identification and monitoring of COVID variants and how mutations can change their infectiousness and speed of spread.  To date, the CDC monitors only a limited sample of those who are fully vaccinated and have serious hospitalizations and deaths, dropping their initial request for states to monitor all “breakthrough” cases.  This data is only voluntary – passive reporting by the county health departments that decide to participate.  This has led to erroneous conclusions about the speed and seriousness of the current COVID-19 Delta surge.

One very bad statistic that is often quoted is this: As of July 12, of the more than 159 million fully vaccinated people in the USA only 5,189 were ever hospitalized or seriously ill, and only1,063 died from COVID-19.  The conclusion that only 0.0033% of those fully vaccinated will get seriously ill (or 0.0007% will die) from COVID-19 is totally misleading.  The reason is that only a small percentage of fully vaccinated folks have been exposed for a short amount of time to COVID-19 in general and the Delta variant in particular.  Until recently the community exposure was only a few percent.  The community spread is now approaching 10% again as testing increasingly returns positive results.  Another popular statement is that of the 170k Americans who have died from COVID this year only 1k were fully vaccinated.  Since this is less than 1% the conclusion is that the Delta surge is a pandemic of only the unvaccinated.  Again this is extremely misleading since the percent of all Americans fully vaccinated at the beginning of the year was very small and only approached 50% recently.

A more relevant and accurate way to assess breakthrough cases and deaths is to look at what has happened recently.  Using the CDC data for the week of 7/13-7/19, we note that 725 serious hospitalized cases and 78 deaths were reported as breakthroughs likely associated with COVID-19.  This should be compared with the 1,978 COVID deaths reported for the week.  Thus 4% (= 78/1978) of all deaths were breakthrough deaths.  These deaths resulted from the infected population over the previous 1-4 weeks which we estimate to be 110,000 in total (see Table below).  This makes the overall lagged case fatality rate, CFR, 1.8% (= 1978/110000).  Segmenting this data into fully vaccinated and unvaccinated folks we estimate that the CFR for fully vaccinated people is 0.3%, far better than the 2.4% experienced by the unvaccinated – a clear incentive to get vaccinated.  This segmentation data also suggests that 30k breakthrough infections occurred over the past 1-4 weeks.  Most of these were asymptomatic or mildly symptomatic so few noticed them and no health authorities tracked them. Anecdotal reports of breakthrough cases among athletes and select populations were dismissed since they were nearly all mild. 

vaccinated unvaccinated            total
Infected (lagged)30,00080,000110,000
Hospital admits7259,27510,000
Deaths (7/13-7/19)781,9001,978
CFR (lagged)0.3%2.4%1.8%

The mRNA vaccines are a remarkable scientific achievement, and much better than most vaccines, but they are not perfect and should not be oversold as such.  They reduce the chance of death by 91% but may only reduce the chance of infection by 40%.  Many fully vaccinated people can still get the virus but their immune systems will have been primed to reduce the probability of serious illnesses and deaths (but not eliminate it).  They are also less likely to carry a viral load large enough to transmit as effectively as unvaccinated people (although some say the Delta variant can increase viral loads a thousandfold), but there is little doubt that they can transmit the Delta variant.  In fact, that they lead to so many asymptomatic cases may be what is exacerbating the latest surge because of the prevalence of silent carriers.  Thus the CDC miscommunicated recommendation to discard indoor masking without verification should be corrected immediately.  Masking and/or social distancing should be recommended outdoors.  Vaccinations should be required for all Federal personnel and for entry into Federal facilities.  The best way to ensure compliance is to require vaccine passports.  Each day’s delay in implementation is costing thousands of Americans their lives and livelihood.   

COVID-19 Surge #5 in the USA – How Deadly?

Since the COVID-19 pandemic began a year and a half ago, there has always been a debate about how serious COVID-19 really is compared with common seasonal flu which kills tens of thousands each year.  Even after more than 600,000 Americans have died and as cases are soaring again the hope is that the death rate in the USA will not be as bad now that half of all Americans have been fully vaccinated. 

The coincident death rate (daily deaths divided by daily new cases) allows us to gauge how deadly a disease is but it has several shortcomings principally due to the fact that deaths lagged infections by a couple of weeks as hospitals and doctors struggle to save patients’ lives.  As reported death counts have an additional problem since some counties and states take several weeks to fully record and report the cause of death.  But since reported death rates are a convenient measure of disease severity and effectiveness of treatment we proposed to use a lagged case fatality rate (CFR = daily deaths divided by an infection curve weighted average of reported cases over the prior 4 weeks).  This adjusted CFR is still just an estimate (since both case and death counts are widely believed to be undercounted), but it allows us to forecast future death counts and to assess whether hospitals and doctors were swamped and patients were unnecessarily lost due to poor planning and shortage of supplies (as they were during the early stages of the pandemic when this ratio was higher than 10% in the USA), and whether treatment methods have improved or not. 

The CFR decreased significantly throughout 2020 even as the USA saw ever-larger surges in infections than the original one last spring.  One major reason is that testing improved so more cases including mildly symptomatic and asymptomatic cases were identified (and the CFR denominator was better measured).  Another is that more effective therapeutics and equipment became available and improved outcomes.  A third reason is that more seniors more vulnerable to COVID-19 took precautions not to get infected and the average age of hospitalized patients declined. 

Unfortunately, the progress seen in 2020 appears to have stalled in 2021 with CFR consistently near 1.8% even though the expectation is that the CFR should have improved further as vaccines became widely available.

  1. As vaccines were rolled out and made available primarily to frontline workers and seniors and those with comorbidities a large part of the vulnerable population should have been removed from the infection pool
  2. The average age of hospitalized patients continued to decline and the very strong CFR age effect should have driven the overall CFR down. 
  3. Improved therapeutics became more widely available.  While monoclonal antibodies were introduced last year, they were only available in limited quantities and that supply constraint should have eased in 2021.

Countering these positive trends were some negative ones:

  1. Many falsely believed that vaccinations protected them fully when the truth is that 95% protection is extremely good but not perfect.  The vaccine made an 80yrs old male 10-20 times less likely to die – about the same vulnerability as an unvaccinated 60yrs old female with 1.5% mortality.  More people letting down their guards may have contributed to keeping death rates high
  2. The new delta variant may be more lethal than the original.  It is known to be 2.3 times as contagious but most scientists believe that it is not any more lethal though no one really knows yet.  
  3. Easing or removal of many mitigation measures such as masking indoors in mid-May by the CDC which mostly impacted infection rates but may have increased viral loads transmitted as well 

The lack of an improvement in CFR is extremely disappointing and troublesome. In the UK where there were more mitigation measures in place to protect the unvaccinated and slow the spread, a significant portion of the infections were breakthrough cases with lower fatality rates helping to bring their overall CFR down.  With the removal of nearly all mitigation measures on 7/19/21 more of the UK infection pool will be the unvaccinated (plus vaccinated but immunocompromised) who will suffer higher fatality rates worsening overall CFR for the UK. 

In the USA, most states removed their mitigation measures this spring so the infection pool remained dominated by the unvaccinated and the CFR has remained high.  We are forecasting that 8,000 Americans will die over the next 4 weeks due to cases and hospitalizations already in the queue.  About 400 of these will be “breakthrough” deaths of fully vaccinated people.  We are forecasting a modest improvement in the USA CFR to 1.5% as masking is reintroduced.  Nevertheless, this fifth wave could be nearly as deadly as the previous two and kill tens of thousands of Americans unnecessarily.   

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