Quantitative analyses on the global coronavirus pandemic

Author: William Ku Page 2 of 11

Florida’s COVID-19 Reporting Change Has Major Consequences

Our blog post about the major change in Florida’s COVID-19 reporting to the CDC has developed into a national story with partisan biases.  A couple of days ago the Miami-Herald “broke” a news story that claimed Florida changed its COVID-19 data recently – something that I had worked with a Sun-Sentinel reporter to break 18 days prior.  Now the story has been picked up by MSNBC, the Wall Street Journal, and other national news services.  However, none of these stories have addressed the full impact of Florida changing COVID-19 cases and deaths from date of reporting to actual date of occurrence.   

1.     While technically correct the new FL method is only used by a few other states to report their deaths to the CDC.  Contrary to the WSJ article’s claim, TX is not using the FL method – or if TX is using the new method they only have a 1-2 day lag in recording deaths. The figures below show how CDC currently stores and displays FL and TX death counts.  As you can see FL death counts show a peak two weeks ago and a drop-off to near zero today.  While TX death count curve shows a steep rise to near-record highs.  The FL data for the last 4 weeks will be continually adjusted upward over the next 4 weeks – delaying accurate information for 4 weeks. 

2.     Allowing some states to report one way and other states to report a different way is a basic Data Science 101 error by the CDC.  You add apples to oranges and you get a meaningless fruit salad.  The CDC according to the WSJ has conceded that some states report the FL way and others such as TX report the traditional way. 

3.     Some states like CA are using actual dates reporting but because they update their data daily, databases and modelers can choose to use either time series in their models.  For FL, though, the wrong death count could be in the system for 7 days (eg. JHU still shows 43,979 as the total cumulative death that was reached and reported 6 days ago for FL). 

4.     If the CDC adds all the states up for the USA total, it distorts the picture of USA death counts and confuses the public and data scientists trying to forecast and advise POTUS.  FL accounts for ~20% of the US total deaths.  The new FL method understates deaths for the last 3-4 weeks which are used by many models to predict future death trends causing them to understate their forecast and causing POTUS to react too late.

Just as good military intelligence is essential for the conduct of a successful war – accurate, timely, and consistent information is essential for successfully winning the war on SARS-CoV-2.  USA intelligence on the COVID-19 pandemic had been poor and has not improved much this year.  Inadequate testing resulting in very high positivity rates, too little genomic testing to understand Delta’s contagiousness and ferocity, dropping breakthrough tracking just when vaccine efficacy may be waning, and switching reporting methodology and allowing states to drop daily reporting in the middle of a pandemic are just a few examples that could cause the USA to lose the war.  The CDC should set the standards for consistent daily reporting and help all states to achieve this.  Viruses do not respect state boundaries and the CDC should not let states dictate what information states give them.  When COVID19 cases are doubling as quickly as every 3 days in some jurisdictions earlier this summer, cases can grow a thousandfold in a month and quickly swamp hospitals causing unnecessary deaths.  Timely, accurate, and consistent information is key to making the right decisions to mitigate the spread and win the war.  

Two mRNA Vaccines Are Not the Same

In the early days of the COVID-19 mRNA vaccine rollout in the USA this year, vaccines were in short supply and people had no choice as to which vaccine to try.  Both two-dose vaccines from Pfizer and Moderna seems to have similar 95% efficacy against serious disease.  Recent studies are revealing significant differences between the Pfizer and Moderna vaccines. 

Moderna has nearly 3X the amount of active ingredients in Pfizer: 100mg vs 30mg.  Moderna created 2.6X more antibodies in patients than Pfizer – with both being negatively correlated with patient age and both declining exponentially over time.  The higher amount of initial antibodies allow Moderna to be more effective and durable against the Delta variant than Pfizer: the risk of a breakthrough case was 2X lower.  While Pfizer is recommending a booster 6 months after the second shot, Moderna is recommending a booster before this winter.  Moderna’s proposed booster has only 50 mg of active ingredients, but it is still proving to be highly effective in phase 2 clinical trials to date.   

As for side effects, a greater percentage of participants who received the Moderna vaccine reported reactogenicity: 82% vs 69% for Pfizer.  Many people (13%) taking Pfizer reported side effects with both doses that sidelined them for 1-2 days.  A small percentage (0.6%) reported symptoms severe enough to require a visit to the ER, and only 0.25% required hospitalization.  It is believed that serious side effects with Moderna are also <1%

If you are immunocompromised and probably did not get full protection from two shots – get your booster shot now unless you had severe side effects.  If you’ve had severe side effects after the second Moderna wait a few weeks for the 50 mg Moderna booster.  Otherwise, on September 20th, all Americans should be eligible for a booster shot.  Get it to improve your protection against severe COVID-19 illness.  Always mask up and social distance for additional layers of protection.     

Some Governors Are Endangering Kids and Prolonging the Pandemic

Many governors in the USA are insisting that they cannot mandate vaccines or mask usage (as in GA), or are actively obstructing localities that try to do so (FL and TX).  Their claims rely on rampant misinformation that kids do not get COVID-19 – or that if they do, they get very mild cases and do not spread it easily, and rarely do they die from it.  This was questionable earlier this year with the initial variants and has become very misleading in the last two months as the extremely contagious and ferocious Delta variant has spread to constitute 99% of all cases in the USA. 

It is increasingly clear that the Delta can and does seriously infect school children, especially those under 12 who cannot be vaccinated yet.  Recent anecdotal stories from Florida have raised alarm and now strong statistical evidence has emerged that reopening schools without mitigation measures may be extremely dangerous to the health and futures of millions of kids while also encouraging the continued spread of the SARS-CoV-2 among all Americans. 

The table below from the Florida Department of Health (FL-DOH) weekly report captures the case trend by age group in FL over the period of 7/29 – 8/19, a period when many schools began to reopen in FL.  Columns 2-4 show the weekly case counts per 100,000 people for the weeks ending in 8/19, 8/12, and 8/5.  These are all extremely high although the over 65 group is below average due to their well-vaccinated status (85%).  The last two columns show the percent change from week to week.  As expected cases were still soaring in the period from 8/5 – 8/12 for every age group with as high as a 23% increase for the under 12 age group.  With schools reopening the virus has continued to surge for that age group – up by 22% for the week 8/12 – 8/19.  Middle school and high school student infections grew by 16%.  Interestingly, this wave appears to have peaked for everyone else.  This is somewhat expected since Delta surges are extremely contagious and fast-growing but they also tend to burn out rapidly after reaching a peak infection of about 100 per 100,000 per day.  At this stage, exponential growth stops as it did in the UK. 

What about the more dangerous outcome of Delta – how fatal is it?  The answer is slowly beginning to emerge as deaths take 2-4 weeks after infection to resolve and then several more weeks to be reported.  The following table from FL-DOH shows that the case fatality rate (CFR = deaths/cases) from COVID-19 is highly age-sensitive with a CFR about 100 times higher for the oldest group (>65 yrs old) than the younger groups (<30 yrs old) over the 19-month span of the pandemic in Florida (column 4).  However, the strong age dependence has evolved with the arrival of Delta.  Death counts and death rates have increased for all age groups but most significantly for the young.  For those age16-29 years old, the lagged CFR [=deaths/(cases from 3 weeks prior)] has increased from 0.03% to 0.17%, or nearly 6-fold.  For middle-aged adults 30-49 years old, it has more than doubled.  Overall CFR has remained near the life-to-date value of 1.4%.  We need to accumulate more data to ascertain how much deadlier the Delta is than the original and earlier variants.  As more people get vaccinated, we expect the CFR to improve.  Unvaccinated kids and young adults will remain big carriers of the disease unless schools adopt stronger mitigation measures and they will also serve to lower the overall CFR.

This early data makes it clear that Florida’s current wave could have peaked already if the governor had not poured more fuel -misleading information – on the fire and supplied more kindling – kids.  Moreover, kids are much more likely to die from Delta than from the original SARS-CoV-2.  Along with the uncertain but potentially debilitating effects of Long-COVID, this makes the Delta variant a major threat not only to the wellbeing of millions of children but also to every Floridian.  Prolonging the contagion increases the possibility of even more dangerous variants developing in millions of Americans that continue to be infected each week.  

COVID-19 Death Counts Reporting in FL Gets Less Transparent

The Florida Department of Health (FL-DOH) convinced the CDC to accept an alternative method for reporting COVID-19 cases and deaths this week that made things less transparent and more confusing at a critical junction of the pandemic.  The FL-DOH has done well in tracking actual and reported dates for deaths and cases but now it has switched the two up in its reporting to the CDC and the public.  The CDC appears to have accepted the new actual date reporting from FL without questions or explanations while most of the other 49 states are still sending the CDC “as reported date” information.  At the end of the day, the two data series wind up in the same place because cumulative cases and deaths must total to the same numbers at all times, but in the interim, there is the potential for misleading conclusions and bad policies. 

report dateCum casecalc diffpre wk casecum deathcalc diffpre wk deaths
12-Aug      2,877,214      151,764      151,415      40,766      1,071       286
5-Aug      2,725,450      134,751      134,506      39,695       616       175
29-Jul      2,590,699      110,724      110,477      39,079       409       108
22-Jul      2,479,975        73,166        73,199      38,670       282         78
15-Jul      2,406,809        45,449        45,604      38,388       231         59
8-Jul      2,361,360        23,747        23,697      38,157       172         32
1-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

Source: The bold numbers are those reported by the FL-DOH (http://ww11.doh.state.fl.us/comm/_partners/covid19_report_archive/covid19-data/)

By going to the actual date of occurrence reporting, data for the previous days are continually updated in a non-transparent way.  For example, the weekly FL-DOH report says the previous week’s deaths total 286 for the week ending August 12th (row 2, column 7 in table above).  But the week’s total deaths can also be calculated by subtracting the previous week’s cumulative total (39,695) from the current week’s cumulative total (40,766) to get 1,071 additional deaths reported for the week ending in August 12th.  The FL-DOH’s 286 is the actual number of people who died during that week AND were reported for that week, but this number needs to be continually adjusted as deaths sometimes take 2 months to verify in FL.  Eventually, the 286 will grow to 1,000 – 1,100 as late death reports drift in.  Similarly for FL-DOH to say the death count is 29 for August 12th (see last red dot on the graph below) may be technically correct but extremely misleading.  Deaths in FL have not gone down over the last two weeks but are in reality rising.  Every day this 29 number will grow but the growth may be concealed from public view.  Without proper explanation, the public will be misled to draw the wrong conclusion about how to slow or end the pandemic.  

The green curve would cause citizens and their government to become more alarmed and more vigilant about adopting sensible mitigation measures such as vaccines, masks, and social distancing.  Rising cases and hospitalizations should have already convinced citizens to do the right thing, but many still argue that until cases result in death they are not concerned.  The red curve might lead the casual observer to say things are not so bad and the government to say that further mitigations are not necessary.  Because pandemics grow exponentially fast, every day’s delay in action now can result in hundreds of dead Floridians. 

The problem is not confined to Florida because Florida has accounted for up to 20% of all US cases and still accounts for 20% of all US hospitalizations, it has an outsized effect on total US numbers.  The declining death count in FL would soften the rising death count seen in every other state in the union, causing the CDC and the US government to adopt bad public health policies.  It could lead other states such as Texas to say “if FL can do nothing and in fact still obstruct public health policies and do well maybe we can do the same thing”.  Texas COVID-19 cases, hospitalizations, and deaths are soaring.   Worse, they may adopt this Florida method of suppressing recent death counts and make themselves look better.   (Something funky happened in California this week but it seemed to have been a one-time restatement; their death counts have resumed rising.)  So we humbly request that the CDC reconsider this change and make Florida report deaths in the same way as every other state which would allow Americans and scientists access to the latest information in the most transparent and uniform fsdhion – otherwise, they must carefully explain why the entire data series needs to be downloaded every day and preserved to get the full picture 

COVID-19 Death Counts in the USA are Rising

President Biden and the CDC are hoping that the US COVID-19 death rate will be better for this current surge.  We are optimistic but have doubts.  The reasons are complex.  For one, the US continues to test much less thoroughly than other best-in-class countries such as the UK.  Thorough testing can identify and stop outbreaks before they become serious surges.  Moreover, identifying a higher number of asymptomatic and mild cases causes the measured case fatality rate (CFR = deaths/cases) to improve since the denominator increases and the ratio decreases. 

In the UK, the CFR appears to have improved significantly from 2.1% for the last wave in January to 0.3% for the current Delta surge.  Part of the reason for the improvement is that the majority of Brits were vaccinated in early 2021 and the death rate for the vaccinated is much lower than for the unvaccinated. 

The US hopes that a similar improvement will be observed.  Unfortunately, this appears to be unlikely for a number of reasons.

1.     The vaccination rate has been slower and lower in the US than in the UK.

2.     The positivity rate is much higher in the US (~9%) than in the UK where it has stayed below 4% throughout this last surge.

3.     The hospitalization rate in the US has already begun to soar. 

4.     The CFR has shown little improvement in the US this year. 

This last point is crucial since it is the best predictor of deaths to come from cases and hospitalizations already in the pipeline.  Lagged CFR is calculated by dividing the average deaths for the past 7 days by a weighted average of cases for the previous 2 – 4 weeks.  Deaths usually take up to 20 days to resolve from case identification.  Then some jurisdictions take up to 2 months additional to report those deaths.  The graph below shows that after the initial confusion in early 2020, CFR improved dramatically and then stabilized around 1.5% for most of 2021.  The fact that it hasn’t improved over the last 12 months is rather disappointing.  It suggests that testing, tracking, and treatment of COVID-19 cases in the US has not improved in that time. 

In recent weeks the CFR has actually deteriorated due to the very contagious and possibly more lethal Delta variant catching an unprepared American population.  We expect the CFR to improve through the rest of the year for an unfortunate reason: the increasing prevalence of breakthrough cases as the effectiveness of vaccines begins to wane.  Since breakthrough cases are more likely to be mild, only a fraction ~0.4% will result in deaths. As more and more people get vaccinated the CFR could drop to the 0.3% seen in the UK.  We can only hope this happens soon.  In the meantime get the vaccine if you haven’t yet, get the booster if your last shot was more than 6 months ago, and wear a mask and social distance as much as you can.  

COVID-19 Breakthrough Deaths are NOT Rare

The Delta variant of COVID-19 is a very contagious and virulent beast.  When better data is required to understand this rapidly evolving virus CDC tracking of COVID-19 cases has gotten worse.  For breakthrough cases due to the Delta variant, only the bare minimum is available.  Nevertheless, they do track total cumulative weekly hospitalizations and deaths in the US (with many caveats).  These data allow us to track incremental weekly data by subtracting the previous cumulative total from the current week’s cumulative total.  The trend is disturbing.

Week EndingCum BK HospitalCum BK Deaths7-day BK Hosp7-day BK Deaths7-day total Hospital7-day total Deaths% of hosp% of deaths
8/2  7,101  1,507    862     244  10,000    2,868   8.5%    8.5%
7/26  6,239  1,263    325     122    6,000    2,133   5.4%    5.7%
7/19  5,914  1,141    725       78    9,000    1,978   8.1%    3.9%
7/12  5,189  1,063      
7/19-8/2   1,912     444   25,000    6,979   7.6%    6.4%

Source: CDC (https://www.cdc.gov/vaccines/covid-19/health-departments/breakthrough-cases.html

Cumulative breakthrough hospitalizations (column 2 in Table above) and cumulative breakthrough deaths (column 3) in the table above are not very useful for analysis since they cover a long period of time when there were only a few fully vaccinated Americans and few Delta variant cases.  For the original and early variants, the mRNA vaccines were extremely effective against infections and near 95% effective against hospitalizations and deaths.  But the Delta variant is much more contagious and possibly more virulent.  Given this uncertainty, it is very important to track how the Delta variant behaves against vaccinated and unvaccinated Americans.  The most recent CDC data releases allow us to do this for the total US.  Columns 4 and 5 give us the 7-day totals for breakthrough hospitalizations and deaths, respectively.  These weekly totals were small and formed a small percentage of the total US numbers until 5 weeks ago when Delta cases started to soar in the US.  Overall breakthrough hospitalizations and deaths began to soar 4 weeks ago.  Over the 3-week period from 7/12 to 8/2, 6.4% of all deaths were breakthroughs (column 9) and an estimated 7.6% of all hospitalizations were breakthroughs (column 8)in the US.  This is happening at a time when about half the US (49.6% as of 8/2) was fully vaccinated and about 83% of all COVID-19 cases were Delta (as of 8/2).  If the mRNA vaccine is 90% effective against death and if the same number of unvaccinated and vaccinated Americans were exposed to SAR-CoV-2 Delta over this time period we would expect only 5% of all deaths to be breakthroughs.  The fact that it is now above 5% is quite troubling.  All else being equal – a necessary assumption in the absence of disaggregated data – 8.5% breakthrough deaths last week implies vaccine effectiveness of 83% against COVID-19 deaths. One factor that may make this ratio high is whether other mitigation factors were employed by the unvaccinated such as consistent mask-wearing or social distancing that lowered the infection rate for this group.  If masks turn out to offer better protection than the vaccine against Delta infection then more unmasked vaccinated people would get infected increasing breakthrough deaths.

Furthermore, the trend has been worsening.  As Delta cases approach 100% of all cases we expect these breakthrough deaths to increase. Of course, as more Americans get vaccinated, the percentage will increase even further toward 100%.  Currently increasing percentages might mean that the protectiveness of the full vaccine may be losing efficacy.  Both Pfizer and Moderna have sought authorization to administer booster shots but the FDA and the CDC are balking, possibly for political and messaging reasons.  This is absolutely unacceptable, particularly for the immunocompromised.  Israel has now authorized booster shots, and they track variants and breakthroughs better than the CDC.  The FDA should also give full approval for the vaccines instead of dragging its feet.  The CDC must begin to track breakthrough cases with more timeliness and more detailed segmentation.  They should view this outbreak as a new spike that requires thorough study and vigilance – testing, tracking, and applying the full arsenal of mitigation measures. Loosening the mask guidance on May 15th was dangerous.   Declaring victory against COVID-19 on July 4th was premature.  Calling this a pandemic of the unvaccinated is an oversimplification that leads to incorrect behavior.

Every American must mask up to reduce infections, vax up to save lives.  

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.   

COVID-19 Vaccines Work Great but Not for 10M Americans

There is no doubt that COVID-19 vaccines are working beautifully to drive down COVID-19 cases in the USA.  With 170M Americans or 51% having had at least one dose of the vaccine, cases in the USA have dropped to a 14-mo low of 5 per 100,000.  

However, there is a significant subpopulation of the USA, 10M or 3%, who may not be fully protected by the vaccines.  These include those (>6M) that are taking immunosuppressive drugs such as steroids used to treat organ transplants, cancers, or other medical conditions, and those who have compromised immune systems due to blood cancers and other diseases.  The original clinical trials for vaccines specifically excluded people who were taking immunosuppressive drugs to get their impressive 95% efficacy results.  Real-life studies were equally impressive since less than 3% of those sampled were immunocompromised.  More targeted real-life studies with immunocompromised patients show more disappointing results.  One JHU study of implant patients showed 46% had no antibodies after being fully vaccinated.  Another study from Israel showed that only 40% of all CLL cancer patients produced any antibodies after being fully vaccinated. 

There are no public databases that track the large scale response of the immunocompromised to vaccines but it is well known that a higher percentage of seniorsincreasing with age, are immunocompromised compared to younger adults.   We suspect that this is one of the reasons why even though senior compliance with vaccinations is very high (86% of everyone over 65yrs in the USA have had at least one dose) seniors continue to get infected and die from COVID-19.  In Florida (FL), the relative infection rate for seniors after falling to a low in April with the success of the Seniors First program is now close to what they were before mass vaccinations began in January, even though a much higher percentage of seniors (88%) have now been vaccinated than the general population (49%).  As more of the rest of the population gets vaccinated this relative contagiousness for seniors may rise further.  The optimistic view is that even for those who have no detectable levels of antibodies from B-cells, other parts of the body’s immune system such as T-cells have been trained after vaccination to fight SARS-CoV-2.  This would be unlikely if the trend we see for seniors in FL continues to worsen. 

What is the solution for this vulnerable part of the population who already have a much higher risk for hospitalization and death due to SARS-CoV-2 and who now seem to gain less from excellent vaccines?  Some people have proposed a third vaccine dose and have seen some success with it.  Others have proposed stopping immunosuppressants temporarily to allow the vaccine to do its work at generating antibodies.  Others have proposed using monoclonal antibodies such as REG-COV as prophylactic.  In the meantime the CDC’s new mask guidance does not apply to this vulnerable group who must continue to mask, social distance, and practice good hygiene until herd immunity is reached.  This means that we must redouble efforts to convince the fence sitters that getting the vaccine can save not just their own lives but the lives of friends and families who may be immunocompromised.

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