COVID-19 Odds

Quantitative analyses on the global coronavirus pandemic

COVID-19 Vaccine Distribution

COVID-19 continues to rage in the USA.  Over the next 4 weeks, 92k Americans will die due to cases and hospitalizations already in the queue.

Effective vaccines are available to slow the spread but distribution bottlenecks will likely delay herd immunity for many months.  In the meantime, the government has changed its guidance today to permit people 65+ and those with pre-existing conditions to get the vaccine now to reduce hospitalizations and the overall case fatality rate (CFR = deaths/cases).  This makes lots of sense. 

The mRNA vaccines level the playing field for older Americans.  It probably doesn’t reduce your chances of being infected by SARS-CoV-2, but if and when you do, you are more likely to be asymptomatic than without it.  That means you are more likely to survive the infection and your likelihood of dying from COVID-19 could decrease by roughly 95%.  This will reduce the extraordinary demand for hospital and health resources.  In fact, the CFR for all age groups could fall below 2%.  The strong caveat though is that SARS-CoV-2 and its variants will remain highly contagious until 80% of the population is vaccinated and herd immunity is achieved.

Demand for vaccines will outstrip supply for months so I would recommend that everyone who qualifies sign up for the vaccine sooner rather than later and avoid the Florida fiasco.  Moreover, releasing vaccines reserved for second doses means that inventory and distribution management will have to be extremely well-tuned to avoid missing second doses at the recommended times.   This is a well-studied problem in business supply chain and inventory management.  However, given the government’s track record to date, this will not be a slam-dunk.  

COVID-19 Third Wave in Florida

The third wave in Florida has been a little more challenging to forecast for fundamental and political reasons.  The third wave in Florida began with the opening of the school year in September and began to be manifest as increased cases in early October (see figure below). 

Hospitalizations began to rise two weeks later in late October (see figure below) and is now 3.66 times higher headed toward a new record. 

Increased deaths did not manifest itself until early November (refer back to the first figure above).  All this was predictable.  The less predictable part was the longer lag time or slower transmission of the virus from kids to older adults and then to grandparents who are most susceptible to fatal outcomes (see figure below). 

This last transfer did not take place in large numbers until December when the weather cooled, holiday gatherings occurred, and more activities moved indoors in Florida.  The mass inoculation of seniors 65+ that just began, and the rapid spread of the B.1.1.7 variant among the young should keep the median age of infectees younger in this third wave.  The net effect is to lower our expectation of the case fatality rate (CFR = cases/deaths) for this third wave to 1.6% from 2.0% for the second wave. 

The slower than expected rise in reported death counts is also somewhat artificial due to changes in the way Florida reports deaths due to COVID-19 that stretched the COVID-19 death reporting from 2 weeks for the first wave to 2-4 weeks for the second wave to 3-8 weeks for the third wave.  In the figure below, with deaths plotted against actual date, you can see that late November and December counts are still incomplete. 

Recently some deaths from September finally got reported in January.  We believe this is due to the FL Governor’s efforts to suppress reporting of deaths to make the pandemic seem less dangerous and justify his laissez-faire pandemic policies.  Hopefully when the new administration takes office, there will be less motivation to politicize scientific data for the pandemic.

Our current forecast for Florida is that cases will peak in late January, hospitalizations will peak in early February and death counts will peak in late February or early March.  With a combination of natural and acquired immunity (via vaccines), Florida could achieve herd immunity by summer and hopefully, avoid the fourth surge.

COVID-19 Variants in the UK and California

The UK and California (CA) are two very different places with different demographics but they are now closely tied as having two of the hottest COVID-19 outbreaks in the world.  The UK infection rate is currently at 0.73% of its total population over the last 2 weeks, second only to the USA at 0.86%, with CA leading at 1.48%. 

Both the UK and CA have instituted masking and stay-at-home orders with varying degrees of compliance and success so it is actually somewhat surprising that these two regions got so hard hit.  Masking compliance is 60% and 80% respectively in the UK and CA, and social distancing compliance is -30% and -40% respectively in the UK and CA.  This bodes ill for other states and countries that have looser mitigation measures.

The UK’s high infection rate is apparently 80% due to the new variant (B.1.1.7) in the UK that contains the N501Y mutation (also seen in a South Africa variant).  While this new variant does not cause more severe illness, it does spread more readily.  This new variant has now been detected in 18 countries including the USA.  This new variant has now been detected in Colorado but it has probably already spread in several other states.  We suspect that many of the new cases in CA are also due to the new variant, although the USA has done very little detailed genetic testing.  This deficiency coupled with the US government’s reluctance to enact a rigorous quarantine on UK travel to the USA leaves the USA highly vulnerable to this and future mutations of the SARS-Cov-2 virus and further spread of the disease. 

Optimizing COVID-19 Vaccine in Florida

The solution to the COVID-19 pandemic is at hand and it could substantially reduce deaths in Florida and the USA.  Both the Pfizer/BioNTech and Moderna vaccines have proven to be highly effective with generally mild side-effects.  One question is how to get them distributed most efficiently to minimize the future death count.  So far healthcare workers and nursing home residents have been the phase 1 recipients.  The CDC has recommended that frontline essential workers such as first responders, teachers, and grocery workers, and those 75 and over should be next in line.  In Florida Governor DeSantis has opted to make those 70 and older go to the front of this second group with the reasoning that they are much more vulnerable than 20-yrs old frontline workers.  I agree.

The overall risk of a population group should determine its order in the line for vaccines.  This means the risk of infection multiplied by the risk of dying after being infected.  Frontline workers could be ten times more likely to get infected since they interact with more people every day.  However, a 75-yrs old has a 200 times greater case fatality rate (CFR = fatality/cases) than a 25-yrs old, with a CFR of 9.0% versus 0.045%, respectively (see blue line in the figure below).  Thus a 75-yrs old would still be 20 times more at risk overall than a 25-yrs old frontline worker.

Moreover, the third wave that is currently raging in Florida which has thus far focused on the young student population is slowly transferring to older adults just as they did in the second wave this past summer (see figure below).  Large family gatherings for Thanksgiving and Christmas will accelerate this transfer and endanger the older more vulnerable population. 

We see this happening in an alarming way in Sumter County which overlaps most of The Villages.  Cases there have been increasing this month (see figure below) and yesterday 76 out of 112 newly confirmed cases were 65+ yrs old.  As noted above this group has a CFR of 9%. 

It could be a close race between the virus and the vaccine to see how many people in The Villages can be vaccinated and saved before they are infected and killed by the novel coronavirus.  To further optimize the effectiveness of the limited supply of vaccines we recommend that those who have acquired natural immunity go to the back of the line of this second group, and to make sure that as many as possible get their first shot of these two-shot vaccines before anyone gets their second shot. 

COVID-19 Third Wave in Florida

Most COVID-19 infections evolve from exposure to positive tests to hospitalizations to deaths. This well-defined pattern allows us to forecast the pipeline of confirmed cases to hospitalizations to deaths with a fair amount of accuracy. For example Thanksgiving travels and gatherings exposed a large portion of the population to the novel coronavirus causing positive test cases to rise now, 7-10 days afterward.  5-7 days after that the serious cases go to hospitals.  Another week later they result in a favorable discharge or death. 

When the community infection rate is high and the positivity measure (percent of tests returning positive) is high, only the serious cases get tested as in the early days of the pandemic this spring.  The average lag time from cases to deaths was only 5 days and the case fatality rate (CFR = deaths/cases) was also high (see figure above).  As testing availability improved and the positivity rate dropped and more asymptomatic and mildly symptomatic cases were identified, the lag time between cases and deaths increased to 15 days in the second wave.  The median lag time between case date and death date is reported is now close to 20 days as some states such as Florida take up to 4-6 weeks to actually report some deaths.  The longer the lag time the more difficult it is to model CFR and forecast the daily death rate.  The summer peak in cases led to some deaths that were reported in a timely fashion but a large number of cases took many weeks to resolve due to real extended times for treatment but also due to inefficiencies in the reporting process.  When we compare cases to the actual date of death, the relationship becomes much tighter (see figure below).  


The peak in daily death count actually followed the peak in case count by 15 days as did the rise and fall in this second wave.  The potential pitfall in this comparison is that deaths associated with the third wave is barely seen in the data as death counts bottomed at the beginning of November and are just beginning to rise (with the data for the last 5 weeks is still incomplete.  Some COVID deniers use this to say that the actual death count is still flat for the third wave – discounting the reality that it is flat because the count is incomplete.   

Comparing cases to the actual date of death also allows us to measure the CFR better.  During the first wave when little was known about COVID-19 and only severe cases were treated and lots of older patients died the CFR was near 4.5%.  During the second wave, younger and asymptomatic and mildly symptomatic cases were uncovered and the overall CFR dropped to near 2.0%.  The third wave involved even younger patients as schools reopened and the CFR is currently near 1.8%.  CFR also improved over time due to improvements in treatment plans (proning) and therapeutics (remdesivir, dexamethasone, and bamlanivimab).  Some of this improvement though could be reversed if hospitals and health resources in the USA become overwhelmed as they are in certain regions of the country.    

Thus far Florida has fared much better than the rest of the country in this third wave partly because of the Sunshine State’s milder weather and hospitals are only filled to half of the peak this past summer (see figure above).  But the increase in national travel for the holidays and a decrease in temperature in Florida could make the third wave worse than the first two in Florida. 

COVID-19 Vaccines and Infections

Currently, there is a very small number of Americans that have gained immunity from vaccination trials.  The FDA would probably approve the Pfizer vaccine by Dec 10th and the Moderna one by Dec. 20th.  By the end of this year, Pfizer and Moderna would have supplied enough vaccines to permit 20M Americans to have had their first shot.  By early next year, 19M Americans would have gained immunity from these two shot vaccines (taking into account the current estimated 95% effectiveness of these vaccines).  Many people estimate that enough vaccine would be available to vaccinate 25M-30M Americans every month in 2021 subject to logistical and psychological constraints (deep blue area in the graph below).  Thus vaccine “herd immunity threshold = 230M” could be reached in the USA by the end of summer. 

Herd immunity could actually be reached sooner than that.  Currently over 14M Americans have gained immunity from being infected by SARS-Cov-2.  The immunity may not be perfect but seems to be at least 99% effective for 6 months.  We project that by yearend 19.5M Americans will have tested positive for COVID-19 (red area).  Due to testing bottlenecks and scarcity, there is a hidden population of asymptomatic and mildly symptomatic cases that we estimate to be twice as big as confirmed cases for a total of 42M currently immune and 55M immune by yearend (red+green areas).  The total infected has been estimated to be as high as 8x by the CDC or 111M currently (red+green+purple areas).  We consider this to be highly unlikely for the USA as a whole even though antibody surveys for small sections of the USA have ranged from 2x to 20x the confirmed population.  If we adopt our best guess estimate for total immunity, we project that it will exceed the threshold for herd immunity by mid-year and stop exponential growth in the USA.     

The CDC has established guidelines for prioritizing vaccinations among different groups of people (healthcare workers, and residents of long-term care facilities). But they omitted to spell out who in those groups should be vaccinated first.  In fact, we believe that everyone should be tested for antibodies before they are vaccinated.  This would allow scientists to:

1.    optimize the distribution of an initially scarce vaccine to those who really need it,

2.    provide a baseline and periodic retests to measure how effectively these new vaccines are producing antibodies

3.   provide us with detailed measures of the true population of infectees.

Pre-Thanksgiving Dip in COVID-19 Cases

COVID-19 cases in the USA have shown a sharp decrease over the last 8 days causing the 7-day rolling average to peak and rollover (see figure below – red squares).  The question is whether this is measuring a real lasting phenomenon – perhaps attributable to local COVID-19 fires burning out, or to mitigation factors taking hold, or to some temporary factor associated with the Thanksgiving holiday.  The answer is probably a combination of all three that will ultimately be overwhelmed by an increase in Thanksgiving transmission.

Some COVID-19 outbreaks have burned so strongly and for so long (3-4 months) that local “herd immunity” may be acting as a retardant to the fire.  For example, in North Dakota (ND) 10.3% of the population has now been confirmed infected (see table below). 

StateConfirmedTestingEst. PopDeathsDeath perFatality
 Infection %Positive %Infection % million
ND          10.3                23          47          920            1,207            1.2
SD            9.0                24          44          943            1,066            1.2
IA            7.2                19          27       2,400               761            1.0
WI            6.6                15          20       3,307               568            0.9
NE            6.5                17          22          989               511            0.8
UT            6.0                  9          11          868               271            0.4
USA            4.2                  7          15  273,077               825            2.0

Given their low testing rate and associated high positivity rate near 23%, the true underlying infection rate could be 5X to 10X higher than reported (higher positivity rates correspond to a higher hidden population of infectees). This means that ND could have passed the “herd immunity” threshold of 60%-70% estimated by most epidemiologists.  South Dakota (SD) is not far behind at 9.0% confirmed with 24% positivity rate.  Six US states (ND, SD, IA, WI, NE, UT) are already above 6% confirmed infection rate and could be approaching the herd immunity threshold in a few months.  Four of these states (ND, SD, IA, NE) has refused to impose any kind of statewide mitigation measures and avoided testing and thus have a high hidden population of infectees.  Hundreds of counties in the USA could be approaching this threshold.  These states and counties could well reach herd immunity before vaccines become widely available in March.  By then it would be too late for vaccines to save lives already irretrievably lost. 

Letting the virus run wild has come at a great price for the Dakotas.  Both states have now joined the unenviable 0.1% club, that is more than a thousand deaths per million population reached by 10 USA states and only 3 countries in the world: Belgium, San Marino, and Peru.  (For reference the USA as a whole is at #10 in the world with 825 deaths per million.  The USA as a whole is far from herd immunity with just 4.2% of the population confirmed infected and an estimated 15%-20% as the true underlying infection rate.) 

Part of the reason for the recent topping of case counts could be due to the wide range of mitigation measures many counties and states have undertaken recently to flatten the curve and deal with the overwhelming demand for healthcare services (current hospitalizations are 56% higher than ever before in the USA).  These measures include mask mandates (which we view as the cheapest mitigation measure), limitations on assembly, curfews, and business/activity shutdowns.  Many of them could take several weeks to cut transmission and to manifest themselves in the data.  Moreover, many of them are not mandatory and depend on widely varying voluntary compliance.  Given the wide spectrum of responses, it will take some time to sort out which has been effective and which have not.

Finally, part of the reason for the recent dip in cases could also be just a matter of timing.  Many young adults including college students got tested for COVID-19 in the days before Thanksgiving, hoping to get negative results and a pass to go home (see graph above).  This raised the number of tests conducted to a record high of 1.98 million tests in the USA on Nov 21st.  91% of these tests came back negative and gave millions “pass” to travel.  Over the last 8 days, the number of tests dropped to 1.28 million on Nov 29th – much of it due to many Americans taking long weekends off for Thanksgiving.  We expect reported tests, cases, hospitalizations, and deaths to increase again soon. 

The incoming Biden administration must take charge of the pandemic war immediately.  We are forecasting that an additional 74.5k Americans will die over the next 4 weeks due to cases and hospitalization already in the pipeline.  Moreover, every day’s delay over the next 51 days will add 2k-3k to the death toll (this mean >100k lives irretrievably lost before Inauguration Day and vaccine public availability) – an avoidable and unforgivably tragic chapter in American history. 

COVID-19 Survival Rates Have Improved?

Amidst the bad news of COVID-19 increasing in the USA for the third time to record levels, there is some evidence that the case fatality rate (CFR = deaths/cases) has improved significantly from spring to summer.  Two large studies of patients in NYC and in England both show significant improvement in survival rates.  We have done a study of cases in Florida and find a similar trend in improvement. 

The figure above shows that cases (brown squares) in Florida first increased in March and then eased in June, only to surge again and burn out by early October.  Since then cases have risen again for the third time and deaths (blue diamonds) appear to have bottomed out and are increasing again.  During the first wave, the first 82,719 cases reported in FL on 6/17/20 were responsible for most of the 3702 cumulative deaths reported on 7/4/20.  This corresponded to an overall CFR of 4.5% (with deaths lagging cases by 2-3 weeks.  The second wave ended roughly on 10/20/20 with 676k more cases which lead to 13.8k more deaths that were mostly reported by 11/14/20.  This corresponds to an overall CFR of 2.0%, roughly a factor of 2 improvement from spring to summer.  The lag time between cases and deaths (as the reported date shown above) increased to 3-4 weeks as reporting lags increased in Florida (real lag time remains about 2-3 weeks). Notice that the scale on the right for deaths is 2% of the scale on the left for cases.  This is what we are predicting for the CFR for the third wave in FL.  A similar pattern is seen in the data for the USA as a whole where the CFR has improved from 6.7% to 1.5% currently. 

The strongest driver of CFR is age and the second wave was caused by many younger adults increasing their activity and getting infected.  We need to check how much a younger median age played into this observed improvement. 

The figure above shows that the improvement from wave 1 to wave 2 is remarkably similar for all age groups.  For example for adults between the ages of 65-74, 12.7% died in the first wave while only 5.5% died in the second wave.  Much of this improvement can be attributed to wider testing (identifying milder cases and cases earlier in their cycle), better hospital practices (e.g. proning rather than immediate ventilating), and better therapeutics (remdesivir and dexamethasone).  A newly approved monoclonal antibody, bamlanivimab, could improve this further. 

One note of caution is that FL and the USA are just approaching the low CFR levels seen in South Korea and other best-in-class countries all along suggesting that much of the improvement is due to the UK and USA finally getting their act together in terms of testing and treatment.  In the spring, USA and UK undertested and missed many asymptomatic and mildly symptomatic cases, and many hospitals were overwhelmed so only the most seriously ill were admitted who then died at a high rate.  Some of the improvements in survival rates could be reversed if hospitals become overwhelmed with equipment and staff shortages in this ferocious third wave. 

COVID-19 Cases in the USA are Rising for the Third Time

The total number of COVID-19 cases in the USA surpassed ten million or 3% of the population today.  The third wave of the Pandemic in the USA is here and it looks extremely dangerous.  For the first time, the number of confirmed cases per week has reached 700,000 or more than 100,000 per day – 50% higher than the peak of the summer wave reached in July (see brown squares in the figure below).  Cases are rising everywhere this time around in contrast to the first wave which was concentrated in the Northeast and the second wave that was concentrated in the Sunbelt. 

This third wave differs significantly from the first and modestly from the second in other ways.  Testing now is much more thorough than the first wave and slightly better than the second wave thus identifying more asymptomatic and mildly symptomatic cases than before (see figure below).  More kids and young adults are being tested now increasing the percentage of silent carriers.  

But the new cases are not all benign as new hospitalizations, albeit with a longer lag time and lower hospitalization ratio have risen steadily since 9/20 (see blue diamonds in the first figure above).  During the first wave patients were so sick they were hospitalized within a few days of diagnosis.  During the second wave, the lag time increased to about a week and those requiring hospitalization decreased by half.  The lag time now appears to be 2 weeks.  Given the rapid increase in case counts, we are forecasting that hospitalizations (currently near 55,000) will exceed the previous peaks of 60,000 by next week and set new records that will stress many hospital systems just a week or two before Thanksgiving. 

Even though hospitals are better prepared this time around with PPE, ventilators, improved treatment techniques (proning), and better therapeutics (Remdesivir, dexamethasone, and monoclonal antibodies), they could still be stressed and cause death rates to exceed those reached this past summer and challenge the horrific levels reached this past spring.  Better medicine plus wider testing and lower median ages had reduced the hospitalization ratio and improved the case fatality rate (CFR) from near 7% to 1.6%. But these favorable factors may be offset by new stresses on the healthcare system.  Deaths rates have already been creeping up since bottoming near 720 per day on 10/17 to near 950 per day (see blue diamonds in the figure below).  We are forecasting that the death rate will double to 1,440 per day by month-end.  The news could get substantially worse if nothing is done immediately.     

Now that the election has passed, the USA must depoliticize the war against COVID-19 and work together to flatten the curve to save lives.  To avoid the worst-case scenarios, pandemic fatigued individuals must agree to wear masks, social distance, and wash hands as recommended by the CDC.  The government must increase testing availability and turnaround times, improve contact tracing, and set up selective quarantining facilities to monitor and reduce community spread.  The Federal government must coordinate equipment acquisition and distribution to ensure no shortages occur this time around.  The next 74 days are crucial if we want to ensure that the case count does not more than double with another 10 million cases and the death count does not increase by more than another 160,000 Americans. 

COVID-19 Cases in Florida are Rising for the Third Time

COVID-19 cases are increasing around the world, in the USA, and in Florida.  In Florida, cases have been rising for the last 5 weeks albeit at a slower rate than many northern states as temperatures have cooled and activities have moved indoors slowly in the Sunshine State.  In Florida, the push to reopen the economy and especially schools have exacerbated the problem.  Since schools have reopened in August it is clear that kids can get infected and high school kids are as likely to get infected as the general population (see graph below). 

College kids and young adults are nearly twice as likely to get infected since they are more mobile and are less risk-averse in general.  While younger kids appear to be less contagious than older kids, their infection rates have been going up with the general population and for kids of elementary school age (5 – 10) it is now about 45% that of the average population.  Even though kids (<18 yrs old) are unlikely to die from COVID-19 (in fact none have died in the last month), a significant portion does get sick.  107 out of 10.7k kids (<18), or 1.0%, have been hospitalized in the last month.  69 FL kids (<18) have been diagnosed with multisystem inflammatory syndrome for children (MIS-C) so far this year.  Perhaps more concerning is that the asymptomatic or mildly symptomatic cases go on to silently infect others (parents, grandparents, and teachers) – increasing the hospitalization and death toll in the community.  We are beginning to see this in the recent increase in the median age of those infected from a low of 35 years old touched at the beginning of September to 39 recently (see figure below).  A similar transfer from young to old occurred this past summer and led to a record surge in deaths.   

This shift to the older generation has resulted in a 24% increase in currently hospitalized from a low of 2,005 reached 10/18 to 2,489 on 11/4 (see figure below).   

Death counts are currently near a 4-month low near 40 cases per day (see figure below).  However, the increased case counts and hospitalizations have led us to forecast death counts will increase soon for the third time this year.   All this happening before the start of the truly cold weather season bode ill for Florida in the coming months. 

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