Daily Rumblings – II

I haven’t done a Daily Rumblings in awhile so will start afresh with a new one. As a reminder these are for shorter late breaking or hot news. I will continue with my longer numbered posts so stay tune for those.

11/3/20

Happy Election Day. Now for some contemporary and I think poignant commentary.

Halloween

Halloween is one of my favorite holidays and I love to goof with the kids who come around. I’m always in some costume. This year we didn’t know what would happen and we didn’t think it was a good idea for families to go romping around neighborhoods, but we were prepared by sitting back and putting the candy out front for the kids to pick from and keeping our distance. We didn’t get a lot of treaters so we walked around a bit. We were happy to see families and kids going around, but there was a disturbing pattern to it. Out of about 8-10 or so families that we saw, in only one were the parents wearing masks. Forget about the kids wearing one. Two families carried an American Flag. I can’t help thinking we got punked by the anti-maskers and they were toying with us in our neighborhood, particularly since it seemed like most of the families came in some car. This realization caused our joyfulness to fade and our contempt to rise when their rebellion would walk up our sidewalk. Hoping for better next year.

Cases, deaths from Trump events

News articles in the NY Times and LA Times reported on a Stanford study that stated that 18 Trump “events are connected to 30,000 infections and 700 COVID-19 deaths …”

This is beyond alarming. Not sure you know that ND and SD are the two most prolific states for cases and deaths per capita. Now what was that motorcycle rally that descended on Sturgis for 10 days in August drawing almost a half million participants? And this wave has penetrated the mid western and central states as well.

So, being a little skeptical I downloaded the Stanford paper (https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3722299). Sure enough it is laden with approximations, but their transmission model looks solid and scientifically sound. What was surprising is that they then did a placebo analysis, where they replicated similar environments and populations that didn’t have such events. Magnificent, even if there are never perfect placebos in this type of analyses, but still it is essential for meaningful results. At least you can attach some statistical probability to the results. In the discussion they state “… examining the experience of a few counties which, according to the preceding statistical analysis, were highly impacted by Trump rallies.” How bad? They are trying very hard not to be controversial. Best to just state verbatim the conclusion:

“For the vast majority of these variants, our estimate of the average treatment effect across the eighteen events implies that they increased subsequent confirmed cases of COVID-19 by more than 250 per 100,000 residents. Extrapolating this figure to the entire sample, we conclude that these eighteen rallies ultimately resulted in more than 30,000 incremental confirmed cases of COVID-19. Applying county-specific post-event death rates, we conclude that the rallies likely led to more than 700 deaths (not necessarily among attendees).”

More distressing is that this is just the beginning of the proliferation from these super-spreader events meaning there could be many more deaths as time goes on. So is a rally really worth 50-100 deaths?

Antibody testing in Orange County indicates high number of Infections

Good science again is getting into the press. A study out of UC Irvine reports on the results of conducting antibody testing (immunity) on 3,000 random residents (https://www.medrxiv.org/content/10.1101/2020.10.07.20208660v1).

The antibody test probes for individuals who have been previously infected and are therefore presumably immune. The results showed a staggeringly high level of infections in OC being 11.5% of the population having had COVID-19. This level was even greater in Latino and low-income neighborhoods at 17% and 15%, respectively.

Let’s look at how this measurement compares to expectations based on deaths and mortality rate. Given about 500 deaths per million in OC and say a 1.0% mortality rate, we calculate 5% total infection [500 / (.005×1,000,000)]. The higher measured rates means that COVID-19 is very contagious and prevalent, but that the death rate is now much less than the 1% that characterized the early pandemic. This is consistent with infection rates infiltrating younger less fatal populations. The important take home is that deaths are concentrated in the elderly and infections are concentrated in the younger. Youths need to understand that they are now responsible for inflicting most of the COVID-19 deaths. I wonder how many of them are seeing a direct association of their infection to older family members dying. It can’t be insignificant.

8/28/20

The Corruption of our National Health Services

I try to avoid politics in my commentary, but unfortunately politics sometimes inserts itself in the most dreadful ways and when it endangers the lives of Americans in order to support crass self-interests, I’m going to speak out. I have been challenged by readers for being political, but I believe I hold all guilty parties accountable for their actions or lack of them from conservatives (the Administration, the mask-averse southern outbreak states) to liberals (most media, California, millennials, etc.). It is about the search for the truth and identifying and solving problems.

In just two days the Administration has twice asserted its dictatorial mandate on two of the most respected and vital independent departments of the government, the FDA and CDC both of which reside under the Department of Health and Human Services (HHS). HHS is headed by Trump designate Secretary Alex Azar, a member of the Cabinet and supposedly our nation’s leading health care expert who by the way has no experience in health care and is the first non-scientist or medical professional to hold that position, being a lawyer from the pharma industry. And by the way he is the 4^th person in that position under our President. But I digress.

First, the Administration rammed an FDA Emergency Use Authorization (EUA) for convalescent plasma and forced FDA Commissioner Stephen Hahn to falsely voice the Administrations claim that it reduces mortality by 35%. Hahn was severely rebuked by the medical profession and has irreparably damaged the FDA’s and his reputation for truthfulness and impartiality. So here’s what’s known. Based on the largest trial to date by the Mayo Clinic, there is no evidence of reduced mortality as this and no trials have been conducted with a placebo control. Instead the data indicate that the 7-day mortality rate ranged from 8.9% to 13.7% for high to low doses of plasma, respectively. The misquoted 35% figure is a relative number and comes from the difference between these percentages [(13.7-8.9)/13.7 = 35%], which is a meaningless comparison without a placebo control and barely showed statistical significance (p=0.048). The 30-day mortality data were even less significant. Totally deceptive reporting by the Administration and FDA. The best estimates for absolute reduction of mortality by plasma infusion are about 3.5%. Worth doing in certain sub-populations, but hardly a breakthrough.

Remember the FDA was also forced to give EUA status to hydroxychloroquine, which the FDA then had to revoke when evidence showed it was more harmful than helpful.

Second, the Administration continues to sabotage coronavirus testing in a fully-admitted effort to suppress the number of cases because it makes the Administration look bad. Now the CDC has changed their guideline to say testing is only required for symptomatic people. The New York Times and CNN quoted CDC officials that the change was “forced down” from the Administration. The majority of transmissions are now from asymptomatic patients, so dah! Yes, we need to test people who are known to have been exposed! Fortunately, most states are ignoring the new CDC guidelines. CDC Director Robert Redfield, whose reputation is already in shambles, had to walk back his comments after a huge backlash by adding that “those who come in close contact with a confirmed or probable COVID-19 patient could be tested.” Could be?!!! This kind of muddled double-speak and ambiguous advice just further confuses the public.

Testing rates, however, are increasing in the U.S. and per capita we are behind only a couple of dozen countries such as Russia, Bahrain, Israel, UAE, U.K., Singapore, Australia, Denmark, Luxembourg, Lithuania, Iceland, Malta, Cyprus, Cayman Islands, Bermuda, Gibraltar. Granted some of these are small countries, but I left off even smaller ones whose testing rates exceed the U.S.

Is Herd Immunity Already Helping?

In my recent post (23. Biweekly Update: The U.S. has Given Up) I noted that countries (e.g., Italy, Spain, France, U.K. Belgium) and U.S. states (e.g., NY, NJ, MI, New England) that had the worst outbreaks have effectively recovered and are holding down the virus. Is this due to having witnessed decimation of lives and health and continuing to have a fear factor about opening up or is there perhaps another contributing factor? I believe both.

There is much discussion about how much herd immunity is needed to tamp down Covid-19. Generally, it is acknowledged that herd immunity of about 60% would slow and eventually eliminate cases and deaths. This comes about because the reproduction number R₀, number of people an infected person will then infect, is about 2.5. This is for a population that is 100% susceptible. However, at 60% herd immunity, the susceptible population is 40% and that gives an effective R₀ (R_e) of 1.0, which is the point where the infection rate stays constant. R_e must drop below 1 for infections to decline. We can model this with the following equation:

R_e = R₀ x (1-P) x (1-T)

where R_e is the effective reproduction number, R₀ is the basic reproduction number, P is the percentage who were previously infected (herd immunity factor) and T is the reduction in transmission rate due to social distancing and caution. If R₀ is say 2.5, then either herd immunity of 60% or reduction in transmission of 60% gets R_e down to 1 and the spread doesn’t grow. A combination of both helps even more.

If 3/5 of all people (60%) become immune then R₀ = 1.0 without any social distancing. But say we can do 40% social distancing and get R₀ down to 1.5 then only 33% herd immunity would be required to get down to R₀ = 1. So, they act together and all immunity helps. NY, NJ and New England are indeed at about 33% herd immunity, so just modest social distancing will keep infections down. I believe that the level of herd immunity in other hot spot populations of the world is sufficient to make it easier to reduce infections with modest social precautions.

A quick way to get a decent approximation of the fraction of the country that has been infected is given by:

(total deaths) / [(IFR) x (population)]

Where IFR is the infection fatality rate. As an example, for Spain we have total deaths = 29,000, population = 46,755,000. So, for an IFR = 1% one gets 6.2% for herd immunity, which is close to what is reported by antibody tests, though these tests have large uncertainties. However, new evidence is that infection is far greater due to asymptomatic patients so this could easily be >10%. We expect similar amounts of herd immunity in other European countries offering some, but not a lot of protection.

Re-infections

Fortunately, SARS-CoV-2 mutates slowly and therefore immunity from a vaccine or infection should be relatively long-lasting. This is unlike the flu virus which mutates rapidly requiring annual vaccination. At the other end of the spectrum are measles, mumps, rubella for which, though also RNA viruses, vaccinations can last a lifetime due to slow mutation.

As for re-infections the jury is still out. My hunch is that this is due to the person not actually having been infected the first time. The Covid-19 test has a 4-5% false positive rate, which means 4-5% of people who take the test register positive when they are really negative. So, if they then get it later it appears to be a re-infection, but is not. This needs to be looked at closer. There has been one verifiable second infection:

https://www.sciencemag.org/news/2020/08/some-people-can-get-pandemic-virus-twice-study-suggests-no-reason-panic

However, is this something to be worried about? Let’s consider some statistics:

Probability of getting Covid-19 once: (70M cases over 7B population = 1%)

Probability of getting Covid-19 twice: (1 case over 70M cases = 0.000001%) at least so far.

There have been reports about antibody levels declining with time giving concern for how long one remains immune. Well it is normal for antibody levels to decline after initial infection, but they are still at adequate levels. This initial surge followed by relaxation to an ambient level is typical of viral infections. After 3 months there are still sufficient defenses to maintain immunity. Let’s thank our memory T-cells.

8/3/20

California Update

I always proselytized that the only reliable data there is on Covid-19 is deaths. Hard to ignore or miscount those. However, deaths are a lagging indicator by 2-3 weeks on new cases and how things are doing in the present. In the past I totally ignored new cases (incidences) and total cases (prevalence) because they were grossly understated due to inadequate testing. Instead I calculated them from the death rates and marched back 2-3 weeks, then forecast forward based on the shape of the curve. Still do that. Now if the inadequacy of testing was at least constant then the trends in cases would have been useful, but this was distorted as testing frequency increased. Now it is fairly constant so trends in cases is an improved indicator. However, over the last couple of months I have started using hospitalizations as an earlier indicator because if you are sick enough to go to the hospital, despite whether you were tested, that means something and then you do get tested. And indeed, it is working out to be a pretty good predictor.

In my 7/22/20 Biweekly Update (Post 22) I showed plots of hospitalizations and death rates for LA and OC and noted where you could see death surges a week or two following hospitalization surges. However, it was also true that the latest hospitalization surge didn’t seem to show a corresponding increase in death rate, but it was expected. Now two weeks later the latest surge in death rate is quite evident as seen in the Figures below. However, the good news is that hospitalizations are falling and therefore we might predict a commensurate decrease in the death rate over the next couple of weeks. Hopefully we are seeing a sustained trend toward decreasing rates of infections.

The Figures below show the death rates for the state of CA and for the U.S. Both populations have undergone a relapse from their peaks in late April. The CA surge is due primarily to the growth in cases and deaths in LA and especially OC. The surge in the U.S. is due to late comer outbreaks, e.g., FL, TX, AZ, and the relapser CA as discussed in previous postings.

Finally let’s look at growth in death rates and deaths per capita for CA counties and then compare that to the rest of the country and the world. A Table is given below. Numbers speak louder than words.

Here are some observations:

• CA death toll grew 411% over the last 3 months though its level of 241 deaths/million still pales relative to the worst hotspots in the country and world. Still it is heading up faster than these other populations.
• For comparison, the new hotspot states are also marching up rapidly in deaths per million: AZ (519), GA (362), SC (348), FL (333), TX (257).
• OC has gone from the lowest to the 3^rd highest per capita death toll of the 9 most populous counties in CA. Its growth over the last 3 months of 1,315% rivals that of Brazil.
• If you dig further at the OC statistics one finds that North County accounts for about 90% of all OC deaths and that Anaheim and Santa Ana represent 51% of the 651 total deaths probably due to having a heavy preponderance of nursing homes.
• Santa Clara, where the CA scare first started, now has a death toll that grew only 72% over the last 3 months. Commendable, but word is that this county is starting to see case counts rising dramatically, so the message is there is no rest for the weary. Everyone is susceptible. Be careful.

More Musings

• Will Hurricane Isaias be good news for the U.S. southeast coast if it keeps people in their houses for a couple of days and reduces infections? We’ll know if there is a dip in hospitalizations and deaths over the next few weeks.
• I have never seen so much traffic in OC, just gridlock in the coastal cities. I know people are going somewhere, but maybe the more time they spend in their cars the less time they spend getting infected.
• Why should we doubt that kids are immune and non-infectious to Covid-19. After all they never get any other virus flus or colds at school and bring them home to infect their families.
• The hope that the corona virus would be seasonal like other flu viruses seems not to be. The U.S. southern states are having major outbreaks and they are not called hotspots just because of Covid-19.

7/9/20

What Me Worry!

There seem to be Alfred E. Neuman’s running around all the governor’s mansions, which is driving people MAD. The figure below is quite astonishing.

Hard to believe that AZ, FL, and SC have the fastest growing rates of confirmed coronavirus cases in the world on a per capita basis (the only way to make comparisons). In fact, there are 16 U.S. states in the top 26 outbreak regions in the world. This is not the way to rev up the economy by turning it off and on and off in fits and starts.

Now I have tried to stay apolitical throughout my blogging, resorting to facts and data and (semi-)dispassionate commentary. And I hope to remain that way, but I will let you form your own opinion on these facts:

• Every state in the figure above except NV and CA were Trump states in 2016. That is 14 of 16 and of those 14 all but two still have Republican governors.
• Of the 28 Trump states in 2016, 24 are currently on the highest 31 outbreak list of U.S. states.

So why is it important to state these facts? Because we need to get to the root cause of the COVID-19 pandemic that is running rampart through most of the U.S.  You cannot solve a problem unless you understand the problem. There is little argument that the current outbreaks are occurring because we were too fast with the trigger in easing social distancing and re-opening businesses. And this practice is glaringly predominant to one political party because of messages I guess they were hearing from somewhere around DC. Unfortunately, you cannot wish or pander your way through a pandemic!

Here is a prophetic comment I made back on May 14 in discussing social easing (Post #17): “It is understandable that we must give great consideration to the economy, but we will be worse off if we socially ease prematurely. Easing as little as 2 weeks too soon could lead to epidemic growth again and require another 2 months of social distancing. That is an atrocious tradeoff.”

….. OK I’ve taken a deep breath and I feel better now.

So again, I am not a shrinking violet and I like to get out and have fun and see friends, but there are safe ways to do it. Wear a mask near people, particularly strangers, don’t shake hands and hug, wash your hands often, avoid crowds as much as you can and do things outdoors. That’s not a lot to ask to help avoid the next 100,000 American deaths.

Other Musings

• Someone needs to talk to the Kardashians to have them make wearing masks cool. We need these to be individual expressions. We should revive masquerade parties?
• What’s with these natives who claim we have a constitutional right to do whatever will infect people and that Gov. Newsom is unjustly depriving us of that right. I suppose it is also our constitutional right to drive 100 mph on the freeways.
• So much for U.S. world leadership when you cannot even vacation in Paris.
• Early in the pandemic the rally cry was flatten the curve. I never liked that because it still assumed the same number of deaths, just spread out further over time. Well in fact what we now have is a flattened curve, but thankfully what we really want is to vanquish the virus.
• To put into perspective the risks taken by front-line healthcare givers, their probability of death now exceeds that of deployed soldiers, race car drivers, and astronauts. Let’s give them respect and above all, let’s not get sick and expose them and everyone else any further!
• Tourism is highly affected by COVID-19, but maybe all the hotspot areas like Italy, Spain, NY, etc. can start a tourism campaign on the premise; “Hey, come visit us; you’ll be safe, we’re all immune!”

7/5/20

A few more updates. Also still relevant is the 7/1/20 entry on California Nightmare.

What’s with them Yutes?

The southern judge could not understand Vinny’s pronunciation of youths in My Cousin Vinny. Well I simply cannot understand yutes at all. They seem to think they are immune to the virus. Well if we look closer maybe they are! The plot below shows infection fatality rate (IFR) vs. age group for COVID-19 and influenza.

Because of the considerable differences in IFR values with age group, we have plotted this on a log scale. One can see that for ages under 50, the chances of dying from influenza are greater than from COVID-19. The latter statistics are still accumulating so the values may adjust, but the conclusion is that they are not that much different until you get to age 50 and over in which case COVID-19 becomes much more deadly (5.6% vs. 0.83% for >64 yr). Currently, the IFR for COVID-19 for all ages is 0.64% (vs. 0.10% for influenza), much less than early estimates of >1%. This is because infections are shifting to younger ages pulling down the IFR.

So, you yutes, you may argue it is OK to party and throw caution to the wind, but if you do, please stay away from your parents, grandparents, aunts and uncles, etc.

How bad is COVID-19?

I have my opinions and I have my facts and sometimes the two collide. So, my opinion is we are in a serious epidemic and we need to exercise as much caution as possible. I didn’t say hole up at home and refuse to work. But if you wear a mask in public, keep your distance, and wash your hands often you will reduce the odds of getting infected by something like 90%, which is good enough for me. However, let’s look at COVID-19 deaths vs. other deaths to put it into perspective.

The figure below shows the running tally of deaths per week over the last few years. One can see the oscillation due to deaths by flu in the wintertime. From these regular death statistics one can easily see excursions from the normal range, which can be attributed to extraordinary circumstances. You can see that clearly for COVID-19 this year. You see perhaps a 15-20% increase in overall deaths. Well does that deserve that much doom and gloom? Well sure as any avoidable death should be avoided. Many of these other deaths are unavoidable, e.g., cancer, old age. But then again maybe many/most of these deaths are also avoidable and we have just gotten used to them (e.g., pneumonia and influenza). The point is the world is not coming to an end and maybe we should look at all deaths more closely to see where we can be putting our efforts to reduce the overall death rate.

So, the Table below takes a closer look at deaths vs. age group. COVID-19 is more deadly than pneumonia and influenza from 2/1/20 to 6/20/20 for all age groups, but the ratio increases with age group. The attributed deaths to COVID-19 indicate that 8.88% of all deaths in the U.S over this time-span was due to COVID-19.

Now wait a second! Why this 8.88% value when the Figure above implies excess deaths of 15-20%. The dark truth is that the number of COVID-19 deaths are probably greatly understated in the U.S. and around the world because of insufficient testing to confirm that deaths in people with COVID-19 symptoms were actually due to COVID-19. Just like cases (prevalence) were/are understated, so are deaths. The likelihood is that there have been closer to and maybe even greater than 200,000 deaths in the U.S., not 135,000 as it is reported today. Further evidence of this is that excess deaths are now tracking more closely to COVID-19 deaths as testing is becoming more widespread.

We have heard arguments, sometimes inferred because of morbidness, that COVID-19 is just causing deaths in people who are already soon to die. Somewhat yes, but statistically not as much as one might expect. Using actuarial tables that give the average life span for each age group we calculated the % of total lifetimes (based on an average of 75 years) that are lost to COVID-19 and that 8.88% figure above for deaths in general comes down to only 7.54% for age-adjusted deaths. So COVID-19 is a killer regardless of age. The big question is whether 8.88% is a cataclysmic disaster or not. I don’t take sides, I just report the data, but again I do come back to we should be working hard to avoid any avoidable deaths, COVID-19 or other.

7/1/20

California Nightmare

Gavin had to pull the plug again today and rightly so. Here is why:

The plots above are for Orange County. Hospitalizations have doubled since May and are up 50% in just the last week alone. Death rates have soared as well. Given that deaths follow infections by about 2.5 weeks and hospitalizations follow infections by about 1.5 weeks, I would predict that the surge in hospitalizations in the last week will lead to a new spike in death rates in the next week or two. You can see this in the data where hospitalization peaks at about 4/5, 4/26, 5/20 and 6/10 leading to death rate peaks about a week later. I’m not sure why the death rate surges are more pronounced than hospitalizations, but death reporting is sometimes spotty especially with elderly care facilities not always being prompt.

Los Angeles has bigger numbers, but not so much per capita. LA was trending down slightly until the last couple of weeks. Here again you can see death rate surges about a week after the hospital surges. Now the downward trend has turned alarmingly upward with hospitalizations increasing about 30% in the last 2 weeks. So, we might expect a death rate surge in LA as well as OC in the next week or two. So, Governor Newsom had no choice.

Now let’s look at the death rates for California as a whole. Pathetic. No sign of recovery, just a persistent plateau and perhaps a new surge. Even worse is that CA is not even the worst state by a long shot.