Vaccine Scheduling and Software

 Software is always a mess, always. Software developers are known to have the users debug their software. Yes, those who pay get to work, for free. In my opinion and my experience this has been a pandemic Microsoft problem. I have spent a good deal of my life doing work arounds with their software. But alas, it was not mission critical. My typical example was Apollo XIII, and the return guidance system. I designed the second backup, a simple sextant with electrical readouts but independent of the computer. No one ever thought it would be needed or at least that is what I thought. Well, history is a bit different.

Now the NY Times states:

When coronavirus vaccines first became available, state health officials in Virginia turned to software recommended by the Centers for Disease Control and Prevention to schedule appointments. But people complained that the software, called VAMS, was too confusing for older adults to use. So the state switched to another system, PrepMod — but that had problems, too. Links sent to seniors for their appointments were reusable and found their way to Facebook, leading to one vaccination event in Richmond with dozens of overbookings. Some of those people threatened health care workers when they were turned away. “It was a nightmare scenario,” said Ruth Morrison, the policy director for the Richmond and Henrico County health district. “People showing up confused, irate, thinking they had an appointment.” State and local health departments around the country continue to face delays dispensing shots, in part because flaws remain in the appointment software tools like those used in Richmond. The problems threaten to slow the vaccine rollout even as supplies and distribution are picking up quickly across the country.

But worse is yet to come:

On Thursday, President Biden said that his administration would send out technical teams to help states improve their websites. He also said the federal government would open a website by May 1 that would allow Americans to find out where the vaccine is available.

 If you think these other messes are bad wait until we get the Feds involved. Regrettably we may regress. We have been playing "whack a mole" for months. I really do not know how many older folks can find their way. I found an entry and still await a final inoculation. Hopefully it works. But the Feds are the last ones to see anything get done. Not to mention the new level of political correctness imposed.

An Observation

 There are 9,000,000 people in New Jersey, rounding off

There have been 720,939 infected, or 720,000 rounding off

There have been 1,619,541 vaccinated first time at least or 1,620,000 rounding off

Thus there are a total of 2,340,000 immune as of today

Or 26% of the population is immune

Or 6,660,000 are vulnerable

The current prevalence is about 33,000 infected walking around

The  new infections per day is about 3,000

Or 45 new infections per day per 100,000 people not immune

Now at the peak we had 4,000 per day

On a population of 8,600,000 vulnerable

Or at rate 46 new infections per day per 100,000 people not immune

Thus our infections are going down not because of anything we are doing better but only because there are fewer vulnerable people! This is epidemiology 101! Nothing has changed EXCEPT the vaccine and more infected.

I wonder why our "Leaders" are not commenting on this at least in New Jersey. This is what Investment Bankers allegedly do for a living, except it is dollars not people. Harvard Business School Case Studies supposedly relishes in this type of analysis. So what  is The Banker up to?

NJ 2021 03 06

 We are going on a year of reporting. Some good news some bad. Let's start:

First, the vaccines are flowing but we must anticipate a delayed effect. Below is the flow of the first two.

This is an interesting but confusing chart. We have taken the ratio of the new infected divided by the vulnerable. Namely the vulnerable are the total population less the formerly infected plus vaccinated. It is increasing which is the surprise. It may be a delay effect but it is worth watching.

This is the new infected vs the percent vaccinated (first) plus infected. Again there is some temporal effects but the flattening is a concern.

The one below is infected plus vaccinated vs time. Vaccinations are increasing at a good pace.

The incremental vaccinated per day is close to 2 million, it should be well above 3.5 by mid April.

This is the Biden curve. He promised what Trump was delivering so it is a slam dunk.

Now for some local data. Here is the town doubling time. It is much too high. The reason, "Kids". Every noon time school is let out and mass crowds of kids assemble for hours and spread the virus. No Public Health controls so we all suffer!

By town here are the doubling times. Surprisingly Morristown is great and Chester Borough is horrible!

The incidence per PoP still shows the Dover cluster. Again having no Public Health structure makes this an unstoppable event.

+

New cases per day of county and town show dramatic difference. The County is decreasing and the town increasing.

The prevalence of 60 people in the town is the beginning of another peak.

The State new per day is flattening at a high level.

The County is actually increasing

The doubling time seems flat at about 200 days.

Death rates seem fixed at 2%

The good news seems to be the final reduction in LTC mortality.

State prevalence is increasing

The County prevalence as well.

Some observations on Demographics. Below is the normalized positives by age. Clearly the spreaders are young 18-29 year olds. These are the ones which spread between and then onto the more vulnerable. School age children not so much.

Second, and as usual, the prevalence is in Hispanic households. This is almost 3:1 to Asians and almost 2:1 with Whites. Again we refer to the ACE2 receptor variants as the driver as well.

Robespierre Redux

 In Thompson's book, Robespierre and the French Revolution, the author notes:

Robespierre was no apocalyptic visionary. He did not believe in letting the tares and the wheat grow together until the harvest. He believed it possible and necessary to root up the tares here and now; and he thought that he saw an end to the business, if revolutionary justice could avoid undue clemency on the one hand and undue severity on the other. His idealism was confined to the people he did not know—the workers. His own class, the bourgeoisie, he viewed realistically. 

 He had nothing of the bureaucrat’s belief that committees, departments, and boards are above bribery or injustice. 

He had always held that the chief danger to the republic would come from its governing class, not from the masses. He disliked armies, because discipline made officers into bullies and esprit de corps enabled generals to become military dictators. He suspected every popular political leader of aiming at supreme power, and saw dictators everywhere—all the more so perhaps if he was fighting his own subconscious desire for dictatorship. What had excluded Marat from the Jacobin fellowship, and especially from Robespierre’s circle, was not his sordid life or his bloodthirstiness, but his candid avowal that a dictator was needed and that he was ready to play the part. Dictatorship was the nightmare that beset the Jacobin bedside: the Revolution had begun as a great liberation from royal-feudal “tyranny”; its second act had been the abolition of the “despotic” monarchy; its third the overthrow of the Girondin bid for absolute control. 

It looked as though it would go full circle and end as it began. Robespierre’s draft for a “shadow” Constitution in 1793 had taken every precaution against this danger— partly by making every office accessible to the ordinary citizen, partly by providing popular checks on misgovemment. 

“The right of resisting oppression [said his Article 25] is a corollary of the other rights of men and citizens”; 

Article 27, “When a government violates the rights of the people, it becomes the most sacred duty of the whole people, and of each separate portion of it, to revolt against it”; and 

Article 28, “When a citizen can no longer rely upon the State to safeguard his rights, he falls back on his natural right to defend all his rights for himself”. 

The final form of the Constitution of 1793, though in some points it fell below Robespierre’s ideals, was in this respect even more plain-spoken. In a series of laconic Articles it declared that: 

“Sovereignty resides in the people: it is one and indivisible, imprescriptible and inalienable” 

“No part of the people can exercise the power of the whole” 

“Any individual who usurps the sovereignty may at once be put to death by free men” 

 “Public office is essentially temporary, and must not be considered as a distinction or a reward, but as a duty” 

 “Crimes committed by the people’s representatives or agents must never go unpunished. No one has the right to claim more inviolability than other citizens” 

“Resistance to oppression follows from the other rights of man” 

 And finally, in words even stronger than Robespierre’s, 

“When the government violates the right of the people, insurrection is for the people, and for any part of it, the most sacred of its rights and the most indispensable of its duties” 

A year later the decree constituting the Revolutionary Government, i.e. the Jacobin regime (December 4, 1793), contained not only an elaborate system for ensuring the efficient supervision of government and local officials, but also a section headed “De la penalite des fonctionnaires publics et des autres agens de la Republique”, which enumerates in twelve Articles the penalties incurred for official offences; they range from deprivation of civic rights and A Republic of Virtue confiscation of property to imprisonment in irons and death. Nor can there be any doubt that Robespierre, whilst disliking the wholesale shooting of rebels, took a special interest in the discriminating execution of Government and local officials.

 It is interesting to see the flow from Monarchy, to Girondins, to Jacobins then Napoleon. Just a set of observations.

 

The P.1 Variant

 New variants are always popping up as we have noted previously. Nature has a brief note on the P.1 variant from Brazil. It notes:

A coronavirus variant detected in the Brazilian city of Manaus might be driving reinfections and the city’s second wave of COVID-19. During the first wave of the pandemic, Manaus experienced one of the world’s highest infection rates: an estimated two-thirds of residents were infected by October 2020, leading some researchers to predict that population-wide immunity might cause new infections to tail off. But in January 2021, researchers identified a novel coronavirus variant, called P.1, during a period of rising hospitalizations in the city and linked the variant to a few cases of reinfection. To characterize the variant further, Nuno Faria, at Imperial College London, and his colleagues analysed viral genomes collected from 184 human samples in Manaus between November and December (N. R. Faria et al. Preprint at https://github.com/CADDE-CENTRE/Novel-SARS-CoV-2-P1-Lineage-in-Brazil/blob/main/manuscript/FINAL_P1_MANUSCRIPT_25-02-2021_combined.pdf; 2021). The variant harbours 17 mutations that alter SARS-CoV-2 proteins. Among the alterations are changes in the SARS-CoV-2 spike protein that have been previously linked to increased transmission and immune evasion.

From the referenced paper the authors note:

 Lineage P.1 contains 10 new amino acid mutations in the virus spike protein (L18F, T20N, P26S, D138Y, R190S, K417T, E484K, N501Y, H655Y, T1027I) compared its immediate ancestor (B.1.1.28). In addition to the abovementioned estimated increase in the rate of molecular evolution during the emergence of P.1, we find, using molecular selection analyses, evidence that 9 of these 10 mutations are under diversifying positive selection .Three key mutations present in P.1, N501Y, K417T and E484K, are located in the spike protein RBD. The former two interact with human angiotensin-converting enzyme 2 (hACE2), whilst E484K is located in a loop region outside the direct hACE2 interface.  Notably, the same three residues are mutated with the B.1.351 variant of concern, and N501Y is also present in the B.1.1.7 lineage. The independent emergence of the same constellation of mutations in geographically-distinct lineages suggests a process of convergent molecular adaptation. Similar to what was observed for SARS-CoV-1, mutations in the RBD may increase affinity of the virus for host ACE2 and consequently impact host cell entry and virus transmission. Recent molecular analysis of B.1.351 suggests that the three P.1 RBD mutations may similarly enhance hACE2 engagement, providing a plausible hypothesis for an increase in transmissibility of the P.1 lineage. Moreover, E484K has been associated with reduced antibody neutralisation and as RBD-presented epitopes account for ~90% of the neutralising activity of sera from individuals previously infected with SARS-CoV-2, tighter binding of P.1 viruses to hACE2 may further reduce the effectiveness of neutralizing antibodies that are competing with hACE2 to bind the RBD. However, it remains difficult to estimate the contributions of the P.1 RBD mutations to transmissibility and neutralisation that may have led to P.1’s emergence at the population level.

 Grinch reports the following SNPs:

aa:orf1ab:S1188L
aa:orf1ab:K1795Q
del:11288:9
aa:S:L18F
aa:S:T20N
aa:S:P26S
aa:S:D138Y
aa:S:R190S
aa:S:K417T
aa:S:E484K
aa:S:N501Y
aa:S:H655Y
aa:S:T1027I
aa:orf3a:G174C
aa:orf8:E92K
aa:N:P80R

 New Jersey reports 2 cases in Hudson County. However this variants seems to attacks specific ACE2 receptors. It is more virulent and its control and mitigation is critical. Hopefully this does not start the process all over again!

Terry's Adventure in Wonderland

 It was a restful day in New York City, March 9, 2020, and I had to see my eye doctor. I knew the Wuhan Virus, as it was then called, was on the march. I saw in the waiting room dozens of patients sitting for their turn. I was prepared. I sat alone by the door, gloves on, isopropyl alcohol at hand, face away from the possibly infected crowd. I gather I was the only one. Yet I had declared a pandemic on February 4, 2020, yet no one seemed to care, especially in New York. Life continued as normal, but just for a few precious hours as the virus cut its deadly path through the city. I returned via the rather decrepit public transit, the New York subway reeking of urine and filth, the Penn Station which makes a Mumbai train station look elegant, and then onto New Jersey Transit, the biggest risk of getting anywhere. I fell asleep on the train.

 When I awoke it was 2021 and there was this White Rabbit (called a vaccine) and I was compelled to follow this creature, perhaps to catch up with it, to see just where it was going. So down the rabbit hole I flew, past web sites shouting that they were not available, that I was not qualified, that it was too late. I knew I must catch this White Rabbit so I tried to fall faster, despite my well grounded understanding of Newton's laws. I swung my arms and hands about my keyboard, from site to site, hour after hour, seeing in the Press that as an older person I was considered incompetent, but undeterred I continued. Down the hole I flew seeing doors slam closed with signs saying, "Prisoners Only", "Smokers Only". "Obese Only", "Press Only", and again and again the signs flew by telling me the White Rabbit could not be found behind any.

 Then, out of pure blind luck, I found one, and it said, "Follow Me". Now this door was an opening to a long winding path. First it said, "Wait here for a month". OK, I thought, at least I got through the door. So I sat, thinking that perhaps as I waited the White Rabbit would somehow appear. But alas, Not. Finally I was told by a sign to gather my things and set out along the road, for a long journey, a very long journey. I wondered if I had enough resources but I must find that White Rabbit. So off I went, hundreds of miles across the terrain of New Jersey, down along the Delaware, then off towards the Atlantic.

 Finally it appeared to be the trail of the White Rabbit. I parked and went to the gate. There were two short fat guards with guns and mace and clubs. They were named Tweedle Dum and Tweedle Dee. They told me to go back to my place, the White Rabbit was having lunch, and not to be disturbed. I thus meekly returned as hundreds of others arrived, I gather also drawn by the White Rabbit.

 Come the appointed hour, I guess the White Rabbit had completed his mid-day nap, Tweedle Dee and Tweedle Dum told us all to line up and proceed. Well it was down the rabbit hole again, a long twisting line down and down with guards checking us to each turn.

 Then out of nowhere I saw the King of Hearts, a somewhat obese man with a balding head and rather poor dentition running about shouting, "Off with their knuckleheads, off with their knuckleheads!" Frankly I had no idea what a "knucklehead" was and why this self-proclaimed King wanted to "off" them. But alas I knew I was somehow still in New Jersey and this may most likely be some South Jersey underworld lingo.

 Finally I saw the White Rabbit, I was nearing him, I could see others closer but as I continued down this part of the rabbit hole, I was almost there. Then, after all the effort, I got next to the White Rabbit, I grabbed his tufted tail, I was there….almost.

 Then I saw this strange creature, a long nose, pock marked face and glassy eyes, with the crumpled top hat, long coat, of some awful shade of green. He then said to me:

 "The White Rabbit can meet you again in three weeks, so you must let go and return then, we will make an appointment for you."

 I turned and spoke to the person next to me and asked, "who is that">

 She replied, "I hear he is called the Mad Hatter, he makes the second appointment."

 "Second appointment! What second appointment, I was here with the White Rabbit now!"

 Then a large caterpillar came to me, and he was smoking some sort of thing, and his head was encircled with smoke. I said, "Hey, this is a non-smoking area."

 The Caterpillar then said, "Plush, plush, poor person, please, plan, properly"

 I wondered just what he said, but then Tweedle Dum and Tweedle Dee escorted us out. But just as I was ascending before me appeared this giant cat, with a fearful grin, and in its churlish manner said:

 "We shall be in contact with your for your return. We shall see you again…."

 Up the rabbit hole I went, travelling hundreds of miles again, but to what I thought, to where, to when?

Upon my return I did get a message from the grinning Ceshire Cat. Well it was half a message anyhow. I was told to return to the rabbit hole, but now I was to be there at dawn, which meant a night time trip, hundreds of miles, during rush hour. All I could think of was returning to the land of the crazed Red King, his pompous assertions and seeing these creatures again. I am still in search of the White Rabbit, and I have the bite in my arm from my first attempted encounter.

 This has been a strange trip to Wonderland….I wonder how Alice managed? But the smiling Cheshire Cat said I must return, will this trip never end, will I get to speak with the White Rabbit, or is this still a dream and I am but on the NJ Transit back home?