Tag: covid-19

Ten million companys’ immunization and contact tracing processes

Pushing responsibility down as far as possible (local government, companies, individuals) is nice in theory, but we keep running up against the reality that people *aren’t* responsible. And we end up with a menagerie of policies that are, best case, uncoordinated and worst case at odds with each other. Go from town to town, you’ll encounter different restrictions. Go from store to store, you’ll encounter different restrictions. I get wanting freedom — I don’t want someone telling me what colour car I am going to drive or what we’ll be doing to relax Friday night. But I don’t see a difference between “the government taking my freedom” and “the company that I work for taking my freedom”. People like to pretend that it’s my choice to work there, thus not really something being forced upon me. Sure, in theory, you can go find a different workplace (University, elementary school, etc) that doesn’t have the restriction to which you object. The practical reality, though, is different. You need money to support yourself – buy food, pay rent, make sure the heat is on – so you cannot just not work. You may not be able to move halfway across the country to work at your perfect employer. Your perfect employer may not have any openings. Or they may elect to hire someone else. Being financially coerced into ceding my freedom isn’t better than the government enacting a restriction.

And there are just some things that are ineffective without a centrally coordinated policy. And that means that, occasionally, you lose the right to chose for yourself.

Math Time – Delta Edition

An update to my previous mathematical analysis of covid transmission now that I’ve seen R0 estimates for this delta variant …

The R0 value for the delta variant seems to be between 5 and 8. Looks like just over 46% of the US population is vaccinated. The vaccines are published as being 90-something percent effective. That makes an effective transmission rate between (5 * (1- (0.46 * 0.95))) and (8 * (1- (0.46 * 0.9))). Between 2.9 and 4.7 — somewhat surprising given the R0 of slightly under 3 that was published at the start of the SARS-CoV-2 outbreak. That means that, as health orders and mandates are lifted, we’re basically exactly where we were a year ago even though about half the population is vaccinated.

A mathematically interesting thing — if you could get the vaccine efficacy up to 100% (a third shot, a tenth shot, a different vaccine, whatever)? We’d still have an effective transmission rate between 2.7 and 4.3 — the value goes down, but not significantly. On the other hand, increasing the percentage of fully vaccinated individuals by 10% gives us an effective rate of transmission between 2.5 and 4.0. Having 70% of the population vaccinated would yield an effective rate of transmission between 1.8 and 3.0. We’d need to get somewhere between 90 and 98% of the population vaccinated to bring the delta variant’s effective rate down below 1 (the point where it would die out naturally)!

That tells me this virus is going to be around for a long time — especially since the R0 for some upcoming variants might be higher. Also, I’m curious to see if the government authorizes a third dose given the minimal impact increasing efficacy has on the effective rate of spread.

Freedom!!?

About a year ago, my boss observed that this entire pandemic sitch is just a nightmare for those with analytical thought processes.. Engineering, science, analytic types. Mathematically? The country was basically in a worse place when the health orders were lifted than it was when the orders were put in place last year. That was astonishing to me. And kind of like the anti-environmentalists who don’t seem to realize they need to drink the water and breath the air … even if you’re vaccinated and have a very good probability of avoiding hospitalization? Getting sick for a week sucks. It sucked ten years ago, it’ll suck ten years from now. But, if you can mitigate your risk of feeling like an elephant is roosting on your chest for a week … what’s the reasonable thought process that leads to someone saying “I’m going to show how very free I am by getting painfully ill”?!

I mean, there are plenty of ways to partake in your American Freedoms that aren’t painful illness. Head out to the range, rent a gun for a few hours, and fire off a couple dozen 50 caliber rounds. Publish a rant against whatever part of government irked you this week. Spend the weekend attending church services for ten different religions. Hell, marvel at the fact there’s not an uninvited soldier camped out in your spare bedroom and that the cops aren’t rifling through your belongings. And that just covers the first five articles in the bill of rights.

In fact …

Article Way to enjoy it
I Spend a weekend attending services for a dozen different churches (synagogs, mosques, etc)
II Hire a gun at a range and spend the afternoon popping off 50-cal rounds
III Marvel at how your spare bedroom is not occupied by an uninvited soldier
IV Notice how the police are not rifling through your personal belongings just because they can
V, VI, VII, VIII Don’t know that I’d commit a crime just to enjoy my right not to provide evidence against myself, be subjected to cruel or unusual pubishment, or experience a speedy, public trial … but you do you.
IX Go to work?
X Oooh, experience all of the things your state does control — maybe hang at the DMV and renew your license
XI Umm … well Michigan hasn’t sued Ohio today. Does that count?
XII Well, you cannot be part of the electoral college … but you CAN vote
XII No more slaves
XIV The state isn’t depriving me of life, liberty and such.
XV My rights aren’t being abridged because of my race
XVI Taxes were withheld from my paycheque this week. Yeah!???
XVII My state has tw senators
XVIII Grab a pint!
XIX I’m a woman, and I can vote!
XX Watch the certification of the election
XXI Grab another pint!

Math Time — COVID Edition

Scott’s dad gets on our cases about being paranoid hypochondriacs (or whatever) because we’re still wearing masks and have Anya in online school for another year. The governor dropped the health orders, after all. Anya is too young to be vaccinated, but he’s safe … and kids don’t get sick anyway. Now, I don’t believe the latter two “facts” — kids do get sick, even if it’s less virulent. And I’ve never seen anything published that indicates vaccinated individuals don’t spread the virus. Just that they don’t feel unwell (which, in my mind, makes them more likely to spread it ’cause they don’t know they are sick … the Yankees having so many vaccinated people test positive sticks in my mind. They wouldn’t have known they were sick if it weren’t for what I assume is routine team-wide testing). And it’s difficult to explain to someone who has already made a decision … but the math just doesn’t support the “it’s all good” attitude people are adopting. I’m not an epidemiologist — I went to school for theoretical physics and work in computer science. I have done a lot of data mining and analysis, so I’ve got a decent understanding of the math side of epidemiology without any of the “so what do we do about it” medical knowledge. That being said … the math side of it can be helpful.

There’s a rate of spread for infections — computer viruses or human, in fact. There’s an initial rate of spread when no one has any immunity / has patched their computer (R0 to epidemiologist). If one person gets the virus, they give it to x people over the course of their infection. This is where you either see the total number of infected people trend toward zero of infinity — that is, if one infected person infects 0.5 (i.e. for every two infected people, you get one more person infected) … eventually the virus dies out. If one infected person infects ten others? This is a ever increasing progression — those ten each infect ten more for 100 infected people. Who each infect 10 for 1000 infected people. Which doesn’t seem bad — but those each infect 10 for 10,000 infected. Then 100,000. For each iteration, the number of infected people is 10^n — 10,000,000,000 is ten iterations down.

But preventative measures get taken — in one case, a computer virus caused my employer to shut down the LAN facing ports on every router in the company. Techs had to walk around with a fix-it CD, clean up every computer on a subnet, and then request the subnet be returned to the network. And, if we saw the virus propagating from that subnet? It got locked down again. Highly disruptive, but effective. And that’s where we were last spring with stay-at-home orders.

There are less severe precautions — computers have anti-virus software that look for virus-like activity for day zero identification. In human terms, that means we’re washing our hands after coming home from an outing. Or, as of last spring, wearing masks. Any of these precautions reduce the R0 value — but it can be difficult to predict exactly how much these actions will reduce the rate of spread.

Vaccines, on the other hand, have a quantified (and published) impact on spread. That efficacy and the percentage of the population that has been vaccinated scale the R0 value. The effective rate of spread is R0 * (1 – ( (vaccine efficacy) * (% of population that is vaccinated) ) ). If a vaccine prevents infection for half of the people who are exposed, then the effective rate of spread after vaccination is R0 * (1 – 0.5 * % of population that is vaccinated)). If a vaccine can prevent 90% of infections from occurring, the effective rate of spread after vaccination is R0 * (1 – 0.9 * % of population that is vaccinated)).

For convenience, I am going to ignore partially vaccinated individuals because I don’t know how effective a partial dose is at preventing transmission. The R0 published last year was around 3 — with about 40% of the population vaccinated with a 95% effective vaccine, that’s an effective rate of spread around 1.86 without other precautions being taken.

Now my numbers aren’t perfect — but this is almost a best-case effective rate of transmission. Another ten percent or so of the population is half-way vaccinated even if I don’t want to get that granular with my maths. But plenty of people got a 80-something percent effective vaccine, too. And the efficacy of each vaccine is reduced against variants. Having an effective transmission rate hovering around 2 seems, to me, like a premature time to cease taking other precautions.

Protesting the Protests

There are some people protesting the stay at home orders – I see videos from outside of DeWine’s daily briefings, and several other states seem to have similar problems. Apart from the question of astroturfing, problem is that there’s very little opportunity for counter-protests. When you go to DC, there are PETA people counter-protesting the people looking to fund medical research (animal testing). There are vegans counter-protesting people looking to increase subsidies in the meat industry. I’ve never seen an abortion protest that didn’t have both sides represented.

These ‘liberate us’ protests? These are people who don’t think they should have to stay at home – they should allowed to hang out at bars, eat in restaurants, shop, party, and … oh yeah … crowd together at protests. The people who think the stay-at-home and shelter-in-place orders are important to protect their health? Seems like a far smaller portion of them would be willing to hang out in Columbus in a protest. Even if they could find masks and whatnot.

Why drive somewhere nonessential? Your car breaks down, and you’re exposed to others (and exposing them to you). You get into an accident and you’re exposed to others (and exposing them to you). Get injured in the accident and you’re adding to the patient load at hospitals. We’re not just staying at home to avoid large congregations. We’re staying at home to create less load for emergency personnel.

Visualization: Percent of Population Infected with SARS-CoV-2

Updated graph for current infection numbers

And the states kinda like Ohio graph where I still think “distance from NYC” is a pretty significant factor in how many individuals are infected. Ohio, going on a month of kids out of school and entering week three of the shelter-in-place order, isn’t seeing the exponential growth some states with similar population numbers have encountered.

Reopening

I keep hearing Trump talk about his decision to re-open the country (and how it’ll be the biggest decision he’s ever made). Begs the question how. And I don’t mean “what is the plan to resume somewhat normal inter-personal interactions” (although the process question needs to be answered). I mean procedurally how is he going to *open* the country? He’s never closed it! Individual states have enacted various protective measures as they see fit. He really think he can overrule, say, Ohio’s shelter in place order? Issue an executive order mandating we all eat at a restaurant this weekend and … what? The FBI is gonna haul me out of the house if I don’t?

Trump Impeachment / SARS-CoV-2 Timeline

The timeline below was posted to a FB group today, but I wanted a more visual format to show how much nonsense  the “impeachment was a distraction from this serious pandemic business” story is. I cross-referenced dates in the timeline with the number of US SARS-CoV-2 infections using archived data from Johns Hopkins through 23 March and the dataset from COVID Tracking (which is current but doesn’t go back far enough to provide correlation with the impeachment dates). There is some overlap, but it’s not like Trump was completely focused on impeachment activity before 05 Feb. Campaign rallies and golfing were his choice distractions. Both of which continued well after the impeachment trial ended.
Timeline with a few additional impeachment-related events added and location info for rally and golf events:
Date # US Infections Detail
18-Dec-2019 0 House Impeaches Trump
18-Dec-2019 0 Trump campaign rally – Michigan
21-Dec-2019 0 Trump maybe golfs – Florida
22-Dec-2019 0 Trump maybe golfs – Florida
23-Dec-2019 0 Trump maybe golfs – Florida
24-Dec-2019 0 Trump maybe golfs – Florida
26-Dec-2019 0 Trump golfs – Florida
27-Dec-2019 0 Trump maybe golfs – Florida
28-Dec-2019 0 Trump maybe golfs – Florida
29-Dec-2019 0 Trump golfs – Florida
30-Dec-2019 0 Trump golfs – Florida
31-Dec-2019 0 Trump maybe golfs – Florida
1-Jan 0 Trump maybe golfs – Florida
2-Jan 0 Trump maybe golfs – Florida
3-Jan 0 Trump campaign rally – Florida
4-Jan 0 Trump maybe golfs – Florida
5-Jan 0 Trump maybe golfs – Florida
8-Jan 0 First CDC warning
9-Jan 0 Trump campaign rally – Ohio
14-Jan 0 Trump campaign rally – Wisconsin
16-Jan 0 House sends impeachment articles to Senate
18-Jan 0 Trump golfs – Florida
19-Jan 0 Trump maybe golfs – Florida
20-Jan 1 First case of corona virus in the US, Washington State.
22-Jan 1 “We have it totally under control. It’s one person coming in from China. It’s going to be just fine.”
22-Jan 1 Impeachment prosecution’s opening arguments and presentation of evidence
23-Jan 1 Impeachment prosecution’s opening arguments and presentation of evidence
24-Jan 2 Impeachment prosecution’s opening arguments and presentation of evidence
25-Jan 2 Impeachment defense presentation
28-Jan 5 Trump campaign rally – New Jersey
30-Jan 5 Trump campaign rally – Iowa
31-Jan 7 Impeachment Senate vote against calling witnesses & travel restriction from China
1-Feb 8 Trump golfs – Florida
2-Feb 8 Trump maybe golfs – Florida
2-Feb 8 “We pretty much shut it down coming in from China.”
5-Feb 11 Impeachment Senate votes to acquit. Then takes a five-day weekend.
10-Feb 11 Trump campaign rally – New Hampshire
12-Feb 12 Dow Jones closes at an all time high of 29,551.42
15-Feb 13 Trump golfs – Florida
19-Feb 13 Trump campaign rally – Arizona
20-Feb 13 Trump campaign rally – Colorado
21-Feb 15 Trump campaign rally – Nevada
24-Feb 51 “The Coronavirus is very much under control in the USA… Stock Market starting to look very good to me!”
25-Feb 51 “CDC and my Administration are doing a GREAT job of handling Coronavirus.”
25-Feb 51 “I think that’s a problem that’s going to go away… They have studied it. They know very much. In fact, we’re very close to a vaccine.”
26-Feb 57 “The 15 (cases in the US) within a couple of days is going to be down to close to zero.”
26-Feb 57 “We’re going very substantially down, not up.” Also “This is a flu. This is like a flu”; “Now, you treat this like a flu”; “It’s a little like the regular flu that we have flu shots for. And we’ll essentially have a flu shot for this in a fairly quick manner.”
27-Feb 58 “One day it’s like a miracle, it will disappear.”
28-Feb 60 “We’re ordering a lot of supplies. We’re ordering a lot of, uh, elements that frankly we wouldn’t be ordering unless it was something like this. But we’re ordering a lot of different elements of medical.”
28-Feb 60 Trump campaign rally – South Carolina
2-Mar 98 “You take a solid flu vaccine, you don’t think that could have an impact, or much of an impact, on corona?”
2-Mar 98 Trump campaign rally – North Carolina
2-Mar 98 “A lot of things are happening, a lot of very exciting things are happening and they’re happening very rapidly.”
4-Mar 149 “If we have thousands or hundreds of thousands of people that get better just by, you know, sitting around and even going to work — some of them go to work, but they get better.”
5-Mar 217 “I NEVER said people that are feeling sick should go to work.”
5-Mar 217 “The United States… has, as of now, only 129 cases… and 11 deaths. We are working very hard to keep these numbers as low as possible!”
6-Mar 262 “I think we’re doing a really good job in this country at keeping it down… a tremendous job at keeping it down.”
6-Mar 262 “Anybody right now, and yesterday, anybody that needs a test gets a test. They’re there. And the tests are beautiful…. the tests are all perfect like the letter was perfect. The transcription was perfect. Right? This was not as perfect as that but pretty good.”
6-Mar 262 “I like this stuff. I really get it. People are surprised that I understand it… Every one of these doctors said, ‘How do you know so much about this?’ Maybe I have a natural ability. Maybe I should have done that instead of running for president.”
6-Mar 262 “I don’t need to have the numbers double because of one ship that wasn’t our fault.”
7-Mar 402 Trump golfs – Florida
8-Mar 518 Trump golfs – Florida
8-Mar 518 “We have a perfectly coordinated and fine tuned plan at the White House for our attack on CoronaVirus.”
9-Mar 583 “This blindsided the world.”
1-Mar 583 Travel lockdown from Europe.
13-Mar 2179 State of emergency declared
17-Mar 6421 “This is a pandemic,” Mr. Trump told reporters. “I felt it was a pandemic long before it was called a pandemic.”
18-Mar 7783 It’s not racist at all. No. Not at all. It comes from China. That’s why. It comes from China. I want to be accurate.
23-Mar 42152 Dow Jones closes at 18,591.93
25-Mar 63928 3.3 million Americans file for unemployment.
30-Mar 160530 Dow Jones closes at 21,917.16
2-Apr 239099 6.6 million Americans file for unemployment.

 

Is it helping?

Schools in Ohio have been closed since 17 March (and a lot of districts stayed home on 16 March). Restaurants have been in delivery and carry-out mode for about the same length of time. We’ve been under a stay at home order since 24 March. And the important question is … is it helping? That’s a difficult question to answer because epidemiological predictions have very broad ranges because most of their inputs are so unknown … and the limited testing makes the data being compared wildly inaccurate. But we’ve only got the data we’ve got, so I thought I’d run some comparisons to see how Ohio is faring.

I selected the four states closest to Ohio in population — PA, IL, GA, and NC. Because these states all identified their first case well before Ohio, I added CT because the first case identified there was 08-Mar and Ohio’s first cases appear on 09-Mar.

State 1st Case Population
PA 6-Mar 12,801,989
IL pre 4-Mar 12,671,821
OH 9-Mar 11,689,100
GA pre 4-Mar 10,617,423
NC pre 4-Mar 10,488,084
CT 8-Mar 3,565,287

It looks like our curve is flattened — although North Carolina, where the first infection was identified earlier than Ohio and their their stay at home order was issued on on 27 March, has identified a thousand fewer cases as of yesterday.

Is proximity to NYC a major factor? CT and PA (as well as NJ, which has a relatively high number of cases) are all right there. But Georgia and Illinois are farther away from NYC than Ohio. Is the number of tests a factor in these case numbers? I’d expected a higher correlation between the number of identified cases and the number of tests administered. GA and CT have fewer total test reports (positive + negative tests) and have more infected people. NC has more reported tests, but fewer cases than OH. PA and IL have more reported tests and more infected people.

Commercial and residential demand

The great toilet paper run of 2020 … may not be panicked hording the way it is portraits in the media. I work from home, but Anya is in school (well, was). And used the bathroom there a few times a week. Back when I worked from an office, I used that bathroom once or twice a day. That’s somewhere between a 30 and 50 percent increase in home bathroom usage. Per person, per weekday.

Food is apt to have a simialr shortfall – kids aren’t eating lunch at school, uni kids are staying home, office workers aren’t going out to lunch. Plus people at home have more time to make breakfast … So goodbye eggs at the grocery store.

Now, if I am right, that means there’s a surplus of the one-ply commercial stuff no one likes. There’s not a shortage – there’s a surplus in the commercial supply sector and a corresponding shortage in the retail one. Which is a lot easier to solve – check out Staples or online warehouses that specialize in office supplies. And restaurant supply centers may welcome smaller scale orders.