Category: Covid-19

I spent a couple days with Excel, futzing with John Hopkins data for Covid-19. The result is charts showing per-capita infections for the 90 most populous countries (confirmed cases per 100K people). They divide up fairly neatly into 5 groups.

First of all are countries that contained the virus quickly. Except for one city in China, their hospitals were not overwhelmed. Life is close to normal for them, now.

This group is about 27% of the global population, mostly in East Asia. That region had a scary experience with the SARS epidemic, so they knew just what to do for the Covid-19 outbreak: quarantines, contact tracing, testing. Local lockdowns when those weren’t enough. Almost everyone wore masks in public, even before the pandemic. They do help.

Next are countries with a low rate that is still growing. These are about 20% of global population. Almost all are Third World or close. That means the low numbers could be from lack of testing, rather than lack of disease. Australia (thicker line) is the outlier. They contained the outbreak for several months, but Covid-19 has recently started to increase again. It’s mid-winter in the Southern Hemisphere, which may be the culprit. That will also be the theme for other countries, later.

For the next three graphs, the vertical scale is compressed by 5x compared to the previous two.

The “getting serious” middle group has exponential growth, with infection rates that are just starting to be dangerous. Columbia (thick blue line) and Mexico (thick red line) are the worst. India (thick green line) is lowest per capita, but it may be under-reported. These countries make up about 36% of global population.

The fourth group had scary rates of infection in March to April, but they are mostly contained for now. Covid-19 snuck up on them, but all these countries responded well. All are First World countries, with 5% of global population.

Then there are the 15 countries already facing a serious impact from Covid-19, with infection counts that are still increasing. You might say these are the basket cases.

Worst of all is Chile (black line), which currently has 1,527 confirmed infections per 100,000 people. That’s over 1.5% of their population. It made the graph too tall for WordPress to handle, so I had to cut it off at the top. Peru (green) is #2 with .91% infected, Bolivia is #11, and South Africa (purple) is #12 and growing fast. Argentina is also exponential, but just below the cutoff I used. All five of those countries are in their winter seasons. That probably is a very bad omen for the Northern Hemisphere, looking ahead to Fall.

The next most bad-growing-worse countries got that way because of politics. USA (#3 red), Brazil (#4 yellow), Saudi Arabia (#6 orange) and Russia (#7 gray) all have autocratic rulers who started out denying that Covid-19 would be a problem. When proved wrong, they still didn’t do much to help fix things. Sweden (#5 light blue) tried a bold experiment, and didn’t shut down. They ended up with more infections, and an economy no better off than the rest of Europe.

All this stuff is just numbers, but it represents many people’s lives. Looking at that steep red line for the US makes me very angry, and very sad. How did we fuck up so badly? But I’d better stop now.

Dennis Kolva
Programming Director
TurtleSoft.com

New York State has been reopening gradually, with a minimum of 2 weeks between each phase. Ithaca entered Phase 4 on Friday, along with most of Upstate NY. Dine-in was allowed in Phase 3, but many restaurants are still takeout-only, or completely closed. All gyms are still closed, as are most bars. Large public events are still forbidden, and masks are required for all indoor public spaces. Outdoors, mask use seems to range from 0% to 70%, depending on location and time. I think it’s declining.

The R_t tracker site currently shows 33 states with increasing infection rates, and only 17 decreasing. New York had a low number through most of April and May, but it gradually inched up. Today it is exactly 1.0. If it stays there, the number of daily infections will remain the same indefinitely.

Since the current number reflects conditions from a couple weeks ago, it is very possible that NYS has reopened too quickly. The ideal balance between safety and economy probably was back at Stage 2 or 3. We will find out about that in a few weeks.

At least Covid-19 is close to contained around here. The county health department is doing almost 1500 tests a week, with only two of them positive on average. Nobody has been hospitalized here since May 29. Nobody local has died yet. Conditions are worse in the bigger cities within a few hours drive, but still tolerable. Even New York City is inching back from the brink.

Sadly, some other states are starting to become very dire. Most of the US reopened too quickly. Governors are starting to crack down, but they will soon find out what happens with exponential growth and a time lag. For example, right now the estimated R_t for Florida is 1.4. That means cases will almost triple before any impact shows, from remedies started today. Florida already has 9500 new daily cases, so it probably will get worse than New York City was in April, and soon.

It’s like watching a slow, enormous train wreck. Too bad it’s not just a train, but the whole frigging country.

Meanwhile, the big question locally is what happens after Cornell reopens this Fall. They just issued a 97 page report about it, but it leaves many details dangling. I think a lot of their plans ignore what students in their late teens and early 20s are like. The local economy is very dependent on the two colleges, so it’s going to be a very interesting ride.

I am pushing 70, so it makes sense to continue social distancing and mask-wearing, even though risks have declined. Most likely that will continue for at least another year. Masks suck, especially in hot weather, but they are a lot more comfortable than a respirator.

To cut down on exposure, the Turtlesoft office is currently open just one day a week. We probably will keep that schedule for most of the summer. Maybe longer. User support is still available by email, and usually by phone.

I spent the stimulus money on scaffolding. So I’m stripping 3 layers of ancient asphalt roofing off my house, and installing metal. It’s also a chance to finish up the exterior painting a bit more safely, and hang new gutters. After that, we’ll see. If QT seems plausible, at some point Goldenseal Pro will consume much more time again.

Dennis Kolva
Programming Director
TurtleSoft.com

According to OpenTable, restaurant reservations in the US increased to 33% of normal, as of yesterday. It varies a lot between states: Rhode Island is close to 100%, while New York, Hawaii and DC are still under 10%. Those numbers are probably a decent indicator for general levels of reopening. The sharp dip yesterday was because it compares to Father’s Day 2019.

The R_t tracker website now shows 19 states with growth multipliers above 1. Arizona leads the pack, while most states in the Northeast are near the bottom. New York was #1 for new cases during most of April and May, but it fell to #8. The action has shifted south and west. Specific numbers vary with each update, but the trend has been consistent.

JUNE 19 UPDATE: the R_t tracker revised their calculation method today. They now show 26 states with growth rates greater than 1 (daily infections increasing). Several states are starting to look very scary.

Since economies are still ramping up, the best guess is that the growth rate will continue to increase. At some point, states with a growth rate much above 1 will run into trouble. Presumably they will then take action to reduce infections.

That means the R_t rate will probably hang out close to 1, pretty much indefinitely. For every infection that ends (via recovery or death), a new one will take its place (on average). Of course there will be large variations in different places.

In a previous post, I talked about containment. It can happen globally if every country reduces infections to zero, until the virus disappears. That’s what happened with SARS and MERS, the two previous coronavirus epidemics. Sadly, it seems very unlikely that containment for this one will ever happen in the US, nor globally. Covid-19 is just too well established. A few island nations have reached zero cases, but that’s still not great. They constantly will need to quarantine all visitors, or risk fresh outbreaks.

For a non-contained disease, the only other end game is herd immunity, which occurs when a critical mass of people are immune. If non-immune people are rare enough, then the disease gradually stops spreading. The amount of immunity needed depends on a lot of factors, but it’s usually between 60% and 90% of the population.

With herd immunity, the disease may eventually die out completely. It may stick around as a minor problem. Or it may return in surges, as each previous wave’s immunity fades away.

There isn’t anywhere with herd-level immunity to Covid-19 right now. New York City is probably the closest, with about 20% showing positive antibody tests. Elsewhere in the US, it’s rarely over 5%.

Doing some very quick math, if 3 months of infections made 5% immune, then it will take 45 months to hit 75%. The curve will be flat, but very wide.

Of course, vaccines are a great way to increase herd immunity very quickly, without all the sickness and death. In the US, roughly 60% of children and 45% of adults got a flu shot in 2018/9. For Covid-19, a recent survey showed 49% who plan to get a Covid-19 vaccination. 20% are unwilling, and 31% not sure.

That probably isn’t enough to attain herd immunity in one swell foop, but it’s close. After a vaccine is available and after half the anti-vaxxers get infected, the US will hit herd levels of protection.

Dennis Kolva
Programming Director
TurtleSoft.com

In past posts I’ve talked about exponential growth when it’s fast and scary, and when it’s close to flat. But there’s also negative growth, with a multiplier of less than 1.

Right now, the R_t Tracker website shows all but four states with R_t like that, from Arkansas (.99) all the way down to Alaska (.63). If they can stay below 1 for long enough, Covid-19 eventually will reach containment.

Here is a chart of exponential growth rates less than one. It shows how the number of new cases of Covid-19 will decrease for each R_t multiplier. The lower the number, the faster the approach to zero.

Right now there are four states with R_t values under .82: Alaska, Hawaii, Vermont, and Montana. All have relatively small, isolated populations. They never had many cases to begin with, and are close to zero now. With local containment achieved, their biggest worry is new cases that come in from elsewhere.

The next lowest state is Connecticut, with an .83 multiplier. They had over 2000 new infections at the daily peak, but the average is about 600 now. At current rate of decline, it will take roughly 50 days to drop by a factor of 10 (to 60 new cases per day). Another 50 days gets it to 6 new cases. The theoretical curve never reaches zero, but with actual humans it’s possible to get there eventually.

Other states with higher R_t values will decline more slowly. Some will be very, very slow.

Exponential curves and R_t charts are pretty, but they are just theory. Actual containment depends on what people do each day: how much they stay home, how much they congregate, whether they wear masks. Just as important is the work of state and local health departments. They have battled all sorts of diseases over the past century, and this is just another for them.

To contain a disease, health departments do whatever it takes to reduce the infection growth rate to something less than one, then keep it that way.

Vaccines are the best way to contain a disease. Many folks are working on them for Covid-19. Next best is contact-tracing and quarantines. If those aren’t enough, then the only recourse left is massive social distancing. Economically, it’s an extremely painful option, but less bad than having many people suddenly sick and dying at the same time.

The ideal way to conquer a dread disease is to get global containment: already accomplished for smallpox, and almost completed for polio. Total containment is very hard work. Health workers must go into poor and war-torn regions and vaccinate enough people to reach “herd immunity”. It also requires plenty of contact-tracking and isolation until the last cases are completely gone. One sad consequence of Covid-19 is that it sets back the efforts to eradicate polio.

The R_t tracker site seems like a very useful tool. However, R_t is based on actual test results. It lags by at least a couple weeks, because it takes time for infections to develop, tests to be processed, and data to be entered into the pipeline. Today’s numbers reflect conditions from when state just started to reopen in early May. The social distance scorecard is probably the best way to predict the future, but it’s a very crude guide based on smart phone locations. It doesn’t adjust for mask use, indoor vs outdoor contact, or sanitation measures. Lately it rates most of the US at D or F, but I think reality is a grade or so better.

As social distancing relaxes, it will be interesting to see how much it affects the numbers. States will probably jump around with changes in weather, policies and people’s behavior. The risk is always there for an outbreak, with a sudden return to scary exponential growth. A single ‘super-spreader’ event can push any state to well above 1.

SARS and MERS were caught soon enough to be 100% contained. Covid-19 became too global, and it’s unlikely to ever reach full containment. Even with a vaccine. However, it can become like measles, influenza and other diseases that are controlled enough to not cause big catastrophes.

Dennis Kolva
Programming Director
TurtleSoft.com

Two months ago, I first blogged about Covid-19. Since then, much has changed. Way more than I expected back then.

OpenTable has a spreadsheet for restaurant visits in 36 states, plus a few other countries. Here is their US data in chart form:

It only took two weeks to drop from normal (Mar 8) to zero (Mar 22). Many Governors shut down their states during that period, but the public was usually ahead of them by a few days. The collapse was close to simultaneous across the whole US, and also in Canada and most of Europe. Reopening started a couple weeks ago in a few states and countries, but it’s still very sparse.

What will Covid-19 do as social distancing relaxes? It may fade out for the summer as flu does. Maybe contact-tracing and moderate distancing will be enough to keep it controlled. Maybe there will be exponential outbreaks. Most people are taking it slow, which helps. Those who rush off to crowded bars and church services will be our guinea pigs.

Meanwhile, most of what I said back in March still makes sense. Here’s a slightly revised recap of my advice for construction companies:

• Stagger work hours & locations. The less time people spend close to each other, the slower disease spreads.
• Be clear with employees and subs. Send them home ASAP if sick, or don’t even let them come in. This might be time to start paying sick leave. Emphasize the need for testing and self-quarantine. Get a non-contact thermometer, and check people for fever.
• Be clear with clients. If you work in client homes, let them know your plans. You might need to add plastic sheeting barriers, and sanitize more thoroughly at day’s end. Switch to outdoor work, if possible.
• Take the usual precautions. Wash hands often. Sanitize surfaces that are touched frequently. Cancel group events. Practice social distancing. Listen to local & state health departments. Most are developing reopening guidelines now. The rules probably will be tweaked as time goes by.
• Wear face masks. Back in March, CDC said not to use masks. Fortunately, their guidance has changed. I think masks may be the #1 way to stay safe, and still run a business. It’s worth elaborating.

Why wear face masks?

Covid-19 spreads mostly by respiratory droplets, which come in a wide range of sizes. Coughing and sneezing produce tons of them. Talking creates plenty. Even normal breathing makes some. The bigger droplets blow out a few feet, then drop quickly. They coat everything with virus gunk- that’s why it’s important to wash hands, and not touch your face.

The smaller droplets (aerosols) linger in the air. They can travel 20+ feet on air currents. Inhale, and they go straight into your airways and lungs. There is debate about how important aerosols are for Covid-19 transmission, but evidence is pretty good that they do cause many infections. Indoor spaces are more risky, especially when people are together there for hours. Air circulation (air changes per hour) makes a big difference.

Snot/saliva/ejected droplets from an infected person will have between 6 million and 2 billion viruses per cc (1 cc = 1/5 teaspoon). Fortunately, the droplets are very small, so only some contain a virus. Unfortunately, there are lots of them. Speaking produces 1,000 to 10,000 small droplets per second. Each cough makes a few thousand mostly bigger ones. Sneezes can make 40K, some of them huge.

Whether a droplet infects you is a matter of chance. Even if you inhale or ingest a virus, many of them get trapped in mucus and never reach a cell. Eventually they exit inside a booger. Others are killed by your body’s innate immune system, which has many anti-viral tricks. It takes a reasonable number of incomings, for even one to infect a cell.

Face masks work in both directions, to prevent that. Outbound, they catch virus droplets that infected people emit into the air and onto surfaces. They make other people safer. Inbound, an N95 removes 95% of aerosols, and almost all larger droplets. Surgical masks are less effective for inbound protection, but still pretty good. Even a bandana is better than nothing.

If everyone is masked, very little gets past the two different filters: one on the cougher, and one on the coughee. The risk of infection goes way, way down. Masks also reduce the odds of getting a really bad infection. I didn’t find any specific data for the effect of initial doses for Covid-19. However, almost all diseases are more deadly if you start with a lot of virus, rather than just a little.

It’s a matter of exponential growth. Once a virus invades a human cell, it starts producing duplicates. Those infect other cells, and it snowballs. The virus count zooms up inside you on a scary steep curve, just like it did globally in March.

Your adaptive immune system has many great ways to kill pathogens, but it takes time to ramp it up. If you started with one virus-infected cell, your defences probably can defeat the infection before it gets too big. You may not even notice any symptoms. Start with a few thousand, and you’ll be very sick. Start with a million or a billion, and you’ll probably die. That’s why Covid-19 kills young, healthy medical workers, especially when they don’t have proper PPE. They absorb a massive dose, the virus starts off strong, and it beats their immune response.

With masks all around, good sanitizing and careful air circulation, you probably can run safe construction projects. At least til Fall.

Dennis Kolva
Programming Director
TurtleSoft.com

As a math nerd, I have a huge crush on Vi Hart. Usually she makes fun math videos, but she just released one that talks about how to unwind from Covid-19. The timeline is probably too optimistic, but otherwise it seems pretty sensible. Political will isn’t there yet to do it nationally, but maybe a few states can start that way.

The founders of Instagram just made a website that tracks R_T, the current rate of increase for Covid-19 in each state. If it’s above 1, infections will increase exponentially. If below 1, they’ll decrease. Just one number for each state, with graphs of how it has changed over time.

Reddit has a few sub-reddits that cover the virus, with interesting links and lively discussions. r/Coronavirus is the most active, with many armchair epidemiologists. r/Covid19 is more science related, with research papers. r/CovidProjects is about mask production and similar pandemic efforts. For random, interesting science, r/Biology and r/Science are also good.

Science magazine has free access to its Covid-19 research articles. Research papers are hard to digest, but they usually have an abstract that is more readable.  Science also publishes articles for the general public, such this one about the way Covid-19 sickness plays out.

Meanwhile, I think the Internet has a big problem with bad information. Rumors and propaganda have always been out there, and people have always believed them. But, production values are better now. It’s easier to present compelling arguments that are wrong. Even dangerous. Bad info makes people do stupid stuff like burning cell towers.

The antidote is science. There are over 30,000 scientific journals out there: everything from Abnormal Psychology to Zygote. Most are extremely specialized, but the best of their research makes it into more general magazines like Nature, Science and Scientific American.  I devoured the latter as a kid, but moved on to the harder stuff.

Science research papers usually take a year or more to be published. The delay is mostly because of peer review. Other experts in the field check them over with a fine-tooth comb. The authors then revise and re-revise. Sometimes more experiments need to be run. Sometimes they need a complete do-over. It’s a grueling process, but the result is accurate info.

The system isn’t perfect, but it’s way more trustworthy than Facebook, Fox News or talk radio.  I’d highly recommend giving it a try. Things have sped up a bit for Covid-19, and serious papers are starting to come in.

Dennis Kolva
Programming Director
TurtleSoft.com

There’s something called the Dunning-Kruger Effect, which says that incompetent people don’t see their own lack of skill. The name comes from a 1999 study, when a Cornell research team tested undergrads for humor, grammar and logic ability. The subjects judged their own talent to be above average at 55% to 75%. Actual competence ranged from 0% to 100%.

The idea has been around for a long time, as in “a little knowledge is a dangerous thing” or “hold my beer”. The paper won an Ig Nobel prize in 2000 because it was so obvious.

I suspect that the results would be different if based on small business owners in their 50s or 60s, rather than late-teen/early-20 Ivy League students. From hard experience, many people learn how to accurately rate their own competence. All it takes is a couple of rashly-made construction estimates, and you quickly gain some (expensive) humility. Likewise, it’s hard to run a successful business long-term if you can’t judge skill levels in yourself and others, and respect them.

Of course, not everyone matures with age. Wisdom seems to come from hard knocks, and some folks are rich enough, pretty enough or charismatic enough to avoid them. Unfortunately, because folks like that are attractive, they often gain power as politicians.

I’d say the recent history of Covid-19 is full of Dunning-Kruger. Too much prideful incompetence in leaders who believe they are much smarter than a virus.

Epidemiologists have been predicting for years that something like Covid-19 would happen. It doesn’t take rocket science to look at H1N1, SARS, Ebola and MERS, and guess that more might be on the way. Those scientists are the real experts, but their voices have too often been drowned out by people in power who have a “gut feeling” that they know better.

Science is hard. It requires patience and discipline, and a willingness to endure tedium without much reward. With rare exceptions, the folks that do it are not charismatic. But, the whole purpose of science is to understand some small bit of reality better. Successful scientists need to be extremely competent in their field.

The path into this mess has many people to blame, or maybe it’s just normal human biases that are at fault. Getting out will need a ton of competence, or it’s going to get much, much worse. The problem is not just the disease, but all the social and economic fallout.

There is a silver lining to all the mistakes: they will provide great data for scientists, over the next few years.

Norway and Finland shut down, but Sweden didn’t. Their counts will be interesting. Angela Merkel is a former research chemist, and Germany has unusually low death rates. Is there a connection? Leaders in Russia, Brazil and the US played down the risks much later than most other countries. That will create interesting data. China and Iran covered up. If their actual numbers ever come out, it’s bound to be worth something.

Dennis Kolva
Programming Director
TurtleSoft.com