Tag Archives: covid-19

“breakthrough malaria vaccine”

Forbes reports a promising malaria vaccine produced by “the Oxford University team behind the Oxford-AstraZeneca Covid-19 shot”. It doesn’t say whether the technology developed for the Covid shot did anything to hasten this vaccine along. It still has some testing and licensing to go through.

The article has some horrifying stats on malaria, which is a major killer of children.

229 million. This is roughly how many cases of malaria there were around the world in 2019, according to the WHO. Around 400,000 died from the disease, which consistently ranks as one of the top ten causes of death in low income countries, despite falling significantly in recent years. Africa is disproportionately affected by the disease, with over 90% of cases occurring there. Children account for almost 70% of deaths. 

Forbes

Doing the math here (journalists, why can’t you do the math for me?), the death rate is about 0.2% of cases. If this is the death rate in Africa (but it could be higher if Africans receive less or lower quality treatment) and the other percentages hold, around 250,000 children in Africa die of malaria each year. From Our World in Data, the death toll in Africa from Covid-19 over the last year is around 120,000.

It occurs to me that countries where people deal with horrible diseases that mass murder children every year might be less horrified by Covid-19, which kills a fraction of older people. Of course I am not saying the lives of poor people have less value or the lives of older people have less value (although this is a perennial debate and people of all ages have a variety of reasonable opinions), but I think you can legitimately ask whether an available dollar should be invested in stopping Covid vs. other horrible diseases people have been dealing with for decades.

and vaccinated people don’t spread the virus…much

The confusion among the public continues. Basically, vaccinated people have a 10% or so chance of getting infected Covid-19 if they are exposed to it. If they are infected, they won’t get seriously ill but they might be able to spread it to un-vaccinated people who might then get seriously ill. If you multiply the probabilities, the odds of getting infected by a vaccinated person and then getting seriously ill are low, and the odds that a given person we are exposed to will be vaccinated is getting higher all the time, so the risk is getting lower all the time. Vaccinated people are being asked to wear masks to help that risk drop as quickly as possible. BUT half the population is hearing “the government is sugar-coating the science” and the other half of the population is hearing “vaccinated people are likely to spread the virus”. Neither of these messages is accurate in my view – I’m hearing the risk is low and getting lower, and we all need to get vaccinated to get the risk as low as possible (which will not be zero, but we can all move on to worrying about other diseases such as antibiotic-resistant syphilis).

about 80% protection against Covid-19 reinfection in a Danish study

When scientists are saying “we are not 100% sure” people who have had Covid-19 will have some immunity to reinfection, many smart people I know are hearing “people who have had Covid-19 have no immunity to infection”. Similarly, when scientists say they are not absolutely sure vaccinated people will not spread the virus (although they are quickly changing their tune on this one as they look at the evidence), people are hearing that vaccinated people are spreading the virus. Here is at least one study showing that when people who had a confirmed infection were tested again three months later, protection against reinfection was pretty good but not perfect at about 80%. It appears to have been lower in people over 65 at about 50%.

The CDC and others have also thrown out 3 months as a minimum amount of time they are confident people are protected against reinfection or protected by a vaccine. I think this is just a conservative estimate in the face of limited information, but again the public is hearing “no protection after 3 months”. In this study, they tested again after 6 months and found no decrease in the level of protection (still about 80%).

So my view is that logic suggests being infected would provide at least some protection against reinfection and being able to spread the virus, and the same for vaccination. I say this because this is how other diseases work. And now the data are backing that up. The science and public health policy communication are still pretty bad, and like a toxic spill, bad communication that takes a few hours can take years to clean up on the surface and there will still be puddles of toxic mess for decades whenever you turn over a rock.

What wild animals were at the Wuhan market?

It seems that the efforts to trace Covid-19 back to bats in the Wuhan province are pretty inconclusive. SARS and MERS were both definitively (?) traced back to bats, so people seem to have jumped to this conclusion. “Similar” viruses have been found in bats, but bats have all kinds of things and the family of coronaviruses seems to be extremely common. The WHO team does say it is extremely unlikely that any of the “several” laboratories studying coronaviruses in the city would have made a mistake leading to emergence of this virus. (This alone raises a few questions for me. Is it unusual for a city the size of Wuhan in China or other countries to have several laboratories with coronaviruses lying around? Or do most big cities have some kind of epidemiological laboratory, and the family of coronaviruses is so common that almost any lab would have examples of it in the fridge? What about the dangerous ones.) They also say definitively this is a natural virus, not a genetically engineered one.

I’ve been to “wet markets” in Singapore and Thailand, which could well be tame compared to the one in Wuhan, I have no idea. I would hypothesize that you have a lot of people working, shopping, and eating in very close proximity to each other. Sometimes you have people doing grosser things, like smoking, or spitting. Cats and dogs sometimes roam freely. And sometimes these markets are air conditioned, I have seen it both ways. So if someone already had the virus, it might have spread between people in the market and have nothing particularly to do with food or wild animals.

But I found it interesting to read what wild animals were actually for sale in the Wuhan market. Do people eat bats, or keep them as pets? (And before you judge as a westerner, be aware people in other cultures are just as horrified by some of our habits and things we eat as we are by some of theirs.)

The so-called wet market had 653 stalls and more than 1,180 employees supplying seafood products as well as fresh fruit and vegetables, meat, and live animals before it closed on Jan. 1, 2020. Days before, 10 stall operators were trading live wild animals, including chipmunks, foxes, raccoons, wild boar, giant salamanders, hedgehogs, sika deer. Farmed, wild and domestic animals were also traded at the market including snakes, frogs, quails, bamboo rats, rabbits, crocodiles and badgers…

Bloomberg

So no bats mentioned. I also find myself thinking about the various “bird flu” and “swine flu” scares of the past. It is often human-livestock contact that gives rise to concerning pathogens, so we should keep that in mind. And of course, there are still plenty of deadly pathogens being spread by mosquitoes, fleas and ticks while we are fixated on this one (admittedly horrific) unusual coronavirus incident.

more free time at home = more babies?

The answer is no. Early in the pandemic, I heard people suggesting that having healthy young couples home more with time on their hands would result in a baby boom. The data show that the opposite is true. On aggregate, people actually make somewhat rational economic decisions about having children. When times are uncertain, a fraction of people decide to postpone plans they might have had to have children, and a certain fraction of those people either miss their window or just change their minds. This shows up in the data.

The article acknowledges that immigration is a potential answer to this. But it is difficult politically, and even if you can convince your population that it is a good idea, you need a good plan to make sure the immigrants can make a positive economic contribution, and you need a plan to ease them into your culture. This doesn’t mean erasing their culture, religion, or language, of course, but nor do you want your culture, religion, or language to change massively in a short time or your country may lose its sense of national identity. Having a sense of national identity while still being relatively trusting and tolerant is a balancing act, and my thought is that you want to allow change but try to make it slow and gradual. Maybe we need a Federal Reserve of Cultural Change to manage this rate.

As a working parent, I also recognize that spending more time at home does not mean more free time for everyone. Working from home full time and taking care of young children who are also home all the time, with no babysitters or minimal support from grandparents and extended family, has been very difficult for many people, including yours truly. If you are not in this situation, those of us who are may chafe a bit when you tell us how “bored” you are. But I also recognize there have been no happy mediums, with part of the population stressed out of their minds and half bored out of their minds, and some of the people who are bored (like grandparents) wishing they could help more but unable to.

some new Covid-related numbers

Here are some new numbers, because I like numbers.

  • The CDC is citing the 100 cases per 100,000 population per day number as the threshold for “high transmission”. Here in Pennsylvania, our health department has been citing this number for when school should go all virtual. But the CDC says elementary schools should be having hybrid (reduced attendance) school right now. Here in Philadelphia our public school children have not been given this chance at any time since March 2020, and it is uncertain whether it will happen before the end of the school year in June. (I’m writing on Sunday, February 14).
  • New data on effectiveness of masks: something like 70-100%, and these studies cited were mostly in public or job settings, not medical settings.

another way to look at slipping U.S. life expectancy

Just in case we need another metric to believe that the U.S. is slipping behind its peers, there is this new study from Lancet, summarized in a Quartz article:

…if the US had a life expectancy equal to the average of countries of comparable wealth (in the study, the group is identified as G7 countries: Canada, France, Germany, Italy, Japan, UK, and US), its population would be nearly half a million more.

It’s not a new phenomenon. The US has trailed the rest of the advanced world in life expectancy since the 1980s, and it’s now 3.4 years shorter than the average of other G7 countries in 2018, the last year for which international data is available. On average, in 2018, people in G7 countries had a life expectancy of 81.9 years, while in the US (prior to Covid-19) it was 78.5 years. In 2018 in Japan, the G7 country with the highest life expectancy, it was 84.2 years.

Quartz

Note that the average we are comparing the U.S. to presumably includes the U.S., so the gap between the U.S. and its peers would be even slightly worse if we were just comparing the U.S. to the average of its peers. Japanese people are living 5-6 years longer than us, on average. This is before Covid-19, of course. Checking Our World in Data, Japan has a reported death rate from Covid-19 of about 55 per million population, and the U.S. of about 1,500 per million population! (I don’t use exclamation points lightly on this blog.)

fun with coronavirus math

Let’s do some coronavirus math! This is a word problem, kids. I’m writing on January 14, 2021, and this post will be horribly outdated, but possibly of historical interest, when you read it.

The total number of cases confirmed to date as of today, in the U.S.: “23.1 million+” (New York Times)

The CDC’s ratio of actual cases to confirmed cases: 7.2 (CDC)

Number of cumulative cases in the U.S. so far: 23.1 million * 7.2 = 166 million (166,320,000)

Population of the United States: 328.2 million (Google)

% of our population that has had the coronavirus = 166 / 328.2 = 51%

% of our population that has been vaccinated: 3.1% (Financial Times)

But all other things being equal (which I am sure they are not), 51% of the people vaccinated will have already had the coronavirus, so the vaccine so far adds 1.6% to 51% of our population. Call it 53% to be generous.

We have heard a variety of estimates on what constitutes herd immunity, but the number 70% seems to be sticking at least in the media (I don’t have a source handy, and need to go do some other things now.) So we might not be that far off. The (painfully) slow but steady vaccine rollout tortoise will eventually get to the finish line, people are continuing to get infected at high rates every day in the meantime, and nobody wants to see another wave from the new variant, but if and when it hits us it might push us over the mark (at a horrific human cost, of course).

One last thought is that at the moment, I suspect we are immunizing people who are more likely to have already had an infection than the population as a whole. We are being told this is the most ethical approach, or the quickest way to lower risk for the population as a whole, or some combination of the two. The ethical statement may be true, although this seems subjective. I thought ethics was not up to ethicists, but rather ethicists were supposed to ascertain what our society as a whole considers ethical, and maybe compare that to other human societies past and present. I haven’t seen public polls of what people think is ethical, although they may exist. I can see a case that the way the vaccine is being rolled out is ethical, but I can also see a case for a random lottery being equally ethical.

Better planning and communication would not just be ethical, they are the common sense need and our government is continuing to fail, fail, fail and people are dying, which is the opposite of ethical governance. To my ears, it is arrogant to hear them lecturing us about ethics.

junkiest junk charts of 2020

Junk Charts is a great blog that takes an example of a data visualization, critiques it systematically, and then either improves it or shows a different way of displaying the same data. The site doesn’t go for overly elaborate graphics, just clear and effective ones. This post has a roundup of the most viewed posts and the author’s favorite posts of 2020.

One thing you probably shouldn’t do is describe interesting graphics in words. Nonetheless, here is some data, which I am not putting in a visual form because it would take exponentially longer than just listing it out:

  • There are 12 graphics covered by the post.
    • 2 scatter plots
    • 3 bar charts
      • 2 horizontal, not stacked – one of these gets changed to a bump chart
      • 1 horizontal, stacked – actually this is more of a “tree plot” where two data points are stacked and then a third is placed underneath
    • 2 pie charts
      • 1 3D pie chart – gets converted to a bump chart
      • 1 is allowed to continue to exist as a pie chart, with minor tweaks
    • 1 “dot matrix” (I’m not even sure if this is the best name, but basically you have empty squares or circles showing the total number of a thing, then some of them get filled in to illustrate how many of that thing fit a certain category)
    • 3 time series plots
      • 2 conventional – although one has two vertical axes, and the author illustrates how the limits can manipulated to suggest to the eye that two trends are related, or not
      • 1 showing shaded regions over time – basically a stacked bar changing over time
    • 538’s election snake

There is something intuitive about pie charts – that is why we explain fractions and percentages to children in terms of pizza or pie, and they grasp it instantly. Pie charts are obviously the wrong way to compare the absolute magnitudes of things.

I do like tree plots. I made one in 2020 and I was proud of myself – it showed the number of acres served by stormwater management controls implemented by three different administrative programs. And then I made a second one where I broke the numbers down further within each of the categories. This was very effective in conveying how much is actually achieved by each of the programs compared to the effort and expense that goes into them.

Resolution for 2021 is to play with “dot matrix” plots at some point (and maybe learn what the best name for these is.) I think these are effective in putting numbers in context of bigger numbers, regardless of units. For example, my city has around 80,000 cumulative confirmed coronavirus cases, maybe 5,000 confirmed active infections (about the number of confirmed cases in the last 10 days), maybe between 80,000 and 800,000 actual cumulative infections, and a population of about 1.6 million. I don’t know how many have been vaccinated at this point, but probably a few thousand. So maybe I would make 16 or 160 boxes each representing a chunk of people, and start coloring them in. Then we could see at a glance how much of the population might have some immunity to the virus right now, and how much does not. You could slice and dice the data many ways. Of course, some people died or moved away, and others were born or moved in. Incidentally, about 2,600 people died of Covid, 400 were murdered, and 120 died in and around motor vehicles. I haven’t seen numbers on suicides or drug overdoses but they are always horrifying. Around 1% of any given population dies in any given year from a combination of preventable and not preventable causes, which is sad but news flash: we are mortal beings.

This site doesn’t do maps, which is fine. I am a big fan of maps. But I have a very simple test – is the data geographic in nature? Then make a map. But often, some other types of graphs and tables will further illuminate the data, and those often work well alongside your map rather than being shoehorned into your map where they don’t really belong. And I also find it clunky trying to do any type of mathematical analysis in mapping software when the analysis is not spatial in nature.

finally, (some) hard numbers on schools and Covid spread

This article from The Intercept cites some recent research studies that put some numbers behind what level of community spread would make opening schools unsafe. The basic idea is that school (especially elementary school) is pretty safe when the level of infection in the community is relatively low, because kids coming to school are not that likely to be infected. But when the level of infection in the community rises, kids coming to school are more likely to be infected and further accelerate the spread.

Even educated people in the general public have a hard time with unit conversions, and this article switches between various units within the article. Come on, guys. Anywhere, here are the numbers from a variety of sources in the article. I’ve done the unit conversions (correctly, I think, but this blog post does not constitute medical advice…)

  • 36-44 per 100,000 population per week (~5-6 per 100,000 per day)
  • 147 per 100,000 per week (21 per 100,000 per day)
  • 35 per 100,000 per week (5 per 100,000 per day)

That seems like a pretty big range, and I am also suspicious whether the reporters have carefully checked the math, given how they jump around even within the article. But let’s assume they have it right. The threshold is somewhere between 35-147 cases per 100,000 per week. The Pennsylvania Department of Education recommends a threshold of 100 cases per 100,000 per week to consider in-person K-12 school. (Although private and parochial elementary schools have been open throughout the pandemic, and public school districts are hit or miss.) The official number for Philadelphia county at the moment (I’m writing this on January 7), which they only update once a week, is 225.9 per 100,000 per week and falling. My unofficial 7-day running average of the numbers the Philadelphia Health Department reports in its daily press releases is 235.0 per 100,000 per week and falling (but looking at a plot, I would say it’s bouncing around and not clearly rising or falling this week). Those of us with children in public school have not had the option of in-person school so far during this school year.