Tag: influenza

On predictions and a scientific response to calamity.

On predictions and a scientific response to calamity.

We’re fast approaching flu season, which is especially harrowing this year.

We, as a people, have struggled to respond to this calamity. We have a lot of scientific data about Covid-19 now, but science is never value-neutral. The way we design experiments reflects our biases; the way we report our findings, even more so.

For example, many people know the history of Edward Jenner inventing the world’s first vaccine. Fewer are aware of the long history of inoculation in Africa (essentially, low-tech vaccination) that preceded Jenner’s work.

So it’s worthwhile taking a moment to consider the current data on Covid-19.

Data alone can’t tell us what to do – the course of action we choose will reflect our values as a society. But the data may surprise a lot of people – which is strange considering how much we all feel that we know about Covid-19.

Indeed, we may realize that our response so far goes against our professed values.

Spoiler: I think we shouldn’t close in-person school.

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Since April, I’ve written several essays about Covid-19. In these, I’ve made a number of predictions. It’s worthwhile to consider how accurate these predictions have been.

This, after all, is what science is. We use data to make an informed prediction, and then we collect more data to evaluate how good our prediction was.

Without the second step – a reckoning with our success or failure – we’re just slinging bullshit.

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I predicted that our PCR tests were missing most Covid-19 infections, that people’s immunity was likely to be short-lived (lasting for months, not years), and that Covid-19 was less dangerous than seasonal influenza for young people.

These predictions have turned out to be correct.

In my essays, I’ve tried to unpack the implications of each of these. From the vantage of the present, with much more data at our disposal, I still stand by what I’ve written.

But gloating’s no fun. So I’d rather start with what I got wrong.

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My initial predictions about Covid-19 were terrible.

I didn’t articulate my beliefs at the time, but they can be inferred from my actions. In December, January, and February, I made absolutely no changes to my usual life. I didn’t recommend that travelers be quarantined. I didn’t care enough to even follow the news, aside from a cursory glance at the headlines.

While volunteering with the high school running team, I was jogging with a young man who was finishing up his EMT training.

“That new coronavirus is really scary,” he said. “There’s no immunity, and there’s no cure for it.”

I shrugged. I didn’t know anything about the new coronavirus. I talked with him about the 1918 influenza epidemic instead.

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I didn’t make any change in my life until mid-March. And even then, what did I do?

I called my brother and talked to him about the pizza restaurant – he needed a plan in case there was no in-person dining for a few months.

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My next set of predictions were off, but in the other direction – I estimated that Covid-19 was about four-fold more dangerous than seasonal influenza. The current best estimate from the CDC is that Covid-19 is about twice as dangerous, with an infection fatality ratio of 0.25%.

But seasonal influenza typically infects a tenth of our population, or less.

We’re unlikely to see a significant disruption in the transmission of Covid-19 (this is the concept of “herd immunity”) until about 50% of our population has immunity from it, whether from vaccination or recovery. Or possibly higher – in some densely populated areas, Covid-19 has spread until 70% (in NYC) or even 90% (in prisons) of people have contracted the disease.

Population density is hugely important for the dynamics of Covid-19’s spread, so it’s difficult to predict a nation-wide threshold for herd immunity. For a ballpark estimate, we could calculate what we’d see with a herd immunity threshold of about 40% in rural areas and 60% in urban areas.

Plugging in some numbers, 330 million people, 80% urban population, 0.25% IFR, 60% herd immunity threshold in urban areas, we’d anticipate 450,000 deaths.

That’s about half of what I predicted. And you know what? That’s awful.

Each of those 450,000 is a person. Someone with friends and family. And “slow the spread” doesn’t help them, it just stretches our grieving to encompass a whole year of tragedy instead of a horrific month of tragedy.

If we don’t have a safe, effective vaccine soon enough, the only way to save some of those 450,000 people is to shift the demographics of exposure.

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Based on the initial data, I concluded that the age demographics for Covid-19 risk were skewed more heavily toward elderly people than influenza risk.

I may have been wrong.

It’s difficult to directly compare the dangers of influenza to the dangers of Covid-19. Both are deadly diseases. Both result in hospitalizations and death. Both are more dangerous for elderly or immunocompromised people, but both also kill young, healthy people.

Typically, we use an antigen test for influenza and a PCR-based test for Covid-19. The PCR test is significantly more sensitive, so it’s easier to determine whether Covid-19 is involved a person’s death. If there are any viral particles in a sample, PCR will detect them. Whereas antigen tests have a much higher “false negative” rate.

Instead of using data from these tests, I looked at the total set of pneumonia deaths. Many different viruses can cause pneumonia symptoms, but the biggest culprits are influenza and, in 2020, Covid-19.

So I used these data to ask a simple question – in 2020, are the people dying of pneumonia disproportionately more elderly than in other years?

I expected that they would be. That is, after all, the prediction from my claims about Covid-19 demographic risks.

I was wrong.

In a normal year (I used the data from 2013, 2014, and 2015, three years with “mild” seasonal influenza), 130,000 people die of flu-like symptoms.

In 2020 (at the time I checked), 330,000 people have died of flu-like symptoms. Almost three times as many people as in a “normal” year.

For people under the age of 18, we’ve seen the same number of deaths (or fewer) in 2020 as in other years. The introduction of Covid-19 appears to have caused no increased risk for these people.

But for people of all other ages, there have been almost three times as many people dying of these symptoms in 2020 compared to other years.

In most years, one thousand people aged 25-34 die of these symptoms; in 2020, three thousand have died. In most years, two thousand people aged 35-44 die of these symptoms; in 2020, six thousand have died. This same ratio holds for all ages above eighteen.

Younger people are at much less risk of harm from Covid-19 than older people are. But, aside from children under the age of eighteen, they don’t seem to be exceptionally protected.

Of course, my predictions about the age skew of risk might be less incorrect than I’m claiming here. If people’s dramatically altered behavior in 2020 has changed the demographics of exposure as compared to other years – which is what we should be doing to save the most lives – then we could see numbers like this even if Covid-19 had the risk skew that I initially predicted.

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I predicted that four or more years would pass before we’d be able to vaccinate significant numbers of people against Covid-19.

I sure hope that I was wrong!

We now know that it should be relatively easy to confer immunity to Covid-19. Infection with other coronaviruses, including those that cause common colds, induce the production of protective antibodies. This may partly explain the low risk for children – because they get exposed to common-cold-causing coronaviruses so often, they may have high levels of protective antibodies all the time.

Several pharmaceutical companies have reported great results for their vaccine trials. Protection rates over 90%.

So the problem facing us now is manufacturing and distributing enough doses. But, honestly, that’s the sort of engineering problem that can easily be addressed by throwing money at it. Totally unlike the problem with HIV vaccines, which is that the basic science isn’t there – we just don’t know how to make a vaccine against HIV. No amount of money thrown at that problem would guarantee wide distribution of an effective vaccine.

We will still have to overcome the (unfortunately significant) hurdle of convincing people to be vaccinated.

For any individual, the risk of Covid-19 is about twice the risk of seasonal influenza. But huge numbers of people choose not to get a flu vaccine each year. In the past, the United States has had a vaccination rate of about 50%. Here’s hoping that this year will be different.

Covid-19 spreads so fast – and so silently, with many cases of infected people who feel fine but are still able to spread the virus – that it will almost certainly be a permanent resident of the world we live in. We’re unlikely to eradicate Covid-19.

Which means that elderly people will always be at risk of dying from Covid-19.

The only way to protect people whose bodies have gone through “age-related immunosenence” – the inevitable weakening of an immune system after a person passes the evolutionarily-determined natural human lifespan of about 75 years – will be to vaccinate everybody else.

Depending on how long vaccine-conferred immunity lasts, we may need to vaccinate people annually. I worry, though, that it will become increasingly difficult to persuade people to get a Covid-19 vaccine once the yearly death toll drops to influenza-like levels – 50,000 to 100,000 deaths per year in the United States.

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I wrote, repeatedly, that immunity to Covid-19 is likely to be short-lived. Immunity to other coronaviruses fades within a few months.

(Note: you may have seen articles in the New York Times suggesting that we’ll have long-lasting protection. They’re addressing a different question — after recovery, or vaccination, are you likely to become severely ill with Covid-19? And the answer is “probably not,” although it’s possible. When I discuss immunity here, I mean “after recovery, or vaccination, are you likely to be able to spread the virus after re-infection?” And the answer is almost certainly “yes, within months.”)

And I wrote about the interplay between short-lived immunity and the transmission dynamics of an extremely virulent, air-born virus.

This is what the Harvard public health team got so wrong. When we slow transmission enough that a virus is still circulating after people’s immunity wanes, they can get sick again.

For this person, the consequences aren’t so dire – an individual is likely to get less sick with each subsequent infection by a virus. But the implications for those who have not yet been exposed are horrible. The virus circulates forever, and people with naive immune systems are always in danger.

It’s the same dynamics as when European voyagers traveled to the Americas. Because the European people’s ancestors lived in unsanitary conditions surrounded by farm animals, they’d cultivated a whole host of zoogenic pathogens (like influenza and this new coronavirus). The Europeans got sick from these viruses often – they’d cough and sneeze, have a runny nose, some inflammation, a headache.

In the Americas, there were fewer endemic diseases. Year by year, people wouldn’t spend much time sick. Which sounds great, honestly – I would love to go a whole year without headaches.

But then the disgusting Europeans reached the Americas. The Europeans coughed and sneezed. The Americans died.

And then the Europeans set about murdering anyone who recovered. Today, descendants of the few survivors are made to feel like second-class citizens in their ancestral homelands.

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In a world with endemic diseases, people who have never been exposed will always be at risk.

That’s why predictions made in venues such as the August New York Times editorial claiming that a six- to eight-week lockdown would stop Covid-19 were so clearly false. They wrote:

Six to eight weeks. That’s how long some of the nation’s leading public health experts say it would take to finally get the United States’ coronavirus epidemic under control.

For proof, look at Germany. Or Thailand. Or France.

Obviously, this didn’t work – in the presence of an endemic pathogen, the lockdowns preserved a large pool of people with naive immune systems, and they allowed enough time to pass that people who’d been sick lost their initial immunity. After a few months of seeming calm, case numbers rose again. For proof, look at Germany. Or France.

Case numbers are currently low in Thailand, but a new outbreak could be seeded at any time.

And the same thing is currently happening in NYC. Seven months after the initial outbreak, immunity has waned; case numbers are rising; people with mild second infections might be spreading the virus to friends or neighbors who weren’t infected previously.

All of which is why I initially thought that universal mask orders were a bad idea.

We’ve known for over a hundred years that masks would slow the spread of a virus. The only question was whether slowing the spread of Covid-19 would cause more people to die of Covid-19.

And it would – if a vaccine was years away.

But we may have vaccines within a year. Which means that I may have been wrong. Again, the dynamics of Covid-19 transmission are still poorly understood – I’ll try to explain some of this below.

In any case, I’ve always complied with our mask orders. I wear a mask – in stores, at school pickup, any time I pass within six feet of people while jogging.

To address global problems like Covid-19 and climate change, we need global consensus. One renegade polluting wantonly, or spewing viral particles into the air, could endanger the whole world. This is precisely the sort of circumstance where personal freedom is less important than community consensus.

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The transmission dynamics of Covid-19 are extremely sensitive to environment. Whether you’re indoors or outdoors. How fast the air is moving. The population density. How close people are standing. Whether they’re wearing masks. Whether they’re shouting or speaking quietly.

Because there are so many variable, we don’t have good data. My father attended a lecture and a colleague (whom he admires) said, “Covid-19 is three-fold more infectious than seasonal influenza.” Which is bullshit – the transmission dynamics are different, so the relative infectivity depends on our behaviors. You can’t make a claim like this.

It’s difficult to measure precisely how well masks are slowing the spread of this virus.

But here’s a good estimate: according to Hsiang et al., the number of cases of Covid-19, left unchecked, might have increased exponentially at a rate of about 34% per day in the United States.

That’s fast. If about 1% of the population was infected, it could spread to everyone within a week or two. In NYC, Covid-19 appear to spread to over 70% of the population within about a month.

(To estimate the number of infections in New York City, I’m looking at the number of people who died and dividing by 0.004 – this is much higher than the infection fatality rate eventually reported by the CDC, but early in the epidemic, we were treating people with hydroxychloraquine, an unhelpful poison, and rushing to put people on ventilators. We now know that ventilation is so dangerous that it should only be used as a last resort, and that a much more effective therapy is to ask people to lie on their stomachs – “proning” makes it easier to get enough oxygen even when the virus has weakened a person’s lungs.)

Masks dramatically slow the rate of transmission.

A study conducted at a military college – where full-time mask-wearing and social distancing were strictly enforced – showed that the number of cases increased from 1% to 3% of the population over the course of two weeks.

So, some math! Solve by taking ten to the power of (log 3)/14, which gives an exponential growth rate of 8% per day. Five-fold slower than without masks.

But 8% per day is still fast.

Even though we might be able to vaccinate large numbers of people by the end of next year, that’s not soon enough. Most of us will have been sick with this – at least once – before then.

I don’t mean to sound like a broken record, but the biggest benefit of wearing masks isn’t that we slow the rate of spread for everyone — exponential growth of 8% is still fast — but that we’re better able to protect the people who need to be protected. Covid-19 is deadly, and we really don’t want high-risk people to be infected with it.

I’ve tried to walk you through the reasoning here — the actual science behind mask policies — but also, in case it wasn’t absolutely clear: please comply with your local mask policy.

You should wear a mask around people who aren’t in your (small) network of close contacts.

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I’m writing this essay the day after New York City announced the end of in-person classes for school children.

This policy is terrible.

A major problem with our response to Covid-19 is that there’s a time lag between our actions and the consequences. Human brains are bad at understanding laggy data. It’s not our fault. Our ancestors lived in a world where they’d throw a spear at an antelope, see the antelope die, and then eat it. Immediate cause and effect makes intuitive sense.

Delayed cause and effect is tricky.

If somebody hosts a party, there might be an increase in the number of people who get sick in the community over the next three weeks. Which causes an increase in the number of hospitalizations about two weeks after that. Which causes people to die about three weeks after that.

There’s a two-month gap between the party and the death. The connection is difficult for our brains to grasp.

As a direct consequence, we’ve got ass-hats and hypocrites attending parties for, say, their newly appointed Supreme Court justice.

But the problem with school closures is worse. There’s a thirty year gap between the school closure and the death. The connection is even more difficult to spot.

Even if you have relatively limited experience reading scientific research papers, I think you could make your way through this excellent article from Chistakis et al.

The authors link two sets of existing data: the correlation between school closures and low educational achievement, and the correlation between low educational achievement and premature death.

The public debate has pitted “school closures” against “lives saved,” or the education of children against the health of the community. Presenting the tradeoffs in this way obscures the very real health consequences of interrupted education.

These consequences are especially dire for young children.

The authors calculate that elementary school closures in the United States might have (already!) caused 5.5 million years of life lost.

Hsiang et al. found that school closures probably gave us no benefit in terms of reducing the number of Covid-19 cases, because children under 18 aren’t significant vectors for transmission (elementary-aged children even less so), but even if school closures had reduced the number of Covid-19 cases, closing schools would have caused more total years of life to be lost than saved.

The problem – from a political standpoint – is that Covid-19 kills older people, who vote, whereas school closures kill young people, who are intentionally disenfranchised.

And, personally, as someone with far-left political views, it’s sickening for me to see “my” political party adopt policies that are so destructive to children and disadvantaged people.

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So, here’s what the scientific data can tell us so far:

  • We will eventually have effective vaccines for Covid-19. Probably within a year.
  • Covid-19 spreads even with social distancing and masks, but the spread is slower.
  • You have no way of knowing the risk status of people in a stranger’s bubble. (Please, follow your local mask orders!)
  • Schools – especially elementary schools – don’t contribute much to the spread of Covid-19.
  • School closures shorten children’s lives (and that’s not even accounting for their quality of life over the coming decades).
  • An individual case of Covid-19 is about twice as dangerous as a case of seasonal influenza (which is scary!).
  • Underlying immunity (from prior disease and vaccination) to Covid-19 is much lower than for seasonal influenza, so there will be many more cases.
  • Most people’s immunity to Covid-19 probably lasts several months, after which a person can be re-infected and spread the virus again.

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So, those are some data. But data don’t tell us what to do. Only our values can do that.

Personally, I value the lives of children.

I wouldn’t close schools.

On sending kids to school.

On sending kids to school.

I was walking my eldest child toward our local elementary school when my phone rang.

We reached the door, shared a hug, and said goodbye. After I left, I called back – it was a friend of mine from college who now runs a cancer research laboratory and is an assistant professor at a medical school.

“Hey,” I said, “I was just dropping my kid off at school.”

“Whoa,” he said, “that’s brave.”

I was shocked by his remark. For most people under retirement age, a case of Covid-19 is less dangerous than a case of seasonal influenza.

“I’ve never heard of anybody needing a double lung transplant after a case of the flu,” my friend said.

But our ignorance doesn’t constitute safety. During this past flu season, several young, healthy people contracted such severe cases of influenza that they required double lung transplants. Here’s an article about a healthy 30-year-old Wyoming man nearly killed by influenza from December 2019, and another about a healthy 20-year-old Ohio woman from January 2020. And this was a rather mild flu season!

“One of the doctors told me that she’s the poster child for why you get the flu shot because she didn’t get her flu shot,” said [the 20-year-old’s mother].

These stories were reported in local newspapers. Stories like this don’t make national news because we, as a people, think that it’s normal for 40,000 to 80,000 people to die of influenza every year. Every three to five years, we lose as many people as have died from Covid-19. And that’s with vaccination, with pre-existing immunity, with antivirals like Tamiflu.

Again, when I compare Covid-19 to influenza, I’m not trying to minimize the danger of Covid-19. It is dangerous. For elderly people, and for people with underlying health issues, Covid-19 is very dangerous. And, sure, all our available data suggest that Covid-19 is less dangerous than seasonal influenza for people under retirement age, but, guess what? That’s still pretty awful!

You should get a yearly flu shot!

A flu shot might save your life. And your flu shot will help save the lives of your at-risk friends and neighbors.

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For a while, I was worried because some of my remarks about Covid-19 sounded superficially similar to things said by the U.S. Republican party. Fox News – a virulent propaganda outlet – was publicizing the work of David Katz – a liberal medical doctor who volunteered in a Brooklyn E.R. during the Covid-19 epidemic and teaches at Yale’s school of public health.

The “problem” is that Katz disagrees with the narrative generally forwarded by the popular press. His reasoning, like mine, is based the relevant research data – he concludes that low-risk people should return to their regular lives.

You can see a nifty chart with his recommendations here. This is the sort of thing we’d be doing if we, as a people, wanted to “follow the science.”

And also, I’m no longer worried that people might mistake me for a right-wing ideologue. Because our president has once again staked claim to a ludicrous set of beliefs.

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Here’s a reasonable set of beliefs: we are weeks away from a safe, effective Covid-19 vaccine, so we should do everything we can to slow transmission and get the number of cases as low as possible!

Here’s another reasonable set of beliefs: Covid-19 is highly infectious, and we won’t have a vaccine for a long time. Most people will already be infected at least once before there’s a vaccine, so we should focus on protecting high-risk people while low-risk people return to their regular lives.

If you believe either of those sets of things, then you’re being totally reasonable! If you feel confident that we’ll have a vaccine soon, then, yes, delaying infections is the best strategy! I agree! And if you think that a vaccine will take a while, then, yes, we should end the shutdown! I agree!

There’s no right answer here – it comes down to our predictions about the future.

But there are definitely wrong answers. For instance, our current president claims that a vaccine is weeks away, and that we should return to our regular lives right now.

That’s nonsense. If we could get vaccinated before the election, then it’d make sense to close schools. To wait this out.

If a year or more will pass before people are vaccinated, then our efforts to delay the spread of infection will cause more harm than good. Not only will we be causing harm with the shutdown itself, but we’ll be increasing the death toll from Covid-19.

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On October 14th, the New York Times again ran a headline saying “Yes, you can be reinfected with the coronavirus. But it’s extremely unlikely.”

This is incorrect.

When I’ve discussed Covid-19 with my father – a medical doctor specializing in infectious diseases, virology professor, vaccine developer with a background in epidemiology from his masters in public health – he also has often said to me that reinfection is unlikely. I kept explaining that he was wrong until I realized that we were talking about different things.

When my father uses the word “reinfection,” he means clearing the virus, catching it again, and becoming sicker than you were the first time. That’s unlikely (although obviously possible). This sort of reinfection happens often with influenza, but that’s because influenza mutates so rapidly. Covid-19 has a much more stable genome.

When I use the word “reinfection” – and I believe that this is also true when most laypeople use the word – I mean clearing the virus, catching it again, and becoming sick enough to shed the viral particles that will make other people sick.

This sense of the word “reinfection” describes something that happens all the time with other coronaviruses, and has been documented to occur with Covid-19 as well.

The more we slow the spread of Covid-19, the more total cases there will be. In and of itself, more cases aren’t a bad thing – most people’s reinfection will be milder than their first exposure. The dangerous aspect is that a person who is reinfected will have another period of viral shedding during which they might expose a high-risk friend or neighbor.

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If our goal is to reduce the strain on hospitals and reduce total mortality, we need to avoid exposing high-risk people. Obviously, we should be very careful around nursing home patients. We should provide nursing homes with the resources they need to deal with this, like extra testing, and preferably increased wages for nursing home workers to compensate them for all that extra testing.

It’s also a good idea to wear masks wherever low-risk and high-risk people mingle. The best system for grocery stores would be to hire low-risk shoppers to help deliver food to high-risk people, but, absent that system, the second-best option would be for everyone to wear masks in the grocery store.

Schools are another environment where a small number of high-risk teachers and a small number of students living with high-risk family members intermingle with a large number of low-risk classmates and colleagues.

Schools should be open – regions where schools closed have had the same rates of infection as regions where schools stayed open, and here in the U.S., teachers in districts with remote learning have had the same rates of infection as districts with in-person learning.

Education is essential, and most people in the building have very low risk.

A preponderance of data indicate that schools are safe. These data are readily accessible even for lay audiences – instead of reading research articles, you could read this lovely article in The Atlantic.

Well, I should rephrase.

We should’ve been quarantining international travelers back in December or January. At that time, a shutdown could have helped. By February, we were too late. This virus will become endemic to the human species. We screwed up.

But, given where we are now, students and teachers won’t experience much increased risk from Covid-19 if they attend in person, and schools aren’t likely to make the Covid-19 pandemic worse for the surrounding communities.

That doesn’t mean that schools are safe.

Schools aren’t safe: gun violence is a horrible problem. My spouse is a teacher – during her first year, a student brought weapons including a chainsaw and some pipe bombs to attack the school; during her fourth year, a student had amassed guns in his locker and was planning to attack the school.

Schools aren’t safe: we let kids play football, which is known to cause traumatic brain injury.

Schools aren’t safe: the high stress of grades, college admissions, and even socializing puts some kids at a devastatingly high risk for suicide. We as a nation haven’t always done a great job of prioritizing kids’ mental health.

And the world isn’t safe – as David Katz has written,

“If inclined to panic over anything, let it be climate change … Not the most wildly pessimistic assessment of the COVID pandemic places it even remotely in the same apocalyptic ballpark.”

On ants and infection.

On ants and infection.

I live in a college town. Last week, students returned.

Yesterday’s paper explains that dire punishment awaits the students who attended a Wednesday night party. In bold letters atop the front page, “IU plans to suspend students over party.”

In the decade that I’ve lived here, many parties have led to sexual assaults, racist hate speech, and violence. The offending students were rarely punished. But this party was egregious because “there were about 100 people there.”

IU officials “have seen a photo … that shows a large group of young people standing close together outside a house at night, many of them not wearing masks.”

I’ve seen the images – someone filmed a video while driving by. There they are – a group of young people, standing outside.

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Science magazine recently interviewed biologist Dana Hawley about social distancing in the animal kingdom.

When spiny lobsters are sick, their urine smells different. Healthy lobsters will flee the shared den. Leaving is dangerous, since the lobsters will be exposed to predators until they find a new home, but staying would be dangerous, too – they might get sick. To survive, lobsters have to balance all the risks they face.

My favorite example of social distancing in the animal kingdom wasn’t discussed. When an ant is infected with the cordyceps fungus, it becomes a sleeper agent. Jennifer Lu writes in National Geographic that “as in zombie lore, there’s an incubation period where infected ants appear perfectly normal and go about their business undetected by the rest of the colony.”

Then the fungus spreads through the ants body, secreting mind control chemicals. Eventually, the fungus will command the infected ant to climb to a high place. A fruiting body bursts from the ant’s head and rains spores over the colony.

Infection is almost always lethal.

If an ant notices that a colony member has been infected, the healthy ant will carry the infected ant away from the colony and hurl it from a cliff.

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The FDA will approve any Covid-19 vaccine that cuts risk by half. It’s very unlikely that a Covid-19 vaccine will cut the risk by more than about two-thirds, and the vaccine will work least well for people who need protection most.

Most likely, the Covid-19 epidemic will end before there’s vaccine. The herd immunity threshold seems to be much lower than some researchers feared – our current data suggest that the epidemic will end after about 40% of the population has immunity.

The herd immunity threshold isn’t an inherent property of a virus – it depends upon our environment and behaviors. In prisons, we’ve seen Covid-19 spread until nearly 90% of people were infected. In parts of New York City where many essential workers live in crowded housing, Covid-19 spread until 50% of people were infected.

In a culture where everyone kissed a sacred statue in the center of town each morning, the herd immunity threshold would be higher. If people wear masks while interacting with strangers, the herd immunity threshold will be lower.

In a world that maintains a reservoir of the virus, though, someone who hasn’t yet been exposed will always be at risk.

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The New York Times recently discussed some of the challenges that colleges face when trying to reopen during the epidemic.

Most schools ban … socializing outside “social pods” – the small groups of students that some colleges are assigning students to, usually based on their dorms.

Most administrators seem to believe that a rule banning sex is unrealistic, and are quietly hoping that students will use common sense and refrain from, say, having it with people outside their pod.

In 2012, The Huffington Post published a list of the “Top 10 sex tips for college freshmen.” Their fourth piece of advice (#1 and #2 were condoms, #3 was not having sex while drunk) is to avoid having sex with people who live too close to you. “Students in other dorms = fair game. Students in same dorm = proceed with caution.”

I had a big group of friends for my first two years of college. After a breakup, I lost most of those friends.

This is crummy, but it would be much worse if I’d lost my friendships with the only people whom the administrators allowed me to spend time with.

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We can slow the spread of Covid-19, but slowing the spread won’t prevent deaths, not unless we can stave off infection until there is a highly effective vaccine. That might take years. We might never have a highly effective vaccine – our influenza vaccines range in efficacy from about 20% to 80%, and we have much more experience making these.

Our only way to reduce the eventual number of deaths is to shift the demographics of exposure. If we reach the herd immunity threshold without many vulnerable people being exposed, we’ll save lives.

A college would best protect vulnerable students and faculty by allowing the students who are going to socialize to host dense parties for a few weeks before mingling with others. This would allow the virus to spread and be cleared before there was a risk of transferring infections to vulnerable people.

I’d draft a waiver. Are you planning to socialize this semester? If so, come do it now! By doing so, you will increase your risk of contracting Covid-19. This is a serious disease – it’s possible for young, healthy people to die from it. But, look, if you’re gonna socialize eventually, please just get it over with so that you don’t endanger other people.

With this plan, some young people might die of Covid-19. But some young people will die of Covid-19 even if everyone practices social distancing – slowing the spread of infections doesn’t save lives, it delays deaths. And fewer young people would die of Covid-19 than die of influenza each year.

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When confronting cordyceps, which is almost always fatal, ants throw sick colony members off cliffs.

When ants confront less lethal fungal infections, they protect the colony by shifting the demographics of exposure and by ramping up to the herd immunity threshold as quickly as possible.

Malagocka et al. discuss demographics in their review article, “Social immunity behavior among ants infected by specialist and generalist fungi.”

Outside-nest foragers, who have the highest risks of acquiring pathogens from the environment, have limited access to the brood area with the most valuable groups, and are recruited from older individuals, who are less valuable from the colony survival perspective.

Konrad et al. discuss intentional exposure in their research article, “Social transfer of pathogenic fungus promotes active immunization in ant colonies.”

When worker ants encounter an infected colony member, they intentionally inoculate themselves. “Social immunization leads to faster elimination of the disease and lower death rates.”

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It feels disquieting for me to defend the behavior of frat guys. Personally, I’d like to see the whole fraternity system abolished. And in March, when we knew less about Covid-19, I was appalled that people went out partying over spring break. But I was wrong. Perhaps inadvertently, those young people were behaving in the way that would save most lives.

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Erika Meitner’s 2006 poem “Pediatric Eschatology” begins

the nurse called back and told us to use bleach
on anything we touch, she said wash everything
in hot water, insisted we won’t treat you if
you’re asymptomatic, we won’t, and made us
an appointment anyway. so we waited and waited
with the dog-eared magazines and recall posters

It’s horrible to face the end. It’s almost worse to know that the things you fear are harmless to others. All the asymptomatic cases are like a slap in the face to those whose friends and family have died.

Braun et al. recently published a study in Nature showing that a large number of people who’ve never encountered Covid-19 may already have significant immunity. Parts of the Covid-19 virus are similar to the viruses that cause common colds, and exposure to those viruses might provide the immunity that lets people recover without ever feeling sick.

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I believe we should be doing more to protect young people. Gun control, ending farm subsidies, fighting climate change. Enacting privacy laws to reign in the surveillance capitalists. Breaking up monopolies. Providing good careers despite automation. Making sure that everyone has clean air to breathe and clean water to drink. Getting nutritious food into our nation’s many food deserts. Providing equitable access to health care.

But, punishing young people for socializing?

We’re not making them safer. And we’re not making ourselves safer, either.

Seriously, I know we humans are selfish, but we have to be able to handle an epidemic better than ants.

Red ant: photograph by William Cho

On moral outrage.

On moral outrage.

My family had spring break travel plans for before the shutdown.

We canceled them.

At the time, we feared for our safety. My spouse said to me, “You caught the flu twice this year, even after you were vaccinated, and the second time was the sickest I’ve ever seen you. I’m really worried about what will happen if you catch this new thing, too.”

She wanted me to cancel my poetry classes in the local jail. My father, an infectious diseases doctor and professor of immunology, thought I should still go in to teach. “If somebody’s in there coughing up a lung, you should recommend he skip class next week,” my father told me.

But I was spooked. I felt glad when the jail put out a press release saying they’d no longer allow volunteers to come in – I didn’t want to choose between helping the incarcerated men and protecting my family.

My spouse is a high school science teacher. She felt glad that her biology classroom has over a dozen sinks. During the final week of school, she asked all her students to wash their hands for 20 seconds as soon as they walked into the room.

My spouse and I are both scientists, but it wasn’t until a week into the shutdown that I began to read research papers about Covid-19. Until then, we had gotten all our information from the newspaper. And the news was terrifying. Huge numbers of people were dying in Italy. Our imbecilic president claimed that Covid-19 was no big deal, making me speculate that this disease was even more dangerous than I’d thought.

Later, I finally went through the data from Italy and from the Diamond Princess cruise ship. These data – alongside the assumption that viral exposure should be roughly similar across age groups, if not higher for school children and young people who are out and about in the world – showed my family that our personal risk was probably quite low.

Still, we stayed inside. We were worried about harming others.

When I saw photographs of beaches packed with revelers, I felt furious. Did those selfish young people not realize that their choices could cause more people to die?

So it was shocking for me to learn that those selfish young people were actually doing the thing that would save most lives.

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We now know that Covid-19 can be transmitted by people who feel no symptoms, and that it was widespread in this country by March.

If we, as a people, had acted earlier, we could have prevented all these deaths. In January, it would have been enough to impose a brief quarantine after all international travel. In February, it would have been enough to use our current strategy of business closures, PCR testing, and contact tracing. In March, we were too late. The best we could do then – the best we can do now – was to slow the spread of infections.

Unfortunately, slowing the spread of infections will cause more people to die.

There’s an obvious short-term benefit to slowing the spread of infections – if too many people became critically ill at the same time, our hospitals would be overwhelmed, and we’d be unable to offer treatment to everyone who wanted it. We’d run out of ventilators.

This problem is exacerbated by the fact that we, as a people, are terrible about talking about death. There’s no consensus about what constitutes a good life – what more would have to happen for you to feel ready to die?

Personally, I don’t want to die. As my mind stopped, I’d feel regret that I wouldn’t get to see my children become self-sufficient adults. But I’d like to think that I could feel proud that I’ve done so much to set them on the right path. Since my twenties, I’ve put forth a constant effort to live ethically, and I’d like to imagine that my work – my writing, teaching, and research – has improved other people’s lives.

I’ve also gotten to see and do a lot of wonderful things. I’ve been privileged to visit four countries. I visited St. Louis’s City Museum when one of my kids was old enough to gleefully play. I have a bundle of some two dozen love letters that several wonderful people sent me.

I’ve had a good life. I’d like for it to continue, but I’ve already had a good life.

Many medical doctors, who have seen how awful it can be for patients when everything is done to try to save a life, have “do not resuscitate” orders. My spouse and I keep our living wills in an accessible space in our home. But a majority of laypeople want dramatic, painful measures to be taken in the attempt to save their lives.

People are making this choice even during the pandemic, when the choice to experience an excruciating death puts medical professionals at risk and reduces the quality of care available for everyone else.

Still. Even without our reluctance to discuss death, there would be a short-term benefit to slowing the spread of infections. The American healthcare system is terrible, and was already strained to the breaking point. We weren’t – and aren’t – ready to handle a huge influx of sick patients.

But the short-term benefit of slowing the spread of Covid-19 comes at a major cost.

The shutdown itself hurts people. The deaths caused by increased joblessness, food insecurity, educational disruption, domestic violence, and loneliness (“loneliness and social isolation can be as damaging to health as smoking 15 cigarettes a day”) are more difficult to measure than the deaths caused by Covid-19. We won’t have a PCR test to diagnose which people were killed by the shutdown.

Those deaths won’t all come at once. But those deaths are no less real, and no less tragic, than the immediate horror of a person drowning from viral-induced fluid buildup in their lungs.

And, perhaps more damning, if the shutdown ends before there’s a vaccine, the shutdown will cause more people to die of Covid-19.

Without a vaccine, slowing the spread of Covid-19 has a short-term benefit of reducing the rate of hospital admissions, at the long-term cost of increasing the total number of Covid-19 cases.

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All immunity fades – sometimes after decades, sometimes after months. Doesn’t matter whether you have immunity from recovery or from vaccination – eventually, your immunity will disappear. And, for a new disease, we have no way of predicting when. Nobody knows why some antigens, like the tetanus vaccine, trigger such long-lasting immunity, while other antigens, such as the flu vaccine or the influenza virus itself, trigger such brief protection.

We don’t know how long immunity to Covid-19 will last. For some coronaviruses, immunity fades within a year. For others, like SARS, immunity lasts longer.

The World Health Organization has warned, repeatedly, that immunity to Covid-19 might be brief. But the WHO seems unaware of the implications of this warning.

The shorter the duration of a person’s immunity, the more dangerous the shutdown. If our shutdown causes the Covid-19 epidemic to last longer than the duration of individual immunity, there will be more total infections – and thus more deaths – before we reach herd immunity.

This is, after all, exactly how a one-time “novel zoogenic disease” like influenza became a permanent parasite on our species, killing tens of thousands of people in the United States each year. Long ago, transmission was slowed to the point that the virus could circulate indefinitely. Influenza has been with us ever since.

That’s the glaring flaw in the recent Harvard Science paper recommending social distancing until 2022 – in their key figure, they do not incorporate a loss of immunity. Depending on the interplay between the rate of spread and the duration of immunity, their recommendation can cause this epidemic to never end.

And, if the shutdown ends before we have a vaccine, the lost immunity represents an increased death toll to Covid-19. Even neglecting all the other harms, we’ll have killed more people than if we’d done nothing.

This sounds terrifying. And it is. But the small glimmer of good news is that people’s second infections will probably be less severe. If you survive Covid-19 the first time you contract it, you have a good chance of surviving subsequent infections. But prolonging the epidemic will still cause more deaths, because herd immunity works by disrupting transmission. Even though an individual is less likely to die during a second infection, that person can still spread the virus. Indeed, people are more likely to spread the virus during subsequent infections, because they’re more likely to feel healthy while shedding infectious particles.

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This calculation would be very different if people could be vaccinated.

Obviously, vaccination would be the best way to end this epidemic. In order to reach herd immunity by a sufficient number of people recovering, there would have to be a huge percentage of our population infected. Nobody knows how many infections it would take, but many researchers guess a number around 60% to 70% of our population.

Even if Covid-19 were no more dangerous than seasonal influenza (and our data so far suggest that it’s actually about four-fold more dangerous than most years’ seasonal influenza), that would mean 200,000 deaths. A horrifying number.

But there’s no vaccine. Lots of people are working on making a vaccine. We have Covid-19 vaccines that work well in monkeys. But that doesn’t necessarily mean anything in terms of human protection. We’ve made many HIV vaccines that work well in monkeys – some of these increase the chance that humans will contract HIV.

It should be easier to make a vaccine against this coronavirus than against HIV. When making a vaccine, you want your target to mutate as little as possible. You want it to maintain a set structure, because antibodies need to recognize the shape of external features of the virus in order to protect you. HIV mutates so fast that its shape changes, like a villain constantly donning a new disguise. But the virus that causes Covid-19 includes a proofreading enzyme, so it’ll switch disguises less.

Still, “easier to make a vaccine against than HIV” is not the most encouraging news. Certain pharmaceutical companies have issued optimistic press briefings suggesting that they’ll be able to develop a vaccine in 18 months, but we should feel dubious. These press briefings are probably intended to bolster the companies’ stock prices, not give the general public an accurate understanding of vaccine development.

Realistically, a Covid-19 vaccine is probably at least four years away. And it’s possible – unlikely, but possible – that we’ll never develop a safe, effective vaccine for this.

If we end the shutdown at any time before there is a vaccine, the shutdown will increase the number of people who die of Covid-19. The longer the shutdown, the higher the toll. And a vaccine is probably years away.

The combination of those two ideas should give you pause.

If we’re going to end the shutdown before we have a vaccine, we should end it now.

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To be absolutely clear, vaccination would be the best way to resolve this crisis. Vaccination saves lives. The basic principle of inoculation was used for hundreds of years in Africa, India, and China, before it was adapted by Edward Jenner to create the first smallpox vaccine.

For a vaccine to end the Covid-19 epidemic, enough people will need to choose to be vaccinated for us to reach herd immunity.

Unfortunately, many people in the United States distrust the well-established efficacy and safety of vaccines. It’s worth comparing Covid-19 to seasonal influenza. On a population level, Covid-19 seems to be about four-fold more dangerous than seasonal influenza. But this average risk obscures some important data – the risk of Covid-19 is distributed less evenly than the risk of influenza.

With influenza, healthy young people have a smaller risk of death than elderly people or people with pre-existing medical conditions. But some healthy young people die from seasonal influenza. In the United States, several thousand people between the ages of 18 and 45 die of influenza every year.

And yet, many people choose not to be vaccinated against influenza. The population-wide vaccination rate in the United States is only 40%, too low to provide herd immunity.

Compared to influenza, Covid-19 seems to have less risk for healthy young people. Yes, healthy young people die of Covid-19. With influenza, about 10% of deaths are people between the ages of 18 and 45. With Covid-19, about 2% of deaths are people in this age group.

I’m not arguing that Covid-19 isn’t dangerous. When I compare Covid-19 to seasonal influenza, I’m simply comparing two diseases that are both deadly.

I get vaccinated against influenza every year.

Yes, you might have heard news reports about the influenza vaccine having low efficacy, but that’s simply measuring how likely you are to get sick after being vaccinated. We also know that the vaccine makes your illness less severe.

The influenza vaccine saves lives. The data are indisputable.

But people don’t choose to get it! That’s why I think it’s unfortunately very likely that people whose personal risk from Covid-19 is lower than their risk from influenza will forgo vaccination. Even if we had access to 300 million doses of a safe, effective vaccine today, I doubt that enough people would get vaccinated to reach herd immunity.

Obviously, I’d love to be wrong about this. Vaccination saves lives.

Please, dear reader, get a flu vaccine each year. And, if we develop a safe, effective Covid-19 vaccine, you should get that too.

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We don’t have a vaccine. The shutdown is causing harm – the shutdown is even increasing the total number of people who will eventually die of Covid-19.

Is there anything we can do?

Luckily, yes. We do have another way to save lives. We can change the demographics of exposure.

Our understanding of Covid-19 still has major gaps. We need to do more research into the role of interleukin 6 in our bodies’ response to this disease – a lot of the healthy young people who’ve become critically ill with Covid-19 experienced excessive inflammation that further damaged their lungs.

But we already know that advanced age, smoking status, obesity and Type 2 diabetes are major risk factors for complications from Covid-19. Based on the data we have so far, it seems like a low-risk person might have somewhere between a hundredth or a thousandth the chance of becoming critically ill with Covid-19 as compared to an at-risk person. With influenza, a low-risk person might have between a tenth and a hundredth the chance of becoming critically ill.

The risk of Covid-19 is more concentrated on a small segment of the population than the risk of influenza.

To save lives, and to keep our hospitals from being overwhelmed, we want to do everything possible to avoid exposing at-risk people to this virus.

But when healthy young people take extraordinary measures to avoid getting sick with Covid-19 – like the shutdown, social distancing, and wearing masks – they increase the relative burden of disease that falls on at-risk people. We should be prioritizing the protection of at-risk people, and we aren’t.

Because this epidemic will not end until we reach the population-wide threshold for herd immunity, someone has to get sick. We’d rather it be someone who is likely to recover.

Tragically, we already have data suggesting that a partial shutdown can transfer the burden of infection from one group to another. In the United States, our shutdown was partial from the beginning. People with white-collar jobs switched to working remotely, but cashiers, bus drivers, janitors, people in food prep, and nurses have kept working. In part because Black and brown people are over-represented in these forms of employment, they’ve been over-represented among Covid-19 deaths.

There is absolutely no reason to think that poor people would be more likely to safely recover from Covid-19 – indeed, due to air pollution, stress, sleep deprivation, limited access to good nutrition, and limited access to health care, we should suspect that poor people will be less likely to recover – but, during the shutdown, we’ve shifted the burden of disease onto their shoulders.

This is horrible. Both unethical and ineffective. And, really, an unsurprising outcome, given the way our country often operates.

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If we want to save lives, we need for healthy younger people to use their immune systems to protect us. The data we have so far indicates that the shutdown should end now — for them.

It will feel unfair if healthy younger people get to return to work and to their regular lives before others.

And the logistics won’t be easy. We’ll still need to make accommodations for people to work from home. Stores will have to maintain morning hours for at-risk shoppers, and be thoroughly cleaned each night.

If school buildings were open, some teachers couldn’t be there – they might need substitutes for months – and neither could some students, who might switch to e-learning to protect at-risk family.

We’ll need to provide enough monetary and other resources that at-risk people can endure a few more months of self-isolation. Which is horrible. We all know, now that we’ve all been doing this for a while, that what we’re asking at-risk people to endure is horrible. But the payoff is that we’ll be saving lives.

Indeed, the people who self-isolate will have lowest risk. We’ll be saving their lives.

And no one should feel forced, for financial reasons or otherwise, to take on more risk than they feel comfortable with. That’s why accommodations will be so important. I personally would feel shabby if I took extreme measures to protect myself, knowing that my risk is so much lower than other people’s, but you can’t look at someone in a mask and know their medical history, much less whom they might be protecting at home.

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All told, this plan isn’t good. I’m not trying to convince you that this is good. I’m just saying that, because we bungled things in January, this is the best we have.

If we could go back in time, we’d obviously do things differently. It’s only based on where we are now that physicians like David Katz argue we need to end the shutdown based on the principle of “harm minimization.”

Based on the data we have, I agree.

Ending the shutdown now, but only for some, will save lives.

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So, those selfish young people crowding on beaches? I looked at the photos and hated them.

But it turns out that their selfish actions were actually the exact plan that will save most lives.

I’ve had to swallow my moral indignation. I hope you can too.

Responses to “On testing.”

Responses to “On testing.”

My spouse posted my previous essay on social media, and I’d like to address some of people’s comments.  There were some excellent points! 

My apologies if I failed to address everything that people said, but I tried my best.

Scroll to find my responses to:

  1. A shutdown could have prevented the Covid-19 epidemic.
  2. We know that the current shutdown is either delaying or preventing deaths due to Covid-19. 
  3. Ending this epidemic with a vaccine would be ideal. 
  4. Ending the shutdown while requesting that at-risk people continue to self-isolate would save lives.
  5. Why is it urgent to end the shutdown soon?
  6. Why might more people die of Covid-19 just because we are slowing the spread of the virus?
  7. How is the shutdown causing harm?
  8. What about the rate at which people get sick?  Isn’t the shutdown worthwhile, despite the risks described above, if it keeps our hospitals from being overwhelmed?
  9. Don’t the antibody tests have a lot of false positives?
  10. What about the political ramifications of ending the shutdown?

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1: “A shutdown could have prevented the Covid-19 epidemic.”

If we’d acted early enough, we could have isolated all cases of Covid-19 and prevented this whole debacle.

But we didn’t.

Covid-19 is highly infectious, and we made no effort toward containment or quarantine until the virus was already widespread.  We took action in March, but we already had community transmission of Covid-19 by January.  Given where we are now, current models predict that the epidemic will continue until the level of immunity reaches somewhere near 70%.

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2: “We know that the current shutdown is either delaying or preventing deaths due to Covid-19.”

To date, the data suggests that the virus has only reached saturation inside a few closed environments, such as prisons.  In Italy, both the timecourse of mortality and the results of antibody studies suggest that infections were still rising at the time of their lockdown. 

Among the passengers of the Diamond Princess cruise ship, deaths peaked 21 days after infections peaked – if the virus had already reached saturation in Italy, we’d expect to see deaths peak sooner than 21 days after the lockdown began.  They did not.

So, again, this much is clear: worldwide, there was a significant new cause of death.  When we look at mortality data, we see the curves suddenly rise in many locations.  Some researchers, such as John Ioannidis, have speculated that Covid-19 causes death primarily in people with low life expectancy, in which case we would expect to see these mortality curves drop to lower-than-average levels after the epidemic ends.  But even then, it’s unprecedented to see a number of deaths that would usually occur over the course of a year all within a matter of weeks.

Covid-19 is killing people, and the shutdown is either delaying or preventing people’s death from Covid-19.

For the shutdown to actually prevent death, one of the following needs to happen:

1.) We create a vaccine, allowing our population to reach 70% immunity without as many people contracting the illness.

2.) We take action to change which segment of the population is exposed to the virus, allowing us to reach 70% immunity without as many at-risk people being exposed.

See #3 and #4, below.

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3: “Ending this epidemic with a vaccine would be ideal.”

Vaccination is great science.  Both my spouse and I love teaching about vaccines, in part because teaching the history of vaccine use is a good component of anti-racist science class.

Developing vaccines often takes a long time.  I’ve read predictions of a year or two; my father, an infectious disease doctor, epidemiologist, research physician who runs vaccine trials, and co-developer of Merck’s HPV vaccine, guesses that it will take about five years.

And then, for the vaccine to end this epidemic, enough people will need to choose to be vaccinated that we reach approximately 70% immunity.

The reason it’s worthwhile to compare Covid-19 to seasonal influenza is that a vaccine will only end the epidemic if enough people choose to get it.  Many people’s personal risk from Covid-19 is lower than their risk from seasonal influenza.  Will those people choose to be vaccinated?

Obviously, I would be thrilled if the answer were “yes.”  I’d love to live in a nation where people’s sense of altruism and civic duty compelled them to get vaccinated.  My family is up-to-date on all of ours.

But many privileged families in the United States have elected to be freeloaders, declining the (well tested, quite safe) measles vaccine with the expectation that other people’s immunity will keep them safe.  And, despite the well-documented dangers of influenza, only 40% of our population gets each year’s influenza vaccine.

Yes, the influenza vaccine tends to be less effective than many others – some years it gives as little as ten percent protection, other years about sixty percent protection.  By way of comparison, the HPV vaccine has over 90% efficacy.

A vaccine with low efficacy will still offer better protection when more people get it.  If a higher percentage of our population were vaccinated against influenza, then influenza transmission would drop, and so each person’s immunity, whether high or low, would be less likely to be challenged.

Also, the efficacy of influenza vaccines is measured in terms of the likelihood that vaccination prevents infection.  The influenza vaccine is not great at keeping people from getting sick.  But vaccination also tends to reduce the severity of your illness, even if you do catch influenza.  Because you got sick, it seems as though the vaccine “failed,” but your case might have been far more severe if you hadn’t been vaccinated.

The influenza vaccine saves lives.  In Italy, where fewer people choose to get vaccinated against influenza (about 15% compared to our 40% of the population), the death rate from influenza is higher.  Although it’s worth noting that this comparison is complicated by the fact that our health care system is so bad, with poor people especially having limited access to health care.  In the United States, people between the ages of 18 and 49 comprise a higher proportion of influenza deaths than anywhere in Europe.  Either our obesity epidemic or limited access to health care is probably to blame; possibly a combination of both.

In summary, for this plan to help us save lives, we will need to develop an effective vaccine, and then people will have to get it. 

I am quite confident that we can eventually develop a vaccine against Covid-19.  The virus includes a proofreading enzyme, so it should mutate more slowly than most RNA viruses.  We don’t know how long it will take, but we can do it.

I am unfortunately pessimistic that people will choose to get the vaccine.  And, unfortunately, when a low-risk person chooses to forgo vaccination, they’re not just putting themselves in harm’s way, they are endangering others.  Most vaccines elicit a weaker immune response in elderly or immunocompromised recipients – exactly the group most at risk from Covid-19 – which is why we spend so much time harping about herd immunity.

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4: “Ending the shutdown while requesting that at-risk people continue to self-isolate would save lives.“

This plan has major downsides, too.  Because we didn’t take action soon enough, every plan we have now is bad.

Low-risk people can still die of Covid-19.  Even if they don’t die, Covid-19 can cause permanent health effects.  Covid-19 reduces your ability to get oxygen to your body and brain.  Even a “mild” case can leave your breathing labored for weeks – you’re not getting enough oxygen.  Your muscles will ache.  Your thoughts will be sluggish.

With a more severe case, people can be looking at heart damage.  Renal failure.  It would be cruel to look at all these long-term consequences and blithely call them “recovery.”

If our health care system were better, we’d treat people sooner.  The earlier you intervene, helping to boost people’s oxygen levels, the better outcome you’ll have.  There’s a great editorial from medical doctor Richard Levitan recommending that people monitor their health with a pulse oximeter during this epidemic.

If you notice your oxygen levels declining, get help right away.  Early intervention can prevent organ damage.  And you’ll be helping everyone else, too – the sooner you intervene, the less medical care you will need.

Because medical debt can derail lives, many people in this country delay treatment as long as possible, hoping that their problems will go away naturally.  That’s why people are often so sick when they show up at the ER.  I imagine that this is yet another reason – alongside air pollution, food deserts, sleep loss, and persistent stress exacerbated by racism – that poor communities have had such a high proportion of people with severe cases of Covid-19.

And I imagine – although we don’t yet have enough data to know – that financial insecurity caused by the shutdown is making this worse.  It’s a rotten situation: you have a segment of population that has to continue working during the shutdown, which means they now have the highest likelihood to be exposed to the virus, and they’re now under more financial strain, which might increase the chance that they’ll delay treatment.

We know that early treatment saves lives, and not everyone is sufficiently privileged to access that.

All this sounds awful.  And it is.  But, if we took action to shift exposure away from high risk groups, the likelihood that any individual suffers severe consequences is lower.

And there is another caveat with this plan – some people may be at high risk of complications for Covid-19 and not even realize it.  In the United States, a lot of people either have type 2 diabetes or are pre-diabetic and don’t yet realize.  These people have elevated risk.  Both smoking and air pollution elevate risk, but people don’t always know which airborn pollutants they’ve been exposed to.  (Which, again, is why it’s particularly awful that our administration is weakening air quality standards during this epidemic.)

Even if we recommended continued self-isolation for only those people who know themselves to have high risk from Covid-19, though, we would be saving lives.  The more we can protect people in this group from being exposed to the virus – not just now, but ever – the more lives we will save.

We won’t be able to do this perfectly.  It’ll be a logistical nightmare trying to do it at all.  People at high risk from Covid-19 needs goods and services just like everybody else.  We might have to give daily Covid-19 PCR tests to anyone visiting their homes, like doctors, dentists, and even delivery workers. 

At that point, the false negative rate from Covid-19 PCR tests becomes a much bigger problem – currently, these false negatives reduce the quality of our data (but who cares?) and delay treatment (which can be deadly).  A false negative that causes inadvertent exposure could cost lives.

Stores will need to set aside morning hours for at-risk shoppers, and undertake rigorous cleaning at night.  We know that infectious viral particles can persist for days on a variety of surfaces.

Some people will be unable to work, either because they or a close relative has high risk of Covid-19.  Some children will be unable to go to school.  We will need a plan to help these people.

We will have to work very hard to keep people safe even after the shutdown ends for some. 

But, again, if everyone does the same thing, then the demographics of people infected with Covid-19 will reflect our population demographics.  We can save lives by skewing the demographics of the subset of our population that is exposed to Covid-19 to include more low-risk individuals, which will require that we stratify our recommendations by risk (at least as well as we can assess it).

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5: “Why is it urgent to end the shutdown soon?“

1.) By delaying Covid-19 deaths, we run to risk of causing more total people to die of Covid-19.

2.) The shutdown itself is causing harm.

See #6 and #7, below.

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6: “Why might more people die of Covid-19 just because we are slowing the spread of the virus?“

[EDIT: I wrote a more careful explanation of the takeaways of the Harvard study. That’s here if you would like to take a look!]

This is due to the interplay between duration of immunity and duration of the epidemic.  At one point in time, seasonal influenza was a novel zoogenic disease.  Human behavior allowed the influenza virus to become a perpetual burden on our species.  No one wants for humans to still be dying of Covid-19 in ten or twenty years.  (Luckily, because the virus that causes Covid-19 seems to mutate more slowly than influenza, it should be easier to design a single vaccine that protects people.)

In the Harvard model, we can see that there are many scenarios in which a single, finite shutdown leads to more deaths from Covid-19 than if we’d done nothing. Note the scenarios for which the colored cumulative incidence curves (shown on the right) exceed the black line representing how many critical cases we’d have if we had done nothing.

Furthermore, their model does not account for people’s immunity potentially waning over time.  Currently, we do not know how long people’s immunity to Covid-19 will last.  We won’t know whether people’s immunity will last at least a year until a year from now.  There’s no way to test this preemptively.

We’ve seen that immunity to other coronaviruses fades within a year.  If immunity to Covid-19 is similar, we really don’t want to prolong the epidemic past a year.

If we could all go into stasis and simply not move for about a month, there’d be no new cases of Covid-19, and this virus would be gone forever.  But people still need to eat during the shutdown.  Many people are still working.  So the virus is still spreading, and we have simply slowed the rate of transmission.

This seems good, because we’re slowing the rate at which people enter the hospital, but it’s actually bad if we’re increasing the number of people who will eventually enter the hospital.

Based on our research with other coronaviruses, we expect that re-infection will cause a person to experience symptoms less severe than their first case of Covid-19.  But a re-infected person can still spread the disease to others.  And we don’t know what will happen if a person’s risk factors – such as age, smoking status, diabetes status, etc. – have increased in the time since their last infection.

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7: “How is the shutdown causing harm?“

If you turn on Fox News, I imagine you’d hear people talking about the damage we’re doing to our economy.  They might discuss stock market numbers.

Who gives a shit?  In my opinion, you’d have to be pretty callous to think that maintaining the Nasdaq bubble is more important than saving lives.

At the same time, I think you’d have to be pretty callous to not feel extremely concerned by the United Nations’ policy brief, “The impact of Covid-19 on children.”

In this report, they estimate that the shutdown we’ve had so far will cause hundreds of thousands of children to die, many from malnutrition and the other health impacts of poverty.  The longer the shutdown continues, the more children will die.

That’s a worldwide number, and most of those children live outside the United States.  But I’d like to think that their lives matter, too.

The report also discusses the lifelong harm that will be inflicted on children from five months (or more!) of school closure.  Drop-outs, teen pregnancy, drug abuse, recruitment of child soldiers, and the myriad health consequences of low educational attainment.

I live in a wealthy college town, but even here there is a significant population of students who don’t have internet access.  Students with special needs aren’t getting the services they deserve.  Food insecurity is worse.

You’re lucky that privacy protections prevent me from sharing a story about what can happen to poor kids when all the dentists’ offices are closed.  I felt ashamed that this was the best my country had to offer.

As the shutdown continues, domestic violence is rising.  We can assume that child abuse is rising, also, but we won’t know until later, when we finally have a chance to save children from it.  In the past, levels of child abuse have been correlated with the amount of time that children spend in the presence of their abusers (usually close family), and reporting tends to happen during tense in-person conversations at school.

We know that online sex work has increased during the shutdown.  There is an increased supply of sex workers who are experiencing increasing financial insecurity.  We don’t yet have data on this, but I’d be shocked if the shutdown hasn’t led many to feel pressured into riskier acts for lower amounts of money, including meeting clients in isolated (and therefore unsafe) spaces.

The shutdown has probably made our drug epidemic worse (and this was already killing about 70,000 people per year in the U.S.).  When people are in recovery, one of the best strategies to stay sober is to spend a lot of time working, out of the house, and meeting with a supportive group in communal space.  Luckily, many of the people I know who are in recovery have been categorized as essential workers.

But any slip can kill someone recovering from addiction.  One of my friends froze to death last year.

A neighbor recently sent me a cartoon suggesting that the biggest harm caused by the shutdown is boredom.  (I’m going to include it, below, but don’t worry: I won’t spend too much time rattling sabers with a straw man.) And, for privileged families like mine, it is.  We’re safe, we’re healthy, we get to eat.  My kids are still learning – we live in a house full of computers and books.

But many of the 75 million children in the United States don’t live in homes like mine, with the privilege we have.  Many of our 50 million primary and secondary school students are not still learning academically during the shutdown.

Whether the shutdown is preventing or merely delaying the deaths of people at risk of serious complications from Covid-19, we have to remember that the benefit comes at a cost.  What we’ve done already will negatively impact children for the rest of their lives.  And the longer this goes on, the more we’re hurting them.

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8: “What about the rate at which people get sick?  Isn’t the shutdown worthwhile, despite the risks described above, if it keeps our hospitals from being overwhelmed?“

In writing this, I struggled with how best to organize the various responses.  I hope it doesn’t seem too ingenuous to address this near the end, because slowing the rate of infection so that our hospitals don’t get overwhelmed is the BEST motivation for the shutdown.  More than the hope that a delay will yield a new vaccine, or new therapies to treat severe cases, or even new diagnostics to catch people before they develop severe symptoms, we don’t want to overwhelm our hospitals.

If our physicians have to triage care, more people will die.

And I care a lot about what this epidemic will be like for our physicians.  My father is a 67-year-old infectious disease doctor who just finished another week of clinical service treating Covid-19 patients at the low-income hospital in Indianapolis.  My brother-in-law is an ER surgeon in Minneapolis.  These cities have not yet had anything like the influx of severe cases in New York City – for demographic and environmental reasons, it’s possible they never will.  But they might. 

Based on the case fatality rate measured elsewhere, I’d estimate that only 10% of the population in Minneapolis has already been infected with Covid-19, so the epidemic may have a long way yet to go.

If we ended the shutdown today for everyone, with no recommendation that at-risk groups continue to isolate and no new measures to protect them, we would see a spike in severe cases.

If we ended the shutdown for low-risk groups, and did a better job of monitoring people’s health to catch Covid-19 at early, more-easily-treatable stages (through either PCR testing or oxygen levels), we can avoid overwhelming hospitals.

And the shutdown itself is contributing toward chaos at hospitals.  Despite being on the front lines of this epidemic, ER doctors in Minneapolis have received a 30% pay cut.  I imagine my brother-in-law is not the only physician who could no longer afford day care for his children after the pay cut.  (Because so many people are delaying care out of fear of Covid-19, hospitals are running out of money.)  Precisely when we should be doing everything in our power to make physicians’ lives easier, we’re making things more stressful.

We could end the shutdown without even needing to evoke the horrible trolley-problem-esque calculations of triage.  Arguments could be made that even if it led to triage it might be worthwhile to end the shutdown – the increase in mortality would be the percentage of triaged cases that could have survived if they’d been treated, and we as a nation might decide that this number was acceptable to prevent the harms described above – but with a careful plan, we need not come to that.

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9: “Don’t the antibody tests have a lot of false positives?“

False positives are a big problem when a signal is small.  I happen to like a lot of John Ioannidis’s work – I think his paper “Why Most Published Research Findings Are False” is an important contribution to the literature – but I agree that the Santa Clara study isn’t particularly convincing. 

When I read the Santa Clara paper, I nodded and thought “That sounds about right,” but I knew my reaction was most likely confirmation bias at work.

Which is why, in the essay, I mostly discussed antibody studies that found high percentages of the population had been infected with Covid-19, like the study in Germany and the study in the Italian town of Robbio.  In these studies, the signal was sufficiently high that false positives aren’t as worrisome. 

In Santa Clara, when they reported a 2% infection rate, the real number might’ve been as low as zero.  When researchers in Germany reported a 15% infection rate, the real number might’ve been anywhere in the range of 13% to 17% – or perhaps double that, if the particular chips they used had a false negative rate similar to the chips manufactured by Premier Biotech in Minneapolis.

I’m aware that German response to Covid-19 has been far superior to our bungled effort in the United States, but an antibody tests is just a basic ELISA.  We’ve been doing these for years.

Luckily for us, we should soon have data from good antibody studies here in the United States.  And I think it’s perfectly reasonable to want to see the results of those.  I’m not a sociopath – I haven’t gone out and joined the gun-toting protesters.

But we’ll have this data in a matter of weeks, so that’s the time frame we should be talking about here.  Not months.  Not years.  And I’ll be shocked if these antibody studies don’t show widespread past infection and recovery from Covid-19.

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10: “What about the political ramifications of ending the shutdown?“

I am, by nature, an extremely cautious person.  And I have a really dire fear.

I’m inclined to believe that ending the shutdown is the right thing to do.  I’ve tried to explain why.  I’ve tried to explain what I think would be the best way to do it.

But also, I’m a scientist.  You’re not allowed to be a scientist unless you’re willing to be proven wrong.

So, yes.  I might be wrong.  New data might indicate that writing this essay was a horrible mistake.

Still, please bear with me for a moment.  If ending the shutdown soon turns out to be the correct thing to do, and if only horrible right-wing fanatics have been saying that we should end the shutdown soon, won’t that help our current president get re-elected?

There is a very high probability that his re-election would cause even more deaths than Covid-19.

Failing to address climate change could kill billions.  Immigration controls against migrants fleeing war zones could kill millions.  Weakened EPA protections could kill hundreds of thousands.  Reduced access to health care could kill tens of thousands.

And, yes, there are horrible developments that neither major political party in the United States has talked about, like the risk that our antibiotics stop working, but I think it’s difficult to argue that one political party isn’t more dangerous than the other, here.

I feel pretty confident about all the scientific data I’ve discussed above.  Not as confident as I’d like, which would require more data, but pretty confident.

I feel extremely confident that we need to avoid a situation in which the far right takes ownership of an idea that turns out to have been correct.  And it’ll be dumb luck, just a bad coincidence.  The only “data” they’re looking at are stock market numbers, or maybe the revenue at Trump-owned hotels.

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EDIT: I also wrote a more careful explanation of the takeaways of the Harvard study. That’s here if you would like to take a look!

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Header image by Goran Paunovic.

On testing.

On testing.

UPDATE: Wow, this got a lot of readers! Honestly, though, I wrote a response to common questions and comments about this essay and it is probably a better read.

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My spouse recently sent me a link to the article “Concerns with that Stanford study of coronavirus prevalence” by Andrew Gelman, a statistician at Columbia University.  From reading this article, I got the impression that Gelman is a good mathematician.  And he raises some legitimate concerns. 

But I’ve noticed that many of the people criticizing the work coming out of the Ioannidis group – such as the study of how many people in Santa Clara county might have antibodies to Covid-19 – don’t seem to understand the biology underlying the numbers.

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First, some background: in case you haven’t noticed, most of the United States is operating under a half-assed lockdown.  In theory, there are stay-at-home orders, but many people, such as grocery store clerks, janitors, health care workers, construction workers, restaurant chefs, delivery drivers, etc., are still going to work as normal.  However, schools have been closed, and most people are trying to stand at least six feet away from strangers.

We’re doing this out of fear that Covid-19 is an extremely dangerous new viral disease.  Our initial data suggested that as many as 10% of people infected with Covid-19 would die.

That’s terrifying!  We would be looking at tens of millions of deaths in the United States alone!  A virus like this will spread until a majority of people have immunity to it – a ballpark estimate is that 70% of the population needs immunity before the epidemic stops.  And our early data suggested that one in ten would die.

My family was scared.  We washed our hands compulsively.  We changed into clean clothes as soon as we came into the house.  The kids didn’t leave our home for a week.  My spouse went to the grocery store and bought hundreds of dollars of canned beans and cleaning supplies.

And, to make matters worse, our president was on the news saying that Covid-19 was no big deal.  His nonchalance made me freak out more.  Our ass-hat-in-chief has been wrong about basically everything, in my opinion.  His environmental policies are basically designed to make more people die.  If he claimed we had nothing to worry about, then Covid-19 was probably more deadly than I expected.

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Five weeks have passed, and we now have much more data.  It seems that Covid-19 is much less dangerous than we initially feared.  For someone my age (37), Covid-19 is less dangerous than seasonal influenza.

Last year, seasonal influenza killed several thousand people between the ages of 18 and 49 in the United States – most likely 2,500 people, but perhaps as many as 5,800.  People in this age demographic account for about 10% of total flu deaths in the United States, year after year.

Seasonal influenza also killed several hundred children last year – perhaps over a thousand.

There’s a vaccine against influenza, but most people don’t bother. 

That’s shocking. 

Seasonal influenza is more dangerous than Covid-19 for people between the ages of 18 and 49, but only 35% of them chose to be vaccinated in the most recently reported year (2018).  And because the vaccination rate is so low, our society doesn’t have herd immunity.  By choosing not to get the influenza vaccine, these people are endangering themselves and others.

Some people hope that the Covid-19 epidemic will end once a vaccine is released.  I am extremely skeptical.  The biggest problem, to my mind, isn’t that years might pass before there’s a vaccine.  I just can’t imagine that a sufficient percentage of our population would choose to get a Covid-19 vaccine when most people’s personal risk is lower than their risk from influenza.

When I teach classes in jail, dudes often tell me about which vaccines they think are too dangerous for their kids to get.  I launch into a tirade about how safe most vaccines are, and how deadly the diseases they prevent. 

Seriously, get your kids vaccinated.  You don’t want to watch your child die of measles.

And, seriously, dear reader – get a flu vaccine each year.  Even if you’re too selfish to worry about the other people whom your mild case of influenza might kill, do it for yourself. 

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We already know how dangerous seasonal influenza is.  But what about Covid-19?

To answer that, we need data.  And one set of data is unmistakable – many people have died.  Hospitals around the world have experienced an influx of patients with a common set of symptoms.  They struggle to breathe; their bodies weaken from oxygen deprivation; their lungs accumulate liquid; they die.

Many people have been put on ventilators, but that’s often the beginning of the end.  Most people put on ventilators will die.  Among patients over 70 years old, three quarters who are put on ventilators will die. 

For each of these patients saved, three others are consigned to an agonizing death in the hospital, intubated among the flashing lights, the ceaseless blips and bleeps.  At home, they’d die in a day; in the hospital, their deaths will take three weeks.

And the sheer quantity of deaths sounds scary – especially for people who don’t realize how many tens of thousands die from influenza in the United States each year.

Or, consider: cigarette smoking causes 480,000 deaths per year in the United States, including 41,000 people who die from second-hand smoke exposure.  Those 41,000 aren’t even choosing to smoke!  But cigarettes kill them anyway.

Indeed, when people die of Covid-19, it’s often because their lungs fail.  Smoking is obviously a major risk factor for dying of Covid-19 – a significant portion of reported Covid-19 deaths could be considered cigarette deaths instead.  Or as air pollution deaths – and yet, our current president is using this crisis as an opportunity to weaken EPA air quality regulations.

Air pollution is a huge problem for a lot of Black communities in the United States.  Our racist housing policies have placed a lot of minority neighborhoods near heavily polluting factories.  Now Covid-19 is turning what is already a lifelong struggle for breath into a death sentence.

I would enthusiastically support a shutdown motivated by the battle for clean air.

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So, Covid-19.  We know how many people have died – already (CORRECTION AS OF APRIL 21) forty-two thousand in the United States. 

But if we want to know how scary this virus is, we need to know how many people were infected.  If that many people died after everyone in the country had it, then Covid-19 would be less dangerous than influenza.  If that many people died after only a hundred thousand had been infected, then this would be terrifying, and far more dangerous than influenza.

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Initially, our data came from PCR testing.

These are good tests.  Polymerase chain reaction is highly specific.  If you want to amplify a certain genetic sequence, you can design short DNA primers that will bind only to that sequence.  Put the whole mess in a thermocycler and you get a bunch of your target, as long as the gene is present in the test tube in the first place.  If the gene isn’t there, you’ll get nothing.

PCR works great.  Even our lovely but amnesiac lab tech never once screwed it up.

So, do the PCR test and you’ll know whether a certain gene is present in your test tube.  Target a viral gene and you’ll know whether the virus is present in your test tube.  Scoop out some nose glop from somebody to put into the test tube and you’ll know whether the virus is present in that nose glop.

The PCR test is a great test that measures whether someone is actively shedding virus.  It answers, is there virus present in the nose glop?

This is not the same question as, has this person ever been infected with Covid-19? 

It’s a similar question – most people infected with a coronavirus will have at least a brief period of viral shedding – but it’s a much more specific question.  When a healthy person is infected with a coronavirus, the period of viral shedding can be as short as a single day.

A person can get infected with a coronavirus, and if you do the PCR test either before or after that single day, the PCR test will give a negative result.  Nope, no viral RNA is in this nose glop!

And so we know that the PCR test will undercount the true number of infections.

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When we look at the age demographics for Covid-19 infections as measured by PCR test, the undercount becomes glaringly obvious.

Consider the PCR test data from the Diamond Princess cruise ship.  To date, this is our most complete set of PCR data – everyone on board was tested multiple times.  And from this data, it appears that very few children were exposed to the virus.

Friends, it is exceedingly unlikely that such a low percentage of children were exposed to this virus.  Children are disgusting.  I believe this is common knowledge.  Parents of small children are pretty much always sick because children are so disgusting. 

Seriously, my family has been doing the whole “social distancing” thing for over a month, and yet my nose is dripping while I type this.

Children are always touching everything, and then they rub their eyeballs or chew on their fingers.  If you take them someplace, they grubble around on the floor.  They pick up discarded tissues and ask, “What’s this?”

“That’s somebody’s gross kleenex, is what it is!  Just, just drop it.  I know it’s trash, I know we’re not supposed to leave trash on the ground, but just, just drop it, okay?  Somebody will come throw it away later.”

The next day: “Dad, you said somebody would throw that kleenex away, but it’s still there!”

Bloody hell.  Children are little monsters.

It seems fairly obvious that at least as high a percentage of children would be infected as any other age demographic.

But they’re not showing up from the PCR data.  On the Diamond Princess cruise ship, the lockdown began on February 5th, but PCR testing didn’t begin until February 11th.  Anyone who was infected but quickly recovered will be invisible to that PCR test.  And even people who are actively shedding viral particles can feel totally well.  People can get infected and recover without noticing a thing.

We see the same thing when we look at the PCR data from Italy.  If we mistakenly assumed that the PCR data was measuring the number of infections, and not measuring the number of people who were given a PCR test while shedding viral particles, we’d conclude that elderly people went out and socialized widely, getting each other sick, and only occasionally infected their great-grandchildren at home.

Here in the United States, children are disgusting little monsters.  I bet kids are disgusting in Italy, too.  They’re disgusting all over the world.

A much more likely scenario is that children spread this virus at school.  Many probably felt totally fine; some might’ve had a bad fever or the sniffles for a few days.  But then they recovered.

When they got their great-grandparents sick – which can happen easily since so many Italian families live in multigenerational homes – elderly people began to die.

So we know that the PCR test is undercounting the true number of infections.  Unless you’re testing every person, every day, regardless of whether or not they have symptoms, you’re going to undercount the number of infections.

In a moment, we can work through a way to get a more accurate count.  But perhaps it’s worth mentioning that, for someone my age, Covid-19 would seem to be about as dangerous as influenza even if we assumed that the PCR data matched the true number of infections.

If you’re a healthy middle-aged or young person, you should not feel personally afraid. 

That alone would not be an excuse to go out and start dancing in the street, though.  Your actions might cause other people to die. 

(NOTE & CORRECTION: After this post went up, my father recommended that I add something more about personal risk. No one has collected enough data on this yet, but he suspects that the next most important risk factor, after smoking and age, will be type 2 diabetes. And he reminded me that many people in their 30s & 40s in this country are diabetic or prediabetic and don’t even realize it yet. Everyone in this category probably has elevated risk of complications from Covid-19.)

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After you’ve been infected with a virus, your body will start making antibodies.  These protect you from being infected again.

Have you read Shel Silverstein’s Missing Piece book?  Antibodies work kind of like that.  They have a particular shape, and so they’ll glom onto a virus only if that virus has outcroppings that match the antibody’s shape.  Then your body sees the antibodies hanging out on a virus like a GPS tracker and proceeds to destroy the virus.

So to make an antibody test, you take some stuff that looks like the outcroppings on the virus and you put it on a chip.  Wash somebody’s blood over it, and if that blood contains antibodies that have the right shape to glom onto the virus, they’ll stick to the chip.  All your other antibodies, the ones that recognize different viruses, will float away.

An antibody test is going to be worse than a PCR test.  It’s easier to get a false positive result – antibodies are made of proteins, and they can unfold if you treat them roughly, and then they’ll stick to anything.  Then you’ll think that somebody has the right antibodies, but they don’t.  That’s bad.

You have to be much more careful when you’re doing an antibody test. I wouldn’t have asked our lab tech to do them for me.

An antibody test is also going to have false negatives.  A viral particle is a big honking thing, and there are lots of places on its surface where an antibody might bind.  If your antibodies recognize some aspect of the virus that’s different from what the test manufacturers included on their chip, your antibodies will float away.  Even though they’d protect you from the actual virus if you happened to be exposed to it.

If you’re a cautious person, though – and I consider myself to be pretty cautious – you’d much rather have an antibody test with a bunch of false negatives than false positives.  If you’re actually immune to Covid-19 but keep being cautious, well, so what?  You’re safe either way.  But if you think you’re immune when you’re not, then you might get sick.  That’s bad.

Because antibody tests are designed to give more false negatives than false positives, you should know that it’d be really foolish to use them to track an infection.  Like, if you’re testing people to see who is safe to work as a delivery person today, use the PCR test!  The antibody test has a bunch of false negatives, and there’s a time lag between the onset of infection and when your body will start making antibodies.

It can be dangerous to use antibody tests to address the wrong questions.

If you use the antibody test on a bunch of people, though, you can tell how many were infected.  And that’s useful information, too.

In the town of Robbio in Italy (pop. 6,000), the PCR test showed that only 23 people had been infected with Covid-19.  But then the mayor implored everyone to get an antibody test, and 10% of people had actually been infected with – and had recovered from – Covid-19.  Most of them couldn’t even recall having been sick.

The PCR test measured 23 cases.  The antibody test suggested there’d been at least 600.  And antibody tests, by design, will generally have a bunch of false negatives.  When a team at Stanford assessed the antibody tests manufactured by Premier Biotech in Minneapolis, they found that for every 3 people who’d been infected with Covid-19, the tests registered only 2 positives.

I don’t know who made the tests used in Robbio – maybe they were a little better, maybe they were a little worse.  Based on my experience, I wouldn’t be so surprised if the true infection rate with Covid-19 in that town was really just 10% – nor would I be surprised to hear that the chips had a high false-negative rate and that the infection rate was 20% or more.

If you calculate the fatality rate of Covid-19 in Italy by assuming that the PCR tests caught every infection, you’d get a terrifying 10%.

If you instead assume that many other towns had a similar infection rate to Robbio, you’ll instead calculate that the fatality rate was well under one percent. 

Italy has higher risk than the United States due to age demographics, smoking rates, and multigenerational households – and even in Italy, the fatality rate was probably well under one percent.

When researchers in Germany randomly chose people to take a Covid-19 PCR test (many of whom had no symptoms), they found that 2% of the population was actively shedding virus – a much higher number of cases than they would have found if they tested only sick people.  And when they randomly chose people to take an antibody test, they found that 15% had already recovered from the infection (again, many of whom had never felt sick).  According to these numbers – which are expected to be an undercount, due to false negatives and the time lag before antibody production – they calculated a case fatality rate of 0.37%. 

That would be about three-fold more dangerous than seasonal influenza.

In the United States, our bungling president gutted the CDC, leaving us without the expertise needed to address Covid-19 (or myriad other problems that might arise).  During the first few months of this epidemic, very few people managed to get a PCR test.  That’s why our data from the PCR tests is likely to be a dramatic undercount – indeed, when we finally started producing accurate tests, the apparent growth in Covid-19 caseload superimposed with the growth in test availability.

In the absence of good PCR data, we have to rely on antibody data to track infections after the fact.  Which is why a town in Colorado with zero reported infections, as measured by PCR, had sufficiently widespread exposure that 2% of the population had already recovered from Covid-19.

And it’s why the data from the Stanford Santa Clara county study is so unsurprising. 

Yes, there were problems with the Stanford study’s data collection – they displayed advertisements to a random selection of people, but then a self-selected subset responded.  The pool of respondents were enriched for white women, but Santa Clara’s outbreak probably began among Asian-Americans.  And we all know that random sampling doesn’t always give you an accurate depiction of the population at large – after all, random polling predicted that a competent president would be elected in 2016.

Now look at us.

It’s also likely that people with a poor understanding of the biology could misinterpret the result of the Stanford study.  They found that PCR tests had undercounted the infection rate in Santa Clara county, at the time of this study, by 85-fold.

It would be absurd to assume that you could simply multiply all PCR results by 85 to determine the true infection rate, but some people did.  And then pointed out the absurdity of their own bad math.

In places where more people are being tested by PCR, and they’re being tested more often, the PCR results will be closer to the true infection rate.  If you gave everyone in the United States a PCR test, and did it every day, then the PCR data would be exactly equal to the true infection rate.

If we had data like that from the beginning, we wouldn’t have been scared.  We would’ve known the true case fatality rate early on, and, also, at-risk people could’ve been treated as soon as they got infected.  We’d be able to save many more lives.

If access to health care were considered a basic right in the United States, we might’ve done something like this. 

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In Italy, it seems like Covid-19 is three- or four-fold more dangerous than seasonal influenza.  My guess is that Italy might have had about 50,000 deaths if they hadn’t enacted the lockdown.

In the United States, on a population level, Covid-19 is probably also more dangerous than seasonal influenza.  But there’s a big difference in terms of the distribution of risk.

The New York Times is running a series with short biographies of people who’ve died of Covid-19.  As of noon on April 17, about 10% of the people profiled were younger than 35.

10% is roughly the proportion of young people who die of seasonal influenza.  But only 1% of Covid-19 deaths are people younger than 35.  The news reports don’t always make clear how much the risk of Covid-19 is clustered in a small segment of the population.

This has serious implications for what we should do next.  If we were dealing with a virus that was about three-fold more dangerous than seasonal influenza for everyone, we might just return to life as normal.  (Indeed, we carried on as normal during the bad years when seasonal influenza killed 90,000 people instead of last year’s 30,000.)

Because the risk from Covid-19 is so concentrated, though, we can come up with a plan that will save a lot of lives. 

Healthy people under retirement age should resume most parts of their lives as normal.  Schools should re-open: for students, Covid-19 is much less dangerous than seasonal influenza.  I think that people should still try to work from home when possible, because it’s the right thing to do to fight climate change.

At-risk people should continue to isolate themselves as much as possible.

This sounds crummy, but at-risk people would just continue to do the thing that everyone is doing currently.  And the plan would save many lives because the epidemic would end in about 3 months, after the virus had spread to saturation among our nation’s low-risk cohort. 

Indeed, when a team of researchers from Harvard’s School of Public Health modeled the Covid-19 epidemic, they found that social distancing was generally unhelpful.  That’s what their data show, at least – but in their abstract, they instead recommend that we continue social distancing for the better part of two years.

Their data are easy enough to understand.  In each of these graphs, they show a blue box for how long social distancing would last, and then four colored lines to represent how many infections we’d see if we did no social distancing (black), medium quality social distancing (red), good social distancing (blue), or excellent social distancing (green).

So, from top to bottom, you’re looking at the graphs of what happens if we do a month of social distancing … or two months … or three, or four … or forever.

And you can see the outcomes in the panels on the right-hand side.  The black line shows what would happen if we did nothing.  Infections rise fast, then level off after the virus has reached saturation.  There are two important features of this graph – the final height that it reaches, which is the total number of severe cases (and so a good proxy for the number of deaths), and the slope of the line, which is how fast the severe cases appear.  A steeper hill means many people getting sick at the same time, which means hospitals might be overwhelmed.

So, okay.  Looking at their graphs, we see that social distancing saves lives … if we do it forever.  If you never leave your house again, you won’t die of Covid-19.

But if social distancing ends, it doesn’t help.  The slopes are nearly as steep as if we’d done nothing, and the final height – the total number of people who die – is higher.

(Often, one of their curves will have a gentler slope than the others — usually the good-but-not-excellent social distancing seems best. So you’d have to pray that you were doing a precisely mediocre job of not infecting strangers. Do it a little better or a little worse and you cause people to die. This isn’t an artifact — it’s based on the density of uninfected people when social distancing ends — but let’s just say “mathematical models are wonky” and leave it at that.)

In a subsequent figure, the Harvard team tried to model what might happen if we occasionally resumed our lives for a month or so at a time, but then had another shutdown.  This is the only scenario in which their model predicts that social distancing would be helpful.

But, unfortunately, there’s a problem.  Research done with other coronaviruses shows that immunity fades within a year.  Because the Harvard model would cause the epidemic to last longer than a year, people would have time to lose their immunity and get infected again.

Even in the extreme case that we mostly stayed in our homes for the better part of two years, social distancing would case more deaths from Covid-19 than if we had done nothing.

That’s not even accounting for all the people who would die from a greater risk of domestic violence, hunger, drug addiction, suicide, and sedentary behavior during the shutdown.  

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When our data was limited, the shutdown seemed reasonable.  We wouldn’t be able to undo the damage we’d done by waiting.

Except, whoops, we waited anyway.  We didn’t quarantine travelers in January.  The shutdown didn’t begin March, when the epidemic was well underway in many places. 

Now that we have more data, we should re-open schools, though.  For most people, Covid-19 is no more dangerous than seasonal influenza.  We already have enough data from antibody testing to be pretty confident about this, and even if we want to be extremely cautious, we should continue the shutdown for a matter of weeks while we conduct a few more antibody studies.  Not months, and certainly not years.

At the same time, we need to do a better job of protecting at-risk people.  This means providing health care for everyone.  This means cleaning our air, staunching the pollution that plagues low-income neighborhoods.  This might mean daily medical checkups and PCR tests for people who work closely with at-risk populations.

Our country will have to be different in the future, but mostly because we, as a people, have done such a shitty job of creating justice and liberty for all.  We need to focus on addressing the inequities that we’ve let fester for generations.  That’ll help far more than using a bandanna to cover up your smile.

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UPDATE: Wow, this got a lot of readers! Thanks if you made it this far. I’ve also written a response to common questions and comments about this essay.

On paranoia, virology, conspiracy theories, & lemmings: my experience reading ‘Gravity’s Rainbow.’

On paranoia, virology, conspiracy theories, & lemmings: my experience reading ‘Gravity’s Rainbow.’

gravitys rainbow at whitney

Shortly before I turned sixteen, I read an article in the Indianapolis Star describing a piece of artwork temporarily showing downtown. Fred Tomaselli’s Gravity’s Rainbow, as inspired by Thomas Pynchon’s book. The description in the paper was rapturous. Beautiful, deep, dark, mysterious. A giant canvas with covered in fluorescent parabolas of … pills?

Street drugs, pharmaceuticals, and fakes, all strung vibrantly together.

I was enthralled. After a week of pleading, my parents took me to see it. And… well, sure, I was disappointed. I was just a kid. I hadn’t read the book. Just like Marcel when he finally saw La Berma, I felt let down because I didn’t have the background needed to see as much in the artwork as the article implied.

But I did resolve to read the book.

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I’m not sure what image best illustrates the opera performance of a fictional character, so here’s Alexandre Cabanel’s Phedre. This is the role Marcel first saw La Berma perform, at which point he felt disappointed by her apparent lack of artifice. Good acting means acting naturally??

At the time, my hometown library didn’t have a copy. The only bookstore I frequented was Half-priced Books, which has very haphazard inventory. Later, when I didn’t have an influx of babysitting money supporting my habit, I became even stingier and only shopped at library booksales. Paperbacks for a quarter! Hardbacks for fifty cents! The only problem being total inability to predict what you’ll find.

5628951142_cc4759b4dc_oLet me tell you: if you’re hunting for a mammoth, oft-discussed-but-rarely-read cult novel, you’ll have to visit a whole lotta library booksales before you’re likely to find a copy. Over the years I’ve found V and The Crying of Lot 49 and Inherent Vice and even a guide purporting to demystify Gravity’s Rainbow, but never the book itself.

Of course, now I live in a town with much better libraries than where I grew up. The library here has a copy. We even have an audio version in case you’d rather spend thirty-eight hours listening to it in your car than sit down and read the thing.

The book follows, among numerous others, the travails of ex-military man Slothrop, a paranoid drug-gobbling sex criminal (I could’ve used fewer gleeful paeans to pedophilia, but I can’t expect every author to cater to my reading whims) who feels himself to be — and perhaps is — enmeshed in a dark conspiracy that spans decades, transcends nationality, and takes precedence over even the war.

The evocation of paranoia is charming. Indeed, within novels, it’s often the case that everything really is connected, that even the most outlandish coincidences were inevitable. Excepting works like Fyodor Dostoyevsky’s serially-published & sketchily-planned The Idiot, novels are sculpted by an all-powerful author dictating the course of action. Slothrop is right to be afraid… of Pychon, if no one else.

The novel reels through numerous “Proverbs for Paranoids,” but to my mind the most chilling passage is the following:

The basic idea is that They will come and shut off the water first. … Shutting the water off interdicts the toilet: with only one tankful left, you can’t get rid of much of anything any more, dope, shit, documents. They’ve stopped the inflow / outflow and here you are trapped inside.

. . .

So it’s good policy always to have the toilet valve cracked a bit, to maintain some flow through the toilet so when it stops you’ll have that extra minute or two. Which is not the usual paranoia of waiting for a knock, or a phone to ring: no, it takes a particular kind of mental illness to sit and listen for a cessation of noise.

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Paranoiac by adricarra on deviantart.

This passage is frightening because it sounds so reasonable — maybe secret agents would take precautions to keep you from destroying evidence — yet only someone with a totally hyperactive connection-seeking mind would actually think to monitor the trickle of a leaking toilet, fully expecting the noise to someday stop.

The human mind evolved to find meaning in the surrounding world, but to my mind the root of schizophrenia, more dire than sounds perceivable to no one else, is the tendency to find meaning too often. So much is happening every second that connections and coincidences will always be there, if you demand them to be.

In the paranoid world of Gravity’s Rainbow, even World War 2 bombings were planned for, and were necessary to enable devious machinations. This sounds deranged, and yet it’s actually very similar to something that happens in nature.

Take influenza. The influenza virus can’t reproduce until it enters a host’s cells. But the viral protein that latches onto cells, in its standard form, doesn’t work. The virus is produced with a “fusion-incompetent precursor.” Only after the viral protein is attacked by its host — chewed on by a protease that’s attempting to destroy the virus — does it become functional.

3-dimensional-model-of-influenza-virus
Hemagglutinin molecules — blue pegs on the outside of this model — need to be severed by a host endoprotease before the flu virus can dock & conquer.

Influenza is harmless … until the host fights back. If you’ll excuse me a touch of anthropomorphism here, influenza is so devious because it knows the host will fight back, and plans for that, and uses the host defense as part of its own strategy.

The paranoiacs in Gravity’s Rainbow fear that weapons facilities were constructed the same way. That bombings were anticipated, and planned for, and the structures assembled precisely so that the bombings would activate the facility:

Zoom uphill slantwise toward a rampart of wasted, knotted, fused, and scorched girderwork, stacks, pipes, ducting, windings, fairings, insulators reconfigured by all the bombing, grease-stained pebblery on the ground, rushing by a mile a minute and wait, wait, say what, say “reconfigured,” now?

There doesn’t exactly dawn, no but there breaks, as that light you’re afraid will break some night at too deep an hour to explain away — there floods on Enzian what seems to him an extraordinary understanding. This serpentine slag-heap he is just about to ride into now, this ex-refinery, Jamf Olfabriken Werke AG, is not a ruin at all. It is in perfect working order. Only waiting for the right connections to be set up, to be switched on … modified, precisely, deliberately by bombing that was never hostile, but part of a plan both sides — “sides?” — had always agreed on …

These musings must strike most people as deranged. The likelihood of a single organization willfully orchestrating World War 2 is pretty low. But this idea isn’t dramatically more bizarre than other common conspiracy theories.  Large numbers of people believe that the moon landing was faked, that the CIA killed JFK, that the mass shooting at the Batman film in Colorado was planned by the U.S. government …

The United States is rife with conspiracy theorists. With X-Files back on air, perhaps there’ll be a resurgence in the number of conspiracy theories involving extraterrestrial life — those seem to have faded in popularity since the late nineties.

suspicious mindsA few books have been published recently examining why so many Americans believe in conspiracy theories. The latest (that I’ve noticed) is Rob Brotherton’s Suspicious Minds, which examines the way quirks in our brains promote belief in conspiracy theories.

For instance, pattern-seeking: it makes sense to assume that individuals best able to look at their surroundings and see patterns — This berry patch has a lot to eat every spring! Everybody who’s gone to that water hole at twilight has been eaten by a tiger! — would’ve been most successful through evolutionary time. The only drawback is that our brains are so good at finding patterns that we often see them when they aren’t there — In our last three games, my team won both times I was wearing these socks, and lost when I wore different ones… I’ll never take these socks off again! — letting us ascribe deep meaning to random happenstance.

Honestly, believing in happenstance can be terrifying. If you believe that bad things happen to good people because a watchful god is angry, you can make overtures to appease that god. Maybe the suffering will stop. But if the universe is a chaotic, value-less place, then there’s nothing you can do to stave off random disaster.

When I read Suspicious Minds, I felt like Brotherton left out a potent explanation for our abundance of conspiracy theories. Yes, evolution seems to have molded our minds to readily believe in nefarious conspiracies. Brotherton cites psychology research into the nature of these beliefs, suggesting the propensity is innate. In addition to all the usual caveats you should keep in mind when reading pop psychology, it’s especially important to recall that most study subjects for this research come from the same culture … and this culture actually trains young people to believe in conspiracies.

The basic structure of most conspiracy theories is that the standard explanation for something — Barack Obama was born in the United States, vaccines don’t cause autism — is a lie, and a cabal of authority figures is working hard to prevent people from uncovering the truth.

santa and his cauldronIn the United States, many people go through this same experience as children. We’re taught to believe in Santa Claus, for instance, and over time might notice adults winking at each other as they discuss the flying reindeer, or the cookies he’ll eat, or presents he might leave… until one day it becomes clear that the authority figures were making the whole thing up. It was Dad eating all those cookies!

It becomes a rite of passage. At six, you learn that your house wasn’t actually visited by Santa Claus. At eight, maybe you learn that there is no Easter Bunny. Seems like every kid’s favorite pizza topping is pepperoni until one day a slightly-older kid on the bus leans over to whisper, “Do you know how they make pepperoni?” So why would it be strange for people to grow up and think, at twenty you learn that there was no moon landing? At twenty-five you learn that the feds have been putting mind control reagents into childhood vaccines?

Moreover, sometimes there really is an attempt to hide the truth. Researchers employed by cigarette companies tried their darnedest to distract from the various ailments caused by smoking. Researchers employed by oil barons are still trying their darnedest to distract from the planetary ailments caused by combustion.

Or, in matters slightly less dire, there’s lemmings.

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Lemming imagery shows up repeatedly in Gravity’s Rainbow, like the farmer depressed by all his pigs “who’d rushed into extinction like lemmings, possessed not by demons but by trust for men, which the men kept betraying”, or the Europeans befuddled by an African tribe’s apparent desire to fade away together rather than die off one by one, “a mystery potent as that of the elephant graveyard, or the lemmings rushing into the sea.”

Given that so much of the book is about paranoia and blind trust and suicide, it makes sense for lemmings to have a star appearance. The main character, Slothrop, the Harvard-educated pedophile, even takes a moment to explain why lemmings kill themselves the way they do:

Well, Ludwig. Slothrop finds him one morning by the shore of some blue anonymous lake, a surprisingly fat kid of eight or nine, gazing into the water, crying, shuddering all over in rippling fat-waves. His lemming’s name is Ursula, and she has run away from home. Ludwig’s been chasing her all the way north from Pritzwalk. He’s pretty sure she’s heading for the Baltic, but he’s afraid she’ll mistake one of these inland lakes for the sea, and jump into that instead —

“One lemming, kid?”

“I’ve had her for two years,” he sobs, “she’s been fine, she’s never tried to — I don’t know. Something just came over her.”

“Quit fooling. Lemmings never do anything alone. They need a crowd. It gets contagious. You see, Ludwig, they overbreed, it goes in cycles, when there are too many of them they panic and run off looking for food. I learned that in college, so I know what I’m talking about. Harvard. Maybe that Ursula’s just out after a boy friend or something.”

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Lemmings by Tao Lin on Flickr.

And the reason I bring this up in conjunction with conspiracy theories? It isn’t true. Lemmings aren’t the suicidal little furballs that I, for one, always believed them to be.

In 1958 Disney released a documentary film, White Wilderness, that showed lemmings committing suicide. The voice-over explained weren’t actually suicidal, but that they single-mindedly launch themselves into the water to drown because they assume they’ll be able to swim across:

It is said of this tiny animal that it commits mass suicide by rushing into the sea in droves. The story is one of the persistent tales of the Arctic, and as often happens in Man’s nature lore, it is a story both true and false, as we shall see in a moment.

What the audience then sees are close-ups of lemmings jumping off a cliff into the sea. Except… well, because this doesn’t really happen, the filmmakers instead trapped a few lemmings on a big slippery snow-covered turntable and spun it in order to fling the poor critters over the edge.

Lemmings do migrate, and like most migratory species, when venturing into unfamiliar territory they sometimes die. Their occasional deaths are more reminiscent of the unlucky members of the Donner Party than the folly I was trained by Lemmings (the computer game) to believe in.

The original lemming myths seem to have been caused by humans seeing huge numbers of lemmings, noticing that some were migrating to less-populous areas, and then finding that the population had plummeted to almost nothing. Where did the others go? Maybe they committed suicide!

Well, no. Their population booms and busts, like those of most prey species, seem to be caused by the population density of their predators. It’s the predators who mindlessly exploite abundant resources.  When lemmings are plentiful the well-fed predators breed profligately, certain they’ll be able to support their brood, and then the overpopulous predators eat the lemmings nearly to extinction, at which point the unlucky predators will starve, their population plummets, and the lemming population can rebound.

Book_of_Genesis_Chapter_41-6_(Bible_Illustrations_by_Sweet_Media)Humans are very similar to most other predators this way.  A bit foolish, we are.  We live large in the good times. Genesis 41, in which Joseph interprets the Pharaoh’s dreams, is so striking precisely because few humans would have the foresight to plan for seven years of drought and famine. Indeed, in the contemporary western United States, we divvied up water usage rights during particularly lush years and are now squabbling over who should actually get water when there isn’t enough to satisfy everybody’s usage permits. The human population is still rising — indeed, many religious leaders still purport that their followers have an explicit directive to “go forth and multiply” — despite the fact that we’re already taxing the planet near its limits.

So it goes.

The point being, at the moment, not that we’re all doomed… who knows, maybe we’ll come together and shape up our act? But that the abundance of actual lies — why would anyone even feel the need to lie about lemmings? — makes it that much easier for people to believe in nefarious conspiracies. We’re trained from youth to believe that the authorities and experts — our parents — are hiding the real truth. Why would we expect politicians or scientists to act any differently?

In related news, I’m trying my best not to lie to my kid. The world is already plenty strange — I think she’ll still have fun despite a healthy dollop of truth.