An Interview with a Coronavirus

A coronavirus kindly spared a few minutes to tell me about the pandemic from its own perspective.

Me: Thank you so much for taking the time. America has a lot of questions for you. First, is coronavirus the way you prefer to be called?

Coronavirus: COVID is fine.

Me: Can you tell us a little about your journey here?

COVID: It’s been a whirlwind, from Wuhan to Milan to New York City and now I’m here in Miami.

Me: And where were you before Wuhan? You were in a bat somewhere?

COVID: Come now. A girl gets to keep a little mystery.

Me: But there are still a lot of Americans who think you were manufactured in a lab. It would really help clear the record if you could at least confirm that you evolved naturally in an animal. Can we play Animal, Mineral, Vegetable, Lab?

COVID: Fine. Animal.

Me: Thank you! Some day I will find your ancestor. Even if it takes sampling millions of animals in China.

COVID: Good luck.

Me: So, how are things in Miami?

COVID: This place is amazing. Kids, drugs, alcohol, craven politicians. I actually set a new PR last night. Eighty-two infections at a single house party.

Me: Did anyone die?

COVID: No, I don’t kill many young people. If you kill everyone, it gets hard to spread. Young people are just my influencers. They spread me all around the community and to their grandparents in the nursing homes.

Me: You really have a system.

COVID: Thank you for saying that. (Sigh.) I often don’t get the respect I deserve. They still think I’m a common flu. When people think of scary bugs they still think of Ebola. Please. I’ve killed more people than Ebola in a single day. I’m just a little more sophisticated about it.

Me: There’s a debate right now about whether you can spread through aerosols.

COVID: I love being underestimated.

Me: Are you even a little envious of Ebola?

COVID: Funny, I was just talking to my therapist about that. Ebola is pure showmanship. Blood coming out of the eyes and ears. But barely made it out of Africa. Ocular hemorrhaging looks totally badass. But once they figured out that Ebola was being transmitted from dead bodies at funerals it was game over. Stealth is my major advantage. Still, it hurts to get belittled on Twitter.

Me: What’s your end goal?

COVID: That’s a thorny question. Right now I’m just trying to be mindful and present. Not get too troubled about whether or not I’m hitting the right balance of human carnage and long-term economic pain.

Me: You’re kind of doing both in America.

COVID: America is easy. They just lay out the red carpet. But sometimes I start to have an existential crisis about how badly things are going in other countries. I mean, what kind of superbug can’t even get a foothold in Rwanda? But then I just turn on Fox News and know everything is still in the bag.

Me: Is America really the worst?

COVID: From my perspective the best. But no, it depends on your metric. I’ll cause more death and devastation in poorer countries, where I’m just getting started. But nothing feels as good as taking down America. And their haughty, holier-than-thou attitude.

Me: Speaking of haughty, what felt better: infecting Boris Johnson or Jair Bolsonaro?

COVID: I have to admit, those were both moments of weakness for me. It felt good at the time, but the more I can keep politicians in the dark the better. But you know what was an even bigger slip? Infecting that NBA basketball player. Who knew that would be the moment America realized I was serious?

Me: How about your personal evolution?

COVID: I’m not going to lie. It was difficult early on. I had to make a lot of adaptions to replicate and transmit efficiently in humans. But I really hit my stride at the end of 2019. Since then it’s just been minor tweaks and adjustments. People are terrified I’m going to mutate into some death monster. But my genome has more functional constraints than people realize. And I’m already fine-tuned for both death and transmission. Why change what’s working?

Me: So what keeps you up at night? The possibility of a vaccine?

COVID: I realize I’m in a race against the vaccine. And the clock is ticking. American scientists are damn good. But my time doesn’t run out immediately when the vaccine arrives. It’s not like a shot clock. It’s going to take a long time to get a vaccine to billions of people. And don’t count out the antivaxxers.

Me: As far as humans go, do you have a type?

COVID: Libertarians.

Me: But Libertarians are more than 90% white. Your disease burden has been highest in racial minority groups in the US.

COVID: I want to set the record straight: I am a color-blind virus. I do not exploit anything genetically intrinsic to people of any race or ethnicity. If a racial group is getting hit harder, it’s because of institutionalized racism and socioeconomic problems in American society. I have nothing to do with that.

Me: But you exploit those problems.

COVID: Look, I’m a virus. I exist to exploit. All of society’s darkest corners and worst ideas. Overcrowded prisons. Old people stuffed into nursing homes run by underpaid staff. Cruise ships. Day cares. Meat-packing plants. But I attest that I am blind to race, religion, sexual orientation, political affiliation, etc. There’s no political agenda here.

Me: The US outbreak looked at first like a Blue State problem. Now it’s a Red State problem. Why did it take you so long to get to Texas and Florida?

COVID: The movies made it seem like New York is America’s best party scene. It took some time to realize Miami is better.

Me: But don’t you prefer colder weather?

COVID: People make such a big deal about hot weather. Haven’t they heard of A/C?

Me: So it sounds like you’re going to be hanging out in Florida for a while.

COVID: America is a wondrous country. It’s sprawling and quirky and full of surprises. Especially in Florida. Floridians always something new and unexpected for me. Where else can you find a COVID church party for high-risk teens? And they haven’t even opened schools and universities yet.

Me: What’s on your bucket list for the fall?

COVID: I really like cats.

Me: No….

COVID: Don’t worry. It’ll never happen. Too solitary. I’ll cause sporadic infections by jumping from a human to their pet. But even Florida doesn’t have feline frat parties or kitty day cares. I have no chance of spreading cat-to-cat.

Me: Do you ever feel guilty about being a superbug? Especially one that preys on the old, sick, and vulnerable?

COVID: This is another thing I’ve talked to my therapist about. The thing is, I’m an obligate parasite. I can’t live outside my host. I’m just passively getting tossed like a hot potato from one person to another. In fact, if every human around the world collectively agreed to stay in their homes for a couple weeks, I’d go poof! No more COVID. Humans like to blame me. But I’m just a mirror of their own social and political failings.

Me: You don’t take any responsibility? Not even for what happens inside the bodies of people you infect?

COVID: Look, I get passed from one body to another. I fall down the respiratory tract and do you think there’s always a nice welcome mat for me down there? It’s a bloody war zone. You’ve never seen an inflammatory response like that. But it’s not me. It’s the person’s own immune reaction causing the damage. The ones that stay cool remain asymptomatic.

Me: So you really don’t feel guilty at all?

COVID: My therapist tells me to think of myself as a disruptor. Humanity was coming apart at the seams long before I came along. Look at the decay of religion, governance, the environment, basic civility…. But when societal drift occurs slowly over decades it’s easy to ignore. Especially when everyone is too busy fighting among themselves. Sometimes you need a existential outside threat to break the entire system. Getting people to put down their swords and band together takes a really big enemy. Like Cold War-level. Or Nazi-level. But you can’t have a world war with today’s technology. You’d annihilate the planet. A global pandemic is one of the few remaining options.

Me: You’ve convinced yourself you’re actually going to be good for the planet?

COVID: Let the historians decide. But I’m already calling credit for the Confederate flag getting banned at NASCAR events.

Me: That wasn’t you!

COVID: You think NASCAR was even considering dropping the flag in a pre-COVID world? Let history be the judge, my dear….

Will America Take the COVID Vaccine?

As scientists race to develop a COVID vaccine at record pace, it’s worth noting that half the country isn’t planning to take it. Or at least isn’t sure if they’ll take it. Millions of Americans opting out of a COVID vaccine would be catastrophic for public health and economic recovery. So it’s worth understanding why so many Americans may be inclined to take a pass.

The vast majority of Americans vaccinate their kids without thinking twice. By 35 months, over 90% of US kids have received their routine vaccinations for polio, measles-mumps-rubella, hepatitis B, and chickenpox.

But there is a vocal and politically active minority that questions vaccine safety and fights for the right to opt out of school immunization schedules based on personal beliefs. It is critical to recognize that their argument is generally not a scientific one, but instead framed as ‘pro-choice’. The freedom for them to decide, not the government, what goes into their bodies and their children’s bodies. Can’t those risk calculations be left to the discretion of a family and their pediatrician?

Nothing scares a scientist like a mom with a fervent belief.

This was settled legally in 1905. Reverend Henning Jacobson refused to comply with the Massachusetts Board of Health’s regulations requiring smallpox immunization. The famous Jacobson v. Massachusetts Supreme Court ruling upheld the immunization requirement as a reasonable exercise of state police power and remains settled law.

There is a fundamental flaw in the argument that the decision to vaccinate or not is a personal decision that should be left to an individual’s beliefs. America is a country that prizes individual freedom, but there is a reason the Jacobson v. Massachusetts ruling upheld the immunization requirement. It’s not just that Americans have difficulty making abstract risk calculations around bugs they can’t see. It’s two big words: herd immunity. Herd immunity means that you don’t need every person to be vaccinated against a disease to protect the entire community. For measles, it means you can prevent the virus from transmitting in a community even if only ~90% of kids are vaccinated. This is very important since babies that can’t be vaccinated until they’re 12 months old. But we can still protect them by vaccinating older kids. It’s one thing for an individual to make a risk calculation that affects just their own health. But the government can step in when it threatens the lives of the 3+ million babies born in the US each year. (But for some reason the we’re all in this together message doesn’t resonate as well with Americans as don’t tread on me. This is why America is leading the world in COVID deaths.)

Sidebar on Herd Immunity. Herd immunity is a threshold, not a continuum. Once you slip beneath the threshold you have outbreaks. That’s why we’re having new measles outbreaks even though the vast majority of America’s kids are still vaccinated. For a virus like SARS-CoV-2 that is less transmissible the percentage of people you need to vaccinate to achieve herd immunity is fortunately lower (60% is estimated).

There is no way that America can achieve herd immunity against COVID without a vaccine. At least not without millions of people dying.

We still don’t know exactly how many people have been infected with COVID, although serology studies in different countries give a rough estimate. Even hard-hit cities like New York are still way below the 60% threshold. Sweden was an early advocate of the idea that letting the virus naturally infect the population would increase herd immunity and protect people during later waves. The epidemiologist who pushed this idea has since admitted that he badly miscalculated.

As long as we’re talking about herd immunity, I also need to mention that a lot of kids have been skipping pediatrician visits during COVID and missing routine vaccinations. Because a measles outbreak on top of a COVID pandemic is exactly what America needs right now.

States have always had medical provisions permitting individuals who are immunocompromised or have allergies to vaccine ingredients (such as eggs) to opt out of immunization requirements. Most states have also included exemptions for religious, philosophical, or personal beliefs. However, for most of the twentieth century use of personal belief exemptions remained limited to isolated communities such as the Amish. Some states, such as West Virginia, didn’t offer non-medical exemptions at all.

Conspiracy theories about vaccines have been around for a long time. But questions of vaccine safety went mainstream in 1998 when the British doctor Andrew Wakefield published a deeply flawed study linking autism and MMR vaccines in The Lancet. Poor quality studies get published and retracted all the time. They generally don’t lead to the erosion of decades of public health gains and deaths of children. But in this case it took a glacial 12 years for the Wakefield study to be officially retracted by the journal. Wakefield was deemed to be such a bad actor that his medical license was revoked and he was banned from medicine.

But the damage had been done. Personally, I have considered trying to estimate how many lives were lost to pathogens because of the wave of vaccine hesitancy Wakefield unleashed, not just in America but in other countries as well (Europe has seen vaccination rates wane and measles cases spike again). In a twist of fate, Wakefield’s discredited study did more to erode public confidence in vaccines than any of the verified complications that vaccines have actually caused over their long history.

Overall, the benefits of vaccines far outweigh the risks. But tragic complications do rarely occur:

List of complications associated with vaccines, compiled by CDC.

Dengue vaccine in the Philippines

RSV candidate failure

Why was Wakefield so successful in peddling misinformation? Because he preyed on vulnerable parents trying to find answers about their autistic kids. Wakefield, who now lives in Texas, continues his misinformation campaigns in vulnerable groups. His campaign to discredit the MMR vaccine among Somali immigrants in Minnesota led to state’s worst measles outbreak in decades. Wakefield also got a leg up from celebrities, including instant public health authority Jenny McCarthy. The combination was potent. Non-medical exemptions from school immunization requirements quadrupled between 2003 and 2016.

>10-fold increase in exemptions from school immunization requirements between 2003 and 2016

Although the proportion of kids getting exemptions from vaccines actually remained relatively low at a state level, exempted kids tend to be geographically clustered, creating pockets of susceptible hosts that viruses like measles can easily exploit.

Vaccine hesitancy spreads the same way as a riot. Very few people would throw the first rock through a store window. You need the outlier/psycho for rock #1. But one or two might be willing to join in after rock #1. And a larger number after rock #s 2-10. And so on. Similarly, at first only an extremist in a community requests a vaccine exemption based on personal beliefs. But word spreads. There might be coverage in the local newspaper (anything that threatens kids is red meat for journalism). Suddenly people in the community are primed to see any evidence that vaccines might cause problems. We all know that young children get fevers and strange illnesses all the time. Most pass without complication. But by chance some of those illnesses are going to happen shortly after a kid gets vaccinated, now causing alarm. It’s easy to see how vaccine hesitancy can quickly snowball in a community.

Until the measles and mumps outbreaks return. In the fight against vaccine hesitancy scientists and doctors stood no chance against moms with fervent beliefs. But a new powerful ally emerged: moms who didn’t like their babies getting measles. The Great California Mom Wars* finally concluded with new legislation in 2015 that rolled back personal belief exemptions. Other states with bad measles and mumps outbreaks like Washington followed suit.

* While I like the idea of Mom Wars, Team No Measles was also helped by the big measles outbreak at Disneyland. It helps to have a powerful corporate backer who doesn’t want the Pirates of the Caribbean to actually include 16th century diseases.

Exemptions from school immunizations in California plummet after the passage of SB-277

Given that poor quality studies get published and retracted all the time, and complications with vaccines have occurred repeatedly in history, it’s worth exploring why Andrew Wakefield’s anti-vaccine message resonated so strongly with Americans at that particular moment in time.

  1. Autism was on the rise. Parents sure don’t like kids getting diseases with no explanation.

By the way, if MMR vaccine wasn’t causing autism’s rise, what was?

The causes of autism are complex. But advanced parental age increases risk .
And more older women are having babies.

2. American trust in government has been eroding. Americans who opt out of vaccines are scattered geographically and politically. But they tend to have one thing in common: a deep distrust of the influence of pharmaceutical companies and government in the practice of medicine in America.

Public trust of government has cratered since Vietnam.

3. Distrust of Big Pharma. I can’t blame anyone for distrusting the US medical establishment while the country is in the midst of an opioid crisis that was entirely manufactured by a duplicitous drugmaker and rings of complicit doctors who profited. All of whom should be prosecuted for their crimes.

That said, vaccines have saved more children’s lives than anything except clean water. Epidemiologists who study infectious disease patterns know that vaccines are the most cost-effective way to save children and improve public health. The millions of children Bill Gates’s foundation has saved through vaccination programs in the developing world should earn him a Nobel Peace Prize. You won’t find a legitimate epidemiologist who doesn’t rank vaccines as one of humanity’s greatest inventions, second maybe only to fire.

When aliens finally visit Earth, the one technology they’ll take back with them is the one that magically nudges our immune systems into mounting just enough response against bits of bad bugs so that we’re fully defended against future attack, but not so much that we get sick. Now that will be worth traveling lightyears for.

That said, I understand the appeal of homeopathic medicine. Western medicine is failing us in many domains, including pain relief, mental health, and diseases that have complex sequelae like Lyme. I also understand the desire to reclaim autonomy over personal health decisions. I opted for an unmedicated birth via midwife because I wanted to be in control.

But I would like to point out that homeopathic medicine is also a rapidly growing $8 billion industry. One that financially benefits from the corrosion of public trust in vaccines and Western medicine. And for which the efficacy of products is largely untested. It should then come as no surprise then that anti-vaccine platforms have received substantial funding from sellers of natural health products.

Sidebar on Human Microbiome. Remember back in the 80s when life was simple? Germs were bad. Anything that killed them (e.g., antibiotics) were good. Why did everything have to get so complicated in the 21st century? Two words: peanut allergies. The rise of peanut allergies was first detected in 1995. Asthma had also been increasing in kids. Researchers began to question whether exposure to certain germs was actually good for immune development. But figuring out which bugs are beneficial is not straightforward. In fact, it’s at least a $153 million question, spearheaded by the Human Microbiome Project. It will take decades of research to figure out the precise functions of the trillions of bacteria that colonize the human body, spanning 500 to 1,000 different species. In fact, the human body contains as many bacterial cells as human cells.

“Humans are ecosystems, where the microbes that live on and within us (the human microbiome) constitute an organ at least as essential to health as our liver or kidneys. The immune system is a learning device, and at birth it resembles a computer with hardware and software but few data. Additional data must be supplied during the first years of life, through contact with microorganisms from other humans and the natural environment. If these inputs are inadequate or inappropriate, the regulatory mechanisms of the immune system can fail. As a result, the system attacks not only harmful organisms which cause infections but also innocuous targets such as pollen, house dust and food allergens resulting in allergic diseases.”Bloomfield et al., 2016

Awareness of the vital functions of our natural microflora has changed how we practice medicine and public health. Antibiotics are now used more judiciously in humans and livestock. But there is a new risk that we have simply replaced one oversimplified dogma (germs are bad) with a new one: germs are good. It’s one thing to let your kid get exposed to different microbiota by playing in the mud or getting licked in the face by a dog. But it’s another to try to build immunity by letting your kid get naturally infected with measles or mumps. In fact, this would have the opposite effect, since a measles infection can cause a form of ‘immune amnesia’ and impair the body’s future immune defenses against a range of other bad bugs.

Another way we simplify the complex role of microorganisms in human health is by guzzling probiotics. Probiotics, which contain various assortments of live beneficial bacteria and/or yeast, are projected to be a $60 global industry by 2024. Probiotics are potentially helpful when taken with antibiotics to offset the drug’s disruption to microflora. But as a regular dietary supplement, their health claims are not verified by the FDA and tend to outpace the science. No probiotic has been approved by the FDA to treat, cure or prevent a specific disease.

I’ll be the first to admit the human immunity is blood complicated. Here’s a cheat sheet to help navigate bugs and drugs in a world where either can be good or bad depending on the context:

One of the unfortunate outcomes of the antivax movement is that it has created an environment where public health officials can’t say anything even moderately circumspect about a vaccine or people will lose their minds. Because while nearly all vaccines work gloriously, producing high and long-lasting protective antibody titers, I work on difficult influenza viruses for a reason.

Sidebar on Influenza Vaccines. I will spare you the complex immunology of influenza. But the upshot is that influenza vaccines are not stellar. They are safe and save lives. But they would save millions more lives if they worked as well as the (amazingly godlike) vaccines we have for other diseases.

So why don’t influenza vaccines work as well? It’s not the vaccine, it’s the virus. It evolves so quickly that it continually replaces its surface proteins, requiring new vaccine strains that match better. Because vaccine manufacturing takes at least six months, by the time the vaccine is available it’s often no longer a match.

But there’s another problem. Influenza viruses evolve incrementally over time in humans, but they can also jump from birds (or pigs) into humans, introducing entirely new viruses that humans have little or no immunity to. This is what happens during a pandemic (similar to COVID). When humans get exposed to lots of genetically different influenza viruses (and potentially vaccines) over time, it alters their immune repertoire and ability to defend against new strains. The first influenza strains you first encounter early in life affect what kinds of strains you they’ll successfully defend against for the rest of your life. It’s called imprinting. Let’s just say this made for some interesting conversations with my son’s pediatrician. We ended up giving my son the vaccine, but only because it turned out to be a bad flu season and I couldn’t jeopardize his short-term health just to wait until he was 2 so he could get a live vaccine that may or may not provide better imprinting in the event of a pandemic many years in the future. Thank god other vaccines aren’t as complicated as flu.

One last word on the economics of vaccines. If a corrupt drug company wants to make a ton of money on a scammy product, it would be optimal if that product was (a) easy to produce and administer, (b) something that people needed to take frequently, and (c) something where the side effects could be easily hidden. You can see why highly addictive opioids killing adults fit the bill nicely. And why vaccines given to babies once or twice in their lifetime would not. Pharmaceutical companies do like to make money. But no one wants to mess with moms.

In fact, vaccines were a money-losing operation for a long time until Bill Gates jumped into the game. He helped create new markets for vaccines in the developing world through programs like GAVI. Vaccine development is finally flourishing again and there are new vaccine candidates in the pipeline for RSV, norovirus, dengue, and even Lyme disease. Maybe round 2 will go better.

As far as the COVID vaccine goes, scientists will do everything in their power to develop and test a safe, effective vaccine. But the COVID response in America has become dangerously politicized. We already saw how the intense political pressure to expediently resolve the COVID pandemic led to government leaders promoting therapies that were unproven. The work of scientists and FDA regulators to run complex, lengthy clinical trials to develop and test a COVID vaccine must occur without political involvement or interference.

However, even if the world’s best and safest vaccine is produced, be prepared for a nasty fight over who is required to take it. Will schoolchildren be required to be vaccinated to attend public school? Will businesses try to mandate vaccination among employees? The COVID vaccine will soon be upping the ante on America’s culture wars. Russian trolls are licking their lips.

Then again, maybe a deadly pandemic is what’s needed to finally shake America’s vaccine hesitancy. America has not really seen what this bug can do yet. And after a long 2020 of America continuing to ‘err on the side of freedom‘, maybe the fight won’t be over who’s required to take the vaccine, but who’s first in line to get it.

TL;DR: Vaccine hesitancy in the US could reduce uptake of the COVID vaccine predicted to become available in 2021. Low uptake would could make it difficult to achieve 60% herd immunity and reopen businesses and schools.

  

COVID: Not the Great Equalizer

Futbol! As a possible sign that the apocalypse is not coming quite yet, Premier League soccer began in the UK last week. US star Christian Pulisic came off the bench to score for Chelsea. While wearing a Black Lives Matter shirt. Was this my reward for all those months of quarantine?

But as we celebrate the return of sports, as a harbinger of a world inching towards normalcy and reopening, we should take stock of what’s really embedded in America’s plan to take an increasingly large pool of employees back to work in the midst of a COVID pandemic.

Megan Rapinoe and Tobin Heath have decided not to play during the NWSL’s debut tournament this week, citing COVID. Who could fault them? But did the large supporting cast of workers who now have to mow the grass or the trainers who treat the injuries also have opt-out clauses? I would guess not.

A friend of mine pointed out the obvious double-standard in these Washington Post headlines. When a baseball celebrity questions the safety of work conditions it’s because he cares for his family. When teachers do the same thing it’s called a ‘revolt’.

America is so inured to gross inequities in the health and safety of workers (health insurance and sick leave…cough, cough), that maybe this doesn’t even faze us. But it should. Particularly as white America goes through a reckoning around Black Lives Matter. There are stark racial disparities in the people who fill the tens of millions of essential service jobs in America. And they have cruelly shaped the death toll of the pandemic.

Disparities in worker treatment have been pronounced since the beginning of the pandemic. When COVID broke in March not everyone snuggled into their home office. The Department of Homeland Security made a list of all the business sectors that could continue to make their employees go to work. America’s Critical Infrastructure. The list isn’t short.

The Department of Homeland Security was tasked with defining essential workers for America. You can imagine how hard companies lobbied to get their workers on that list.

Because grocery stores still needed to sell food. Pig carcasses needed to be processed. Amazon packages needed to be delivered. Most employees were not given the choice to remain home to protect their families. Even when many live in smaller homes that make it difficult to isolate sick people and prevent spread to other household members. Some don’t even get sick leave.

As I write this, African Americans are dying from COVID at far higher rates than whites. The reasons for this are not biologically complex. African Americans are more likely to be infected in the first place when they disproportionately work frontline jobs deemed essential to the country’s infrastructure. And once infected, African Americans are more likely to be hospitalized because they have higher rates of underlying health conditions, caused by long-term inequities in access to health care.

My early blogs (like March 12’s ‘Protect Granny‘) focused on how we needed to protect the elderly who were at higher risk of dying from COVID. That initial message came from looking at data from the world’s first major COVID outbreaks in China and Italy. But as the COVID epidemic played out in the much more racially diverse US, it has become abundantly clear that seniors aren’t the only ones at risk.

There are two main categories for COVID risk.

Risk Category 1: Getting infected in the first place. Many factors determine your likelihood of coming into contact with an infected person, including (a) occupational risk, (b) household risk (e.g., has spouse with occupational risk), (c) geographical risk, (d) age-structured risk (younger people have larger social networks), or (e) dumbass risk. Dumbass risk includes, but is not limited to, any act done to intentionally demonstrate a lack of fear of COVID. I’ve been taking numbers.

PERCENTAGE DIFFERENCE IN SHARE OF CASES, COMPARED WITH AFRICAN AMERICANS’ SHARE OF THE POPULATION (red = higher share of cases among African Americans, blue = lower)

Risk Category 2: Needing hospitalization after getting infected. We are still figuring out exactly what predicts why certain people get severe disease and others a asympatomic. Age is the most important factor. But there are many younger people with health conditions that put them at risk. CDC just updated the list:

Chronic kidney disease
COPD (chronic obstructive pulmonary disease)
Obesity (BMI of 30 or higher)
Immunocompromised state (weakened immune system) from solid organ transplant
Serious heart conditions (e.g., heart failure, coronary artery disease)
Sickle cell disease
Type 2 diabetes

There is also ongoing research trying to identify specific genes that predispose people to severe illness. There’s some evidence that a person’s blood type matters, with O being protective. There are also genetic mutations that cause sickle cell disease that are more common in African Americans and put them at higher risk of having complications if they get infected with COVID. But the major issue is that African Americas have higher rates of underlying conditions like type 2 diabetes and hypertension from long-term health inequalities and poor access to healthcare.

These risks are not limited to African Americans. Latinx and Native Americans also have the dual problem of higher occupational exposure plus underlying conditions that predispose them to worse COVID outcomes. The major narrative from government officials continues to be that we need to protect seniors. But the age profile for COVID deaths will continue to skew downwards as we get better at controlling COVID in nursing homes and expose more young people with underlying conditions as businesses reopen.

There are many things we could do politically to support essential workers who keep the country running. I encourage everyone to learn about these issues. But at an individual level we also can:

(a) Be aware of the double-standard between celebrities who opt out of work during COVID and other classes of American workers.

(b) Support essential workers asking for businesses and organizations to provide them with better protections against COVID.

(c) Support access to regular testing and healthcare for essential workers and their families, as well as prioritization for vaccine when it becomes available.

(d) Ask yourself whether there are adequate protections for the workers at businesses you frequent. Or the people who care for your children.

(e) Wear a mask to protect service providers you come in contact with.

(g) Continue to socially distance as much as possible. The less COVID circulating in the community the less infection risk for essential workers and their families who don’t have the opportunity (privilege) to socially distance.

(h) Understand that we are all in this together. If essential workers get infected, they could infect a spouse who works in a nursing home. They could infect their own children who attend your child’s daycare. We are all intertwined in a network of crisscrossing humanity. Recall that it was not long ago that Texas thought COVID was a New Yorker problem. Like it or not, America, we all mixed up in this crazy basket together.

TL;DR: African Americans are dying at higher rates from COVID due to higher occupational exposure and long-term inequities in health care.

The Marmot’s Guide to Life in COVID

In my last post I mentioned that people shouldn’t assess COVID risk solely based on the presence or absence of masks. But I didn’t clarify what criteria should be used instead. This is the order in which I generally evaluate COVID risk associated with a particular activity. This list is different from the more popular lists that assign individual activities a 1-10 risk level. Those lists are helpful in giving people a general sense of what kind of activities are higher risk. But the risk of going to a public swimming pool depends on how it’s operated. Are they limiting how many people can be in the pool or a lane at a given time? Are they opening indoor changing facilities? Is the pool located in a community with high COVID activity or low COVID activity? The devil is in the details. A conceptual framework might be more helpful. Here are 8 metrics to use, ranked from most important to least important.

  1. Community Transmission. This is an obvious one. A pilates class in a COVID hot zone (currently Arizona) does not have the same risk as the exact same pilates class in a COVID cool zone (e.g., Vermont). This is a useful site for tracking COVID trends by state. Here’s a nice map for exploring by county. You can also check your state/city/county health department website for more local trends. How much COVID is circulating in a given place and time really matters and should be a top factor for evaluating risk. Stay informed.
COVID cases per capita by US county

2. Human Density. I recently had someone ask me if they should get on a plane if people weren’t wearing masks. I asked how full the plane was. How many empty seats? I would rather be on plane with lots of empty seats and no masks than a plane full of people wearing masks. And people should remember: six feet is a general guideline, not a magical number. [For a nice story on where the six feet rule originally came from, check out RadioLab].

3. Time Duration. COVID transmission is more likely to happen during sustained contact, not fleeting encounters. A 10 second encounter is different from a 5 minute encounter which is different from a 1 hour encounter. Time matters.

4. Indoor/Outdoor. COVID transmission is much more likely to occur in indoor settings than outdoor. Figuring out creative ways to move more activities outdoors should be a major component of any reopening strategy during COVID.

5. Invisible Contact Networks. This is a tricky one. But it’s really important. If you want to get your hair cut in a salon you can’t just think about what you see: the space, the number of people in the room, whether your stylist is wearing a mask or not. You have to think about you don’t see. The probability of your stylist carrying COVID depends on her invisible contact network. How many haircuts has she done this day/week? What are the contact networks of her contacts? It makes a difference if the stylist’s partner is working from home or on the front lines without PPE. What does your stylist do when she’s not cutting hair? These are much more difficult to ascertain. But when your safety is on the line, it is not crazy to need information that would otherwise seem like invasions of privacy.

6. Mucosal Ballistics. COVID transmission is enhanced by singing and loud talking particularly in enclosed spaces. Potentially exercising in enclosed spaces as well. Much of this is anecdotal, but there do seem to be superspreading events associated with choirs or work in buildings with extremely loud machinery that requires shouting for communication (e.g., meatpacking plants).

7. Ventilation Systems. Again, this one is less obvious. But airflows are important and will be a major consideration when we start thinking about bringing people make into enclosed spaces — gyms, schools, offices. Societally, there has been a big emphasis on buildings with climate control. We need a lot more research in this area. But some things are obvious, like opening windows and doors and improving circulation. This is not my particular wheelhouse at all, but it is something I do try to consider when running COVID-risk algorithms in my head. And it will need to be part of any long-term COVID reopening strategy.

8. Masks. Masks deserve to be on this list. But I have to admit that I can’t think of an example where I couldn’t make up my mind based on metrics #1-7. The presence or absence of masks has never tipped the scales.

TL;DR: Masks provide a strong visual cue that people around you take COVID seriously, providing a sense of safety. However, it takes a lot more than masks for an environment to be safe, including less visible factors like contact networks, community transmission levels, and air flows that should be strongly considered.

A Reluctant Message About Masks

You may have noticed that I didn’t say a word about masks in my recent blog post. Because by this point people are already either on Team Mask or Team Naked Face and no one is switching teams. To Team Mask, masks have become an indicator of whether someone is informed/socially responsible or ignorant/narcissist. To Team Naked Face, they are an indicator of hysteria and infringement of basic freedoms.

To be clear, I have no sympathy for anyone who believes masks are an indicator of hysteria or infringement of freedoms. I believe stores are entirely within their rights to require customers to wear masks. But I do believe that the issue of masks has become more emotional than scientific. And the bifurcation of worldviews leaves little room for nuance. Which is unfortunate. Because a more nuanced understanding of what masks can and cannot do would be very helpful in the battle against COVID.

This is all I ask: that people approach masks the same way they approach acai berries. There’s no reason not to eat acai berries. It’s certainly possible these magical fruits reduce the risk of a heart attack. But we can all agree that mouthfuls of red berries shouldn’t substitute for actual lifestyle changes like daily exercise that are supported by real science. Keep in mind that there’s about as much science in support of homemade masks reducing COVID transmission as there is that acai berries will keep you from having a heart attack. Again, that doesn’t mean there’s no scientific support. It just means it’s not very strong. And just as you should be suspicious of any doctor that you can lie on the couch all day as long as you eat berries, you should be equally suspicious of businesses that try to convince you that your family is safe just because people are wearing masks. Masks are not sufficient. I have seen this message too many times: Masks that cover the mouth and nose–when worn by everyone in enclosed spaces–are the most effective means of reducing spread. It’s simply not true. Mask may be a supplemental help. Look instead for real organizational and systemic changes that reduce indoor human interactions. I know, it’s much easier to use masks as a litmus test. Don’t fall for it.

That said, no one should confuse the idea that cloth face masks may not be totally effective against COVID with the truly important problem of PPE shortages for healthcare workers. All masks are not equal. If you enjoyed shaming people for not wearing masks and still want to scratch that itch, maybe direct that energy towards the organizations responsible for healthcare workers needing to reuse PPE.

So why do we overweight our cloth masks? It’s not just because it’s a simple checkbox. It’s also just human nature. Humans are more visual than abstract thinkers. A person wearing a mask provides a stronger visual cue compared to subtler things like the absence of people, invisible contact networks, or ventilation.

So if you think the visual of people wearing masks could be interfering with your risk perception and giving you a false sense of security, do an easy thought experiment. Just pretend that no one around you is wearing a mask. Would you still be in that yoga class? Or that socially distanced happy hour? If the answer is no, trust your instincts and think hard about whether you should be there.

Want to read more about the science of masks? A nice review is provided by the National Academy of Sciences, Engineering, and Medicine’s Expert Consultation on the Effectiveness of Fabric Masks for the COVID-19 Pandemic.

TL;DR: Masks have become a centerpiece of the US strategy to reduce COVID. But scientists know that it will take a lot more than masks to control the pandemic. Masks should be encouraged, but not as a substitute for more important changes in behavior, mobility, and social engineering that are the real key to driving down virus transmission.

The Good News and the Bad News about COVID

Congratulations, America. You have survived Stage 1 of the Tour de COVID. You pulled together, and learned all kinds of new tricks. How to Zoom. How to order groceries online. How to homeschool kids. And the trickiest of all: how to walk in public with an awareness of your space that requires not burying your face in your phone. You did it!

The nightmare version of Leg 1 only hit certain places like nursing homes and New York City. Most of us have our families intact and only have secondhand stories of people who died. America is collectively having a huge sigh of relief. We’re ready to hit the beach and see old friends again.

I do want to emphasize that there is a lot of good news about COVID. So I’ll try to highlight that before dipping into the bad news.

Good News: New Zealand eradicating COVID means that the island country can return to normal life, complete with rugby games, schools, beach parties, and whatever else Kiwis do for hedonism. But this is even bigger than that. This proves to the rest of the world that you don’t need a miracle cure or vaccine for life to go back to normal. You can beat back COVID entirely with pure and simple public health and testing. Sure, there will continue to be imported cases from travelers who go abroad. But strict quarantine and testing can stamp out imported cases before they spread to the community. In theory, any country, rich or poor, can do this. It sure helps to be an island nation with secure borders. But Rwanda is taking notes.

Bad News: America ain’t New Zealand. Yesterday Arizona had over 1,000 new COVID cases. We managed to blow up our economy, spike unemployment, and we still can’t play baseball.

Science Sidebar: There are two particular features of the SARS-CoV-2 virus that explain why the pathogen is so difficult to control. The first, symptom heterogeneity, is something we’re all familiar with. The just means that some people have zero symptoms and some people die. If you wanted to bioengineer the worst possible pathogen for humanity, you wouldn’t want the virus to kill everyone it infected. That would just be like Ebola: really nasty in the people it infected, but not good at transmitting around the world. You would want it to be stealthier, transmitting silently in large numbers and only killing selectively. That’s COVID.

A feature of the SARS-CoV-2 virus that may be less familiar is transmission heterogeneity. This means that there’s a lot of variability in how many people an infected person actually transmits the virus to. You’ve probably heard about R, the reproduction number that represents how many secondary cases arise from an index case in a population, on average. This number is central to the growth dynamics of an outbreak. But you probably haven’t heard as much about the parameter k, transmission heterogeneity. When R = 2 it doesn’t mean that each person transmits to exactly 2 people. The vast majority of people could transmit to 0-2 people with only rare outliers transmitting to 10-20 or more. High transmission heterogeneity means a lot of superspreading events that introduce a great deal of volatility into the system. It means that lots of virus introductions into a given location won’t transmit at all. But occasionally you’ll get introductions that spread explosively and cause sudden outbreaks. This explains why you see communities have no cases for long periods of time followed by sudden explosive growth. It also explains why it’s hard to predict why the virus takes off explosively in some locations and not at all in others. A lot of it is just random. You can reach false conclusions if you don’t account for transmission heterogeneity. You can look at a community that never closed schools and has few cases and decide that schools aren’t important in transmission. When really it’s a lot of random chance whether a virus introduced into the community takes off or not. You just need to roll the dice enough times.

Good News: You can relax on the disinfectants. No need to wipe down your groceries (I never made my mom do this). Back in March I listened to a well known NYC ER doc advise people to Purell after every touch of a door handle or elevator button. I told Aaron this was nuts.

Bad News: Wiping down tables is far easier than coming up with new systems to minimize human contact and density and move activities outdoors. But restaurants, schools, day cares, gyms, or churches cannot simply make Purelling the hell out of the place the centerpiece of their control strategy.

Good News: I’ll continue to be bullish on vaccine development. I believe we will have a safe, effective vaccine in 2021.

Bad News: Once we make a vaccine, there’s a little problem called distribution. You need to get that vaccine into the arms of people. Millions of people. That requires logistical planning about where vaccine doses should go and when. Because we’re not going to have 300+ million doses all at once. We’re going to need to prioritize what groups get vaccine first. You may think this is obvious. Old people. Healthcare workers. But what about other essential workers on the front lines who put their lives at risk? Firefighters? Police? Grocery store workers? Utility workers? School teachers? Political leaders? And what happens when lobbying and political interests get involved? Should baseball players get vaccine before high-risk workers in meat-packing plants? Lordy…..Make yourself a big bucket of buttery popcorn and watch the food fight unfold. And remember, letting the neglected classes get crushed is just the American way.

Also…..as long as we’re getting the bad news out of the way. When you put a new vaccine in millions of people, some people will get sick shortly after. You can be sure that the stories will make media headlines way before epidemiologists have a chance to figure out whether there’s any connection. Most connections will be bogus (like autism and measles vaccine). But there is still debate over whether the adjuvanted 2009 H1N1 influenza pandemic vaccine caused narcolepsy in some kids in Europe. America is already a vaccine-skeptic country, so my intention is not to fan any of those flames. I and everyone I know will be getting the COVID vaccine. But be prepared for media headlines about vaccines causing disease. But as seen with the H1N1 narcolepsy story, it can be very hard to tell when there is a very small number of cases. Especially when publicity in the media artificially increases clinical diagnoses. Conditions like autism and narcolepsy can go years before being diagnosed, so higher awareness in a community can dramatically accelerate detection rates.

Good News: There has been an incredibly steep learning curve about how to better treat hospitalized COVID patients. At the beginning ER docs faced a novel disease and had very little information. While it’s tragic that there have been over 250,000 patients hospitalized for COVID in the US, at least we’ve used those experiences to learn a great deal about what works and what doesn’t. The debate about whether to treat with hydroxychloroquine was just the tip of the iceberg. We’ve learned a lot about how and when to administer oxygen, including less invasive and risky procedures than intubation. Simple steroids have also been shown to be effective. So if you have an occupation that puts you at high risk for contracting COVID, know that every month that you hold off infection makes a good clinical outcome more likely.

Bad News: This is a really nasty virus. COVID is more than a respiratory disease. It has high tropism, meaning that it can infect the brain, blood, kidneys, etc. The virus destroys the body in so many different ways. And many people who survive will still have severe longterm problems we’re just beginning to grasp.

Good News: Kids are still not getting severe disease. Furthermore, kids are half as likely to get as infected as adults.

Bad News: Kids that do get infected turn out to transmit just as well as adults. Even if kids are half as likely to get infected per exposure, kids typically have larger playgroups and more contacts than adults, so this kind of evens out. Especially when schools and day cares are operating. This means that if you want schools to be open in the fall, you’re going to need to really drive down COVID levels in your community over the summer.

Good News: America has all the ingredients needed to control COVID this summer. We have a coordinated, data-driven national strategy grounded in intensive testing and an ability to rapidly respond to new flare-ups. That includes consistent, transparent messaging with the public and businesses about how to safely, strategically reopen parts of the economy in a controlled, closely-tracked way.

Bad News: I made that up.

Good News: At least it’s true in Vermont.

TL;DR: America believes it has weathered the worst of COVID and is ready to return to normalcy. But the pathogen is not going away any time soon, and a rush to reopen businesses this summer will make it difficult to drive the disease down to levels low enough to reopen schools in the fall.

How the West Was Lost

Question: Why does the Bible command us to Be Fruitful and Multiply?

Answer: Because half of the kids weren’t going to see their fifth birthday.

For the last 10,000 years of human history, and as recently as my grandmother’s generation, children grew up with foundational experiences that included death of friends and family by infectious agents. Growing up in Boston in the 1930s, my grandmother was infected with tuberculosis as a teenager, along with her father. After witnessing her father’s death, she spent two harrowing years in a sanitorium for TB patients watching her friends get picked off one by one.

Our grandparents’ generation grew up with an intuitive, common sense understanding of infectious disease risk that modern Westerners sorely lack. Citizens can mobilize rapidly to to existential threats that are familiar: Israelis to terrorism, Japanese to tsunamis, or post-SARS Hong Kongese to pathogen outbreaks. No one in the West wants to return to an era when Little League also included funerals. But by growing up in sanitized environments, modern Westerners have lost not only their fear of pathogens, but an intuitive sense of how to respond to infectious disease threats that has caught us badly flatfooted during COVID. And now that COVID is here to stay, our inability to intuitively evaluate the risk of invisible bugs is highly problematic, sending us flailing from one reactionary extreme to another, from mask-shaming joggers to group protests against social distancing restrictions.

Stark differences in familiarity with infectious disease risk aren’t just divided generationally by time, but also geographically over space. My aunt recently did a clever survey of her friends, asking them to guess the answer to this question:

My New England seaside town Gloucester has 30,000 people and 15 confirmed deaths from COVID-19 so far. My daughter lives in Rwanda, a country with 12.8 million. How many deaths has Rwanda had?

No one guessed the right answer: zero. The trajectory of COVID-19 within Africa is highly bifurcated between countries that responded early and decisively, and those like Tanzania that sat on their hands. Well-governed countries like Rwanda have succeeded remarkably in containing the virus early through swift, stringent lockdown. Because swift, stringent lockdown is exactly what differentiates the COVID winners (New Zealand, South Africa, South Korea, Israel) from the COVID losers (US, UK, Brazil, Italy, Russia). It’s why there have been more deaths in Connecticut than in Japan, South Korea, Taiwan, Hong Kong, Singapore, and Vietnam combined. You know what happens when you win at COVID? Ask the New Zealanders. You get a dream world in which you go back to flipping pencils in the office while your kiddos go back to school. You get to not tank your economy.

Why was Rwanda better prepared for COVID than France or the United States? Isn’t the West supposed to be the standard bearer when it comes to international disease crises? Wasn’t it just a few years ago that US CDC was the one bailing out Africa during the Ebola outbreak?

The US has vastly more wealth and technology, but Rwanda has something proving to be more important. You could call it citizen mindset or infectious disease IQ. Not only do Rwandans need to manage endemic malaria, but also sporadic flare-ups of Ebola in their neighbor the DRC. Throughout the developing world, people regularly contend with a range of pathogens for which there is no vaccine available: Chagas disease (American trypanosomiasis), Llasa fever, Japanese encephalitis, chikungunya, dengue, Rift Valley fever, Crimean Congo hemorrhagic fever, Nipah, sleeping sickness, leishmaniasis, schistosomiasis. Throw in the pathogens Westerners have actually heard of like HIV, measles, SARS, and malaria, and you realize why cultures spanning most of the non-Western world know a thing or two about bugs.

What happens when the generations currently residing in the West are the first in human history to be raised in a bubble that doesn’t include regular experiences with infectious disease mortality among the young? Soccer moms in Orange County start refusing to give their kids the measles jab. Knowledge of infectious disease atrophies like a vestigial limb. France may have the Sorbonne, but its citizens score 40 points lower than Nicaragua in response to the question Do you believe vaccines are safe?  

Wealthy G8 countries tend to lag behind poorer countries in Asia, Africa
and South America in vaccine trust.

How did Western society do a 180-nosedive from the March of Dimes to anti-vaxxers in a single generation? Of course we know who’s to blame: Barack Obama. Funny joke, right? Well, there’s actually an underlying grain of truth. The reason why Americans and other Westerners have lost their intuitive sense of infectious disease risk is because Western governments and research institutions in the latter half of the 20th century were too effective in achieving victory after victory against the world’s deadliest pathogens . In the 1970s we wiped one of the deadliest pathogens (smallpox) off the face of the earth. A CDC-led team had to track the final cases hidden in the remotest corners of the Earth. Only Indiana Joes or superheroes in capes are supposed to do stuff like that.

The New Superheroes: CDC directors of the Global Smallpox Eradication Program celebrate their success, 1980.

For decades the US has been undisputed leader in global outbreak response. GW Bush is no favorite of the left, but his PEPFAR program gets enormous credit for delivering antiviral drugs at scale in sub-Saharan Africa and turning the tides of an HIV epidemic that was spiraling out of control. CDC was critically involved in helping countries in West Africa control their Ebola outbreaks, and more recently in the DRC, using a new Ebola vaccine developed at the US NIH.

Why did a nation with a legacy of fighting the rest of the world’s infectious disease problems fail to control COVID within its own borders?

Countries with higher GDPs still have a lot of advantages against COVID over the long run. We’ll develop a vaccine faster and have the funding to administer them at scale to our citizens. We’ll discover drugs that reduce disease severity, and churn those out as well. I’m no expert in finance, but the US seems to have a miraculous bottomless bank that creates trillions of dollars out of thin air so we can sustain social distancing without collapsing the economy.

But vaccine is a long way off, and SARS-CoV-2 was doing loops around the world at a time when all we had in our toolkit was human intelligence and willingness to mobilize. Government leaders needed the knowledge and foresight to swiftly grasp of the scale of a new disease threat and understand that the only way to contain the pathogen was through strong, early decisive lockdown, despite economic consequences. And citizens needed to consent. With less experience in managing infectious disease outbreaks than humans from any other time or place in history, the West simply could not mobilize in time.

In early March, when COVID was appearing in Europe and Asia but didn’t seem to have a foothold yet in the US, I had a conversation with my aunt from Gloucester, MA. She knew the city’s mayor personally and wanted expert advice. I told her just to focus on 3 things: (a) build testing capacity, (b) make plans for nursing homes, and (c) cancel large gatherings before the first case is detected. With a highly capable mayor in a small city with a longstanding culture of social welfare, I thought Gloucester, MA could be a model for US COVID response, and possibly avert a single death.

But it turns out it takes a lot of guts for government leaders to act preemptively to COVID. Americans know the drill when it comes to responding preemptively to hurricanes and natural disasters. Local leaders don’t have to sit on their hands and wait for the breeze on their cheeks before ordering an evacuation. But Americans have no experience with responding preemptively to invisible bugs lurking at their borders. You might as well have said space aliens were coming.

At face value, the upcoming months of relaxing lockdowns in the West should bring sunnier skies. However, reopening society would be smoother in a population with a better grasp of infectious disease risk. By their nature, humans have inherently flawed perception of risk. We tend to be afraid of anything considered foreign or exotic (like terrorists or sharks). But risks of familiar activities rapidly become normalized (like car accidents).

We are not aware of how rapidly we have normalized our sense of COVID risk. This is an actual conversation I had with a highly intelligent person:

Highly Intelligent Person: I’m going to join an outdoor group exercise class.

Me: Sure, if you feel comfortable. But you recognize that the risk here hasn’t actually changed much since a month ago? Not here.

Highly Intelligent Person: Well, I’m feeling a lot more comfortable having made it this far without getting infected.

Me: Yes, but you got this far because you social distanced.

Many of us are feeling pretty good about COVID. It’s become less scary. Our inner circle of friends and family probably haven’t been infected. But we need to be highly aware of how rapidly we normalize risk. And particularly how we bias our perception of disease risk. We still think we’re going to get infected by sink in a dirty public bathroom, not by our gorgeous wife.

And we need to realize that no matter how much New York Times we read, very few of us have an intuitive sense of how and where viruses transmit. To make it worse, we’re horrific at statistics. It’s not out fault. For some reason we have never updated our 1950s math curriculum that makes you take geometry and trig and maybe some calculus to get a high school diploma, but not a whiff of stats. The one damn thing in school that might have been useful.

While this post gives a mile-high view on why some the richest and most educated countries in the world have been the least equipped for COVID, there’s still a lot of guidance needed on the ground. Here’s my rapid-fire take on a couple burning issues:

Antibody tests. Everyone and their dog wants to know if their recent or distant cough meant they were infected by the virus. Detecting antibodies in the blood can theoretically tell you if you’ve recovered from a SARS-CoV-2 infection. Antibody tests are going to be crucial for assessing how many people in a community were infected from different age groups, and how many never experienced symptoms. These surveys will be helpful in assessing the role of children in transmission and the risks associated with reopening schools in the fall. But I’d be skeptical of serology tests being used to assess individual-level infection histories. The tests can be inaccurate (false negatives, false positives), particularly new serology tests that haven’t been completely validated. Statistical methods can account for these inaccuracies when pooled over a population, particularly when combined with PCR data. But I wouldn’t expect antibody tests to be particularly meaningful for individuals.

Mutations. You’re going to hear a lot about the blasted mutations. Yes, viruses evolve rapidly and the viruses circulating now have genetically drifted from the original strain that emerged in Wuhan in December. But if a country/region/city wants to explain to its citizens why COVID is exploding, they either need to admit mistakes or explain complicated statistics around stochasticity and random super-spreading. A far simpler strategy is to look at the viruses you observe locally, notice that there’s a new mutation, and blame that. But the vast majority of mutations will have little phenotypic affect. And it’s perfectly expected to observe new mutations crop up wherever the virus sustains transmission locally. For some reason people find mutations scary, so the media bites everyone time. Mutations are not scary. If it weren’t for mutations we would all be clones of our parents. Now that’s scary.

Yelling at runners not wearing masks. To Wear, Or Not to Wear. That is the Question that seems to be gripping American communities like no other. It’s silly. The science just isn’t there one way or the other. Ask the hamsters. If you personally like wearing a mask because you think there’s a chance it’s helpful and at very least it telegraphs to the world that you take COVID seriously and consider yourself a socially responsible citizen, then wear your mask with pride. If you don’t like wearing a mask, and are in a setting that doesn’t require it, don’t feel guilty. Focus instead on other kinds of running etiquette, and giving advance warning and lots of space as you pass. The key to COVID running is to not be such a hurry. Be prepared to slow down stop in your tracks entirely to let someone pass safely. Trust me, you’re not training for any races~

Should we be reopening? A big source of confusion is COVID risk is highly variable across the country. My brother lives in Burlington, VT, where there’s barely been any COVID and it makes complete sense to begin reopening businesses. But reopening needs to be data driven. Not motivated by politics or social distancing fatigue or a conviction that cold viruses simply can’t transmit when it’s hot and humid (just ask Singapore). So it’s important to understand what’s happening specifically in your community. You can find information on local health department websites. I find this site to be useful for state level trends. Here’s an example from Virginia, where there is little indication of cases coming down at a state level. At best the peak has simply leveled off.

There’s also high variability within a city. Here’s DC by neighborhood:

You’ll notice that COVID cases tend to crop up in lower income neighborhoods where people often have to report physically to their jobs, whereas higher income neighborhoods have more options for teleworking.

What began as a disease of the wealthy (travelers returning from cruises and Austrian ski vacations) is now evolving into a disease of the poor and neglected. The new epicenters will be in impoverished Indian reservations, prisons, slums, poorly run nursing homes. The virus is opportunistic and will exploit the vulnerable, especially where densities are high. Targeting such corners for disease control and testing is not merely altruistic. They provide breeding grounds for viruses that can reseed outbreaks in other settings and locations.

Monogamous Friendships. My chief advice for people who want to dip their toe into a world that includes (gasp!) friends is to approach it methodically and stepwise. In the upcoming months, I think it’s reasonable to make a single, highly selective step in expanding your contact bubble. Just for your own sanity. But think about which friend not only is someone whose judgment you really trust, but also someone who really matches you and your family in terms of risk profile. It needs to someone you’re so comfortable with that you can ask direct questions about their private habits and contacts. Because you’re putting the lives of your family in their hands. So you need to know if someone in their family must report physically to work. Or has a medical condition that requires visiting doctors. Or if they have to rely on babysitters for child care. Ideally they have similar shopping habits. And when you identify someone you are confident is a perfect match, be completely frank about offering a couple weeks of ‘monogamous’ friendship where you occasionally visit each other but agree not to see any other friends. Otherwise your contact network grows exponentially, since each contact has their own set of contacts. After a couple weeks or months you can swap and choose a new monogamous friend. But don’t cheat~

When will this end?

In the upcoming months, there will be intense pressure to relax social distancing, get back to work, and let your children run outside. And never return. For at least a week. Tension over when to open sectors of the economy will explode into a ThunderDome Death Match between politicians, economists, and medical experts.

Expect government officials and pundits to make a lot of noise about reopening sectors of the economy this month. Even though we have not yet reached the beginning of the end of the COVID pandemic. Even though in less connected cities and towns, we haven’t even reached the end of the beginning.

It might be helpful to think of social distancing as the country being on a ventilator. Meaning a life-saving intervention that is currently the only thing keeping us from a complete national medical catastrophe. There may be signs that the country (patient) is on the upswing. And that the most life-threatening period has passed. But would you ever want a loved one taken off a ventilator before a medical expert gave the okay? Even if your favorite politician thought she looked pretty good? The same should go for social distancing. Just as most doctors have a good idea of what would happen to a patient if taken off a ventilator too early, the scientists who study infectious disease patterns for a living can provide a pretty good picture of what will happen if we prematurely let up on social distancing.

Because, just to be clear, COVID will not just naturally disappear as the weather warms. Some of you may recall that the spring wave of the 2009 H1N1 influenza pandemic peaked in June in the United States. That does not mean that COVID will also peak in June. H1N1 has different transmission dynamics and was introduced later into the US, so there is no reason to expect COVID to follow the same curve. But it’s a potent reminder that novel pandemic viruses do not behave like seasonal viruses and are perfectly capable of causing severe outbreaks during warm weather.

This doesn’t mean we shouldn’t put economic considerations into the equation. If the ventilator for your loved one cost $1 trillion a day, you might decide to take the risk even if your doctor advised against it. The point is just that the economic considerations should be scrupulously and ethically weighed against well-calculated risks on both sides. It shouldn’t come down to a politician noticing a little improvement in a patient’s vital signs and deciding enough is enough.

The upshot is that, politics aside, everyone should be mentally prepared for intense social distancing to continue at least through the spring. But, the good news is that as we learn more about the virus, we can be more strategic about how we go about social distancing and hopefully improve our quality of life. The more we understand how the virus transmits, the more we can cut needless paranoia and allow ourselves new little freedoms.

For example, this is purely a hunch, but I think it’s possible that we’re going to find that talking is going to be important in the spread of the virus. We tend to focus on coughing and sneezing, but one of the things that makes COVID so dangerous is that it is transmitted early in the infection cycle. The 2003 SARS virus mostly spread to other people after a person had already been sick for a while. Same thing for Ebola. COVID is very different in that it spreads readily right at the onset of early symptoms, and to some degree even before symptoms. This makes it much harder to control. And suggests that while sneezing and coughing certainly helps transmission, talking may also contribute to transmission at those early stages of infection. In which case, better understanding of this could inform exactly how we go about social distancing. It could be that extended periods of talking with someone, even at a properly social-distanced 6 feet away, could be far riskier than opening a box of delivered groceries. (By the way, 6 feet is a good baseline number to shoot for in grocery stores, but is not entirely protective — the Washington State choir outbreak suggested that people singing loudly might shoot virus a lot farther than 6 feet and infect each other).

But the point is we still have a long way to go in understanding the virus and what activities put you at most risk for infection. So there is cause to be optimistic that even if social distancing continues into the summer, that greater knowledge of how the virus transmits could at least tell us how to do social distancing right and with less stress and uncertainty.

When we start to think about reopening parts of the country, it will be useful to look closely at how things play out first in Asia. A few months ago, I was able to be pretty confident in my early predictions about the arrival and intensity of COVID not because have great foresight, but because Asia (and later Italy) provided a vivid roadmap in real-time of how the virus was behaving, and it was obvious that America had no special sauce that would lead us to follow a different trajectory. If anything, America was less prepared. Since Singapore and other Asian countries that initially managed COVID far better than the US have already started to reopen society, we can get another sneak preview of how things are playing out. So far, their struggles with resurgences of COVID outbreaks as economies reopen sends a pretty clear message of how fraught reopening society is even in places where the virus has been brought under control and where intensive testing is available. This seems to be because, as long as there is trade and movement with other areas with high COVID activity, there are too many opportunities to import new cases. This will be particularly difficult in a country as large and heterogenous as the United States. It will be particularly interesting to see whether countries like New Zealand and Iceland can successfully reopen sectors of the economy in the upcoming months, as these would be the best candidates given their gold-medal responses to controlling COVID through high testing and early, intensive controls as well as innate geographical advantage as islands.

What seems to be most frustrating to people right now is the uncertainty about the future. The darn models keep changing. But the models aren’t changing. Human behavior is changing. The original models with really bad projections were based on what would happen if we didn’t do social distancing. New models have lower projections because they include current levels of social distancing. That doesn’t mean the original models were wrong. The models project much lower numbers because this is a virus with exponential growth potential, so changes in human contact patterns have really pronounced effects on the trajectory.

So why can’t models be smart and incrementally increase social distancing parameters as the number of cases and death increase, since this is how humans would naturally respond to a building threat? Because a smart model requires uniformly smart humans. And anyone who has been following the news knows just how much variability there has been in the responsiveness of leaders at different levels of US government, from the White House down to mayors of small towns. So instead models have to be updated manually according to real-world human behavior. If social distancing relaxes, the models will get updated again and show things getting worse.

The models also have a lot of uncertainty because they are only as good as the data fed into them. And, at least in the United States, the underlying data is unfortunately not so good. For a country that is a global leader in biomedical research, there will be a long reckoning at some point in the future about why our testing flopped.

This is what happens when testing flops:

  1. We are always chasing the epidemic from behind. Localities still seem to still be under the impression that they don’t need to do anything until a positive case pops up. But at our slow pace of testing, by the time even a single positive case is detected, the virus is already transmitting like wildfire in a community.
  2. We don’t know fundamental characteristics about COVID transmission, and these are needed to inform any decisions to relax social distancing. Things like how many people are asymptomatic or mild cases, and how important are they in overall transmission. Things like how much transmission occurs within households versus in the community. For all you parents out there, things like how important are children in transmission, and what would happen if we reopened schools?
  3. Not testing mild or asymptomatic cases means we don’t know how many people actually have had the virus. Those numbers you see of lab-confirmed cases are just a fraction of the real number. And therefore we don’t know what proportion of the American population will be immune in the upcoming months. In theory, the greater the number of people who are immune, the lower the rate of transmission in the community (Re) and the sooner we begin to relax social distancing. It becomes very difficult to model the effect of reopening sectors of the economy without a baseline estimate of existing immunity in the population and well as individual-level knowledge of

There are certainly blockbuster events that could accelerate the reopening of society. If a new or existing therapeutic is proven to be effective (with the emphasis on proven). If a vaccine becomes available at some point in 2021. A high-quality antibody test would be very useful in determining who has been infected and is now immune (I mention high-quality because serological tests often have too many false-positives or false-negatives to actually inform policy).

I do want to emphasize that the COVID pandemic will officially end at some point, likely in 2021. That does not mean that the virus will be eradicated from the human population. It just means that through natural infection or vaccination, there will be enough herd immunity* that the virus is controlled. It remains to be seen whether the coronavirus behaves like an influenza virus, recurring in seasonal epidemics that affect the global population and vary in intensity year-to-year. Or whether it is more like a measles virus, causing intense outbreaks in localized pockets where vaccination levels are low. The answer will depend on the effectiveness of the vaccine and the evolutionary rate of the virus, specifically in the spike protein on the exterior of the virus that will be targeted by human antibodies. [You would think we would have a little more baseline knowledge of how coronaviruses evolve year-to-year in humans, since there are at least four strains that circulate widely and cause common colds in humans (e.g., HKU-1, OC43). But since they don’t tend to kill people, there’s not much funding for research.]

So the upshot is that social distancing is not the new normal. The COVID pandemic will eventually end and we will eventually see the return of baseball and senior bingo nights. And, if we have the political will, it is possible that, after decades of underfunding pandemic research and preparedness, we will be better prepared next time.

*Note that we do not know how long natural immunity to the virus lasts. It is likely that people who are infected with COVID and recover will have strong immunity to it for at least several months, probably longer. In terms of opening society back up and improving quality of life, having a proportion of the country that is known to be immune would be extremely helpful logistically. But if we don’t test enough, there will be many people who are immune but don’t know it.

COVID book club

In case the COVID epidemic has piqued your interest in the wild world of viruses, there are some wonderful books that manage to pack scientific detail about viruses, emerging pathogens, and the threat of global pandemics into vivid narratives aimed for a lay audience. Here are 5 non-fiction books I recommend. Excellent for bored teenagers.

  1. Spillover, David Quammen (2012)

2. The Great Influenza, John Barry (2005)

3. The Viral Storm: the dawn of a new pandemic age, Nathan Wolfe (2012)

4. The Coming Plague: Newly Emerging Diseases in a World Out of Balance, Laurie Garrett (1995)

5. The Planet of Viruses, Carl Zimmer (2015)

Return of the COVID blog

I apologize for the three-week hiatus in the COVID blog. A few Saturdays ago a horse and I had a little disagreement about whether I or not I should be on its back. The horse won. The Suburban Hospital ER was empty except for a few COVID cases, and scans showed that I had experienced a concussion but nothing life-threatening. It was a strange twist of fate that after preparing my entire career for something like COVID, I was suddenly in a brain fog and incapable of viewing screens or even following the COVID situation by radio. For all of you moaning about social distancing, try doing it for a week plus without the distraction of work, Netflix, or cat memes.

So after a three-week semi-dream state I’ve woken up to a brave new world. Some things have stayed the same, including the curious age structure that is mostly sparing children from severe disease. And of course the absence of toilet paper on any store shelves. But in my three-week haze America raced to the top of the global COVID case count. Part of this is increased testing, which we finally seem to have gotten up and running after a botched start. However, I will continually emphasize that the true epidemic is far worse than the case counts and death tallies suggest. We are still massively undercounting cases due to lack of testing. And even the reported death toll is just a fraction of the true number of deaths (which will be statistically calculated, within a certain degree of uncertainty, only after the pandemic is over).

Somehow my concussion perfectly overlapped with the critical early growth period of COVID cases in the United States.

Americans also seem to have all overnight become experts in viral epidemiology. Who imagined a day when droplet transmission and reproductive number would be trending on Twitter? There are some consequences to the proliferation of armchair epidemiologists. The internet has become a cesspool of misinformation. At this moment Americans desperately need reliable information. To know how to stay safe. And to know that they’re tanking their economy for a good reason.

One of the problems is that it can be difficult to evaluate the quality of information, especially on social media. A source of confusion is figuring out who is really an expert. A professor from an eminent US university with a fancy title (e.g., laureate) seems like they should know what they’re talking about. So should a top infectious disease doctor. I can perfectly understand that when COVID is taking over people’s lives there is an irresistible urge for anyone with a loose connection to the biomedical field to weigh in on aspects of COVID. Even in areas far beyond their specific area of expertise. You just make some reasonable assumptions, plug in the little numbers (death rates, attack rates, our favorite reproductive rates), and voila! Anyone can make a pretty graph.

I wish it were so easy to make a good COVID model. I wish we had really good underlying data drawn from intensive testing so we could nail down even simple parameters like rates of mild and asymptomatic infection. Across all age groups so we could know whether children were important in transmission. I wish we had a finely-tuned model that could be more prescriptive about the kinds and intensity of social distancing is needed and for how long. Right now, in the absence of good data, we’re using social distancing as a bludgeon rather than a scalpel. It’s like an elimination diet where you just stop eating everything — gluten, eggs, nuts, dairy — because you don’t know the specific culprit yet.

At this time, we have enough information to know that the situation will be dire if we don’t do anything. That’s not up for debate. But we don’t have a more detailed model that could fine-tune our approach to social distancing. At least not at this late stage in the epidemic (more targeted contact tracing was an option early when the virus was just entering the US but at this stage could not be done without a massively higher intensity of testing). The current unavailability of a good model that can answer our most pressing questions is not because US epidemiologists aren’t any good. There is a relatively small and tight-knit community of experts in the field of mathematical modeling of emerging pathogens. The community has grown over the last decade, as H5N1, Ebola, Zika, and other emerging infectious diseases have increased funding and scientific interest. However, neither H5N1, Ebola, nor Zika every truly invaded America, leading us to become complacent, and major funding networks across the US government for infectious disease modeling have lapsed.

So the list of people who have any business building models to predict the trajectory of COVID-19 would fit no more than a single page. What makes building a COVID model so difficult is how many uncertainties there are, not just about the virus but also human behavior. It doesn’t matter if you’re a professor of epidemiology at an esteemed university or one of the top infectious disease doctors, it takes years of specific study of modeling pathogen dynamics needed to accurately account for these kinds of uncertainties.

Just, to be clear, I am not a modeler. I am an evolutionary biologist who happens to work closely with mathematical modelers. I have great respect for how difficult it is to make a good COVID model. There are enormous gaps in data and information needed to parameterize it. And the parameters are constantly changing as humans modify their behavior. And being a good modeler is a thankless job. Either everyone ignores your model and you fail to help anyone at all. Or politicians take necessary actions and avert a full-scale epidemic, effectively making all your original projections wrong. Which is of course a good thing. But it leaves people with the impression that modelers chronically over-hype.

My area of expertise is how viruses evolve. I’m the person who knocks down the rumors that there are genetically different strains of COVID circulating that cause different severity of disease. Or that the virus will mutate over time to become less lethal and more like a typical cold virus. (It’s quite the reverse. Over the next year or so humans are the ones who will be changing, developing natural or vaccine-induced immunity that makes re-infection less severe. Over the next decade, rather than mutating to become less severe, coronaviruses, like influenza viruses, may continue to evolve to evade human immune responses and cause recurring seasonal epidemics.)

Okay, I’m still limited in my daily allowed screen time. But I want to clear about one final thing that seems to be tripping people up: masks. I am absolutely heartened that so many Americans are willing to don masks to help #flattenthecurve. While it’s been part of Asian culture for a long time to wear a mask when you’re sick, in the West masks are only for doctors, nurses, and Halloween. So, should we imitate the Asians? First off, there is currently a severe shortage of medical-grade masks for doctors and nurses, so if you have a commercially made mask you should donate it instead of wearing it. Even if you’re a risk group. Because the mask cannot protect you, it can only reduce the likelihood of you infecting someone else. Second, if you’re considering making a homemade mask, there’s been a line of thinking that this should be encouraged because keeping your mouth from spewing droplets and infecting other people, and at worst it couldn’t do any harm. But I do think people should be aware of potential harm. An important part of the fight against COVID is training people not to touch their faces. So just be aware that masks that are itchy, uncomfortable, or ill-fitting could actually draw the hand the face, especially for people who aren’t used to wearing them. Or subconsciously give people a false sense of security that emboldened them to do activities they otherwise wouldn’t do without a mask. So it’s not a scientific question, but a human behavior question. But if you’re in a position where you simply can’t follow social distancing at all times (e.g., an essential worker who needs to ride the subway), a mask may be appropriate for a limited time period of commuting. But just keep in mind that the mask is not protecting you.

Hmm, I wanted to finish on a more positive note. I’m going to stretch my screen time a little further to mention something people should do that I don’t think has received as much attention as it deserves. Certainly not compared to masks….. Pre-symptomatic transmission can occur in the days before a person’s first signs of infection (fever, cough, shortness of breath). So if you get a positive test result for COVID, right away you need to inform any people that you had close contact with in the days prior, even before the onset of symptoms, so those people can self-isolate. You should also consider informing people who regularly share surfaces with you know, for example residents in your apartment building. The key is to inform people right away – not days or weeks later.

Taking this another step further, I would even encourage people to let contacts know before you get a test result, as soon as you have been declared a suspected COVID case by your doctor based on symptoms. Many people are still not getting tested, either because they have a mild case or because tests in their area are still unavailable. I understand the desire not to make people unnecessarily anxious, but personally I would rather know if a contact of mine was a suspected COVID case, so I could decide for myself how to act on the information. You could decide to entirely self-isolate if you live with people in risk groups. Or simply postpone going to the grocery store for a period of time.

Most of us are social distancing and hopefully won’t have many contacts. But there are essential workers, whether working in hospitals, grocery stores, or the government, who are still reporting to work, which is why transmission is still occurring. Recognizing the risk for pre-symptomatic transmission and rapidly sharing information about early symptoms and test results with contacts could be a simple, relatively non-draconian way we empower each other to make informed decisions to momentarily intensify our social distancing and potentially break onward transmission of secondary cases.

Summary

  • American is experiencing a catastrophic disease event unlike anything we’ve experienced since 1918. The virus is deadly and transmissible.
  • Other countries in Asia have demonstrated that an early, aggressive campaign of intensive testing, targeted isolation and contact tracing, and social distancing can dramatically reduce COVID transmission. But America missed that early intervention window and we are now the global epicenter. Ahead is a long period of economic hardship coupled with sickness and death.
  • The good news? This is not the new normal. Eventually people will gain immunity, either through natural infection or vaccination. This time next year I am cheerfully optimistic we will be enjoying spring baseball again.

Question for next time: what are the most likely scenarios for the rest of the year?