OT: Covid-19 Neck Sharpies Part III: "Immune." You keep using that word.

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I interrupt this current crisis to remind you of that other crisis that still exists. Remember that thing we were talking about a week ago? Yeah, still there, very much doing its Worldwide Tour thing. 

Previously:

Part I. Hello: Antibody (April 25)

Part II. The Tests, the Tests, the Tests (April 26)

Part III: “Immune.” You Keep Using That Word. I Don’t Think It Means What You Think It Means.

TL;DR:

1. Immunology is weird and unpredictable. Many things you think you know are probably wrong. "Immune" is a complicated concept in the actual world.
2. Your positive antibody test is probably a very good thing, especially if you've had a confirmed case, got sick, and got over it. We don't yet know if testing positive for antibodies, getting sick, and recovering--or getting vaccinated-- will actually keep you from getting COVID-19 again for a good long while, but the answer is probably yes, and exmperimental data is so far so good.
3. Asymptomatic carriers have the comparable viral loads to symptomatic patients, and are probably more infectious, not less.

So you’ve decided to test positive for SARS-Cov-2 antibodies. Congratulations. That’s really super. Do you want a cookie?

You either got sick with a confirmed case of COVID-19 or you took a serum antibody test (reminder, it looks for antibody against the virus, not the virus itself) and it looked like one of these:

(step back to Part II if you’re not sure how to read those strips)

You just dropped a little blood onto that serological test strip and got back strip C, D, or E. Interpreting the results means we can tell you some general things that are probably true, but not definitely true. You’ll understand why in a minute.

BUT FIRST A FEW WORDS FROM OUR SPONSORS

Werner Heisenberg, Patron Saint of Uncertainty (file photo)

Doubt is to certainty as neurosis is to psychosis. The neurotic is in doubt and has fears about persons and things; the psychotic has convictions and makes claims about them. In short, the neurotic has problems, the psychotic has solutions.

---Dr. Thomas Szasz, the Yogi Berra of psychiatry: (fn10)

So now would be a good time for this message board and the rest of America (and probably the planet) to quit dry-humping the leg of certainty and get comfortable with reasonable probabilities. Which is like making out with someone pretty hot but who you wish had popped a Mentos a minute ago.

Even with perfect technology and unlimited amounts of clean data, we can’t know everything. If we could, smart people could simultaneously determine the position and spin of an electron and I’d be able to pair up all my socks. They can’t and I can’t. Because it can’t be done, you feel me?

“Probably” is a sensible and scientifically sound way to make public health policy in These Uncertain Times. About the only time "probably" isn't good enough is when you're talking about the safety of vaccines and therapeutics. 

/end of rant vis-à-vis certainty

OK then. Let’s get back to those test results.

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SCENARIO ONE: I never felt sick. I got the serum antibody test anyway. It says I’m IgM+/IgG- (Strip C). How did that happen?

This result is kinda like: you found footprints inside your property/fence line, but it doesn’t look like the intruder got into the house. You don’t know who it was and wouldn’t recognize them again if you saw them. But, yay, they didn’t get in. A little disconcerting, though. Creepy, even. But no sirens. No commotion. No mugshot of the bad guy who trespassed. Perp(s) looks to be gone.

Result Probably Means: If you got test result C, it’s probably because of nice work first by the non-specific defenses (see below), then by Paul Blart and the Weird Guys getting things stopped early. IgM antibodies aren’t going to benefit from the Beilein Effect next time around (go back to Part I if you need a refresher), but they saw something they recognized on the SARS-Cov-2 virus and sponged up enough of it to clear the infectious viral particles before things got worse (fn11).

Nice work Blart. Have another donut.

Here’s where the difference between a viral exposure and an infection becomes useful to think about.

So there’s a chance your exposure (to a viral orc horde) wasn’t enough to lead to an actual infection (of target cells), but was enough to trigger detectable viral-specific IgM (Blart arrives on a Segway). The virus might have reached target cells, but you'd expect some symptoms to show up after a while.

By way of viral analogy, if you shared needles with/had a blood transfusion from/had unprotected sex with an HIV+ person, you were exposed. You're not infected with HIV unless you test positive for it because it's taken up residence in your T-cells. 

To get into a target cell and become more than an inert, lifeless piece of code, the virus has to survive at least:

1) exposure to the external environment between hosts

2) skin and other physical barriers

3) non-specific immune cells

The second and third represent innate immunity (also frequently called "non-specific" though that's kinda misleading)(fn12).

Innate immunity is like the fence around your yard, the thorny bushes behind them, the dog that will happily lock it's jaws on anyone who jumps the fence. It doesn't matter who it is, they are facing the same obstacles to get into the house.

The adaptive or specific barriers are things like the Ring doorbell camera or peephole. Now you're specifically recognizing potential threats and distinguishing them from harmless visitors. And you learn from past experiences.

So, like even the pluckiest spermatazoa in a middle school sex ed film, a virus needs to arrive in numbers to reach the promised land. You're not getting sick because your hand picked up one virus particle ("virion") from a door handle and then you touched your face. You're sick because you picked up 10^something particles then touched your face. Wash your hands. Stop touching your face. 

Speaking of loads. Let's talk about viral load. heheheheh, I said "load."  It's kinda important (fn13a). It means about the same thing as “dose” when you’re talking about the initial infection, but after that it simply means how much virus is there in the patient at any given time. With COVID-19, usually peaks about when symptoms show up and starts slowly declining as the specific immune response kicks in (fn13b).

Note that PCR tests for the virus might be false negative before the symptoms show up. The symptoms might never show up if the initial infection is with so few virions they get wiped out with just innate immunity (happens all the time) plus a dash of IgM.

Q. So is an COVID-19 asymptomatic person less infectious?

A. No. And it's actually worse than that. Asymptomatic people not only carry viral loads as high as symptomatic patients (fn14), they are shedding more virus and likely MORE infectious, not less (fn15). Crikey. But that's why masking asymptomatic people is probably the single most useful thing we can do from the public health point of view (fn16). Also, wash your filthy hands.

Most likely the viral load in Scenario One was below the threshold that is going to make most people sick. The technical term you know was coming is coming, and it's called the ID50 ("Infectious Dose 50"). That’s the number where 50% of people exposed to that initial dose will actually get infected. 

Sometimes, the infectious number is a good bit lower than the amount needed to make someone feel sick, but that depends mostly on how effective the immune system is. 

Vis-á-vis masks, this is where the benefit is supposed to kick in. Suppose you have two people, one of whom is infected, one is not. Both have the opportunity to mask up (assume cloth masks):

The thinking is that if you catch the big droplets as they spew out of the infected mouth, then catch a few more before it gets to the uninfected person, you've moved to a better place on that dose curve. In this completely made-up example, you drop from a 70% infectious dose to about a 30% infectious dose if both are masked up (in truth, the mask on the infected individual probably matters more, but both help). That's a massive win for public health if scaled up. If either or both is wearing a properly-fitted N95, you're probably talking about a spot on the curve way down in the bottom left corner. 

Numbers matter because when the virus hits the beach like troops landing at Nasal Normandy, it’s a race between viral replication and the immune system’s ability to raise a defense, including but not limited to antibody-producing B-cells specific for the virus.

Lesson of Scenario One: You best bring numbers or you gonna get Blarted, got it Porkins?

(I like to call Coronaviruses “Porkins” because they have the fattest genome in the virus world. I'm not saying you should body-shame viruses or rebel pilots, but just how much room could there really be in an X-wing cockpit, anyway? I know, look who’s talking, Paul Blart)

The non-specific or “innate” immune system with a little boost from our Mall Cop (IgM) representing the initial specific, “adaptive” immune system was sufficient to keep the intruders at bay because the viral load wasn’t that high to begin with, or you were just born with awesome innate immunity or something. 

Or you just got tested the day before symptoms kicked in and IgG will be showing up in a few days.

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SCENARIO TWO: I got infected/sick. This time I’ve got IgM+ and IgG+ on the test (Strip D). This is good, right?

Yeah, this is good in the sense you’re putting up a fight and the cops are on the scene. Sorry you’re not feeling well. Intruders kicked the door in or climbed in through a window. That is upsetting. But booby traps went off. Tarantulas were deployed on the intruder’s face. Your house is getting busted up a little but it's for the greater good. And you got a good look at the dudes who got inside. 

From now on, we’ll specifically keep an eye out for these punks

This result is kinda like: Perp(s) is/are still on your property/in your house. Sirens are going off (cytokines). Mall Cop (IgM) showed up like last time. Armed cops showed up (IgG). Weapons are drawn. Shots are fired (cytotoxic cells kill things tagged with the IgG). 

Result probably means: The full-blown infection raised a highly specific immune response and the virus is probably in retreat by now. IgG on the scene means the full range of immune cells are probably being recruiting to the scene, so even if it’s not over, at least you’re fighting. Arrests are made. Mugshots are taken (immune memory). 

Lesson of Scenario Two: It’s not great to feel sick, but you’re probably creating a solid antibody response. Whether you’ll be immune to the next challenge by the same invader depends on whether you’ve created memory cells that are effective and durable, and we can’t tell that by looking at the positive IgG test. Right now, all we know is there's a fight, and you're doing what you should be doing.

Q. So I've got the right antibodies. Even the really good kind. Why isn't that enough?

A. Yeah, this whole post would have been a lot shorter and probably more useful if I'd just started and ended with this question. The answer is that some antibodies are neutralizing, and some are not.

Neutralizing antibodies are (a) what you're hoping to (and probably will) make during the course of an infection (b) what pharma companies are racing to produce en masse so they can save the world and make billions on treatments, and (c) what other pharma companies are hoping to stimulate with vaccines to induce people to make their own neutralizing antibodies so they can save the world and make billions.

You test for neutralization in vitro like this:

 

If it binds with good affinity ("stickiness") but doesn't neutralize, it's probably because the antibody binds the right protein (the spike), but not in exactly the right place to stop it from entering the cell. Binding but not really stopping is kinda like this:

#42 (Ronnie Lott): good binding affinity, bad neutralization

#58 and #29: bad at everything

The lesson is, sometimes you're grabbing, you're just grabbing in the wrong spot. Or in Lombardian terms, "GRAB GRAB GRAB. NOBODY TACKLING." If the spot you bind to isn't the spot the virus needs to interact with the receptor, you might slow it down a little, but you're not stopping it.

Q. So why the hell do we even bother making antibodies that aren't neutralizing?

A. Because antibody (B-cell) generation is random. You don't know what you haven't seen yet, so the strategy is to take the genes you're born with and rearrange them in tens of billions of combinations to recognize as many different shapes as possible (fn17). Three-dimensional shape at the binding region is what makes one antibody specific (picky) for one thing, and another antibody specific for another thing.  Same for affinity (sticky). We do the same thing with the receptors on T-cells, which I haven't gotten into (and won't).

A non-neutralizing antibody could still be somewhat helpful aggregating viral particles and clearing some of them out of the system, or triggering the cascade of events that an IgG antibody helps to kick off, and all that is better than nothing. But the virus is getting into the target cell if it gets close enough, even with non-neutralizing antibodies attached. 

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SCENARIO THREE: I got sick with confirmed COVID-19. I recovered. I tested negative by PCR. A few weeks later, I test IgM-/IgG+ (Strip E).

This result is kinda like: Things are quiet again. Perps are off to jail or dead. You've still got the mugshots (memory B cells). If they show up again, cops will be all over them. Your property is reasonably safe.

Result Probably Means: If you tested D or E, you have at least a few virus-specific IgG antibodies and associated memory B-cells ready to make the leap from 3-star to NBA first-rounder upon a second exposure. Which means a second exposure will go well for you and poorly for the virus. Probably.

Lesson of Scenario Three: The same dudes will have a tough time invading the same home again, because you're not stupid. You’re probably hearing about things like herd immunity and “immunity passports” in your readings. These things are based on distinguishing “maybe” (bad) from “probably” (good). We're not going to reach herd immunity without a vaccine because reaching that number in a country our size would optimistically cost around a million dead people. 

Q. Cool, #immun4life amirite? Aren’t we done here? Where is my "Immunity Passport"?

To clear customs with your Immunity Passport, you're depending on those antibodies being

1) neutralizing (see above)

2) persisting as memory cells

"The Persistence of Memory Cells" by Salvador Dali

The immune response to coronaviruses can be weird, and that was appreciated in the literature at least 30 years ago. “Weird” meaning things like reinfections with the same strain of virus were observed as far back as 1990 (fn18), suggesting the formation of long-term memory cells might be defective, but all evidence currently is that no one is getting reinfected (early reports look to be more about bad testing than genuine reinfections) and that people are generating neutralizing antibodies. 

Where do memory cells come from?

Not pictured: Helper T-cells that give the B-cells an assist in becoming memory cells.

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Q. So what does "immune" mean to you?

A. In a perfect world we don't live in, immune means we either get sick once or get vaccinated and never have to worry about it again for life. That happens sometimes, but rarely, even with the best vaccinations (if vaccines worked perfectly the first time, we'd never need booster shots, would we?).

In our world, we're often immun-ish, which means the probabilities have slid in our favor thanks to improving the quality and quantity of players that can help us. We're equipped to go compete and win. We can literally live with that. Probably.

At the end of the day, the battle at both the micro and macro level is mostly about tempo. Can we as a society bend the curve down so the hospitals aren't overwhelmed? Can the virus infect and replicate fast enough to generate enough new virions to keep reaching new cells and new hosts? Can we buy our immune systems some extra time when things start going bad or calm them down if they're doing more harm than good (we'll talk about that if I get to Part IV)?

Imagine Lucy is probably IgM in this scenario since she's the front line. Or she's the innate immune system. Either way, she doesn't have to get everything, just keep the numbers manageable for Ethel.

That makes Ethel the IgG or just the whole adaptive immune system.

Things go well for a while, but if you fall behind, it tends to build on itself. "Immune" doesn't mean the conveyor belt stops or everything goes perfectly. "Immune" means given enough time, they'll get the chocolate wrapped. Sometimes you just gotta accept that you're playing from behind for a bit. 

On the other hand, if you panic, things go bad in a hurry. It's called a "cytokine storm," and you've probably heard of it at this point (fn19). In a nutshell, it's a complex cascade that overwhelms the system with inflammatory messages (secreted immune molecules like interleukins and TNF-alpha) between immune cells.

So basically, it is to the immune system what Facebook is to our political system. 

Once this process gets tripped, you're in a spiral you can't easily get out of. The whole immune system works because it has built-in amplification mechanisms. That becomes a bad thing when the thing you're amplifying is panic.

EPILOGUE: Three Lies

If you’ve ever been to Harvard Yard (fn20) you probably met seen this impressive statue, the base of which reads (you can squint your eyes at the above or you can trust me):

JOHN HARVARD

FOUNDER

1638

All of those things are wrong. The school was founded in 1636, John Harvard was not the founder, and that’s not John Harvard, it’s just some schmuck who sat for the artist since they had no clue what the not-Founder looked like two centuries earlier.

If Harvard had built a statue for the immune system, it’s probably inscribed with something like this:

GET SICK ONCE, GET IMMUNITY FOR LIFE

HEALTHY PERSON=GOOD IMMUNE SYSTEM

THE IMMUNE SYSTEM DISTINGUISHES SELF vs. NONSELF

Yeah. No. Not really.

We just talked about the ideal world that is the first of these. The real world is messier.

The second is based on the thing we touched on when we were discussing where B-cells and T-cells come from (fn17 again). You're born with a massive deck of unshuffled cards in your specialized immune cells, and in order to have a strong immune system, you need to shuffle and shuffle and shuffle and redeal until you get billions of combinations of genes ("VDJ recombination") that can recognize billions of unique (or close to unique) three-dimensional shapes.

Like your financial portfolio, an undiversified immune portfolio is a disaster waiting to happen. Diversity is generated from the genes you inherited and the vagaries of luck. It's not based on broccoli and vitamin C versus double-bacon cheeseburgers or quiet meditation versus SERENITY NOW, though those things are relevant to generally maintaining the engines.  

Stress management is good. Good diet is good. Exercise is good. None of these things reshuffle your immune genes. Two identical twins won't have the same immune cards to play. It's just luck, man. Not having the ideal B or T cells to respond to SARS-COV-2 doesn't mean there was some problem with your immune system. It just means random things are random.

The third is mostly beyond the scope of this post. See (fn21) for an overview.

The immune system is designed to do two things and it does them well:

1. fight pathogenic invaders
2. confound the predictions of very smart people (VSPs) (fn22)

It's superb at both. For example, it may very well turn out COVID-19 may not even be an infectious respiratory disease at all. It could be that it's actually an infectious blood vessel disease. What, what? Yeah, there are unknown unknowns, and if we knew what they were, they'd be known unknowns, you dig?

Your ship may be coming in. You’re weak but not giving in. You’ll go out fightin’ all of them. For what it's worth, some centenarians are beating this virus (fn23). That's despite what's called "immunosenesence," otherwise known as "old immune systems are like old bones and joints and act accordingly." That tells you even a sleepy immune system can pull through given a low enough initial viral load and enough time to sort things out. Better to just stay out of the fight if you can.

Next up later this summer (I'll regret saying this, I'm sure): 

COVID-19 Neck Sharpies Part IV: Treatment and Vaccines

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Footnotes

(10) The quote-a-minute Hungarian-American (1920-2012) Szasz, most well known for his tome The Myth of Mental Illness, had a number of gems, e.g:

“The stupid neither forgive nor forget; the naive forgive and forget; the wise forgive but do not forget.”

“Men love liberty because it protects them from control and humiliation from others, and thus affords them the possibility of dignity. They loathe liberty because it throws them back on their own abilities and resources, and thus confronts them with the possibility of insignificance.”

“Why don't you have a right to say you are Jesus? And why isn't the proper response to that "congratulations"?”

“Formerly, when religion was strong and science weak, men mistook magic for medicine; now, when science is strong and religion weak, men mistake medicine for magic. ”

“In the United States today, there is a pervasive tendency to treat children as adults, and adults as children. The options of children are thus steadily expanded, while those of adults are progressively constricted. The result is unruly children and childish adults. ”

“Boredom is the feeling that everything is a waste of time; serenity, that nothing is.” 

“Every act of conscious learning requires the willingness to suffer an injury to one's self-esteem. That is why young children, before they are aware of their own self-importance, learn so easily; and why older persons, especially if vain or important, cannot learn at all.”

“If you talk to God, you are praying. If God talks to you, you have schizophrenia”

(11) In the last decade, the idea that IgM+ B-cells may also play a role in the development of memory has gained traction, though IgG remains the dominant subtype factor in secondary immune response.  See, e.g., Kurosaki T, Kometani K, Ise W. Memory B cells. Nat Rev Immunol. 2015;15:149–59

(12) Calling the innate immune system "non-specific" is kinda wrong. It's actually exquisitely specific, but it's specific in a completely different way than B-cells and T-cells are specific. Instead of highly specific 3D protein shapes, innate immunity looks for repeating patterns on things like bacterial cell walls and other bad guys. 

(13a) "It's not whether you were exposed to the virus. It's how much." New York Times, 29 May, 2020. 

(13b) To et al., Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study. Lancet Infect Dis 20(5):565-574 (May 2020).

For most patients, the viral load of SARS-CoV-2 was very high at presentation [of symptoms] and declined steadily.

(14) Zou et al., SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients. N Engl J Med, 382:1177-1179 (19 March, 2020).

The viral load that was detected in the asymptomatic patient was similar to that in the symptomatic patients, which suggests the transmission potential of asymptomatic or minimally symptomatic patients. These findings are in concordance with reports that transmission may occur early in the course of infection and suggest that case detection and isolation may require strategies different from those required for the control of SARS-CoV.

(15) He et al, Temporal dynamics in viral shedding and transmissibility of COVID-19. Nature Med 26:672-675 (15 Apr 2020).

We observed the highest viral load in throat swabs at the time of symptom onset, and inferred that infectiousness peaked on or before symptom onset. 

(16) Leung et al, Respiratory virus shedding in exhaled breath and efficacy of face masks. Nature Med 26:676-680 (3 Apr 2020). https://www.nature.com/articles/s41591-020-0843-2#auth-14

(17) VDJ recombination. Basically, imagine three decks of cards. One has a dozen unique cards, one has a few hundred, one has a few thousand. Each player gets dealt hands made up of one from each pile, which means potentially billions of unique combinations. That's how your antibody repertoire comes together. You have billions of B-cells each with unique antibody binding regions because your genes shuffled and dealt when each B-cell was being made. Those decks are called the variable (V), diversity (D), and joining (J) clusters of genes, hence the name "VDJ recombination." 

(18) Callow, K.A. et al, The time course of the immune response to experimental coronavirus infection of man. Epidemiol Infect, 105:435-446 (1990)

(19) An immune system in panic does more harm than good. Cytokines (messengers between cells), and specifically interleukins (inter=between, leukins=immune cells), are the normal way the system communicates at a distance through the blood. When panic sets in, cytokines like interleukin-6 (IL-6) get overproduced (the "storm"), and an overhyped system starts destroying tissue and blowing up the plumbing. For a review, see Tisoncik et al, "Into the Eye of the Cytokine Storm. Microbiol Mol Biol Rev 76:16-32 (March 2012). 

(20) Pro Tip: don’t pahk yah cah in Hahvahd Yahd

(21) The classic paradigm of immunology is that the immune system distinguishes self vs. non-self or "foreign" antigens. The problem is that's inconsistent with a lot of observable phenomena, e.g. moms not rejecting a gigantic foreign alien creature in the womb (no, the fetus is not shielded from maternal immune cells). Also, vaccines should be able to work just by injecting a foreign protein into you. But they don't. They need something called an adjuvant to stir up the immune system at the same time, or you usually won't respond to the thing being injected.

In the mid 1990s, a former Playboy Bunny named Polly Matzinger started pointing out some of these things when she was running a lab at the NIH and it caused people to pull their hair out the way actual bunnies get their hair pulled out for fur-lined coats and gloves (you ever seen this? sheesh). But they didn't disprove her point: something is wrong with the fundamental paradigm. She called it The Danger Hypothesis because she believed the immune system is looking for dangerous things, not foreign things. A little review here.

(22) Example of confounding VSPs: an immune molecule called interleukin-2 (IL-2) is critical to making key parts of the immune system communicate with each other, especially the famous T-cells. A team of researchers created a mouse missing the IL-2 gene just to show what many VSP already knew: a mouse without IL-2 will not be able to generate much of an immune response.

Except that exactly the opposite thing happened. The immune system in these mice didn’t lay down like Brett Favre laying down for Michael Strahan, it went buck wild like Brett Farve blowing up some poor OC's carefully diagrammed play. VSP were like:

That's why they play the game. This happens all the time. It is happening right now with COVID-19. We just aren’t sure how yet.

(23) https://abcnews.go.com/International/106-year-believed-oldest-covid-19-survivor/story?id=70182773