Dr. Peters' UPdates

“OK we get it. To make a vaccine, you just identify the pathogen (COVID-19 SARS-CoV-2), remove the bits that seem to kill people and keep the bits that elicit a protective immune response, and Bob’s Your Uncle. Time to inject into people, right? How do we figure out if our vaccine is a lemon?”

OK, you get that this is tricky, right? That viral pathogenesis can be caused by viral replication, but ALSO can result from the immune response to the infection (key threshold concept in virology)? And when that happens, a vaccine can make things worse, by enhancing a pathogenic immune response, right? This can result from Antibody Dependent Enhancement of disease, remember? And that has actually been proven for other coronaviruses? And anyway, it is becoming clear that severe COVID-19 disease can involve immune dysregulation and cytokine storm, so vaccine testing might be fraught, right? Have you been paying attention at all?

“Yeah, yeah, sure, sure. Whatever. We need a frickin’ vaccine and we don’t need a lot of noise from mister negative ninny, here. Let’s get this done. What are the steps before mass vaccination?”

Ok, normally we do an “exploratory stage”=basic research. Then a “Preclinical Stage” involving animal studies to figure out safe vaccine dosing and safe method of administration. Then, in the US we make an “Investigational New Drug (IND)” application to the FDA, with our data and proposal for Clinical Studies. Then we do a “Phase I Vaccine Trial” where we round up 100 or fewer volunteers, give them the vaccine, and see how they respond. We are looking for people a LOW risk of getting the disease in the first place. Safety is primary concern, do they get sick from the vaccine? We monitor the crap out of these people, and also measure their immune response, especially if we have “correlates of protection” to examine. For this Phase I, maybe no placebo, or open label meaning everyone knows who got the vaccine. If that goes well, we go to a “Phase II Vaccine Trial” where we round up several hundred people, and definitely bring in a placebo group, and extend the findings of Phase I. Here we are focused on safety, immunogenicity just like Phase I, but are looking at dosing, schedule of immunizations, maybe method of vaccine delivery. We might even throw in some volunteers who are at higher risk of disease, see if they are protected at all. If that goes well, we are off to “Phase III Vaccine Trials.” This is when we look for more rare adverse events. Say a rare adverse event occurs in just 1/10,000 vaccine recipients. Our trial needs 60,000 subjects (half vaccine half placebo) to detect it. We also look to see if the vaccine works, the real money question. To do that we simply see how many vaccinated persons get disease, compared to placebo, over time. If the vaccine works, and nothing really bad happens, then off to “Approval” by FDA, vaccine manufacturing, and widespread use. Then we embark on “Phase IV Vaccine Trials aka post-licensure trials” which continue to test for safety, effectiveness, etc. That utilizes the “Vaccine Adverse Event Reporting System (VAERS)” where anyone can report potential adverse events, and the CDC monitors that reporting to look for rare adverse events, and try to figure out of there is causation.

“Wow that was super boring. This ‘medical education’ thing is painful. So we basically give the Vaccine to a few people to see if they do OK, then give it to lots of people to see if it protects from disease. How often do these trials give disappointing results?”

Most of the time. “Seriously?” Yes, see attached case studies from FDA for examples of how and why.

“OK, so it is a good thing that there are like 100+ COVID-19 SARS-CoV-2 vaccines in development, got it. How do we SERIOUSLY speed up this process? I need a haircut.”

Well, we hacked out the entire Exploratory and Preclinical phases for COVID-19 SARS-CoV-2 by relying on research in the Coronavirus field. We just made some vaccine candidates and started Phase I trials for 6 of them so far. No messing around.

“Great. How are we measuring the immune response, to see if any of these are working?”

Tricky. We need something we don’t have, which is a “correlate of vaccine protection.” That might be an anti-SARS-CoV-2 antibody level that, when achieved in a vaccine trial subject, shows that they are protected from disease. Could be antibody levels, could be measures of the cellular immune response. The thing is, we don’t have that data, we don’t know what that is. We can make some inferences from work on SARS and MERS, see attached paper, especially discussion under “Correlates of Protection.” This is pretty soft.

“Phase I trials are ongoing for some vaccines, great. How can we speed up Phase II and III? Phase III sounds like it could take a LONG time.”

Well, Phase III is partly about detection of rare adverse events, and it is nearly impossible to speed that up, but you can shift that to Phase IV/post-licensure and assume additional risk. But Phase III is largely about vaccine effectiveness, and that CAN be seriously sped up by “controlled human challenge studies.” Yes, this is as terrifying as it sounds. First step, get low-risk healthy volunteers and do a dose-escalation study where you don’t give them any vaccine, and inoculate them with COVID-19 SARS-CoV-2, so you know what dose makes most volunteers sick, but isn’t so huge that they get extra-sick. Terrifying. Once you nail that down, you get more volunteers to receive either placebo or candidate vaccine, then inoculate them all with COVID-19 SARS-CoV-2, and see if vaccination results in protection, and study the crap out of them for every correlate of protection you can think of, plus clinical diseases. Then if that goes OK, do another one with more subjects. Then move to licensure if the vaccine works.

You are not serious.

I am totally serious, see attached paper on COVID-19 challenge studies by some bioethicists. The sooner we have a protective vaccine, the more lives will be saved. This is really risky though.

How do you recruit volunteers for such a study? People could die.

See [https://1daysooner.org] where volunteers are already lining up.

How can we speed up manufacturing and distribution?

By just manufacturing vaccine doses on large scale, right now, without knowing if the vaccines are safe even work at all. That is exactly what is happening now.

So how soon, if all goes perfectly, and we do the human challenge thing and manufacture now?

Unbelievably soon, maybe this fall.

“There are now nearly 100 COVID-19 SARS-CoV-2 vaccines in development for sure, probably many more, of all different types. Why so many? How are they selected? What is the science informing these choices?”

You will be asked by patients, family, friends about your thoughts on COVID-19 vaccine development, indefinitely. Let’s dig in.

What do we need to know about a respiratory virus to design a vaccine candidate?

The goal of an effective vaccine is to develop a biologic that we can provide a healthy person, that will result in a protective immune response. So we need to know if infection by the pathogen itself makes a protective immune response. If it does, we are in business. (If it doesn’t (HIV), we are looking at a VERY heavy lift to design a vaccine.) We need to find survivors whose healthy immune systems fought off the infection, and figure out exactly how they pulled it off. (Innate or adaptive immunity or both? Did the immune response help or make disease worse? Did just a couple of antibodies to a specific protein do all the protecting, or what?)

OK this rudimentary information is crazy hard to figure out for a novel pathogen. It’s pretty hard to just round up a bunch of COVID-19 survivors and inject a bunch of SARS-CoV-2 in their noses, and see how they do. (Actually Challenge studies like this ARE under consideration for vaccine assessment.) Before we would even THINK about designing a vaccine, we might need decades of intense basic research to characterize the disease and immune response, develop an animal model for testing, figure out which immune responses are protective, if humoral we need to figure out which viral proteins and which antigenic domains are the protective antibody targets, on and on. We haven’t done ANY of that for SARS-CoV-2, so how the heck have these shmoes put together vaccine candidates within months of SARS-CoV-2 emergence? Obviously, they are relying on the decades of research and vaccine development on Coronaviruses, especially SARS-CoV-1 and MERS-CoV. Fortunately, that work is REALLY beautiful, done by scientists motivated by predictions of the pandemic we are now in experiencing. The structure of the SARS major viral antigen, Spike protein, was resolved at the atomic level by 2005.

So the design of all these vaccine candidates is based on research on other related pathogens? Yep. Have we developed vaccines for any of these other Coronaviruses?

Yes, none shown to protect humans, all in preclinical phase.

Does 100+ COVID-19 SARS-CoV-2 vaccine candidates mean what I think it means?

Yes, it means that everyone is taking a shot at this, hoping something works, but no one knows what is really likely to work, if anything. Are we screwed? Not really, this is how science actually works all the time, pretty much. Thoughtful failure after failure, every failure scrutinized and shared, every tiny success a step forward. This is where scientists live, baby.

So what DO we know about Coronavirus that has informed the design of these many vaccine candidates?

Neutralizing antibodies and T-cell immune responses can be raised against multiple SARS proteins but mainly target the S protein. The SPIKE is a trimer of S proteins. SPIKE is involved in receptor recognition, virus attachment and entry, it is the MAJOR target of vaccines. GO AFTER Spike, with a vaccine. S protein is a class I viral fusion glycoprotein, like HIV Env, influenza HA, paramyxovirus F and Ebola glycoprotein. S protein is CLEAVED during viral entry into S1 and S2. Angiotensin-Converting Enzyme 2 (ACE2) is a SARS-CoV (classic) receptor, also true for SARS-CoV-2. The part of S protein (and SPIKE) that binds to ACE2 is the Receptor Binding Domain (RBD). Antibodies targeting the RBD seem especially good at neutralizing viral infection. Vaccines have been designed using all of S protein, or just the RBD.

OK, so before SARS-CoV-2 showed up, how were we doing with making vaccines for SARS (classic) and MERS?

See attached reviews for deeper dive. In short, lots of animal studies (including non-human primate studies) showed feasibility and immunologic response, but only 2 MERS vaccines made it to Phase I and none for SARS (classic).

So as soon as we had a gene sequence for COVID-19 SARS-CoV-2, everyone slotted S protein full length or the predicted RBD into all kinds of vaccine vectors, hence the giant list of vaccines in development?

Yep, that is it. Although basic research on this organism is moving VERY quickly and will inform vaccine design.

Animal Models for COVID-19 SARS-CoV-2?

You bet—ferrets and cats are permissive of infection, and non-human primate models have been described too.

We are going to have vaccines in no time!

Yes, definitely true, human trials are ripping along at simply incredible speeds. But remember that we need a vaccine that works.

Now that just sounds negative—we need some positive energy! Optimism!

Hey, I am a super optimistic guy. But there is reason to think this might not go perfectly smoothly. Antibody-dependent enhancement (ADE) of viral infectivity and diseases has been reported for some coronaviruses. Specifically feline infectious peritonitis virus (FIPV), a vaccine not only didn’t work, but resulted in accelerated infection linked to antibodies to the virus. A SARS-CoV- classic vaccine seems to have made ferrets worse, causing hepatitis and liver necrosis in those immunized. In an in vitro study of SARS-CoV, antibodies to SPIKE potentiated infection of coronavirus into target cells.

What does the possibility of COVID-19 SARS-CoV-2 ADE mean for vaccine development?

We don’t know, but we need to be super careful. Vaccines could enhance disease, as in Dengue. But ADE isn’t a deal-breaker for vaccine development, we have an effective Dengue vaccine now after all, but its deployment is super complicated given potential for ADE. See 2 opinion papers, brief, for perspective.

“Why are we supposed to stand 6 feet away from each other to prevent SARS-CoV-2 transmission? Why not 5 feet? Why not 7 feet?”

“What is the deal with SARS-CoV-2 in poop?”

Speed Review of Hospital Infection Control stuff:

http://intranet.wakehealth.edu/departments/infection-control/coronavirus/ppe/ The different types of hospital isolation can be confusing, “Contact Precautions, special enteric precautions, airborne precautions, etc.” Remember that you can look on the back of the signs on the door for information about which agents and situations requiring each type of isolation. ALWAYS observe the isolation requirements posted on the door even if you and the team think they are wrong. NEVER let a patient or family member see you disregard an isolation sign, they will conclude that you are endangering a patient. Attached is a reminder of how to put on and take off PPE, we follow CDC recommendations, review this before returning to the wards. The quick reference one-page guide I attached is out of date, not endorsed by our institution, it just gives you a sense of the complexity of this enterprise. When in doubt call infection prevention for clarification.

What is the data underlying the 6-feet or more recommendation on the news so much, with COVID-19?

There has been a great deal of work done through the past century on respiratory virus transmission. Coronaviruses and other respiratory viruses can remain viable in droplets that fall on surfaces, and smaller aerosolized particles. (For useful visual image in considering aerosolized particles, think of someone smoking, and the cloud of smoke that you can see.) Transmission dynamics are complicated, involving virus viability, environmental conditions, air flow, surface type, on and on. So where does “6 feet” come from? Mostly, it comes from “shoe leather epidemiology” in which contact tracings are done to figure out who actually contracted disease in an isolated outbreak. And the most controlled settings that these “natural experiments” have occurred has been on airplanes.

Most relevant is the attached NEJM 2003 paper on SARS transmission in an airplane, and the passengers that got infected were clustered in the few rows closest to the index patient, directly in front or behind. Before this study, the conventional wisdom was that large-droplet spread would occur only within 36 inches. But this study changed that thinking, leading to other work on airplanes and a sense that greatest risk was within about 2 airplane rows, about 6 feet. Additional meta-analysis on the 2-row rule (see attached) isn’t particularly rigid. A very nice modeling study (Lei et al attached) compares transmission of Flu, SARS CoV (pre-COVID-19) and norovirus, to suggest that Flu transmission is best explained by close contact route, norovirus by fomites, and SARS CoV by all 3 routes (close contact, airborne, and fomites). Fascinating quote, “The predicted infection risk from the fomite route for aisle seat passengers if 2.2 times higher than that for non-aisle seat passengers. The aisle passenger-to-non-aisle passenger relative risk in the outbreak (9.5) is much higher than 2.2, and may be attributable to a small sample size of secondary cases.” I have generally preferred a window seat. But now I REALLY prefer a window seat.

What about EBOLA and airplanes?

Ebola really doesn’t transmit much on airplanes, see attached.

What about SARS-CoV-2 being found in poop?

As you recall from Virology, Coronaviruses are enveloped viruses, and generally enveloped viruses are not transmitted by the fecal-oral route. This because they are less stable, and more likely inactivated by transmission through the GI tract. Still numerous studies are documenting SARS-CoV-2 in human stool. Here is the thing—virtually all of those studies are just looking at nucleic acid presence in stool not viable, replication-competent virus. The very high levels of SARS-CoV-2 RNA in stool does raise concerns that this enveloped virus is able to pass through stool replication-competent though, that is concerning.

Enter a REALLY good paper you should consider reviewing, Wolfel et al, pre-published by Nature, attached. These guys really dig in to do a virological assessment of patients with SARS-CoV-2, actually trying to culture replication-competent virus from stool, and they weren’t able to do it despite also seeing lots of viral nucleic acid in stool. They do not say this finding is conclusive, they note that the viral RNA in stool of SARS-CoV-2 is much higher than MERS virus, for example.

“How good is the SARS-CoV-2 diagnostic testing? Is it good? Are some better than others? What is the deal?”

SPEED REVIEW: I have yet to take any board exam, initial or renewal, USMLE or specialty or subspecialty, in which I was not asked at least 2 questions about test sensitivity, specificity, positive and negative predictive value.

https://en.wikipedia.org/wiki/Sensitivity_and_specificity

https://en.wikipedia.org/wiki/Positive_and_negative_predictive_values

I really like the table on this particular Wikipedia site, but really this same 2 x 2 table is EVERYWHERE in every board review book you will find.

Sensitivity of a SARS-CoV-2 diagnostic test would tell us the probability that the test would be actually positive in a person who actually is infected with SARS-CoV-2. It is calculated from the ubiquitous 2 x 2 table by dividing the number of true positives by the number of persons with actual disease. High sensitivity is super desirable when you REALLY don’t want to miss any cases. We REALLY don’t want to miss cases of SARS-CoV-2 we are trying to mitigate/contain a deadly virus. High Sensitivity, hardly any false negative.

Specificity of a SARS-CoV-2 diagnostic test would tell us the probability that the test would be actually negative in a person who actually does NOT have SARS-CoV-2. It is calculated from the ubiquitous 2 x 2 table by dividing the number of true negatives by the number of persons do NOT have actual disease. High specificity is super desirable when you have a lot of diseases that look a lot alike, and you need to distinguish one cause from another. A very specific test for SARS-CoV-2 would be super nice because COVID-19 can look so much like influenza disease, and both are circulating at the same time. High Specificity, hardly any false positives.

Positive Predictive Value of a SARS-CoV-2 test would tell us the probability that a person with a positive test, actually is infected with the virus. This is calculated from the 2 x 2 table by dividing the number of true positives by the number of total test positives (true positives plus false positives). To be honest, the PPV is really the statistical test most useful to a clinician in my opinion, it is conceptually appealing and straightforward. (How likely is it that my patient has SARS-CoV-2 if this stupid test is positive? That is the PPV.) KEY TEACHING POINT: The PPV of a test is super slippery, it is always changing, it depends entirely on the “pre-test likelihood of disease” or the prevalence of disease in the population you are testing. So, at this moment, the PPV of ANY SARS-CoV-2 test is way higher in Manhattan than in Winston-Salem, because the prevalence of COVID-19 is so much higher in NY right now. ANY influenza test has a WONDERFUL PPV during flu season, but that number is in the toilet in the middle of summer. When I get a call about a kid with a positive rapid flu test in January, I am thinking, hey, this kid has flu. But the SAME test in July, I am thinking this is almost certainly a false positive, why the heck did anyone bother doing this test?

Negative Predictive Value of a SARS-Cov-2 test would tell us the probability that a person with a negative test, actually is NOT infected with SARS-CoV-2. This is calculated from the 2 x 2 table by dividing the number of true negatives by the number of total test negatives (true negatives plus false negatives).

So everyone tests us on this stupid math, so let’s take it out for a spin! What is the sensitivity, specificity, PPV and NPV for the SARS-CoV-2 PCR test in widespread use in the US?

Answer, I have no idea, and I can’t figure it out. It is incredibly frustrating. I thought I would have this great educational update on core board stuff, then give you data to give you a nuanced way to interpret all the news reports on testing accuracy. I got nothing.

“Seriously? Nothing at all? No clue whatsoever?”

Not that bad. I never thought that we would know the PPV or the NPV of these tests, because our disease prevalence is all over the place and those numbers are slippery. Sensitivity and Specificity are what I am looking for, and there is some stuff on that. The attached paper by Ai et al comparing 2 diagnostic testing methods, PCR and chest CT scans, illustrates the difficulty in figuring this out.

The reason we don’t really know for sure about how these tests perform in the clinical setting, is we are still trying to get a handle on how the virus behaves—does it shed in the nasopharynx throughout disease, or only early on, before it sets up shop in the lungs? NP or throat swabs best? Standardizing specimen collection is necessary for determining Sensitivity and Specificity of a test in the clinical setting, and we aren’t there yet. These tests probably are pretty good, with a likely sensitivity and specificity of over 90% (for both) for these tests, based on extensive data from other viruses. The way they get a ballpark idea of how well these tests are working is by using laboratory “simulated” clinical samples with known quantities of lab-isolated virus, and also comparing new PCR assays to older PCR assays, by comparing performance on clinical samples.

What about the new rapid tests? Are they any good?

The Abbot rapid SARS-CoV-2 test hyped at the White House uses nicking enzyme amplification reaction (NEAR) technology. (If you want to geek out on what that is, see the “amplification chemistries” review I have attached, that is a really deep dive.) But yes, these tests are all probably pretty comparable to PCR in their capacity to amplify nucleic acid of viral pathogens.

CT Scans? What is the deal?

We can think about CT findings as a COVID-19 disease test, with a sensitivity, specificity, positive and negative predictive value. Indeed, we can apply that thinking to physical exam maneuvers, and we often do. (For example, what is the sensitivity, specificity, positive and negative predictive values for the Kernig and Brudzinski signs for detection of bacterial meningitis? They are TERRIBLE, so we don’t emphasize those skills in CS1/2 courses.) It turns out that CT scans of patients with COVID-19 have a pretty characteristic appearance, and used in concert with laboratory testing, are quite useful.

Will SARS-CoV-2 resurge in the fall, to become a seasonal respiratory virus in our region? Do we really not have a clue about that? Why is this a total mystery?

"Whoever wishes to investigate medicine properly should proceed thus: in the first place to consider the seasons of the year . . .” Hippocrates (circa 400 BC)

Respiratory viruses are seasonal, obviously. Why?

See lovely review by Moriyama et al attached. We return to the R₀, or basic reproductive number for a respiratory virus. The R₀ for respiratory viruses often increases during the winter months, then drops in the summer. The reason for this change in R₀ is multifactorial. There are changes in the environment, human behavior, immunity.

Are all Respiratory viruses worse in the winter?

NOPE. Influenza, endemic Coronaviruses (see attached paper on coronavirus seasonality), and RSV peak in winter, but others like adenovirus are year-round. Non-rhinovirus enteroviruses are summer viruses (see fig 2 of review).

So what are the environmental factors that impact R₀ for respiratory viruses?

Mostly changes in temperature and humidity, sunlight too. But here is the thing, we work in crowded spaces year round, inside. It isn’t like we are outside all summer hunting and gathering and huddled together in a cave all winter for warmth. We overwhelmingly work inside all year, sharing the air, crowding together no matter the weather. Still, the relative humidity indoors drops in winter big time with indoor heating, and the air change rate indoors drops significantly in winter when buildings are heated.

To break it down, humidity affects both the stability of the virus, as well as its transmission.

First Stability. Virus transmission by droplets happens with big fat droplets that we touch and squish onto our mucous membranes, or tiny droplets that float through the air and we inhale. The humidity, or vapor equilibrium in the room, affects evaporation from the droplets, and the concentration of virus in the droplets. Weirdly for flu, the stability of the virus in these droplets is best at low humidity and high humidity, but worse in the middle range. Looking at other viruses, the stability of the winter viruses is highest at low temp and humidity, but the stability of summer and all-year viruses are higher at high humidity and temperature. Remember that these viruses, to a virologist, are WAY different from each other.

Then transmission. Researchers have studied the crap out of flu, which can be transmitted by droplet AND aerosol, and these are affected differently by temp and humidity. They think in temperate regions (like us) winter brings dry warm indoor air and the flu gets into droplets that are desiccated by the low humidity, and can float around more, so more aerosol spread. But at the equator, the air is more humid, and the droplets filled with flu stay fat, and settle on surfaces, and transmission occurs by contact spread.

What about host factors and seasonality?

This is super interesting see review. Mucus layer, our first line of defense. If we breathe a bunch of dry cold air, our mucus gets dehydrated and doesn’t’ work well. Second line of defense, epithelium, and dry air impairs the capacity of epithelium to repair itself quickly. So cold dry air reduces ciliary activity and kills bronchial epithelia, and this is why ventilated patients get warm humidified air from their vents. Wearing a mask in winter might actually protect us by keeping our noses nice and warm, to improve our antiviral defenses!

What about innate immunity?

Holy crap, the host interferon system doesn’t work as well at lower temperatures. People still working to figure this out. Also, short daylight of winter may knock down phagocytosis and mess with macrophages due to vitamin D deficiency.

What about adaptive immunity?

Heat definitely changes CD8+ T-cell function in mice, but get the temp too high then it drops.

Bottom line

Seasonality of respiratory viruses is super complicated, an interplay of environmental factors and host immunity, and structural characteristics of the virus affecting stability and transmission, probably a lot of physics and structural biology and droplet chemistry and circadian rhythm stuff, and eons of viral co-evolution with the human immune system, and we don’t have a great handle on this.

What about the other bad Coronaviruses like SARS (classic) and MERS?

SARS (classic) made people super sick but had a very low R₀ and everyone was terrified it would become seasonal, but it didn’t because it just left the human population fully. MERS keeps showing up, also has a low R₀ and really doesn’t circulate in humans, it is a camel virus. Each year it pops into humans from camels, but the low R₀ for human-to-human transmission means it isn’t maintained as a circulating human virus.

Where to these endemic respiratory viruses go in the summer?

KEY CONCEPT: these viruses don’t “Go” anywhere. Just because we aren’t seeing disease, doesn’t mean the viruses aren’t still infecting humans and replicating in them, and getting passed along. People can shed these viruses asymptomatically, acquire them, have low level replication and prolonged shedding, etc. R₀ drops but doesn’t go to zero. Then yearly environmental changes cause R₀ to increase and we see lots of respiratory disease.

So will COVID-19 SARS-CoV-2 become an endemic virus that establishes some kind of seasonal pattern like endemic Coronaviruses -OC43, -229E, NL63, and -HKU1?

Given what we know about SARS-CoV-2 shedding in asymptomatic persons, potential for prolonged shedding, etc. I would agree with the experts that suggest this as a pretty likely possibility, you can decide for yourself. But we shouldn’t just freak out—our population immunity is rapidly evolving with overall immunity growing, our current pandemic is occurring in the context of a completely novel virus. 2009 pandemic strain H1N1 has been circulating ever since that scary first year, for example, and enhanced human immunity (vaccination and immunity after wild-type infection) has moderated disease burden.

(I put the Hippocrates quote up top to give the impression that I am an old-school scholar, hunched over crumbling parchment in a rare-book section of a European reading room, making jokes in Latin with librarians wearing reading glasses on chains around their necks. But I think we all know I just copied that out of a random paper on virus seasonality to try to look smart.)

“If someone gets COVID-19 SARS-CoV-2, when do they stop shedding virus? When are they no longer contagious?”

Viral “clearance” is necessary to render the host non-infectious to others. To answer the incredibly important and relevant questions above, we have to do a deeper dive into the “Cellular Immunity” arm of the adaptive immune response to Coronavirus. Cellular immunity is important in coronavirus clearance, but also important in pulmonary pathogenesis with immune-mediated lung damage being an undesirable outcome. Clearing an intracellular pathogen from a host requires the elimination of the infected cells.

Speed Review

Cell mediated immunity is adaptive, but no antibodies involved. Naïve T-cells are mature but haven’t yet encountered an antigen. These Naïve T cells are converted into activated T cells after encountering antigen-presenting cells (APC’s) like macrophages, dendritic cells, and sometimes B cells. The APC’s take the antigenic peptides and load them onto the MHC (major histocompatibility complex) molecule of the cell, then present that to the receptors on the naïve T cells. That “activates” the T cell.

The “activated” T cells belong to one of 3 different classes. Cytotoxic T-cells that kill infected target cells by apoptosis, TH1 cells that activate macrophages, and TH2 cells that stimulate B cells to make antibodies. Cellular immunity also stimulates cells to make a lot of cytokines. So, Cell-mediated immunity is super important in the antiviral response, and is critical to viral clearance especially through Cytotoxic T-cells (AKA CD8+ T-cells or killer T-cells). (Recall that activation of CD8+ T cells happens when class I MHC on the APC binds to the the T-cell receptor, and the MHC constant portion is also bound by the CD8 molecule on the T cell.)

When Cytotoxic T-cells go to work on an infected cell, they release cytotoxins perforin and granzymes. The perforin gets the granzymes into the cytoplasm of the infected cell and trgger the caspace cascade, that leads to apoptosis of the cell (aka programmed cell death), and Bob’s your uncle. There is a way that Cytotoxic T-cells can trigger apoptosis of an infected cell just by interacting with its surface, but the cascade makes my head hurt. Something to do with FAS ligand. (Don’t share this summary with real immunologists. They will get pissed off and yell at me, this is way oversimplified.)

Respiratory Virus Disease and Cellular Immunity

OK back to our threshold concept that viral disease is often caused by immune response as much or more than by viral replication. Given that cellular immunity is all about killing host cells that are infected with viruses, it is pretty easy to imagine that respiratory viruses infecting the lung tissue could lead to some serious damage. That is what we are seeing in patients infected with SARS-CoV-2, and management of cytokine storm is important. The immune system has to clear the virus, but do it in a way that doesn’t destroy the host. For nice fairly brief review, see attached article with overview of a bunch of respiratory viruses.

So when does a patient infected with COVID-19 SARS-CoV-2 disease stop shedding virus?

Wow, that is a super good question, obviously relevant to control of viral spread in our communities. The answer is, it depends. Attached is a very recent paper looking at this for SARS-CoV-2 from investigators who examined 16 patients in Beijing China. They swabbed their throats to look for Viral genetic material by PCR, to try to figure out the “shedding window” for viral presence in these samples after clinical recovery of the patient. Half of their patients were still shedding after recovery, one patient shed for up to 8 days. The authors cite to earlier studies describing much sicker patients, one study showed shedding 12 days after symptoms resolved, and another showing shedding up to 20 days. IMPORTANT CAVEAT: These studies look at PCR evidence of viral presence in nasopharynx—looking for genetic material. They are NOT looking at virus culture in cells, which would directly measure the amount of replication-competent virus. If a host has lots of virus in NP, the PCR would be positive even if all the virus was covered in antibody and was non-infectious. STILL, PCR is a pretty reasonable way to look at likely shedding of replication-competent virus.

So what makes someone shed virus for a longer time?

Well, this isn’t exactly rocket science. If cellular immunity is required for viral clearance, then anything that suppresses cellular immunity is likely to prolong viral shedding. Steroid treatment! Other immunosuppressive therapy in very sick patient! Immunodeficiency from congenital defects, acquired immunodeficiency including cancer treatment, etc.

So how do we really know when someone recovered from SARS-CoV-2 infection is done shedding the virus?

Well, ideally we would test the patient to confirm they are PCR negative, and then end isolation. However, we don’t have testing access right now. So what do we do? Well, we do the best we can. Below are the CDC guidelines regarding how to handle recovered patients in outpatient setting, with no tests. HOWEVER, if a patient has been really sick, is immunocompromised, on steroids, it would make a LOT of sense to advise that recovered patient to maintain self-isolation longer than the recs below. These recommended times frankly seem pretty short to me given the papers I have sent to you. But there you are.

4/1/20 CDC Guidelines for ending isolation after SARS-CoV-2 Infection

https://www.cdc.gov/coronavirus/2019-ncov/hcp/disposition-in-home-patients.html: For outpatient isolation without access to testing to determine presence of virus in NP: At least 3 days (72 hours) have passed since recovery defined as resolution of fever without the use of fever-reducing medications and improvement in respiratory symptoms (e.g., cough, shortness of breath); and, At least 7 days have passed since symptoms first appeared.

Guidelines for ending isolation for hospitalized patients more elaborate: https://www.cdc.gov/coronavirus/2019-ncov/hcp/disposition-hospitalized-patients.html, Testing to demonstrate that shedding has concluded is definitely preferred, sicker patients may shed longer.

I send along this paper published yesterday, because it strikes me as particularly important and informative:

Cardiovascular Implications of Fatal Outcomes of Patients With Coronavirus Disease 2019 (COVID-19). JAMA Cardiology.

It seems that COVID-19 disease caused by SARS-CoV-2 may cause more myocardial disease than appreciated. Certainly as we discussed in Virology core course, respiratory viruses cause viral myocarditis, coronavirus among them. This is pretty rare though. However, a finding that Coronavirus causes higher incidence of myocardial damage would fit very nicely with the finding that the elderly are at much higher risk of severe disease and death. That the mechanism may be related to inflammation/cytokine storm is intriguing, and something we can treat.

I just cut and paste this section straight out of the paper, really fascinating.

Potential Mechanism Underlying Myocardial Injury

The current study demonstrates that patients with underlying CVD and other comorbid conditions are more prone to experience myocardial injury during the course of COVID-19. For patients with underlying CVD, including hypertension, coronary heart disease, and cardiomyopathy, viral illness can further damage myocardial cells through several mechanisms including direct damage by the virus, systemic inflammatory responses, destabilized coronary plaque, and aggravated hypoxia. Therefore, patients with CVD are more likely to experience myocardial injury after COVID-19 infection and higher risk of death.

However, it is also notable that the 16% of patients with underlying CVD but with normal TnT levels had a relatively favorable outcome in this study. These data suggest that myocardial biomarkers should be evaluated in patients with CVD who develop COVID-19 for risk stratification and possible early and more aggressive intervention. Although the exact pathophysiological mechanism underlying myocardial injury caused by COVID-19 is not fully understood, a previous report showed that in 35% of the patients with severe acute respiratory syndrome coronavirus (SARS-CoV) infection, the SARS-CoV genome was positively detected in the heart. This raises the possibility of direct damage of cardiomyocytes by the virus. SARS-CoV-2 may share the same mechanism with SARS-COV because the 2 viruses are highly homologous in genome. In the current study, plasma TnT levels were significantly positively linear correlated with plasma high-sensitivity C-reactive protein levels (Figure 2), indicating that myocardial injury may be closely associated with inflammatory pathogenesis during the progress of disease. Viral particles spread through respiratory mucosa and simultaneously infect other cells, which could precipitate a cytokine storm and a series of immune responses. Huang et al5 highlighted that in patients with COVID-19, the imbalance of T helper 1 and T helper 2 responses resulted in a cytokine storm, which may contribute to myocardial injury. The release of inflammatory cytokines after infection may cause reduction in coronary blood flow, decreases in oxygen supply, destabilization of coronary plaque, and microthrombogenesis."

As for patient selection, this sentence certainly got my attention: "Among 187 patients with confirmed COVID-19, 144 patients (77%) were discharged and 43 patients (23%) died." Our colleagues at the Seventh Hospital of Wuhan City, China have done some seriously heroic work.

“What is the deal with SARS-CoV-2 and our immune systems? No treatment, no vaccine, hardly any tests, all this personal-protective equipment everyone is talking about looks a lot like trash bags that people put over their scrubs. I sure hope our immune systems step up here. . .”

Our immune systems are highly evolved and pretty spectacular, and have long been locked in mortal combat with respiratory viruses. The literature is incredibly confusing and complicated, definitely more than a one-pager. Let’s break it down, you can dive back into fundamental immunobiology as much as you would like. Coronaviruses have evolved to evade the immune response like every other pathogen.

Our immunity to coronaviruses is innate and adaptive. But our immune response can be both protective and pathological in COVID-19, recall our threshold principle that viral disease is often a manifestation of the immune response to infection, sometimes more than viral replication. So to understand treatment for COVID-19 in the ICU, we need some clue about the immune response so we know what the heck is going on. Cytokine storm and Macrophage Activation Syndrome are being actively discussed as complicating Coronavirus disease in critically ill patients, and I am being asked to consider IL-1 and IL-6 blockade in these patients. What, you ask? Let’s get in the game.

Adaptive immunity includes the Humoral immune response (antibody production) and that is critical for neutralization of coronaviruses, blocking viral entry into cells by binding to the spike glycoprotein. T cell immunity is just as important. CD4+ T helper cells are key for development of specific antibodies, and CD8+ cytotoxic T cells are really important for killing infected cells and viral clearance. So, antibodies neutralize Coronavirus, T-cells help with that and also clear infection. (This is a ridiculous oversimplification, but there you go). Setting adaptive immunity aside. . .

Innate immunity: I want to focus on this for now. Anatomical barriers, inflammation mediated by macrophages, dendritic cells etc. that produce histamine, leukotrienes, etc., Complement system, does all this ring a bell? It is complicated and sprawling.

Innate Immunity includes innate leukocytes (NK cells, mast cells, eosinophils, basophils) and phagocytic cells (macrophages, neutrophils, and dendritic cells) and these cells identify and eliminate pathogens. One of the coolest areas to read about are the Pattern Recognition Receptors on these cells that recognize molecules that are found in coronaviruses but NOT us, and when they bind these molecules the cells activate and release inflammatory mediators. These receptors can be membrane bound on the cell (like Toll-like receptors super cool and other ones), or floating around in the cytoplasm (like NOD-like receptors and RIG-I-like receptors).

OK. So along comes a Coronavirus, and our innate immune system uses a bunch of different proteins to recognize this invader.

These include Toll-like receptors, RIG-I-like receptors, and others. These proteins activate the antiviral Interferon system (IFN-alpha/beta or “type 1 interferons”), which are cytokines that are produced and secreted by cells that encounter viruses (or virus parts). These interferons then go bind to the TON of cells that express the IFN-alpha/beta receptor. Binding there activates the JAK-STAT pathway in those cells, that pathway makes a transcription factor that goes to the nucleus to activate our “antiviral gene expression program.” This actually regulates hundreds or thousands of genes that have antiviral, immunomodulatory, anti-proliferative functions, crazy complicated. These actually block lots of viral functions: entry, polymerase function, protein translation, RNA stability, budding, apoptosis, on and on.

So Coronaviruses have evolved to dodge these innate immunity mechanisms. They inhibit Interferon induction amazingly well, in part by hiding their dsRNA that are produced during viral replication in double-membrane vesicles. But there are a bunch of Coronavirus proteins that participate too—viral proteins that sequester host immune cascade factors, again super complicated. These proteins block Interferon signaling and increase interferon resistance.

RELEVANCE TO ICU:

Circling back, it seems that our ICU patients with Acute Respiratory Distress Syndrome are having “cytokine storm” and the uncontrolled inflammatory response is causing lung inflammation. So super-smart Dr. Alycia Taxter send an e-mail about IL-1 inhibition (Anakinra, Canakinumab) and IL-6 inhibition (Tocilizumab and Sarilumab), the rheumatologist think we should use these drugs. So we would check a ferritin to assess for Macrophage Activation Syndrome and if ferritin is high, use these drugs. See Lancet paper attached that Dr. Taxter sent me.

Please don’t share this ridiculously oversimplified summary with any immunologists. They will roll their eyes and start talking to me slowly, using small words.

Briefly, in a study published in 2007, it was reported that viruses very clearly are associated with olfactory dysfunction. Long before then, viral upper respiratory infections were identified as causes of olfactory dysfunction. This particular study was done in Japan, was fairly small (24 patients), and the investigators look for 10 different respiratory viruses. In 15 of the patients, they found a virus in nasal washings (by PCR), and in 10 cases these were respiratory viruses. Mostly these were rhinovirus, but Coronavirus and parainfluenza virus was identified. Anyway, the symptoms of anosmia lasted in many cases WAY longer than other URI symptoms and nasal obstruction.

In an incredibly interesting and unexpected development, a very large percentage of SARS-CoV-2 infected patients have developed anosmia/hyposmia. A letter (see Canvas) summarizes some of this data very briefly.

"In Germany, it is reported that more than 2 in 3 confirmed cases have anosmia. In South Korea, where testing has been more widespread, 30% of patients testing positive have had anosmia s their major presenting symptom in otherwise mild cases."

This group proposes that the finding of anosmia/hyposmia may be useful for early identification of patients with COVID-19 disease. Fascinating.

“What is the deal with the NIH Vaccine Trial that started 3/19/20?”

WHAT ARE THE DIFFERENT KINDS OF VACCINES: Recall the different classes of vaccines in use: live attenuated, and inactivated, and subunit vaccines. You have learned all about this stuff in immunology and elsewhere.

Click here for a list of all vaccines used in the US

Click here for a list of all US vaccines, with vaccine type

As you review this table, you might ask, “which ones of these are RNA vaccines?” None of them. There are no RNA vaccines approved for medical use at all.

WHAT IS AN mRNA VACCINE: RNA vaccines work by introducing an mRNA sequence encoding a disease-specific antigen into a person’s cells. These cells translate the mRNA in the vaccine to produce the antigen which is recognized by the immune system. They can be made MUCH faster and cheaper than traditional vaccines, allowing for faster responses in outbreak settings. They can be delivered by needle into muscle, blood, lymph node or directly into organs, even by nasal spray or needle free into skin. There are 3 types: 1. non-replicating mRNA (simplest). 2. a self-replicating mRNA called self-amplifying replicon (RepRNA) technology which are large self-replicating RNA molecules derived from viral genomes. 3. In vitro dendritic cell non-replicating mRNA vaccines in which a persons dendritic cells are extracted, transfected with non-replicating mRNA as in 1, and re-injected into the patient.

ARE OTHER GROUPS WORKING ON CORONAVIRUS VACCINES? Yes a lot in fact. Most are working on RNA vaccines, but I was able to find at least one company report suggesting work on an inactivated vaccine.

HOW LIKELY ARE THESE VACCINES TO BE PROTECTIVE? We don’t know, but vaccine development isn’t a sure-thing.

Important—we don’t really need a vaccine to completely protect us from disease, although that would be nice. A vaccine that reduces disease severity would be wonderful. We need to keep people out of the ICU’s, keep them from dying.

WHY NOT STREAMLINE VACCINE TESTING HERE? WHAT IS THE DOWNSIDE? Well, a vaccine could make the disease worse. That is not just hypothetical, it really happens.

DENGUE: A vaccine is “sort of” available since 2016, but it is not recommended except in rare cases. Initial infection with dengue fever might not cause severe disease, however due to the phenomenon of antibody-dependent enhancement, subsequent infection with a different serotype can lead to severe hemorrhagic fever and death. If you are infected once with dengue you should probably take care to avoid subsequent encounters with dengue fever. So Vaccine development for Dengue has been fraught, and the vaccine we have is only deployed in special settings to reduce the risk of severe disease in persons known to have had Dengue in the past. This is a special case, and we have known to be careful here because of the clinical observation of antibody-mediated disease enhancement in this particular disease. We DO NOT see this kind of effect with wild-type Coronavirus disease.

RESPIRATORY SYNCYTIAL VIRUS: For both RSV and Measles, there have been vaccines made that actually made disease worse in vaccine recipients. A particularly heartbreaking story was the formalin-inactivated RSV vaccine (the “lot 100” vaccine) tested in the late 1960s that caused children to be MORE susceptible to severe disease, and 2 children died. This experience set RSV vaccine work back decades, and we still don’t have an RSV vaccine. (RSV vaccine work has been heroically advanced and there are promising candidates now.) The point is that VIRAL PATHOGENESIS is not simply a result of viral replication! Rather the immune response to the infection can cause very significant pathology, most definitely true for respiratory virus disease! This is a vital “threshold concept” in virology, and underscores the need for very deliberate and careful testing of vaccine candidates.

"What is the deal with Chloroquine and SARS-CoV-2?”

THRESHOLD CONCEPTS ABOUT VIRAL PATHOGENESIS: Antiviral drug discovery is really challenging, any thoughtful discussion must be based on an understanding of viral pathogenesis. The KEY CONCEPT here is that viral pathogenesis may be caused directly by viral replication, but NOT NECESSARILY. There are MANY examples of severe respiratory viral disease caused primarily by the host immune response, and pulmonary inflammation, and cytokine storm, and Macrophage Activation Syndrome, etc. These mechanisms are definitely under consideration in severe COVID-19. Look at the abbreviated slide set. Just finding a drug that inhibits virus growth in vitro (in a lab on some cells) does NOT mean it will be useful for treatment. It just isn’t that simple.

CORONAVIRUS CELL ENTRY: Briefly, SARS-CoV-2 likely enters the host cell by receptor mediated endocytosis, and in the host endosome there are cellular proteases that cleave the spike protein to trigger viral entry into the cell cytoplasm. See abbreviated slide set for review, and new slides #15 and #16 for quick visual summary.

WHAT IS CHLOROQUINE: FROM THE CDC Website 3.23.20. Hydroxychloroquine and chloroquine are oral prescription drugs that have been used for treatment of malaria and certain inflammatory conditions. Chloroquine has been used for malaria treatment and chemoprophylaxis, and hydroxychloroquine is used for treatment of rheumatoid arthritis, systemic lupus erythematosus and porphyria cutanea tarda. Both drugs have in-vitro activity against SARS-CoV, SARS-CoV-2, and other coronaviruses, with hydroxychloroquine having relatively higher potency against SARS-CoV-2 ^[1,4,5]. A study in China reported that chloroquine treatment of COVID-19 patients had clinical and virologic benefit versus a comparison group, and chloroquine was added as a recommended antiviral for treatment of COVID-19 in China ^[6]. Based upon limited in-vitro and anecdotal data, chloroquine or hydroxychloroquine are currently recommended for treatment of hospitalized COVID-19 patients in several countries. Both chloroquine and hydroxychloroquine have known safety profiles with the main concerns being cardiotoxicity (prolonged QT syndrome) with prolonged use in patients with hepatic or renal dysfunction and immunosuppression but have been reportedly well-tolerated in COVID-19 patients

HOW DOES CHLOROQUINE WORK: Antimalarial—it gets into the parasitic digestive vacuole which is acidic, then prevents the parasite from managing heme which is toxic to the parasite.

For rheumatoid arthritis—the drug inhibits lymphocyte proliferation, enzyme release from lysosomes, oxygen metabolite release from macrophages, etc.

ANTIVIRAL: Primarily, it is thought that the antiviral effects of Chloroquine and related drugs is caused by raising the pH of the host cell endosome, thereby inhibiting viral entry. Also, these drugs are used as anti-inflammatory drugs, so it may be that benefit is gained by reductions in the production of pro-inflammatory cytokines. THIS IS NOT NEW AT ALL: see review on this topic in Lancet ID from 2003, attached.

DO THESE DRUGS WORK AGAINST COVID-19 SARS-CoV-2: I hope so. Really. But the evidence to date is very thin. It definitely works in vitro (see recent paper file Chloroquine in vitro SARS-COV-2 3.2020). But really, that had LONG been established in other Coronaviruses, I think any virologist would be gobsmacked if this drug didn’t work to reduce viral replication in vitro for this new coronavirus.

The really important question is whether Chloroquine or related compounds actually work to treat COVID-19 disease. Attached is the only report, published in Bioscience Trends (COVID-19 Brief report), that honestly doesn’t share any data at all. It is little more than a press release.

So, basically, Chloroquine has long been known to have antiviral properties, but there remains no published evidence that Coronavirus disease is modified by these drugs.

Relevant questions:

“With so many people on Chloroquine for Malaria and rheumatologic diseases, has anyone noticed that they are less likely to suffer from colds, given that endemic coronaviruses cause 15-30% of colds?” Answer: Nope, not as far as I can tell.

“With so many people on Chloroquine as an anti-inflammatory/immunosuppressive medication, has anyone noticed that these patients are more likely to get really severe viral diseases especially coronavirus?” Answer: Nope, not as far as I can tell.

“15-30% of all human colds is a lot, and if someone sold a safe drug that worked really well on coronavirus, it seems like they would get super rich.” Answer: Yep, seems like if Chloroquine (or other marketed drugs shown to have in vitro activity for coronaviruses) were just super incredibly promising, we would have data examining their effect on coronavirus colds. But we don’t.

I really, really, really hope these drugs, or some other licensed drug(s) work to keep COVID-19 patients out of the ICU’s. And I have no problem in this emergency situation with clinicians just trying this stuff in hope that there might be some benefit. But when Dr. Fauci reminds everyone that we need data to assess the effectiveness of these drugs, he is TOTALLY RIGHT. Otherwise, we are just flying blind, giving drugs that we think might help but maybe don’t, and may even make things worse.

We are hearing a lot of discussion about the “Great Influenza” of 1917-18 as a comparison to our current COVID-19 SARS-CoV-2 pandemic. I thought it might be interesting to you to review what really happened in that epidemic, from a scientific/medical standpoint. The attached short review from a medical historian is fascinating.

Teaching points:

-The influenza A virus pandemic of 1918 is an extreme example of influenza-bacterial co-pathogenicity.

-In the post-antibiotic era, the association between influenza and bacterial pneumonias has been less dramatically evident due to widespread antibiotic use, mechanical ventilation, and relatively few autopsy studies.

-During the 1957 Asian influenza pandemic in the US, hospitalizations for bacterial pneumonias increased substantially, with S pneumoniae, H influenzae, and S aureus most often isolated.

-During the 1968 Hong Kong influenza pandemic one series of 127 patients in NY showed 16% with bacterial pneumonias, 40% of those were fatal.

-Influenza FAMOUSLY is associated with serious bacterial infections. BUT THIS IS NOT TRUE OF CORONAVIRUSES.

An interesting basic science study was published in 2008 by Dr. Fauci, who we are hearing about a lot in the news just now. In this study, Dr. Tony Fauci and colleagues examined lung tissue from 58 autopsies and reviewed path and culture data from 109 autopsy series from 1918.

Morens DM, Taubenberger JK, and Fauci AS. Predominant role of bacterial pneumonia as a cause of death in pandemic influenza: implications for pandemic influenza planning. JID 198:962-70, 2008.

“The majority of deaths in the 1918-1919 influenza pandemic likely resulted directly from secondary bacterial pneumonia. . .Less substantial data from the 1957 and 1968 pandemics are consistent with these findings.”

“We believe that the weight of 90 years of evidence, including the exceptional but largely forgotten work of an earlier generation of pathologists, indicates that the vast majority of pulmonary deaths from pandemic influenza viruses have resulted from poorly understood interactions between the infecting virus and secondary infections due to bacteria that colonize the upper respiratory tract.”

Relevance to Coronavirus Epidemic:

-this is a very different virus than influenza. Many severely ill patients with COVID-19 (disease) SARS-CoV-2 (the virus) have been treated empirically with anti-bacterials, but we really don’t know the incidence of bacterial co-infection in severe COVID-19. In SARS epidemic the contribution of bacterial co-infection was not considered particularly important.

The radiographic findings of lung disease in COVID-19 do not suggest acute bacterial pneumonia, those CT scans show multifocal, patchy disease. But it is notoriously difficult to obtain bacteria from patients with acute bacterial pneumonia, they seldom have positive blood cultures for example, so questions remain.

“What are Superspreaders and Cloud Patients, and what relevance does this have to the ongoing COVID-19 (SARS-CoV-2) Pandemic?”

Discussion and data surrounding the “Superspreader” concept is often confusing and garbled, especially with regard to the spread of respiratory viruses. There are “superspreaders” (infected people) and “Superspreader events” (not what we are talking about here).

FIRST THE MATH: The rate of spread of any epidemic depends on “the average number of secondary cases generated by one primary case in a susceptible population.” This is described mathematically as the “Basic Reproduction Number” or R₀. Generally speaking, if this number is below 1, then the epidemic spread cannot be self-sustaining, because a primary case infects less than 1 secondary case. This is not exactly rocket science. This number changes during the epidemic, and we talk about the “effective reproduction number” or R_t. This number gets lower with implementation of control measures, and a drop in susceptible individuals during the epidemic. Again, no rocket science here, the whole reason you are all sitting at home is that we are trying to drive down R_t. An effective vaccine would drive down R_t.

The “Basic Reproduction Number R₀” and the “Effective Reproduction Number R_t” are average numbers for infected persons in the population. Thus, some persons will have a low number (reclusive, meticulous hand hygiene after pooping in appropriate receptacle, wears mosquito repellent, doesn’t have sex, coughs into elbow) and other persons will have a high number (socially gregarious, gets drunk and poops in the punch bowl, delicious to mosquitoes, sexually promiscuous, enters loudest cough contest.) Mathematically, an individual with a high R would be considered a “superspreader.” Simple. Enough math.

RELEVANCE TO NON-RESPIRATORY VIRUS EPIDEMICS: Super-spreaders are extremely well described in lots of epidemics, particularly GI pathogens and Sexually Transmitted Diseases, etc. Typhoid Mary, an Irish Cook named Mary Mallon, is believed to have infected 51 persons with Typhoid. R=51. She was quarantined for 3 years and agreed not to work as a cook, they released her. However, she changed her name and moved from kitchen to kitchen to find work, and the typhoid researcher (Soper) couldn’t track her down. Then after a big outbreak the police tracked her down, arrested her, and she was forcibly quarantined from 1915 until her death in 1938. Famous Super-spreader, actual R probably way higher than 51.

RELEVANCE TO RESPIRATORY VIRUS EPIDEMICS: Obviously, a person with a respiratory virus could drive up their R number by just traveling a lot while infectious, failing to conform to social distancing efforts, etc. MORE INTERESTING is the question of whether or not an infected person could be just way more contagious than most others, due to co-pathogenicity.

The Cloud Baby was described in 1960 by Eichenwald, who reported that newborns colonized with S. aureus dispersed large numbers of bacteria and were highly contagious when co-infected with respiratory viruses. In 1972 Gwaltney extended these observations to pneumococcus. The Cloud Adult was described by Sheretz here at Wake Forest in 1996, they had a surgical ICU outbreak of Methicillin-resistant S. Aureus during which one health care worker was colonized with the outbreak strain, and had a minor respiratory viral infection during the outbreak. It appears from these reports and other animal studies that co-infection of a respiratory virus could increase transmission of a respiratory bacterial pathogen.

This is highly relevant to our understanding of the great influenza epidemic of 1917-18. Influenza virus is famously associated with bacterial pneumonia and co-pathogenicity. However, Coronavirus is NOT. And it does not seem that the respiratory disease from SARS, MERS, or COVID-19 SARS-CoV-2 is due to bacterial co-pathogenicity.

RELEVANCE to SARS Hong Kong outbreak in 2003: A doctor that treated SARS traveled to Hong Kong for a family wedding, infected like 16 people there, they returned home the world over.

RELEVANCE TO COVID-19 (disease) caused by SARS-CoV-2 (the virus): The Centers for Disease Control and Prevention Korea apparently identified a single case that participated in a gathering of the Shincheonji Church of Jesus, the Temple of the Tabernacle of the Testimony, this resulted in a jump of 70 cases. This superspreader has been identified as “Patient 31.”