KNOW YOURSELF, KNOW YOUR ENEMY...AND WE COULD WIN A HUNDRED (COVID-19) BATTLES WITHOUT LOSS

Remdesivir, mRNA vaccines, the catastrophic COVID-19 test kit, and our very own immune system

DISCLAIMER: For the past couple of entries, I've done my best to shift the focus of COVID-19 information away from medicalized solutions like drugs and vaccines for a few reasons:

1) If we invested as much financial and human capital into our public health systems and healthcare infrastructure as we invest in our military, we wouldn't be in the mess that we are in today. This TED talk by Bill Gates from 5 years ago eerily predicts the calamity of the COVID-19 pandemic, given the health infrastructure at the time. We weren't ready then and we are seeing that we are still grossly underprepared now. We need to invest in global health equity and stronger health systems.

2) The science behind the tests and drugs and vaccines being developed aren't incredibly nuanced for our day and age. We've had the privilege of seeing various disease outbreaks that have equipped us with advanced knowledge of the biology of these pathogens. We can adjust the applications of our knowledge but we have a foundation to build off of. The issue we face right now is how we regulate this information, and by we, I mean Big Pharma and the governments that they're in bed with. Reports from today found that the President of the United States tried to lure biotech into developing an exclusively American COVID-19 vaccine. (Again, nationalism isn't going to save us.) At least for now, Germany's CureVac is still free to work on developing the vaccine, free from capitalist limitations. As we learned from yesterday's toilet paper segment on price gouging, why would we do this knowing that the world is suffering?

3) If we focus too much on the seemingly miraculous pills and potions, we lose sight of greater concerns of accessibility. The reality is that even when we find a cure or a vaccine, we can only roll out so much at a time. How do we decide who gets dibs? Chances are that disenfranchised people in our communities and low-income countries who are disproportionately affected by the pandemic aren't first priority. This is why it is so important to be mindful of the social distancing measures. Prevention is the best kind of medicine so we should emphasize the need to devote our resources to addressing transmission instead of a cure.

Now that we have established all that, we can cautiously dip our toes into the ~science~ behind the tests, vaccines, etc. There is a lot of information in the media about all this and I hope that understanding some of the basics of these fancy treatments will help you manage your expectations.

Let's start with what we have to work with right now: the COVID-19 test.

Being a student at UNC-Chapel Hill (yes, I'm plugging my school) means that I have the privilege of being on the same campus as some of the world's top researchers. Many of them have been working on developing tests based on the WHO's protocol since mid-January, but are facing delays waiting on authorization from the FDA, dealing with the lengthy government approval process, and not receiving information about how much labs will be reimbursed for conducting research. As someone who goes through multiple pipette tip boxes and tubes of antibodies on a weekly basis, I can say that even simple sequencing protocols add up quickly.

Wait, but South Korea has tested so many people? How is that possible? Why is there such a big difference with the US? America really dun goofed again...

The graphic below was done by an artist who beautifully illustrates various data sets.

See, the WHO already had test guidelines available based on international efforts. Here is the chain of events: Chinese scientists uploaded a copy of the virus's genome (A-C-U-Gs) online on January 10 so that virologists around the world could start working on developing a test. On January 21, Christian Drosten's team in Berlin, who also discovered the original 2003 SARS virus, submitted the first protocol for testing for SARS-CoV-2. This protocol would become the basis of the WHO's protocol. Soon after, the US declared that it had developed its own protocols and refused to use the non-American ones.

There is a long convoluted story of how federal restrictions on testing further delayed the ability to devise a good test but in essence, the CDC distributed tests that were faulty. A reagent in the kits that were sent out in the first week of February was found to be contaminated and resulted in a number of false positives. This means that a number of people who may not have been infected came up positive. Despite this, if you read into the article, it is clear that the faulty test was an issue but the implosion of the US economy and healthcare system during critical weeks of action actually falls on the hands of its Presidential Office.

Politics aside, what actually went wrong and how does the test work? The test relies on the bread and butter of any wet lab - polymerase chain reaction testing (PCR). This stuff isn't super-complex (ahem, Mr. President it's pretty basic science) - I learned about it in 10th grade and have been performing it since the summer after my Freshman year of college.

In PCR, you essentially follow 3 steps: 1) Breaking the two strands of DNA apart to expose the nucleotide sequence (denaturation). 2) Short sequences that we make called "primers" bind to the DNA sequence (annealing). 3) A polymerase enzyme builds off the primer and makes a complementary sequence to the DNA. The idea is that you want to make many many many copies of the sequence (amplify them) so that you can screen for the presence of the virus.

The WHO's protocol specifies the NAAT (nucleic acid amplification test) of real-time reverse transcription PCR (rRT-PCR) for COVID-19 testing. This is because the virus has RNA, while the human samples are made of DNA and we have to build RNA from DNA. Put simply, we use a different enzyme than in normal PCR but the main point of amplifying the genetic material from the sample to compare to the known COVID-19 virus genes remains. The current COVID-19 tests screen for 2 genes and if both are detected then the test is deemed positive.

COVID-19 has been identified as a lower-respiratory disease so I believe they swab the naso-oropharyngeal airway (they poke a long Q-tip down your throat at the drive-thrus) and send the sample to be processed. The lab then takes the human samples and prepares a master mix in a little tube containing nucleotides, primers, and water to which the sample is added. They then stick it in a fancy machine that changes the temperature over time, then they pull out the solution and run it on a gel beside an indicator that shows what a sample with both genes looks like. If the processed sample and the known positive sample match, then you know that person has COVID-19.

EXCEPT, in the case of a false positive which is what happened with the CDC's tests. The thing is that PCR can be finicky and is very susceptible to contamination (flashback to the summers spent in a Micro/Molecular lab where I learned that the hard way). A good way to test for faults in the reagents is to also run a negative control with your samples. This would be a sample that has the master mix but none of the contents from the swab, was run in the machine with the other samples, and run on the same gel. In theory, without the swab, there should be no genes showing up. If there are, you know there is something funky in the reagents. Ultimately, nothing too complicated but we need to reduce the government barriers that are delaying the testing.

Now, what about that vaccine?

Earlier today, the NIH released a statement about clinical trials for the mRNA-1273 vaccine starting in Seattle. It uses mRNA, which is a molecule that provides instructions for what amino acid-based proteins the cell needs to make. This vaccine's mRNA prompts human cells to express harmless virus protein spikes on their surface which are supposed to elicit an immune response. The idea is that your immune cells will recognize the spikes as "non-self" threats and launch molecular warfare to get rid of it - antibodies!

Remember how we talked about viral spikes in the first blog? Y-shaped antibodies produced by your B cells will bind to those viral spikes. The thing is, that your body doesn't inherently have antibodies that readily attack a virus it's never seen before - it develops them after your body fights off infection. Hence, introducing the virus structure to your immune cells without the risk of actual virus pathogenicity (no genetic information for viral reproduction) primes your immune system so that if you do contract COVID-19, your B cells are prepared to quickly launch antibodies and clear the virus. Immune cells in your body, macrophages, will see these bundles of antibodies surrounding the viruses and will engulf and digest them.

Currently, they are testing to see if this vaccine will be effective in priming the immune response. Will the body make antibodies that will be effective against an actual COVID-19 infection? Is there any potential that it could hijack our macrophages or other immune cells? We are months out from the answers to these questions and more so even if we have a plan devised, manage your expectations about the vaccine being deployed too soon.

And finally, let's briefly touch on the news of an effective antiviral for COVID-19: remdesivir.

(Yes, another school plug.)

Dr. Ralph Baric and his lab the Gillings School of Global Public Health are testing a broad-spectrum intravenous antiviral drug. The great thing about remdesivir is that it may be effective against viruses other than SARS-CoV-19. Perhaps ones we have yet to encounter.

We've actually known about this basis of this drug for about a decade now. Descendants of the original compound, 3a, have been used by Gilead Sciences to develop remdesivir. It was developed as a general antiviral candidate (broad-spectrum). It was even proposed as a treatment for Ebola, but was found less effective in comparison to other treatments. So far, we've seen positive results when tested on other coronaviruses like MERS and SARS, but we are just beginning the clinical trials (literally just today).

The drug works on blocking the virus from multiplying in infected animals. Like we've talked about before, a virus needs RNA polymerase in order to make more copies of itself so if we can stop this enzyme, we can stop the infection. Remdesivir acts by mimicking the appearance of one of the RNA nucleotides, adenosine, so that the RNA polymerase adds it to the elongating chain instead of adenosine and this terminates the chain of genetic replication of the virus. The genome never gets completed and the virus cannot replicate.

If we're really getting into the nitty-gritty of molecular science, the reason why the chain gets capped is because of a reactive hydroxyl group (hello again O-Chem). As we know from grade 10 science (wow it just keeps coming up), DNA is double-stranded and antiparallel. We build from 5' to 3' all the time and in order to continue to build upon the chain, we need a hydroxyl group on the 3' end of the chain. This 3' hydroxyl group performs a nucleophilic attack on the phosphates of the nucleotide and we continue to build the chain with each successive nucleotide with its 3' hydroxyl. Remdesivir is an analog of the base but without the 3' hydroxyl so it gets added to the chain, but RNA polymerase cannot detect where to continue adding bases without the -OH. We have seen this type of drug application multiple times before, particularly, in the development of HIV antivirals. (Wow, Dr. Peifer and Dr. Duronio I hope that if you ever read this, you're proud.)

Despite some of these successes, COVID-19 is not Ebola and is not HIV so we can be hopeful, but hopeful with a healthy degree of skepticism.

So now you know a little more. But again, please bear in mind that these magic bullets aren't the perfect solution for several reasons. There are a lot of reasons we need to zoom out and look at the bigger picture of finding an end to this pandemic. Beyond the molecular scope of our therapies, we must dig deep and approach COVID-19 with a biomedical lens through stronger global public health systems that prioritize global health equity.

STRAINING THE FABRIC OF OUR SOCIETY - TOILET PAPER

Why you may have seen fights break out at Costco and why this neglect of social distancing actually fairs worse for your health

A good amount of the later part of this blog was inspired by a thread on the importance of social distancing this week. Check it out here.

In the past 24 hours, I've received a number of suggestions for potential topics for today. However, upon receiving three separate messages:

"Why are people mass buying toilet paper?"

"Why are people selling out of toilet paper but not food?"

"TF is up with the toilet paper (panic - is overreacting more harmful or helpful?)"

...I realize that the people want toilet paper and they want toilet paper now.

To answer the question of "why" people are panic buying toilet paper, there are a number of explanations we can look at.

From an economic standpoint, the mass closure of facilities, certain services, etc. has left a lot of people scrambling to find another source of income. In the United States, there has been a lot of back and forth on the issue of paid sick leave packages. COVID-19 is exposing the fact that the very fabric that holds America together is made up of low-wage laborers who are not afforded the ability to take sick leave when needed. As of Friday evening, an agreement was reached with the White House on legislation that would allow some workers affected by COVID-19 to take up to 10 days of paid sick leave at partial public expense. A large number of low-wage workers who live paycheck to paycheck are currently in a very vulnerable position with no definitive end. Not that this applies to everyone, but mass buying high-demand items in the midst of this crisis and price gouging have become a way of obtaining income. Even Canadians (some of the most courteous people on the planet...I mean...am I not just the nicest person you know? Haha...jk...unless...) have been guilty of exploiting the scarcity of toilet paper, hand sanitizer, Lysol wipes, and a number of other crisis items.

The social system itself has failed the people and put many in a position of desperation. However, hoarding and price-gouging make the situation worse for everyone. If the vast majority of the population doesn't have the means to look after themselves and their hygiene, they cannot contribute to the greater collective effort of preventing disease.

From a hygiene perspective, this Time article suggests that the urge to stockpile toilet paper goes back to the fundamentals of humanity: we eat and sleep and poop. From our days of potty training to fully functioning adults, toilet paper has always been there. Hence, it is programmed in our system to actively seek out toilet paper as a product necessary to fulfill our fundamental needs. (Obviously, we've moved on from plucking leaves from the forest. Mankind has shown its strong preference for bulldozing natural habitats.)

If food is also essential to our survival, why toilet paper shortages and not food? If you've been to a Walmart in the past few days, you know that shelves that once displayed bread, cereals, grains, ramen, and other low-priced non-perishables are also barren. However, there has been a little more hysteria over hoarding toilet paper. For starters, food has a variety of substitutes. If you can't find the jar of Nutella you need, chances are there is something else you're willing to consume somewhere in the store. On the other hand, there is no substitute for toilet paper. Well, I suppose you could opt for baby wipes or saw a roll of paper towels in half, but it isn't quite the same. There is also a degree of psychological comfort that stems from seeing the barren space on your shelf occupied by several bulky rolls of toilet paper instead of a small avocado.

Digging deeper into some of the psychology behind panic buying, we should investigate the "zero risk bias". Over the past few weeks, people have been asked to put a very abrupt pause on their lives. Schools have closed, travel restrictions have pressured people to flee travel destinations to return home, employees are transitioning to working-from-home, and those who do not have that option may be left jobless. The world has been told to cancel plans and remain indoors indefinitely as there are several factors that elevate exposure risk.

Are you immunocompromised? Are you at risk of occupational exposure? Have you traveled to regions with high rates of infection? Are you stressed, thus straining your immune system? Have you been present at large public congregations such as the toilet paper sale version of Black Friday at the Walmart down the street?

This is where the zero risk bias comes in. With multiple factors that put us at risk, we are irrationally disposed to eliminate ONE category of risk as opposed to working on reducing EACH category of risk. You read that correctly. We would rather fix one problem and ignore the potential to resolve everything else. Eliminating one risk entirely seems like we are eliminating a greater proportion of our mental strain. We disregard the quantitative validity of the situation to focus on stepping back into our comfort zones. Therefore, we are biased toward the appealing but less effective option.

We have established that people would rather eliminate the risk of being "unclean" during potential quarantine by ensuring they have an excessively sufficient supply of toilet paper. This bias occurs at the expense of abiding by the recommended social distancing orders. But here is why keeping your distance is particularly important right now...

As we are all probably aware by now, SARS-CoV-19 can be carried by an asymptomatic individual for about 14 days. Recent reports state that the median incubation period of COVID-19 is 5 days and that symptoms are not present in over 97% of cases until 12 days after infection. In North America, we are at the very beginning of this incubation and transmission-risk period. Testing is particularly limited at the moment (I know the WHO has screwed up in the past but I don't know why the US didn't take the damn test kits!!!), and people aren't being tested unless they are appropriately symptomatic (see below) which means that as I blog there is currently the highest number of infected people who don't even know that they're infected walking around.

Even if you didn't travel to high-risk areas or knowingly come into contact with an infected individual, chances are that you contracted it from someone who wasn't coughing and feverish but was infected (ahem, Rudy Gobert). By the time people who were infectious but asymptomatic develop symptoms realize that they were infected in about a week, well, they would have already infected everyone who did not isolate themselves this week. Even without symptoms, people who unknowingly have COVID-19 are contagious the entire time between when they become infected until they develop a fever.

The CDC has advised that people cancel or postpone events with over 50 people for 8 weeks. Yes, this seems a bit extreme (and I am currently freaking out about the likelihood of not being able to walk in my college graduation ceremony in front of my family), but you don't have to lock yourself up for 8 weeks. Do the math. In about a week or two when everyone who was infected starts to present symptoms, then you definitively know who to avoid. And if you were good about keeping isolated during these critical 14 days, then you know it's fairly safe to slowly start to see people you know are not symptomatic and could not potentially be carrying the infection (because they too practiced social distancing).

As much as authorities can bar you from campus (ugh, I just wanted to ease my mind with PCR in my lab), gardens (rip Duke Garden senior grad photos), bars (I didn't want to celebrate my 22nd birthday anyway), if you linger in the boba shops it is OVER for us all! We must be accountable for our own health, and more importantly, the health of the vulnerable, if we want to have any shot at flattening the curve. Otherwise, before we know it, instead of toilet paper shortages, society will suffer a shortage of ventilators and ICU beds.

As the article referenced above states, we need to pressure officials to close ALL schools and public spaces and cancel public events for the time being. Sleepovers, hangouts, and parties need to be put on hold if there is any risk of potential infection. I know FOMO sucks, but please don't be that friend that flies back from Italy and shows up at the apartment of people who have tried to adhere to social distancing orders. Get some fresh air but keep your distance. Minimize the amount of time you spend in enclosed public spaces like stores and restaurants - make food at home but order take-out meals instead of eating-in if you can't cook (and tip well!). And if you are symptomatic, even if it is "just the cold and not COVID-19", please stay home.

Note that in especially small and densely populated areas, like college towns, the infection is able to spread rapidly across the entire population. Social distancing has a significant impact on mitigating disease transmission.

Click this link to see the source of the graphic below and other incredible illustrations of the COVID-19 situation.

So to answer the question about overreacting: underreacting poses catastrophic risks far greater than overreacting. Yes, measures are currently rather extreme, but the hope is that people abide by them so that we don't end up with an overburdened healthcare system and a tragically high number of completely preventable deaths. This does NOT mean you should hoard toilet paper - quite the opposite really. Instead, try to understand why you feel the panic about the things you cannot control and choose to focus on the things that you can control. As small as it seems, the choice to practice social distancing for even one day makes a huge impact.

Only if we follow through on our promises to protect the greater good of society, will we be able to see the peak and decline of this outbreak. As of this update from the past hour, the US currently has over 3000 cases of COVID-19. The New York Times predicts that the infections in the US could peak at 9.4 million without interventions. But if we abide by aggressive public health interventions starting TODAY, there is hope that the peak can fall to 3 million.

For the time being, take advantage of actually using social media to be social. I've sincerely enjoyed reconnecting with new and old friends over the past few days thanks to video chat. (There is really no point in trying to flex vacation photos featuring your envy-worthy abs. We all know that the airline industry is currently dead and nobody is really flying.)

In closing, I want to remind everyone to take this time to reflect on their own privileges. I know that feeling restricted and isolated is far from ideal, but consider everything that you have that others do not at this time. If you have the ability to stay home from school or work, consider how fortunate you are to not worry about where the next paycheck or meal is coming from. If you had to book an expensive flight back into the US, be thankful that you have the resources and legal protection to get you home. If you are upset about not being able to go out to restaurants and events freely, think about how lucky you are to have an immune system that is strong enough to enable you to even consider leaving your apartment.

Capitalism if fragile. The system is broken. Current leadership is failing and the fate of the world rests in the hands of civil society. Maybe this is a disaster. Or perhaps this is an opportunity for us to rise to the occasion in the small and simple ways that we can.

You care capable. What you do next? That's up to you.

THE SOAP BAR IS MIGHTIER THAN THE SWORD

Soap vs hand sanitizer...pero, por qué no los dos?

So last time on the Quarantine Chronicles, we talked a little bit about the structure of SARS-CoV-19 and how that allows the virus to jump between different species. Considering how people have been hoarding Purell like it is the end-of-days (and I assure you that although we have lost every major sports league season, for the time being, we will survive), I think it's worth digging into the question of soap vs hand sanitizer, and other disinfectants.

Storytime: flashback to my Sophomore year of college. I sat in the front row of my Intro to Medical Microbiology class (shoutout to Dr. Cramer who in part inspired this blog) and watched one of my closest friends wipe down a chair with a Lysol wipe for 10 minutes in front of the lecture hall of some 200 undergrads. The point she was trying to make (thanks Ryan for being a trooper!), was that although disinfecting wipes claim to "eliminate 99.99% of viruses and bacteria", they are only effective if used properly. And unless you wipe down your surfaces for 10 minutes, I can guarantee that you have been doing it wrong. Both Dr. Cramer and the Centers for Disease Control and Prevention stated that "disinfection usually requires that the product remains on the surface for a certain period of time"...or as illustrated in lecture, that the surface must be visibly wet for 10 whole minutes. If you read the fine print of your Lysol wipes, the label even specifies 4 minutes. Do it! I dare you!

The length of this video is longer than you wipe down your surfaces and it isn't even enough. Also, hello Moonlight Dance Crew hoodie!

The active ingredient in these wipes are quaternary ammonium compounds ("quats" for short) which have been found to irritate the skin, lungs, and negatively affect reproductive health. They are effective when used properly, but don't go wiping your hands with them out of hysteria. Wipe down surfaces (ahem, like your grimy phone) as directed and rinse off the residue from your skin to prevent irritation.

As mentioned before, fomites aren't our biggest concern for COVID-19. Good old 10th-grade science taught us that similar molecules interact more strongly with each other than dissimilar ones. Example: the phospholipid bilayer! Polar heads would rather assemble together and tuck away the hydrophobic tails.

A Twitter thread by Dr. Palli Thordarson of the UNSW Sydney School of Chemistry does a great job of digging into the ~supramolecular chemistry~ behind this debate with respect to responding to COVID-19.

SARS-CoV-19 is held together by hydrogen bonds and hydrophilic interactions and when it interacts with similar surfaces like fabric and skin, hydrogen bonds can form between these surfaces and the virus. When the virus interacts with more dissimilar surfaces like porcelain or steel, the virus does not form those bonds and remains stable for some time on those surfaces. If someone coughs on their hand, the virus binds to the skin's surface and when people shake hands then the viruses transfers to another person. Hence, person-to-person transmission is the biggest issue, so let's talk about getting our hands dirty and how to appropriately clean them.

For starters, it is important to note that the type of virus also determines its ability to be infectious and what agents we should use to effectively destroy them. The general anatomy of a virus includes nucleic acids that make up the genes of the virus (DNA or RNA) and a protein capsid that holds the nucleic acids. Building on this basic anatomy, viruses can either be naked (just the genetic material and the protein coat) or enveloped by a lipid bilayer. This seemingly simple difference has a rather significant impact on the virus' ability to survive. Naked viruses are more resistant to disinfectants because the outermost protein capsid can withstand detergents and mechanical damage. Whereas lucky for us (I mean, comparably), the COVID-19 virus is enveloped. This outer lipid layer is much more susceptible to detergents and mechanical damage. If we can destroy this outer layer, then the virus is not infectious anymore.

Note: The image below and information supporting the text above can be referenced to McGraw-Hill.

This interference with the virus' lipid envelope is how alcohol and alcohol-based hand sanitizers work on the virus. Again, no envelope = no infection. Hand sanitizers that are more than 60% alcohol will effectively kill the virus. In this case, a passing percentage does the trick. Before you try to steal your lab's giant container of 100% alcohol, know that water is necessary to catalyze the reaction that allows alcohol to denature the virus' structure. AND, before you try to make your own home-made concoction of hand sanitizer with the leftover vodka from the Spring Break party that never happened because of quarantines...know that 80 proof vodka is only 40% alcohol and will NOT save you from COVID-19. (Don't drink it either! The details of that are an entire post on its own.)

Going back to the point made earlier, surfaces need to remain wet for a period of time in order for the necessary molecular reactions to occur. Alcohol is volatile and evaporates quickly, which also poses another challenge for disinfecting. Additionally, depending on the family of the virus, concentrations between 60% and 90% alcohol will be specific to different families.

So, hand sanitizers are effective and a great idea when you can't get to a sink. However, hand washing WITH SOAP (none of that 3-second rinse after you use the toilet stuff!) is more effective so do so as often as you can.

What is so great about soap? Let's revisit the reference to similar molecules interacting from above.

Amphiphiles in soap are fat-like substances that are structurally similar to the lipids in the viral envelope. These molecules can compete with the lipids in the virus membrane and also outcompetes the interactions between the virus and the skin so the virus cannot attach to the organic surface. Alcohol is capable of dissolving the viral lipid membrane at the appropriate concentration but is overall not as effective as soap in disrupting these molecular interactions.

So there you have it! As Dr. Thordarson writes, COVID-19 is a "nano-sized grease ball" and regardless of the size of the viral particles, soap is incredibly effective in pulling-apart these grease balls.

In summary:

Lysol wipes with their fancy "quats" kill viruses but only when used properly and they should not be used on skin.

Alcohol and alcohol-based hand sanitizers are great for when you can't get to a sink but can fail if the concentration is too low (or high), if your hands are greasy, and if you get sweaty palms. (Don't go on that awkward sweat-inducing date with someone who may be infected.)

Soap is essentially a fail-safe option, provided that you scrub into the nooks and crannies of your skin for 20 seconds (even if it isn't specifically antibacterial!).

I know that the world feels like it's coming to an end and that the current lack of an available vaccine or antiviral medication seems discouraging. However, the science behind public health messaging pushing hand-washing doesn't lie.

Keep calm, and wash on (with soap)!