Sunday, March 15, 2020

Pandemic! Not just a game for science nerds.

Unless you've been sequestered somewhere with no internet or newspapers or you've just awoke from a medically induced coma, you've heard there is a virus currently spreading across the planet. I'm adding my voice to the masses that are talking about it. But you love my stories. So, sit back and relax, I mean you're quarantined anyway right? Let me tell you a story about icebergs, exponential growth, flattening the curve, and what preparedness should really look like (hint: it doesn't include hoarding toilet paper). 

Before we dive in, let's learn a little bit. The virus that everybody is talking about right now is called SARS-CoV-2, or Severe Acute Respiratory Syndrome Coronavirus number 2. It causes an illness called COVID-19, or Coronavirus Disease 2019. SARS-CoV-2 and COVID-19 should not be referred to as "China Flu" or "Wuhan virus" or "Wu Flu." If the outlet you are getting your information from has used any of those terms, turn the channel or close your browser window; you are not receiving accurate, helpful COVID-19 information. 

Transmission electron microscope image of SARS-CoV-2; Credit: NIAID RML

There are a whole bunch of coronaviruses out there in the world that infect animals, including humans. There are now seven coronaviruses known to cause disease in humans. Four of them, called the endemic human coronaviruses, are among the viruses that cause the common cold. The other three, SARS-CoV (the first), MERS-CoV, and SARS-CoV-2 are considered highly pathogenic; they can cause severe illness and death. The highly pathogenic coronaviruses are most likely bat viruses that get passed to humans from a different animal. For SARS-CoV it was masked civet cats; for MERS-CoV it's dromedary camels. We're still determining the animal associated with SARS-CoV-2, but do we know the initial outbreak in Wuhan, China is heavily associated with live-animal markets.

The current outbreak of SARS-CoV-2 has been classified as a pandemic by the World Health Organization (WHO). A pandemic is an epidemic that has spread globally. The outbreak first emerged in late December 2019 when health care workers in Wuhan, China noted a marked increase in cases of pneumonia of unknown etiology. That is, pneumonia for which we don't know the cause. At 3:08pm CDT on March 15th, 2020 there are 162,687 cases of COVID-19 reported by cities, states, provinces, counties, and countries across the planet Earth. This is according to a dashboard created by the Johns Hopkins Centers for Systems Science and Engineering. This dashboard is interactive and just a lot of fun...if you're into that sort of thing. Which I am, a lot. The WHO also has a dashboard. What times we live in! Data nerds unite! 

Unfortunately, the COVID-19 numbers are just the tip the iceberg and since the reproductive number is greater than one in a naive population, we're seeing exponential growth. In some places the cumulative number of cases is doubling every day, but thankfully we can see that with measures such as social distancing and testing and isolation we have seen successes in slowing the spread. Okay, okay that was a lot of jargon. Let's learn what it all means.

Tip of the iceberg: 
The iceberg analogy is used frequently when discussing any disease, including infectious diseases. The tip of the iceberg reflects the cases we know about. They have tested positive or are highly suspicious due to illness contact with infected persons or from places where the transmission is occurring. The part of the iceberg we see above the water is much smaller in comparison to the part under the water. There are many people with COVID-19 that we don't know about. They are asymptomatic or have mild illness. Or they were very sick but didn't get tested due to lack of knowledge of care providers, lack of tests, lack of testing reagents, or stringent guidance for who should be tested early on and some places still using that guidance because the system is already overwhelmed.

Credit: Dr. Bhoj R Singh

Reproductive number:
In its purest form, the basic reproductive number (often written as R0 and spoken as R not, which is actually spelled "R naught," because the English language is ridiculous). Anyway. In its purest form, the basic reproductive number is the number of people that any one infected person can go on to infect over the life of their illness, assuming a population with no immunity. It's not necessarily a constant; it can change if the population develops immunity naturally or by vaccination. Or if public health measures slow the spread. During a pandemic like the one we are in now, an R-naught of greater than one means transmission is likely to occur and an R-naught less than one means transmission is less likely to occur. Current research suggests the R-naught for SARS-CoV-2 is greater than one and is, on average, between two and three. Each person with COVID-19 may infect 2-3 people over the course of their illness. Some will infect more; some will infect none.

Exponential growth:
Here's a quick and dirty explanation: case number increases by the number of itself, over time. 8, 16, 32, 64 rather than 4, 5, 6, 7, 8 which is linear. In an epidemic, an important figure related to this growth is called the epidemic doubling time; the time between the doubling of numbers, reported in days for COVID-19. The doubling time is a moving target and is reflective of the situation at any given time and in any given place. The doubling time in China right now is less than that outside of China; the outbreak in China is on the way down and most everywhere else is on the way up. Exponential growth is currently unfettered; it won't stop until everyone is infected, or we have prevention by vaccination or other means. Which brings us to the next point: flattening the curve, community mitigation, and social distancing.

Flattening the curve, community mitigation, and social distancing:
If we're all going to become infected with SARS-CoV-2, let's not all get sick at once. Can we agree? We (collectively as humans) do not have enough ventilators in the world for every person that needs one if they become severely ill with COVID-19 and for those who are already on ventilators due to influenza, cancer, trauma, lung fibrosis, and many other reasons. Let's use the example of panic-buying toilet paper. Each store has a pretty good stock of toilet paper in times of calm. You may have noted on occasion "Why on Earth are there two full rows of toilet paper at this store?" No? Just me? Okay, fine. Normally, even if say 10% of shoppers on any given day are buying toilet paper, there's plenty left on the shelves for the next day and up until the store can restock the shelves. But if 80% of shoppers buy toilet paper at the same time one day, the shelves will be bare, and the store will have to put out everything they have in the stock room. Then the next day, 80% of those shoppers buy toilet paper. Now the shelves are bare and there's nothing in the back. And I'm rationing the three rolls I have left and I had to buy a four pack of cubes of tissues instead the three pack of full packages I usually buy and allergy season has already started. You monsters! I digress. The same thing that will happen in our health care system if we all get sick at once. It's been estimated that around 15% of COVID-19 cases will have severe illness that requires hospitalization and 5% will need intensive care. A portion of the 80% with mild illness may also require hospitalization for pneumonia. We simply do not have enough beds, gloves, gowns, masks, ventilators, dialysis machines, etc. for everyone to get sick all at once. See the "Alert Kitty" below. Flattening the curve is not about making sure our numbers are low in total, it's about spreading them out over time. See the "Lazy Kitty." 

Credit: Dr. Anne Marie Darling

How do we become the lazy kitty? By community mitigation and social distancing. Communities should cancel all large gatherings such as parades, conferences, rallies, concerts, sporting events, schools, etc. You as an individual should avoid crowds, consider doing your grocery shopping online or go to the store when the parking lot is relatively empty. Avoid mass transit if possible or at least try to keep 6 feet between you and the people around you. Wash your hands often and always when you get home from being out in the world. Work from home if that's a possibility. Don't go to work or restaurants or grocery stores if you are sick, even with a cold. Keep your kids home if they are sick. Be a lazy kitty. Help out your elderly and disabled neighbors by offering to shop for them or set them up with a food delivery app if they have a smartphone or tablet. But don't you dare go over there if you are sick or have been exposed to COVID-19. This disease is very deadly for the elderly. Keep them safe.

What preparedness for COVID-19 should actually look like:
  • Make sure you have at least a two-week supply of your prescription and over the counter medications
  • Make sure you have a two-week supply of food and essentials like diapers and toilet paper. TWO WEEKS. Not a supply to last until the end of days. I don’t know how much toilet paper y’all go through in two weeks, but if it requires you to buy 72 rolls, I’m concerned.
  • Create a plan for your family in the event that your household is quarantined or curfews are enacted in your community. This is already happening in the U.S. Hoboken, New Jersey has instituted a curfew from 10pm to 5am, nightly.
And now we come to the portion of the program where we answer viewer questions. I asked my friends and family to give me their burning COVID-19 questions. I've tried to answer to the best of my abilities with the available information. Reminder that this virus is still very new and the answers I found now are subject to change as we learn more.

How long does illness with COVID-19 last? 
  • We don't know for sure. This is a new virus and researchers are working diligently to figure all of this out. 
  • This was the hardest one for me to find an answer for. I've looked at countless journal articles associated with the current outbreak, but almost none have data on time to recovery. What I did found out though is it turns out the "80% have mild illness" figure that we keep seeing out there includes mild pneumonia as well as what I would assume is actual mild illness. So, there's that. Definitely not just "the flu." 
  • I've seen data showing that if pneumonia develops, it's about a week after one starts to feel sick with cough and fever.
  • One case report of an individual with cough and fever who developed mild pneumonia around day 9 of illness that likely was only diagnosed because he was in the hospital (after testing positive, not because he was that sick). This is the first case reported in the U.S. He started to get better on around day 12, but at the time the article was released in late January, he was still hospitalized so we don't know exactly how long his illness lasted in total.
  • One case report of an individual sick with high fever, cough, and fatigue for three days and then recovered. This is a case in Germany that caught COVID-19 from an asymptomatic colleague. 
  • There is a report of 12-32 days from symptom onset to recovery. This is a tiny case study of four medical professionals who all developed mild pneumonia and were treated with antivirals.
  • I have seen modelling studies using a time to recovery of 21-22 days. These are studies that use available data to estimate how an epidemic will play out. And I do remember seeing this 21-day figure in an early report coming out of China, but I can't find the source again. It was looking at hospitalized patients and showed 21 days from onset to recovery and also 21 days from onset to death for those who died.
  • Bottom line: 
    • You'll be sicker longer if you develop pneumonia (be aware of difficulty breathing). 
    • Risk of severe illness requiring hospitalization or of death increases significantly with age over 60 or medical conditions like heart disease, high blood pressure, lung disease, cancer, diabetes, pregnancy (current or recent), kidney, or liver disease.
How long is an infected person contagious?
How does the virus spread (droplet vs airborne)?
  • All available evidence supports that the virus SARS-CoV-2 is spread person to person by respiratory droplets.
  • These respiratory droplets come out of your mouth and nose when you speak or sing or simply breathe and they hang out in the air a little while and then fall. When you sneeze or cough, you expel the droplets much farther. See this great Science Friday video of a sneeze! This is why we keep telling you to sneeze into your sleeve.

  • The virus does not appear to persist in the air like airborne viruses such as the virus that causes measles. That virus is also expelled when coughing or sneezing, but it can remain in the air for up to two hours in its infectious state. A person with measles may sneeze in an elevator and then leave. An hour later, an unvaccinated person enters the elevator and breathes. They are now infected and may go on to develop symptoms. An hour later! There isn't any evidence to support that the virus that causes COVID-19 is spread this way.  
  • Evidence does suggest, however, that the virus can be transmitted by touching inanimate objects or surfaces contaminated with SARS-CoV-2 and then touching your mouth, eyes, or nose.
How long does SARS-CoV-2 live on surfaces?
  • Researchers looked at available data for human coronaviruses (the ones that cause the common cold), the first SARS-CoV, MERS-CoV, and other similar animal viruses. What they found is that human coronaviruses can remain infectious on surfaces for up to 9 days. This varies widely depending on the type of surface (hard vs soft, glass vs metal) and other conditions such as humidity, temperature, and how much virus is present. 
  • These studies are done in laboratories where conditions can be controlled, which is not the case out in the real world.  
  • Don't panic! The studies also show that these viruses are readily removed from surfaces using appropriate disinfectants for the recommended amount of time. More on that next.
What about those wipes by the carts at Target and other stores?
  • Disinfectant wipes and sprays:
  • Check the label where it lists the bacteria, fungi, and viruses that it is active against. Look for human coronavirus or other similar viruses or viruses that are harder to kill than coronaviruses (like Norovirus and other calciviruses). 
  • The EPA has a wonderful list that you can check your product against.
    • Check the label for the EPA Registration number, or EPA Reg. No. and enter that number into the search bar. If your product shows up, it can be used to disinfect SARS-CoV-2. 
    • Follow the instructions for the virus listed in the EPA table and on the label of your product. There will be a specific contact time. This is the amount of time the surface must remain wet in order for disinfection to occur
    • Some products have a very long contact time which can be difficult to achieve. Others, the contact time may only be a few minutes. 
  • Wipes by the carts at Target and other stores:
    • Specifically the blue cart wipes at Target stores in Minnesota: I got lucky the other day at my Target in that I saw a roll of the blue wipes at an empty register waiting to be placed in the cart wipe container (that doesn't tell you what they are or how to use them). The active ingredient of those wipes is 0.12% benzalkonium chloride and that is not on the EPA list of disinfectants to use against SARS-CoV-2. 
    • At other stores or Target if the wipes aren’t blue, check to see if the wipe's product name is on the container. If so, search for it on the EPA website. If not, try to find a manager and ask for the name of the product or the EPA registration number.
    • Consider this though: Will you wait 4 minutes, ensuring the cart handrail remains wet for the whole 4 minutes, before going about your shopping? Did the person before you? Or behind you?  
    • I'm not saying don't use the wipes, they will clean off the boogers and potential fecal matter left by the toddler that was sitting there before you. But they're not really for true disinfection.
What of Africa and other places with low numbers? Why no spread of COVID-19?
  • Wait for it...
    • In Africa, there are outbreaks in South Africa and Algeria and five more countries reported cases on Saturday 3/14/2020
    • In the U.S., as of 4:00pm CDT on 3/15/2020 every state except West Virginia has reported at least one case.
    • Remember the iceberg analogy. 
  • Depending on the capacity to test (kits, reagents, trained personnel), it may be that only the sickest or highest risk or those with obvious links to known cases are being tested.
  • Low numbers do not necessarily mean that there aren’t any cases or that there isn’t any spread.
Why weren't we more prepared in the U.S.?
  • Funding for public health isn't usually a priority when there are so many programs competing for dollars. 
    • Research from the American Public Health Association shows national investment in public health capabilities needs to be around $32 per person and we are, as of October 2019, spending $19 per person.
    • State and local health departments are underfunded and often working with bare bones staffing; this includes public health laboratories.
  • State public health laboratories were required to use the CDC-developed assay and until those labs were up and running, only CDC was doing testing for the entire country.
    • Only those with strong epidemiological connections to the outbreak in China and symptoms of illness were being tested early on. 
    • This no doubt allowed COVID-19 to spread silently. Mild illness usually does not lead one to a doctor's office or hospital. 
    • The first roll out of the test kits included faulty reagents that set testing back by a couple of weeks.
  • Dr. Anthony Fauci said, "The system is not really geared to what we need right now. That's a failing. Let's admit it."
Can I get it from a dog? Do dogs or other pets get infected or spread COVID-19?
  • You may have heard of the dog in Hong Kong that tested positive for COVID-19. The dog's owner had COVID-19 and to be honest, I don't really know why the dog was tested. The original report is behind a paywall. All other reports I've read on veterinary sites state that the dog did not have symptoms of illness.
  • There is no current evidence to suggest that pets play an important role in the spread of COVID-19.
    • However, if you have COVID-19 the recommendation is that someone else care for your pet or service animal. 
    • If that isn't possible, then wash your hands before handling your pet or service animal and avoid snuggling and kissing. 
    • YEAH RIGHT. Sorry Maxdog, if I get COVID-19 you're coming down with me!
Maxdog aka Maxwell Copernicus aka the Best Chihuahua Ever

What am I doing to be safe at work and other places?
  • My coworkers and I in the public health lab and in laboratories all over the world take precautions every day, regardless of COVID-19 or any other infectious disease.
  • We wear gloves, lab coats, and eye protection when in the lab.
  • We only open direct patient samples in a biosafety cabinet that is working properly to keep the air inside the hood.
  • We wash our hands frequently while working in the lab and every time we leave the lab. 
  • I am washing my hands when I come home from being out in the world. I'm not currently doing much else different because, as an introvert, I've been social distancing my whole life! And I have allergies so not touching my face is just not an option. All kidding aside, I do have tickets to a drag show in a couple weeks and I'm keeping a close eye on how things play out. I will follow the guidance of the Minnesota Department of Health and the CDC.
Should I travel?
  • I can't answer this for you. You have to take a number of factors into account.
  • My advice is to pay attention to the CDC's travel website in general, and the COVID-19 page specifically. They have recommendations for international travel, cruises, frequently asked questions, and things to consider for travel within the U.S.
And last, but certainly not least:
Can I catch COVID-19 while having sex in a hot tub?
  • I know this was a cheeky question, but I'm answering it anyway!
  • Short answer: It depends! Does your partner have COVID-19? Then the answer is yes, you can catch COVID-19 while having sex in a hot tub. Sorry.
  • You're more likely to get "hot tub rash" though, which is a skin infection caused by Pseudomonas aeruginosa. Yuck.
Y'all. I think this is the longest post I've ever done! I mean, it is a pandemic after all, so I guess it's warranted. Let's recap a few key points, shall we?

1. SARS-CoV-2 is the virus that causes an illness called COVID-19.
2. COVID-19 has spread globally, and the WHO has officially called it a pandemic.
3. The virus spreads easily from person to person through close contact and also from touching contaminated surfaces and then touching your mouth, nose, or eyes.
4. Most people who catch COVID-19 will have fever and cough. Some people develop mild pneumonia. Others get very sick and need to be hospitalized. People are dying, particularly the elderly and those with medical conditions.
5. Older age or medical conditions such as heart disease, high blood pressure, lung disease, cancer, diabetes, pregnancy (current or recent), kidney, or liver disease significantly increases your risk of severe illness requiring hospitalization or of death.
6. Nationally and globally, our health care system cannot handle it if we all get sick at once, so we need to practice social distancing.
7. Check on your elderly and disabled neighbors.
8. Wash your hands.
9. Don't hoard toilet paper. Or cold medicine. Or bottled water. Or tissues.
10. Don't have sex in a hot tub. Unless it's your personal hot tub. That no one else ever uses. Then maybe.

Be safe out there. 
World Health Organization:
Centers for Disease Control and Prevention: