My Coronavirus Concerns

Since December I’ve watched with wide, open eyes the spread of the coronavirus. I’ve tried to stay away from the news media for the most part except for print to keep track of numbers of sick and deaths in given areas. This is going to be way outside what I generally talk about but there’s so much going on it seems worth giving this a deep dive.

My area of expertise is in disease outbreaks. I have a Masters of Public Health in Epidemiology (the study of epidemics) and my area of expertise is in disease outbreaks, prediction, and prevention. Movies like Outbreak and Contagion make me happy. Books like The Hot Zone and Tom Clancy’s Executive Orders are enjoyable to me on a deeply academic level. I do deeply enjoy studying disease epidemics.

If you want my take away message scroll all the way to the bottom.

About a decade ago I moved my area of expertise from human disease outbreaks to plant-based outbreaks. Many of the fundamentals are the exact same. The advanced techniques I learned as human prediction methodology I now apply to plant based systems, helping farmers maximize their profits as thin as those profits may be. I firmly believe food security is one of the most important risks any economy faces, which is why I made the move that I did.

2019-nCoV-CDC-23312 without background.png
Illustration of a coronavirus. The red colored blobs that look like towers protruding from the surface are proteins that are used to identify the uniqueness of each virus. These proteins are also used to create vaccines.

I’ve watched China during the SARS and the later MERS outbreaks in the Middle East when I was still a student and saw little fanfare. The disease didn’t spread extremely rapidly. It peaked rather quickly and the US wasn’t really hit too hard. This is different, very different.

SARS, MERS, and COVID-19 (this most recent coronavirus) all belong to a family of viruses known as Coronaviridae. Coronavirus outbreaks are common and include the ‘common cold’ type of symptoms. Symptoms generally include coughing, sneezing, similar to a general respiratory viral infection. Humans get infected from human to human contact and more infrequently human to animal contact, more on that later.

Coronaviruses are an RNA virus which is important when we look at replication and speed of mutation. RNA viruses generally have a faster mutation rate than DNA viruses because RNA viruses lack a checking mechanism DNA viruses contain when their nucleic acid is replicated.

Coronaviruses are commonly found in birds and bats. It’s not always lethal in those groups and they act as a reservoir. So when bush meat is consumed or wild animals infected with these viruses are consumed, sometime that virus can hop from one species to another and we get outbreaks of novel pathogens. The occurrence of species to species jumping is rare but when it happens the new host population has no immunity to it, the immune system has never seen it before so it takes longer to mount a resistance to it meaning it tends to spread quickly and be more severe. People eat wild caught game all the time on a daily basis and these jumps occur every few years. Looking at the entire picture they are very rare.


I can absolutely understand why people are worried. It’s a very healthy reaction. This virus spreads via the air, spray droplets, general daily contact. It’s a scary thing to know there is a pathogen going around in the world you can’t see and don’t know if you’ve been infected. I absolutely get it. If I lived in a major city like New York or LA, I’d likely be more worried and take more precautions than I do living where I live which is rural, doesn’t have a major airport in the state and doesn’t have international tourism to speak of.

This new virus is appears to be more contagious that SARS. We’re still trying to figure out how deadly it is or it’s case-fatality rate. If you become sick, what percentage of people die. Right now, a good estimate is around 3%. MERS and SARS had much higher case-fatality rates which decreased the spread oddly enough. It has been as high as 12% in Iran but that number has dropped to 3%. In China, it’s nearer 3.5%. In full honesty, I don’t trust the Chinese statistics though. China has often falsified information that makes the country look bad and faked official state documents for appearance (watch the Chinese gymnastics team, they’re not all 16 and previous gymnasts have admitted it too). This happened during the SARS outbreak; at the time China relied heavily on tourism for their economic growth beside manufacturing.

The state department of the US has issued travel warnings to mainland China, South Korea, Iran and now Italy. Japan will likely be next here shortly as the State Department believes travelers should reconsider their travel.

If you become sick, you were exposed 5-7 days ago. That’s pretty long, the seasonal flu is about half that. The longer incubation period (time between contracting the virus to showing symptoms) means that’s another several days someone is possibly infecting people without showing symptoms, taking precautions, staying at home. The current quarantine period is 14 day, which might not be enough after I watched someone cough all over their child after going through that process. As an epidemiologist that was horrifying and that gentleman should have immediately been taken back to quarantine and tested for the virus. Epic levels of disturbing going on.

Source: NYTimes

The above graphic has the case-fatality running up and down. Higher on the list = more likely to kill. Across the bottom is the R0 (R null or R not). This value is the number of people each infected person infects, which equates to how quickly does it spread. Meales has an insane R0 or 15. For each person infected they can infect 15 people, it spread super fast during outbreaks which is we developed the MMR (Meales, Mumps, Rubella) vaccine. The current coronavirus has an R0 between 2 and 4, we’re not 100% sure yet. Things are changing too fast to pin it down accurately. The Spanish Flu had an R0 of 2.1. The case-fatality rate of Spanish Flu was around 2.5%, the novel coronavirus is around 3-3.5%. The impact of modern medicine at stopping epidemics before they become the Spanish Flu type numbers of infected people can’t be understated. 500 million people were infected with the Spanish Flu, we’re only at 118,000 right now with the novel coronavirus.

Spanish FluCOVID-19 (3/10/2020)
World Population2 billion8 billion
Transmission Rate1-2 persons2-4 persons
# Infected500 million118,000+*
# Dead40-50 million4,200+*
Very similar potential between the two viruses, but very different eras they inhabit. Modern medicine and our current understanding of viral infection and human physiology is light-years ahead of what it was in 1918. We have antibiotics to treat secondary infections. We have proper cleaning and sterilization techniques. Even though world travel has exploded, it’s also easier to control that travel and identify persons potentially infected.
*One note is that we have no numbers from North Korea. They say they have 0 patients. I can confirm that is absolutely impossible given the current state of the pandemic and what we know of the disease spread and N. Korea’s economic dependency on China. It’s likely horrible in N. Korea as they have limit healthcare capabilities and much of the population is underfed to malnourished.

Those as highest risk of dying due to the novel Coronavirus are those over 60 and those who have an underlying disease. The deaths in Washington State have all been associated with a nursing facility.

As I type this New York just announced their second confirmed case. That’s around 110 cases in the US, with a little over 60 on the West Coast (California, Oregon, and Washington). Those areas heavily affected right now, are pretty much all near major airport hubs. The west coast being affected isn’t surprising as there is more direct travel between China, South Korea, and Japan than to cities like Atlanta, Dallas, and New York City.

Edit: New cases are occurring all over the US as people return from trips or acquired the disease from infected areas of the United States.

Precautions I’d recommend to anyone

The basic precautions of washing your hands frequently should be continued, especially before eating. We’re still in flu season and that works well at preventing the flu. If you travel public transit carry around hand sanitizer and use it after exiting public transit. Try not to touch your face.

We’re not at the point that we should be walking around with face masks. In many Asian countries this is a common sight even without the disease outbreak. Some wear it as a precaution to getting sick while traveling public transit and others to prevent breathing in pollution and dust particles. It’s a super common sight and doesn’t correlate much to the current outbreak.

We don’t need to be running around with HazMat suits and gloves either. Gloves don’t do anything for you if it’s contaminated and then you touched your face. You just contaminated yourself.

If you are sick and have sick days, take them. Stay home if at all possible is you’re sick. This holds true if you have the flu or a novel virus. Imagine if you infected someone at work who takes care of their 80 year old grandmother or mother and then she was infected and died because of it.

If you work in a school and can provide or can get disinfecting wipes do so. Principals and teachers who travel the halls during the day doing checks can wipe handles quickly with a disinfecting wipe during their route. It doesn’t add much time since you’ll already travelling that route to get from A–>B and the wiping action doesn’t have to be a full clean. A quick wipe in step can do wonders. Same thing for bathrooms, clean the knobs on the water faucets if you don’t have automatic taps, same with towel dispensers. You’ll be surprised how much that will help outbreaks in schools of everything from the flu to the common cold. DO NOT USE homemade disinfecting cleaners. Essential oils won’t work Karens of the world. Use bleach or tested bleach alternatives. Otherwise you potentially set yourself up for a lawsuit and no school needs that.

Don’t buy into the BS salesmen going around trying to sell you something right now. You aren’t sick, generally speaking your risk is low of getting infected anyway. You’re risk of dying is rather low as well if you are in good general health.

How an Outbreak Progresses

All outbreaks will follow one progression if left unchecked. We call this a logarithmic curse or S-curve. An outbreak will start with a slow progression (the bottom of the S) before entering a logarithmic (very rapid) growth (center of the S) before it plateaus at the top as the outbreak has infected it’s maximum number of people, resistance is found, programs to prevent transmission are successful, etc. We can change how far along that progression and dramatically change the outcome of an epidemic.

  1. We catch it early, before logarithmic growth begins. This includes quarantines and travel restrictions as the first and easiest methods.
  2. Shutting down schools and business (China, Japan, South Korea, and 1 school in New York have already done this)
  3. Government Programs – passing out face masks, water, etc. this decreases contact with potential persons and makes sure everyone has basic necessities of life. People do die of starvation during disease outbreaks.
  4. Martial Law – forcing people to stay indoors, no contact with neighbors. Incredibly difficult to do. China has already started to take some of these measures it would appear. Military personnel have been seen running drills and many businesses and schools have been shut down and food service has been significantly altered under some form of military involvement.
  5. Vaccination programs if available (we are still at least 1 year away but it is being developed). Vaccine programs are the most successful programs we’ve developed with modern medicine. Viral diseases are best prevented using this method and as a result measles, polio, and smallpox have largely been removed as a major contributor of death and economic losses. Smallpox was eradicated. Polio is almost eradicated as well.

There are literally hundreds of things that can be done to prevent a disease from spreading and it depends on the disease. An airborne program won’t work for a water borne disease and vice versa. I’ve only listed most common to most extreme as they appear to be happening with this particular outbreak.

We are at the bottom of the S-curve meaning intervention procedures can have the largest impact right now if successful, which is why every country has begun their precautions. The ideal situation right now is that we never hit the logarithmic growth and we plateau now. I doubt strongly we’ll be able to do that. I think we’ll see some type of rapid increase but hopefully it will plateau quickly. Those intervention methods will have proved successful if that is indeed what happens.

Edit (3/8/2020): It would appear that we’re in the log growth phase based on the resources listed below. Don’t be surprised if we hear of more extreme limitations on movement like the resent restrictions in Italy. One March 1 we had roughly 1800 new cases per day. We’re now at 4800 new cases per day.

Resources I’ve Been Watching

The NYTimes has a great tracking map that pools resources from the CDC, Johns Hopkins University, US State Dept., National Health Commission of the People’s Republic of China, and World Health Organization to name a few. Other state and national agencies are also pooled as their information becomes available.

Johns Hopkins CSSE Coronavirus Tracker (or this link for the full description) has great information regarding early reporting and current methods of outbreak prevention being deployed. The interactive dashboard is updated regularly and gives as specific information is being reported.

Sorry but it’s another NYTimes article. But it’s a good one. But it does answer 6 questions most people seem to have regarding the outbreak. There’s also good infographics regarding how diseases spread.

Take Home Message

This isn’t the seasonal flu, so don’t let anything tell you ‘Oh it’s just the flu. It’s no big deal’. It should be taken seriously and does pose serious issues if not taken seriously. It could become the new Spanish Flu outbreak, that is within the possibilities; although, unlikely. But it is worse than the seasonal flu in both case-fatality and speed of spread.

  • I’m watching with curiosity and to know where the disease is and how bad it is.
  • I’m NOT buying face masks.
  • I AM washing my hands more
  • Spring Break has me concerned as many people are planning to go to Italy. We will very likely see a spike in confirmed cases in about 3 weeks.
  • Those most at risk continue to be elderly and immune comprised persons. If you are sick, please do not visit those persons out of precaution.
  • Overall, I’m not worried yet. The world economy will not be destroyed. This will not be as bad as the Spanish Flu outbreak of 1918. This will not be bubonic plague.
  • Beware of those selling cure all solutions right now. It happens every outbreak and preys on people’s worst fears

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.