Screen shot from https://healthmap.org/covid-19/

Coronavirus SARS-CoV2: 03/17/2020

You don’t want your throat or lung cells to get the SARS-CoV-2; spread love with your actions instead.

I’ve been laying low these last two weeks watching the pandemic unfold. I was getting updates from a friend in South Korea on the numbers a little bit faster than the news updates were putting them out. I was hoping it could be contained, and it started looking good for a while and then parts of the quarantine ended and the numbers shot up. Of course, people were itching to travel. It would seem people cannot be talked out of traveling, especially when they only have something that feels like minor cold or flu symptoms for people younger than 40.

The other factor was that it started spreading from people who didn’t have any signs of the virus. People made it past the screening because the had no symptoms or didn’t have a fever. Fortunately, we now know a little more about how the virus moves. Unfortunately, the virus gets around. We now know you can likely catch it from 6 feet (2 meters) away [CDC: How it Spreads page].

What do we know about the virus and the disease?

[If you need it, I’ve made a glossary towards the end.]

COVID-19 symptoms can be distinguished from flu symptoms by one main factor: It does not cause a runny nose. That being said, one can still have a runny nose if one is infected with multiple viruses (Wu et al.). The other give away is developing a dry cough. The other symptoms in order of severity are: Fever, Dry Cough, Fatigue, Sputum production (that’s thick mucus in the lungs), Shortness of breath, Muscle pain/joint pain, Sore Throat, Headache, Chills. Less common symptoms are: Nausea/vomiting, Nasal congestion, Diarrhea. Symptoms typically start with fever then progress to a dry cough.

We’ve heard that the incubation period is 14 days, but WHO says “people with COVID-19 generally develop signs and symptoms, including mild respiratory symptoms and fever, on an average of 5 days after infection.” and that the incubation period can vary from 1 to 14 days. There has been one reported case of incubation lasting 27 days. According to Lauer, Grantz, et al. there’s a 0.1% chance some people will not show signs until after 14 days.

There have been reports of asymptomatic transmission. On January 24 a 33-year old professional felt ill with a sore throat, chills and muscle aches. The next day he developed a fever and a productive cough. He returned to work 3 days later. He contracted the virus through a business meeting with a business partner who was asymptomatic until January 26 on her flight back to China. Her symptoms were mild. This means that there is an asymptomatic mode of transmission. Two other coworkers also became sick from this one person returning to work. None of them had severe illness. [Roethe et al. 2020]

The implemented traveler screening processes seem to be ineffective. According to Hoehl et al., two passengers tested positive out of 114 passengers who had cleared through all the medical checks. All of these people had no fever and showed no or mild signs of infection. The two travelers who were infected stayed healthy with no fever. There was only a faint rash and slight swelling in the throat in one traveler. [Hoehl et al. 2020; see Tong et al. 2020, Wu et al. 2020, and this article for another set of examples.]

Researchers found evidence strongly suggesting the virus can cause infections in both the throat and in the lungs. This is unlike the virus that caused SARS which only infects the lungs. The worst part of the throat infection (which is mild) peaked around the fourth day after onset. The immune system generally kicks in and starts killing off the virus within the second week. Whatever gets coughed up from the lungs seems to remain infectious into the third week. The most contagious part seems to be before symptoms and until the immune system starts producing antibodies in the second week (that’s when the viral load is the highest and the most shedding occurs). The results suggest it is transferred via droplets and not just through direct contact. [Woelfel, Corman, Guggemos, et al. 2020] There’s additional evidence that it infects intestines and can infect kidneys and heart (Yan et al. 2020).

The median time from onset to recovery is 2 weeks (note, that’s not the average just the center of the distribution indicating that it is equally probable it will be lower or higher). Severe and critical cases may last anywhere from 3 to 6 weeks. There are several ways the disease plays out:

• 81% experience mild symptoms. This ranges from no pneumonia to mild pneumonia.
• 14% experience severe symptoms. This ranges from shortness of breath to fluid filling the lungs.
• 5% experience critical symptoms. This ranges from respiratory failure, septic shock, and/or multiple organ failure. Of these, slightly less than half died an excruciating death (this represents the 2.3% case fatality rate).
• 19% of people will have a terrible experience with COVID-19 and will likely need medical support.

Here’s a handy chart to help discern how vulnerable those around you are:

One paper suggests that China only tested 5% of it’s cases, so the data may not be the most reliable. That also means that South Korea might actually be more representative (except for differences in demographics). Let’s compare South Korea on March 11 with the data from China:

Now to get a sense of the difference between the flu severity and the severity of COVID-19, here’s yet another chart:

The other important factor to discuss is the number of people one infected person will infect (the reproduction number). It just so happens to be 2.3 people according to the Chinese cases. According to Lai et al., it has a reproduction number 2.24 to 3.58. This is more than the seasonal flu by anywhere from 2 to 3 times. Each person infected by the flu will only spread it to 1.3 other people. There is no vaccination nor have our bodies developed a resistance to this virus. One more concern is the virus does not seem to be effected by weather or temperature.

Here’s a chart comparing it with more viruses:

One might be tempted to derive a proxy between average life expectancy in a country and the death rates. It could start to explain the differences between countries based on the accumulated health damages based on lifestyle. However, the statistics would really be modulated by available care — since without adequate care, more fatalities will result from the 19% of people who will experience more severe symptoms.

Those 19% of infected people are the reason why we need to try everything we can to flatten the curve, including fighting misinformation (I’ve seen some people spread around information saying that COVID-19 starts out with so much of a runny nose it feels like you’re drowning). If the 19% of infected people in an area exceeds the number of beds available in the hospitals, a much larger portion of those 19% will die horrible, untimely deaths.

There are some people who believe that this won’t be enough because the US only has about 924,100 hospital beds, and only about 160,000 ventilators for those in the 19% who would need it. If that’s realistically the limit of critical care, things will become really terrifying for those 19% of people who need better care after the first 800,000 cases of COVID-19. Those numbers could be refined a little bit more by including the study “Clinical characteristics of coronavirus disease 2019 in China” which states only 5.1% of patients needed non-invasive ventilators and 2.3% required invasive, yet the total percentage of patients on ventilators was 6.1%. If that’s the case, assuming the infections are spread out and not all in one location, after we reach 2.6 million infections we will have run out of ventilators. So this means that after anywhere between 800,000 (0.24% of the US population) to 2,623,000 (0.8% of the US population) cases in the US, we will have exhausted our supply of mechanical ventilators and more people will start dying excruciating deaths.

Given the results of “Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts” it would be impossible to fully contain and control the outbreak under much better conditions than the ones we have. Given the mild symptoms that 81% of people experience, it’s quite possible that there are many, many more cases in the US which haven’t been tested or confirmed. People are likely blissfully spreading the virus because they just don’t feel that sick. Nevertheless, we should all just stay home for the sake of those who are at risk.

What Can I Do To Make It All Better?

You should be minimizing you exposure to places where potential carriers of the disease are and have been. You should go meditate in your room and try to find stillness in the chaos that surrounds us. You should be in prayer. You should become a part of a rent strike. Maybe you should organize an online hack-a-thon like it’s 2009 in Portland, OR again. Check in with everyone you know and make sure they are doing well. Try to help meet peoples needs while protecting them.

If you take any medication or natural remedy, you could still get infected and be a carrier, even if you have no symptoms. So please be considerate of others and don’t act like we’re all invincible. Remember 19% percent of us will have severe to critical symptoms.

In America, there are now places, like San Francisco and Seattle, which are shutting down. Other places in the world have been doing similar things. Some people have been expressing regret at not following the suggestions to practice social distancing or quarantine. While we have no systems in place to adequately support people in the absence of their jobs, it is the right thing to do from an epidemiological perspective. It sucks, but we need to remember what it is like to be real human beings again and return to inhabit our world and not the systems we’ve built around us.

One least thing: If you have any more questions, please check with the WHO Myth busters page and the WHO Coronavirus disease (COVID-19) advice for the public page. Ask me questions and I’ll see what I can answer.

Daily data for Mainland China in Orange. All other countries in Yellow. Total recovered in Green. Screen shot from: https://www.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

Glossary

Here’s my basic definitions of things you might need to look up:

• SARS-CoV-2 — This is the specific name for the virus. While scientist were trying to figure out more about the virus, it was referred to as Novel Coronavirus (2019-nCoV).
• COVID-19 — This is the specific name for the disease the virus causes.
• Inoculation — This is the stage at which a virus is introduced into a persons body. This could happen like so: A person gets a virus on them, they touch their eye and the virus gets washed into their nasal cavity where it proceeds to attach itself to a host cell and injects the RNA it carries. It could also be as simple as someone walking past someone who coughed, inhaling a teeny-tiny droplet with a few viruses in it, and then those viruses attaching to cells in their lungs.
• Incubation — The host cell continues making copies of the virus until it explodes, releasing thousands of copies of the virus. This repeats until symptoms show up.
• Shedding — When host cells explode (lysis is the technical term), the corresponding release of viruses is called shedding. Once the viruses are shed several things can happen depending on which cells are infected. If a lung cell is infected, a shed virus could be exhaled (if it doesn’t stick to other cells very well) or coughed up in liquid in the lungs. Same goes for nasal passages.
• Onset — This is when symptoms start to appear.
• The time from inoculation until onset is called the incubation period.
• Progression — The period starting at the onset of the infection where the symptoms get worse as the infection progresses more and more.
• Prodromal Period — The period between the onset of symptoms and the full development of symptoms. In this list of terms, it is the first part of the progression stage. At this stage a slight fever might occur along with aches.
• Death (optional for most people) — What it says on the can. This really only happens if you don’t go into remission.
• Remission — The infection is getting better and our immune system is able to successfully fight off the infection.
• Recovery — This is the point at which symptoms have stopped being an issue and one feels normal again. Shedding may still persist past recovery.
• Transmission rate/R₀ (“R-naught”) — Basic reproduction number. This is the number that estimates how many people a person infected with a virus will infect while they are shedding the virus.
• Asymptomatic — Without symptoms. I just put this here for completeness.

Citations

1. Max Roser, Hannah Ritchie and Esteban Ortiz-Ospina (2020) “Coronavirus Disease (COVID-19) — Research and Statistics”. OurWorldInData.org. Retrieved from: https://ourworldindata.org/coronavirus
2. Lauer SA, Grantz KH, Bi Q, et al. (2020) The Incubation Period of Coronavirus Disease 2019 (COVID-19) From Publicly Reported Confirmed Cases: Estimation and Application. Ann Intern Med; [Epub ahead of print 10 March 2020]. doi: https://doi.org/10.7326/M20-0504
3. Wu X, Cai Y, Huang X, Yu X, Zhao L, Wang F, et al. Co-infection with SARS-CoV-2 and influenza A virus in patient with pneumonia, China. Emerg Infect Dis. 2020 Jun. https://doi.org/10.3201/eid2606.200299
4. Rothe, C., Schunk, M., Sothmann, P., Bretzel, G., Froeschl, G., Wallrauch, C., … & Seilmaier, M. (2020). Transmission of 2019-nCoV infection from an asymptomatic contact in Germany. New England Journal of Medicine. DOI: 10.1056/NEJMc2001468
5. Hoehl, S., Berger, A., Kortenbusch, M., Cinatl, J., Bojkova, D., Rabenau, H., … & Neumann, P. (2020). Evidence of SARS-CoV-2 infection in returning travelers from Wuhan, China. New England Journal of Medicine. DOI: 10.1056/NEJMc2001899
6. Tong Z-D, Tang A, Li K-F, Li P, Wang H-L, Yi J-P, et al. (2020) Potential presymptomatic transmission of SARS-CoV-2, Zhejiang Province, China, 2020. Emerg Infect Dis. 2020 May. https://doi.org/10.3201/eid2605.200198
7. Woelfel, R., Corman, V. M., Guggemos, W., Seilmaier, M., Zange, S., Mueller, M. A., … & Bleicker, T. (2020). Clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster. medRxiv. DOI: https://doi.org/10.1101/2020.03.05.20030502
8. Elizabeth Cohen (2020) Infected people without symptoms might be driving the spread of coronavirus more than we realized. CNN. March 14. Updated March 16, 2020.
9. Yan, R., Zhang, Y., Li, Y., Xia, L., Guo, Y., & Zhou, Q. (2020). Structural basis for the recognition of the SARS-CoV-2 by full-length human ACE2. Science. DOI: 10.1126/science.abb2762 https://science.sciencemag.org/content/early/2020/03/03/science.abb2762
10. Andy Kiersz (2020) Coronavirus death rates in South Korea reinforce a frightening pattern of how the disease affects older people. Business Insider. March 11. Retrieved from: https://www.businessinsider.com/coronavirus-death-rates-by-age-south-korea
11. Lai, C. C., Shih, T. P., Ko, W. C., Tang, H. J., & Hsueh, P. R. (2020). Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and corona virus disease-2019 (COVID-19): the epidemic and the challenges. International journal of antimicrobial agents, 105924. Retrieved from: https://doi.org/10.1016/j.ijantimicag.2020.105924
12. Brian Resnick (2020) Covid-19 is not the flu. It’s worse. Vox. March 13. Retrieved from: https://www.vox.com/science-and-health/2020/3/13/21176735/covid-19-coronavirus-worse-than-flu-comparison
13. File:Covid-19-curves-graphic-social-v3.gif. (2020, March 15). Wikimedia Commons, the free media repository. Retrieved 01:47, March 16, 2020 from https://commons.wikimedia.org/w/index.php?title=File:Covid-19-curves-graphic-social-v3.gif&oldid=404474046.
14. Tomas Pueyo (2020) Coronavirus: Why You Must Act Now. @tomaspueyo on Medium. March 10. Updated March13. Retrieved from: https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca
15. Joscha Bach (2020) “Flattening the Curve” is a deadly delusion. @joschabach on Medium. March 13. Retrieved from: https://medium.com/@joschabach/flattening-the-curve-is-a-deadly-delusion-eea324fe9727
16. Patti Neighmond (2020) As The Pandemic Spreads, Will There Be Enough Ventilators? NPR. March 14. Retrieved from: https://www.npr.org/sections/health-shots/2020/03/14/815675678/as-the-pandemic-spreads-will-there-be-enough-ventilators
17. Guan, W. J., Ni, Z. Y., Hu, Y., Liang, W. H., Ou, C. Q., He, J. X., … & Du, B. (2020). Clinical characteristics of coronavirus disease 2019 in China. New England Journal of Medicine. Retrieved from: https://www.nejm.org/doi/full/10.1056/NEJMoa2002032
18. Hellewell, J., Abbott, S., Gimma, A., Bosse, N. I., Jarvis, C. I., Russell, T. W., … & Flasche, S. (2020). Feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. The Lancet Global Health. Retrieved from: https://www.thelancet.com/journals/langlo/article/PIIS2214-109X(20)30074-7/fulltext
19. Jocelyn Gecker and Janie Har (2020) Life in San Francisco area screeches to a halt amid shutdown. AP. March 17. Retrieved from: https://apnews.com/07672ee6aded6e8ac5954c07676eb926
20. Gabe Guarente (2020) Governor Orders Shutdown of Washington Restaurants and Bars for Dine-in Service. March 15. Retrieved from: https://seattle.eater.com/2020/3/15/21181203/washington-shut-down-restaurants-and-bars-statewide-for-dining-in
21. Mattia Ferraresi (2020) A coronavirus cautionary tale from Italy: Don’t do what we did. Boston Globe. March 13. Retrieved from: https://www.bostonglobe.com/2020/03/13/opinion/coronavirus-cautionary-tale-italy-dont-do-what-we-did/?utm_source=pocket-newtab