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Basic Information About Viral Pathogens & The Current State Of Information About COVID-19


As we ‘shelter in place’ as a means of controlling the spread of the Novel Corona Virus, first diagnosed in November of 2019, it is a good time to evaluate not just COVID-19 but viruses in general. But first, a little perspective on the numbers game.

The following reasons indicate that COVID-19 fatality rate will be far lower than the 2% or higher currently proposed:

  1. The mortality rate is the number of patients who die divided by the number of patients known to have the disease.
  2. Most people infected develop mild symptoms and may not even go to the doctor.  They are not counted, which artificially increases the mortality rate.
  3. The fatalities are often associated with our elderly and with people who have an underlying medical condition, comorbidity, similar to seasonal influenza fatality cases.
  4. Given the national and international travel it is most likely that there are a great many cases that have already come and gone.  This means that the denominator, identified population infected, will continue to grow at a rate much faster than the number of fatalities. 

An article in the New England Journal of Medicine states “If one assumes that the number of asymptomatic or minimally symptomatic cases is several times as high as the number of reported cases, the case fatality rate may be considerably less than 1%.” 

We have an excellent example of a worst-case scenario provided by the Japanese when they quarantined a cruise ship with over 3,700 people and only had 707 people test positive and only managed to kill off 6 people, mostly over 80 years old, which gives us a 0.8% fatality rate.  This IS higher than the yearly influenzas fatality rate, 0.1- 0.2% but much less than the last SARS outbreak which took 2% of those infected. 

So, what did the Japanese do wrong?

  1. Confined all passengers to their rooms but did not do anything to the ventilation system, which was not effective in removing virus particles and did not provide 100% outside air to each room.
  2. Allowed staff, including those testing positive and those actively ill, to eat together and sleep in quarters where they could spread the infection amongst themselves.  Then had them prepare and deliver food.  
  3. Did not instruct, or did not enforce, staff to use the PPE provided properly.  Instagram pictures showed crew delivering food with one of the respirator straps hanging under his chin.
  4. Pictures show passengers lining up for testing without face masks or gloves, so they were exposed to infected passengers and touching potentially contaminated surfaces at the testing site as well as from and to their rooms.  As well as standing next to potentially infected passengers and crew.

The following reasons indicate that COVID-19 fatality rate will most likely be far lower than the 2% or higher currently proposed:

5. Only 707 people out of 3,700 tested positive for the virus.  Yes, they are following the passengers and yes, some are now testing positive, but you would expect a much higher affected population for an easily transmissible disease.

6. Most people infected develop mild symptoms and may not even go to the doctor.

7. The fatalities are often associated with our elderly and with people who have an underlying medical condition, similar to flu fatality cases

8. Given the national and international travel it is most likely that there are a great many cases that have already come and gone.  This means that the denominator, identified population infected, will continue to grow at a rate much faster than the number of fatalities.  

Corona viruses have crown-like spikes on their surfaces and are divided into 4 main subgroups:

  • Alpha
  • Beta
  • Gamma
  • Delta

There are 4 human coronaviruses that cause the common cold:

2 are Alpha

  • 229E
  • NL63

2 are Beta

  • OC43
  • HKU1

Colds are not fatal.

There are currently 3 corona viruses that jumped species from animals to humans:

  • 2019 Novel Corona virus, also called: nCoV, COVID-19, SARS-CoV-2, and HCoV-19
    • Strains: SARS-CoV-2 nCoV-WA1-2020 (MN985325.1) and SARS-CoV-1 Tor2 (AY274119.3) 
    • origin Wuhan Hunan seafood market in 2019
  • SARS Severe Acute Respiratory Syndrome, also called: SARS-CoV. 
    • origin South Eastern China, 2003-2004.
  • MERS Middle Eastern Respiratory Syndrome, also called MERS-CoV.
    • The CDC states that camels are the reservoir, but bats are most likely the source.  Saudi Arabia, 2012

The above mutated viruses can be fatal.

Comorbidities are preexisting conditions that make the patient more likely to contract the disease and/or more likely to have a more severe reaction.  Comorbidities for corona viruses include:

  • History of smoking 
  • bacterial co-infection 
  • high blood pressure
  • 60 or more years old
  • cardiac issues
  • diabetes 
  • hepatitis
  • pneumonia
SymptomsSeasonal InfluenzaColdsSARS 2003MERS 2012COVID-19 2019
Incubation period, time from exp. To symptomsAverage 2 days, or 1-4 days1-3 days2-7 days2-14 days Average 5 sometimes up to 21 days5-14 days In Wuhan: 5.2 days* CDC: unknown WHO: 0-24 days
Asymptomatic casesXX
Mild casesXX
Muscle achesXXX
Runny/stuffy noseXX
Sore throatXX
Cough XXStarts 2-7 days after onsetXX
Weakness X
FatigueX, up to 3 weeks
Nausea/vomiting Abdominal painX
Diarrhea1 in 5 casesX
Kidney DiseaseX
Duration average14 days7-10 days7-10 Days
Case Fatality Rate, CFR2019: 0.1%0%10%35%2.3%
Secondary illnessesBronchitis, pneumoniaMost develop pneumoniaPneumonia and kidney failurePneumonia, ARDS
Infectious periodDay before thru day after symptomsThe day before thru 7 days after symptomsWhile symptomaticUp to 30 days after symptoms startPrior to symptoms and after symptoms dissapate
Viability on surfaces outside of body48 hours24 hours, on hands ≤an hourOver 20 days3. On plastic48 hours4 on steel & plastic at 20’C & 40%RH72 hours on plastic and stainless steel Copper 8 hours Cardboard 24hrs
R02018: 1.863-42.0-6.7***2.2

*The basis for the 14-day Medical observation period for people who have been exposed.

**SOB Shortness of Breath

R0 pronounced R nought, also known as the Reproductive Number, is the average number of people who will be infected by one person.  An R0 that is less than one is good, the higher the R0 the more people one infectious person can infect.  This measurement of infectivity is calculated by:

  1. The likelihood of contact between the infectious person and the susceptible person.
  2. How the disease spreads, aerosol, direct contact, etc.
  3. How long it can survive outside of the body.
  4. The Hang Time, for aerosol transmission, how long the infectious particle remains in the breathing zone of other people.
  5. If, and how long, asymptomatic people are infectious.
  6. Where the disease is found.
  7. Social, demographic, and cultural characteristics will make the R0 vary between locations.                                                                                                                                    ***MERS R0 for 2014 in Jeddah was 3.5-6.7 while in Riyadh it was 2.0-2.8

The R0 for smallpox, polio, and rubella range between 5 and 7.  Ebola, while thought to be very contagious, has an R0 of only 1.5-2.0 this disease is transmitted by contact with blood.  Whooping cough is transmitted via aerosol inhalation and it’s R0 is 5.5.  Measles particles have a 2-hour Hang Time which plays a major factor in the very high infectious rate of 12-18 R0.

It should be noted that R0 assumes everyone is susceptible, there is no immunity, and only relates to how many people will eventually be infected.

**Click on the picture to view the MicrobeScope graph


When the virus in the person ends up outside of the person this is called viral shedding and it is how a virus is shared to the people around you.

Direct Transmission: Inhalation

Whether we are speaking, sneezing, coughing, or just sitting there breathing, we are exhaling liquid particles from our respiratory system.  Have you ever watched the Outbreak movie starring Dustin Hoffman?  Do you recall the scene in the theater where the exposed and now sick and infectious lab tech is coughing, and spewing out droplets that are shown floating around the theater inhaled via the nose and into the mouths of the people around him?  No?  Well, now Is probably not the best time to go watch that movie.  

That scene stuck with me and this Novel Corona virus, COVID-19, potential pandemic got me thinking about the accuracy of that mode of transmission of a virus.  So, I did a little research, citations below, and found out that there are a LOT of variables that come into play with airborne transmission of infectious material.  

  1. Mode of transmission: a cough has a lot less Volume, 6×10-8ml, than a sneeze, 1.2×10-5ml, so the sneeze is more effective means of transmission.

Viruses are 17-300nm long, 1,000x smaller than bacteria, 300 to 10,000nm, which are smaller than human cells.  So you can imagine how many will fit in a sneeze or cough droplet

2.The number of coughs and sneezes that occur before you can get the heck away!  This is both concentration and duration of exposure.

3.Which virus they have because they each have different parameters

4.Viral load: how much virus is being shed (given off), as in how many viral particles are there in the droplets?  

This depends on the virus.  Influenza A has a peak shedding the first day of acute respiratory symptoms and the number of particles decrease steadily after that.

We know that COVID-19 is infectious long symptoms appear and that some people do not develop symptoms but can still transmit the disease.  We do not know how infectious they are but there have been reports of active infections that have been traced to asymptomatic people.

5.The force of the cough or sneeze compared to how close you happen to be standing next to them.

6.Where the particulate gets deposited in your body, did it hit the target?  They float around until they collide with a cell with compatible receptors and receptor binding proteins. 

a. Respiratory viruses that produce coughs, sneezing, mucous producing, headaches and fever, usually target the cells that line the respiratory tract or gut.

b. HIV targets Lymphatic T-Cells which is like taking out the security guard before robbing the bank.

7.As with chemicals ‘the dose makes the poison’.  Arsenic can make your hair shiny or it can kill off an inconvenient witness.  Same with viruses, where is the tipping point, the dose that gets you sick?

a. If you inhale, get deep into the lungs, Influenza A 0.7-3.5 Plaque Forming Unit, PFU’s, 50% exposed will get sick.

b. If the virus just gets into the nasal mucosa then you need 89-224PFUs to really feel it.

8.Where the virus laden particulate is deposited depends on the size of the droplet containing the virus which depends on how much water evaporates which depends on the difference in humidity between where the particle came from, nice hot moist body, and where you are, which is usually much less humid and colder.

Remember when hang time applied to footballs or basketballs, or how long an athlete stays in the air after jumping?  Well, forget it, we’re safety professionals now.  Hang time means how long an infectious particle will stay in the air where the people you are responsible for are exposed.

So, particle deposition depends on

a. Size, the larger the particle the faster it falls, contaminating some surface.

  1. Evaporation makes the cells smaller.
  2. Aggregation, viral particles sticking together makes them larger.

    b.  Smaller particles can stay suspended for several minutes to be inhaled and small enough to the target cells in your respiratory system.                                                                                 

Indirect, or Surface transmission

In some scenarios contact transmission is the most important route, in others it’s airborne infectious particles.  Hands that touch contaminated surfaces can then self-inoculate you if you touch your face, the mucous membranes of the eyes, nose or mouth.

Factors influencing having enough viable infectious material on a surface to be transferred to your face or mucous membranes depends on several factors:

  • Strain variation, for example, one strain of COVID-19 is only viable on cardboard for 8 hours while the other one can transmit an infection within 24 hours.  Since you cannot test every surface the time listed in the table is the longest.
  • The titer (concentration of virus) on the surface
  • The surface type.
  • The suspending medium
  • Mode of deposition
  • Temperature
  • Relative humidity
  • The test method, does the media the sample is transferred to have the right mix of nutrients for it to grow?  If not, you get a false negative. 
  • Some test methods will only tell you if it’s there, not if it is still infectious.

Assessing different responses for different countries.

United States’ CDC response to SARS

CDC worked closely with WHO and other partners in a global effort to address the SARS outbreak of 2003. For its part, CDC took the following actions:

  • Activated its Emergency Operations Center to provide round-the-clock coordination and response.
  • Committed more than 800 medical experts and support staff to work on the SARS response.
  • Deployed medical officers, epidemiologists, and other specialists to assist with on-site investigations around the world.
  • Provided assistance to state and local health departments in investigating possible cases of SARS in the United States.
  • Conducted extensive laboratory testing of clinical specimens from SARS patients to identify the cause of the disease.
  • Initiated a system for distributing health alert notices to travelers who may have been exposed to cases of SARS.

United States response to COVID-19, first case confirmed on January 21, 2020:

  • The CDC could not get tests approved by the FDA 
  • The test developed by the CDC had “technical challenges”.
  • The FDA instructed laboratories that they could develop tests but not use them without first passing the FDA’s “approval, clearance, or authorization” process.
  • February 24th state government labs petitioned the FDA for permission to develop and use their tests.
  • The FDA permitted an emergency streamlining of the regulatory approval process and directed the labs to provide less paperwork for clearance, an EUA application.
  • February 29th the FDA allowed tests to be used provided the EUA application was submitted within 15 days.  For more information see the JAMA article.
  • Initially the CDC limited testing to only those with known exposure.
  • March 3rd Vice President Pence instructed the CDC to remove limits on testing.
  • March 16th the FDA announced that it would allow states to over see state government developed tests.
  • The FDA has also allowed private sector companies a fast track to getting more COVID-19 test kits produced.
  • As of March 19th 71,000 people have been tested and there are more than 7,000 cases. 
  • Thousands of tests are being tested by government health labs.
  • The tests will be used to spot new outbreaks and decide where to put resources.
  • In the absence of an ability to identify people who have COVID-19 or who have been in sufficient contact to have contracted COVID-19 cities and states are 
    • Closing schools. 
    • Posting attendance limits for meetings and entertainment.  
    • Sports leagues are canceling events.
    • Restaurants are closed.

South Korea’s response to COVID-19, first case confirmed on January 21, 2020:

  • January 27th summoned representatives from over 20 non-government controlled medical companies to a conference where top infectious disease experts instructed them to develop and produce an effective COVID-19 test.
  • Fast tracked regulatory approval process.
  • February 3rd, less than 7 days later, one company’s test was approved and February 12th a second company’s test was approved
  • By March 19th over 290,000 people have been tested and spot checked the results to ensure the tests were effective.
  • This allowed them to aggressively track down and test anyone exposed to patients that tested positive.
  • South Korea has been removed from some country’s prohibited travel lists.

Italy’s response to COVD-19, first case confirmed on February 20, 2020 during the peak of their influenza cases along with an unusually high number of pneumonia cases.

  • February 21st the first person to person infection is identified.
  • The first country to ban flights from China.  Which could have led to travelers coming by other routes and not disclosing they were at risk.
  • Italy has Emergency Medical System for cities like Milan and the Lombardy region and has created a screening process for patients presenting with COVID-19’s symptoms or from areas with known cases of COVID-19.  They coordinate
    • Patient flow to hospitals and specialized facilities.
    • Address specific issues about bed resources and emergency department overflow.
  • March 8th the number of cases increased by 50%.
  • March 9th Italy placed residents, 60 million, on lockdown.
  • March 10th Italy has tested over 42,000 people, more than other European countries.
  • Italy has one of the oldest population in world.  
  • It also has 24 of the 100 European cities listed on the Swiss air monitoring platform IQAir, 24   
  • Italy has the largest outbreak outside of Asia.
  • Italy’s mortality rate was 4% on March 10th.

1Journal of Occupational and Environmental Hygiene, 2: 143–154 ISSN: 1545-9624 print / 1545-9632 online Copyright c 2005 JOEH, LLC DOI: 10.1080/15459620590918466 Toward Understanding the Risk of Secondary Airborne Infection: Emission of Respirable Pathogens Mark Nicas,1 William W. Nazaroff,2 and Alan Hubbard1 1School of Public Health, University of California, Berkeley, Berkeley, California 2Department of Civil and Environmental Engineering, University of California, Berkeley, Berkeley, California

2Viable Viral Efficiency of N95 and P100 Respirator Filters at Constant and Cyclic Flow Paul D. Gardner,1 Jonathan P. Eshbaugh,2 Shannon D. Harpest,2 Aaron W. Richardson,2 and Kent C. Hofacre2 1U.S. Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 2Battelle Memorial Institute, Columbus, Ohio Journal of Occupational and Environmental Hygiene, 10: 564–572 ISSN: 1545-9624 print / 1545-9632 online Copyright c 2013 JOEH, LLC DOI: 10.1080/15459624.2013.818228

3Chan KH, Peiris JS, Lam SY, Poon LL, Yuen KY, Seto WH. The effects of temperature and relative humidity on the viability of the SARS Coronavirus. Adv Virol 2011;734690.

4van Doremalen N, Bushmaker T, Munster VJ. Stability of Middle East respiratory syndrome coronavirus (MERS-CoV) under different environmental conditions. Euro Surveill 2013;18. pii: 20590.