Understanding the World of Viruses and Outbreaks

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Understanding the World of Viruses and Outbreaks
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By Robert Bernstein

SEC - A Viral Lecture: Understanding the World of Viruses and Outbreaks - Dr. Carolina Arias, Assistant Professor, UCSB Department of Molecular, Cellular and Developmental Biology 3-11-20.

Dr Carolina Arias specializes in virus-host interactions in her UCSB research lab. We were fortunate that she was able to speak to us at the Science and Engineering Council about the current situation with the COVID-19  coronavirus.

Here are my photos from her talk.

Arias explained that we are exposed to viruses every day. They are constantly traveling the world. She expressed frustration that diseases like measles are on the rise due to misinformation by "anti-vaxxers".

She noted that Ebola is still happening. And she reminded us of the harm done by the Zika virus during its peak 2015-2017.

"Don't Panic!" That was her message that she took from "The Hitchhiker's Guide to the Galaxy" and wanted to convey to us.

Panic can be more damaging than the disease and it can make people do crazy things. We are seeing this now with the bizarre hoarding behavior in stores of items like toilet paper.

Arias offered this quote from two times Nobel Laureate Marie Curie: "Nothing in life is to be feared, it is only to be understood. Now is the time to understand more, so that we may fear less."

Unfortunately, at this time we don't understand much. The situation is rapidly evolving. This virus was first discovered in December 2019.

So, what is a virus? Arias noted that she has two young children and they are constantly carrying them! A virus is a bit of genetic material encased by proteins.

She offered an image of an influenza virus.

Viruses are not living organisms. The Oxford English Dictionary says, "Life is the condition that distinguishes us from inorganic matter. The capacity for growth, reproduction and continual change preceding death."

Viruses need a host. Viruses are "obligate intracellular parasites". The virus hijacks the host cell to turn it into a virus factory. They are "pirates" of the cell and often kill the cell when they are done with it.

Viruses infect all kinds of organisms. Farm plants and animals, included. China last year had a pig virus that killed most of the pigs in China.

Have you ever seen a blue "roly poly" bug (or pillbug)? The blue is caused by an iridovirus that forms crystals on the surface.

Viruses can infect tobacco, yeasts, amoebas and bacteria. We are full of viruses that infect the bacteria in us. They outnumber the bacteria by ten to one.

Not all viruses cause disease.

Some viral diseases are common. For example, the common cold and herpes. Arias studies a specific herpes virus that infects the eye. The average adult gets 2-3 cases of the common cold each year. More for children.

We don't die of colds or herpes simplex.

Other viruses are rare. For example, rabies or West Nile Virus.

Sometimes, disease numbers rise in a certain area. This is called an "outbreak".

Last year there was a measles outbreak in Los Angeles County. One person exposed 500 people in a couple of classrooms. 100 of those could not show they had been vaccinated. It was controlled after it was identified.

Outbreaks can expand. An infected person may not be identified and may not seek medical attention.

An epidemic is defined as "an outbreak of disease that spreads quickly and affects many individuals at the same time." A pandemic is an epidemic that has affected an entire country or the entire world.

As of March 11 the World Health Organization (WHO) declared that COVID-19 is officially a pandemic. The day before it was officially calling it just an "outbreak"! Arias said that the delay in calling it a pandemic was more political than scientific.

What are coronaviruses? Coronaviruses are a large family that includes mild viruses like some common colds all the way to serious viruses like MERS.

20-30% of common colds are due to coronaviruses.

Despite some rumors, COVID-19 was not engineered in a lab! But some coronaviruses will mutate naturally.

The 2002 SARS outbreak was the first realization that coronaviruses could be serious. SARS had a 10% death rate. There were 8,000 cases of SARS. After containment there were no other cases except some sporadic ones.

The 2012-13 MERS outbreak was 30% fatal. There were 2,000 cases. Because it was so damaging to patients, most were in the hospital. They were able to infect some health care workers in the hospitals but they had little access to infecting others outside the hospitals.

COVID-19 is a bigger challenge because people can walk around infected for awhile without knowing they have it. Thereby infecting other members of the public.

This virus started out being called the "Wuhan Virus" because of where it was first observed. It was then called "Novel Coronavirus 2019". It is now called COVID-19, but the full official name is SARS-CoV-2. It is related to SARS. But it did not evolve naturally from SARS.

Coronaviruses can be spread by animals. COVID-19 started in an animal market in Wuhan, China. It began in bat populations. They don't die from it. They can in turn infect other animals that humans come in contact with more often.

In the case of SARS, the more common animal that was the intermediary was the civet cat in China. This animal was often eaten for food. The sale of civet cats was banned, but it continued in the black market.

MERS resides in dromedary camels. Human adult males are most likely to get MERS because of their interactions with these camels.

The current COVID-19 origin is still a mystery. We know it came specifically from the Wildlife Market in Wuhan. But the specific animal is not known. There was a rumor that pangolins were involved. That is now known to be incorrect.

COVID-19 is known to be carried by bats. That version is 96% similar to the human version. But the intermediary reservoir animal is not known.

The outbreak started close to New Year's Eve on December 31, 2019. It was observed to be a form of pneumonia with no known cause. The genome was sequenced and it was known in days to be a new coronavirus.

Looking back, we know that the first appearance of the first symptoms occurred in a patient in early December 2019.

Arias presented this timeline showing how fast this has happened:
December 31 – That mystery pneumonia
January 7 – Isolated with genome
January 11 – 41 were known to be infected
January 20 – First US case
January 30 – WHO declared a Global Emergenc

Arias showed graphs of cases in China and outside China. Cases in China plateaued due to massive action there. But in the rest of the world it is still on the rise.

February 26 was the first US case of unknown origin, in California. This is worrisome because it means that people may carry it with little or no symptoms.

February 29 was the first US death.

March 6 Trump signed an $8 billion emergency spending bill. This should have happened earlier according to Arias.

The availability of tests affects reported cases. Testing will be based on symptoms, not on demand. Numbers are clearly not accurate now since so little testing has been done in the US.

COVID-19 is an RNA virus. This is error prone every time it replicates. Viruses don't care if lots of mistakes are made because so many are made. This makes it easy to trace by observing mutations. The rate of these mutations allows determination of how long it has been in a given population.

It is possible to look at the outer package of the COVID-19 virus to identify it.

California is one of the most affected states so far. Mostly in the north of the state so far. Washington State and New York State are also very much affected. It will keep spreading. As of the time of her talk, there were 1,000 US cases. 31 deaths. And 15 people who recovered.

The symptoms are fever, cough and shortness of breath. That is not very descriptive. Common influenzas have the same symptoms.

2-14 days after being infected the symptoms appear.

It can be caught by being within 3-6 feet of someone with an active fever for more than two minutes. It is spread by droplets from coughing from deep in the lungs.

Just touching someone is not immediately a problem. It has to enter your body through eyes, nose or mouth. This is why it is important to wash hands frequently. Hand sanitizer is an alternative if hand washing is not possible. We unconsciously touch our faces and that is the problem. It helps to make a conscious effort not to touch our faces, but hand washing is more effective in practice.

Droplets will settle on surfaces and can spread from there. Think of it like a bad version of influenza. Surfaces can be sanitized with Clorox or Lysol.

The main complication of COVID-19 is pneumonia.

Why is it so severe? Most viruses thrive in the upper respiratory tract. This is true for the common cold and most versions of influenza.

But COVID-19 only thrives deep inside the lungs, in the alveoli. That is what it targets. This is by definition a form of viral pneumonia. Antibiotics do nothing to help.

So far COVID-19 seems to have a 2% mortality rate. In comparison SARS was 9.6% and MERS was 34%.

Pre-existing conditions make a big difference in the mortality rate for COVID-19. It is just 0.9% with none. Being old is itself a risk factor in addition to specific conditions.

There are no vaccines for this virus, nor for most viruses. Nor are there any antiviral agents for this one. In the case of influenza, it is possible to take the antiviral Tamiflu within 48 hours and it will shorten the case by about one day. There are also antiviral agents for HIV, herpes and hepatitis C.

There is an attempt now to repurpose antivirals for this disease. One that is being studied is Remdesivir. But it won't be soon enough to stop the spread for now. It has to be studied to determine if it works. If it does anything bad. And if it can be used prophylactically or if it can only be used as a treatment.

A vaccine will take a year or more to develop.

There are "super responder" patients who get the disease quickly but also clear it quickly from their bodies. It is good to study such people to get a clue about treatment. This helped with Ebola.

With regard to face masks, she advises against using them if you are healthy. You will end up putting your hands to your face more often if you are wearing a mask. That actually increases your risk of infection. Masks can be helpful if they are worn by those who are already infected to keep them from infecting others.

"Social Distancing" is effective. Avoid being close to other people. Avoid hand shaking and other unnecessary contact.

If you have a fever you should contact your health care provider. 100.4 degrees Fahrenheit is the threshold of concern. If you have a fever, please stay home.

She trusts what Anthony Fauci is saying at the Centers for Disease Control (CDC).

The CDC also offers advice on how to survive while staying home during a quarantine.

Children will be OK if they get this disease. But it is important to make sure they don't pass it along to older people who are at risk. The Swiss government opted to keep schools open so the kids are not going to stay with their grandparents!

There are many unknowns right now. We don't know how long it can be transmitted after a person has had it. It takes days to get test results even if one can get tested. It is not even known if getting the disease gives permanent immunity. And we don't know what are the long term effects on the lungs or the rest of the body from getting this disease.

Someone asked Dr Arias if she had a favorite science fiction movie that was related to epidemics. She said that in fact the movie "Outbreak" got her into the field!

In summary, she said:
Wash your hands
Protect others by staying home if you are sick
Wear a mask to protect others
Avoid groups and unnecessary touching of others
And Don't Panic!

I will add that this presentation was provided by the Science and Engineering Council of Santa Barbara. They host monthly talks on local technical innovation as well as providing scholarships and other services to encourage young people to go into science and engineering careers.

Here is more information about the Science and Engineering Council: https://www.scieng.org/

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25 Comments

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Gibraltar_Roadster Mar 14, 2020 07:21 PM
Understanding the World of Viruses and Outbreaks

Known as a phographer and environmentalist, Robert demonstrates that he is an excellent writer and explainer. This write up is a fine contribution to the community, however I would like to pick two nits. I object to the relatively cheaper shot taken at the anti-vaccine viewpoint since places like Denmark are already pioneering highly intrusive legislation which could lead to severe "forced vaccine" trends in connection with quarantine policies. Secondly I object to the notion that we should just accept the expert consensus that the presence of a probable bioweapons research lab in Wuhan China is not suspicious and worthy of investigation. Thirdly, we are not "panicking" we are just stocking up and want results from government. Overall , four and a half stars for the report, and five stars for the photos.

Gibraltar_Roadster Mar 14, 2020 08:18 PM
Understanding the World of Viruses and Outbreaks

Alternative hypothesis is neither a "view" nor a theory. Jumping to no conclusions whatever, I merely point out that Wuhan Institute of Virology is a Biosafety level 4 (BSL-4) lab, the highest and most dangerous level. I agree that in all probability the line we are being told that the virus emerged from the wet markets is accurate. But there has been no transparent inquiry and it is completely possible that there was an unscheduled release of the highly infectious virus if a lab worker picked up the virus. I personally met a young Ph. D. researcher who was inadvertantly infected with plague while doing his work. I resent these posts attributing "views" when I merely raise the possibility that we are being snowed when official government scientists and others assure us that the cause was the wet markets. (I accidentally double posted by hitting reload and in this snide retort it is insinuated that I am so kind of knuckle dragger who deliberately double posted thinking that would improve my case. ) I certainly hope that the Edhat moderator does not spin this dialogue, especially since I am merely arguing to wait for the facts, and am being subjected to what borders on personal attacks. Jeez. Factual references (22): https://en.wikipedia.org/wiki/Wuhan_Institute_of_Virology#References

jqb Mar 14, 2020 08:46 PM
Understanding the World of Viruses and Outbreaks

"I object to the relatively cheaper shot taken at the anti-vaccine viewpoint " -- Robert simply reported what Dr. Arias said ... there's no rational basis for dinging him for that or calling it a cheap shot (relative or otherwise). And the statement is factual: diseases like measles ARE on the rise due to misinformation by "anti-vaxxers". The truth of this is independent of anything that Denmark is doing or how anyone feels about it. It's also a fact, readily observed, that "bizarre hoarding behavior" and panic is occurring, whether that describes your own behavior or not. And there's nothing in Robert's article saying that people "should just accept" anything. If you want to believe, contrary to all the evidence, that the Wuhan Institute of Virology is a bioweapons research lab (your own link says otherwise) and that the virus originated there, that's up to you. But Robert has a different approach, so he stated that COVID-19 started in an animal market in Wuhan, China because that's the current best understanding of the available facts. https://thebulletin.org/2020/03/why-do-politicians-keep-breathing-life-into-the-false-conspiracy-theory-that-the-coronavirus-is-a-bioweapon/

jqb Mar 14, 2020 09:32 PM
Understanding the World of Viruses and Outbreaks

A sober factual analysis. Bioweapon: very unlikely, and promotion of this idea is problematic for U.S.-China relations. Accidental release from a lab researching the animal sources of coronaviruses: less unlikely. Crossover from animal to human: the prevailing view. https://www.foreignaffairs.com/articles/united-states/2020-03-05/us-chinese-distrust-inviting-dangerous-coronavirus-conspiracy

jqb Mar 14, 2020 10:55 PM
Understanding the World of Viruses and Outbreaks

"I never even hinted that this virus was being developed as a weapon itself, just that the lab was probably involved in defense related research" -- hmm ...
"I object to the notion that we should just accept the expert consensus that the presence of a probable bioweapons research lab in Wuhan China is not suspicious and worthy of investigation" -- looks like a pretty big hint to me. If the lab is just defensive, then there's nothing suspicious about it. As for investigation, see the Foreign Policy article I linked. Over and out, permanently.

EastBeach Mar 14, 2020 11:17 PM
Understanding the World of Viruses and Outbreaks

Another great summary Robert, thank you! Looking at your linked photos, I still can't wrap my head around the fact that viruses aren't "living" organisms. They seem to have such malevolent intent :)

jqb Mar 15, 2020 12:06 AM
Understanding the World of Viruses and Outbreaks

Viruses are tiny organic machines that replicate themselves by parasitizing the mechanisms of cells. In the process, they destroy those cells and damage the organisms they are part of, and get expelled where they can invade other bodies to continue their activities, but there's no intent, any more than if someone falls into a woodchipper, the woodchipper intends to destroy them--it's just the nature of woodchippers. Whether viruses are "living" is just semantics ... the biological definition of life is something like "open systems that maintain homeostasis, are composed of cells, have a life cycle, undergo metabolism, can grow, adapt to their environment, respond to stimuli, reproduce and evolve". Viruses have some of these properties, and the rest are provided by the cells they parasitize. Compare to cancer, which occurs when cell reproduction goes awry and doesn't respond to the shutdown signals from the body ... they're sort of "too" alive. They're "malevolent" in that they don't "care" about the rest of the body and don't function as part of it (so no homeostasis).

EastBeach Mar 15, 2020 12:01 PM
Understanding the World of Viruses and Outbreaks

I appreciate your reply JQB. My original post had a smiley face so was said partly in jest :) But in times like this, science-based action is what's going to get us over the hump. So talking about how viruses work is a good thing.

jqb Mar 15, 2020 12:38 PM
Understanding the World of Viruses and Outbreaks

Thanks. I of course understood that you don't think that viruses are actually malevolent (note: no scare quotes in that case), which is why I put the word in scare quotes just as you did. Mostly I wanted to get at this idea that there's a bright line dividing "alive" and "not alive" ... there isn't; it's just semantics. Science recognizes this and has done so ever since the concept of vitalism was refuted by the synthesis of urea, but the concept lives on in the general population. The OED definition of "life" that Robert provides is left over from these pre-scientific notions ... life does not divide us from the "inorganic" -- bodies are still organic after they are dead. The chicken in your freezer is organic. Organic molecules have been found on rocks in space that probably do not derive from living organisms. Viruses are organic. Life is defined by the functions it performs ... homeostasis, reproduction, growth, etc. Viruses perform some of these functions but not others, and some they perform only by taking over the mechanisms of living cells, so whether viruses are alive is a judgment call, not a fact of nature.

jqb Mar 15, 2020 12:40 PM
Understanding the World of Viruses and Outbreaks

Oops, you didn't put "malevolent" in scare quotes, it's "living" that you quoted. But it was obvious from "seem to" and the smiley and the rest of the context that you weren't being literal.

two abbys Mar 14, 2020 11:28 PM
Understanding the World of Viruses and Outbreaks

Thank you Robert, you have provided a great service posting this clear and credible information with all of us. I have shared the link to several friends.

Gibraltar_Roadster Mar 15, 2020 01:01 AM
Understanding the World of Viruses and Outbreaks

RE: Viruses. EASTBEACH nobody thought that you really think that they are "malevolent". Anyway...if anyone can debunk this it would make for an interesting read: https://www.popsci.com/new-evidence-that-viruses-are-alive/

EastBeach Mar 15, 2020 01:11 PM
Understanding the World of Viruses and Outbreaks

I found the Popular Science article interesting . My takeaways about the researchers' theory are ... cells and viruses may long ago have shared a common ancestor, one that consisted of cell plus virus, evolution caused the virus to branch away from the cell (by simplifying rather than getting more complex), when a virus "attacks" a cell and is able to replicate it (in a sense) now looks like its ancient ancestor.

jqb Mar 15, 2020 01:32 PM
Understanding the World of Viruses and Outbreaks

Simplification is known to happen in parasites, which evolve from autonomous organisms and may shed mechanisms that are no longer needed because they are provided by the host. See https://phys.org/news/2020-02-henneguya-salminicola-microscopic-parasite-mitochondrial.html for a striking example. Here's another interesting article discussing the genetic origin of viruses: https://cosmosmagazine.com/biology/what-came-first-cells-or-viruses However, the genetic origin has nothing to do with whether they are "alive", any more than a corpse is alive just because it once was, or a stillborn baby is alive just because its parents were.

Bird Mar 15, 2020 11:11 AM
Understanding the World of Viruses and Outbreaks

Thanks, Robert! I have been wondering what, exactly, is a virus and how does it differ from a bacterium ...and how, for instance, viral pneumonia differs from bacterial pneumonia --- and why viruses are not affected by antibiotics while bacteria are. Your posting gives a good start on understanding!

jqb Mar 15, 2020 01:06 PM
Understanding the World of Viruses and Outbreaks

Bacteria are complex single-celled organisms with various organelles inside of them, including the nucleus that contains their chromosomes ... they are autonomous critters, much larger than viruses which are just a shell containing a strand of DNA or (as with coronavirus) RNA. Bacteria are much like the cells of your body, except that your cells function as part of a whole rather than being autonomous (although some cells, like the white blood cells, are pretty close). Antibiotics disrupt the functioning or reproduction of bacteria, but since viruses are just these tiny packets that don't have life functions, they aren't affected. However, since viruses have a lipid (fat molecule) shell, they are destroyed by soap (externally). Vaccines stimulate your immune system to develop antibodies that destroy specific pathogens (that is, the vaccine works against just one pathogen), either viruses (e.g., measles) or bacteria (e.g., diptheria). Pneumonia is an infection of the alveoli in your lungs, and can be caused by bacteria, viruses, or fungi.

Ant lion Mar 15, 2020 01:03 PM
Understanding the World of Viruses and Outbreaks

Great summary. However the jury is still out on pangolins as a possible intermediate host. The first coronavirus studied from pangolins is about 90% similar to covid 19, which may be a hybrid of bat and pangolin viruses or simply a virus in one of the 2 that has not been sequenced yet.

jqb Mar 15, 2020 01:15 PM
Understanding the World of Viruses and Outbreaks

Yep. Note that COVID-19 is the name of the disease; SARS-CoV-2 is the name of the virus that causes it--bats carry coronaviruses but are apparently immune to the diseases they cause (why is not well understood). Robert's nice report is slightly confused about this (which is understandably common).

sbrobert Mar 16, 2020 09:40 PM
Understanding the World of Viruses and Outbreaks

Here Dr Arias has made this talk available online when she gave it to a different audience: https://www.mcdb.ucsb.edu/news/all/2020/new-virus-block-sars-cov-2-and-covid-19-pandemic

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