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Send in the Clones...don't bother they're here!

That title is not totally appropriate of this post, but I have had it in my mind for a while but have not done a post on clones. Since the subject of this post - viruses - mutate (essentially "clone" themselves) and reproduce by asexual duplication (essentially "cloning") this gave me the opportunity to use it. Hey, I like it.

I wanted to do an informational post on viruses. There is a lot of concern (understatement much?) today as I write this as we are in the midst of a viral pandemic caused by the SARS-CoV-2 virus, which causes Covid-19. This is not meant to be a scientific treatise, study, or paper. I will take liberties with certain processes and descriptions, but it is factual to the best of my knowledge and research. I am not a scientist, doctor, or medical professional. I am a lifelong student of almost anything and have studied health/medicine/diseases for most of my life with emphasis placed on this study when my wife was diagnosed with an incurable rare disease in 2005 - Multiple System Atrophy, FYI.

What is a virus? I would wager almost 100% of adults have been told they have a "virus" or 'viral infection" at some point in their life, but does everyone understand what they are? Everyone has had a cold, "stomach bug" (which we inadvertently sometimes call food poisoning, when it is not), cold sore, flu, or other sickness/issue caused by a virus. Viruses are very, very prevalent in the world. They live in animals, bodies of water, soil, humans - really anywhere. More than 30,000 different virus isolates are known today and grouped into more than 3,600 species (219 of which are currently known to infect humans), in 164 genera, and 71 families. There are discussions below on the major classes of viruses. Now, most viruses cannot live but in a certain environment. (see below for an additional explanation, but viruses do not actually "live". However for simplification I will use this term in most cases - again, NOT A SCIENTIFIC paper) That is good for us as humans as the vast majority of viruses are in the category of not being able to infect/live in us. The bad news is: viruses are always mutating. That means a virus that cannot infect humans can (and do) mutate into a form that can infect humans. 

Viruses are not "alive" in a sense that we were taught about in science/biology class. Some of you probably remember seeing something like this:

The seven characteristics of life include:
  • responsiveness to the environment;
  • growth and change;
  • ability to reproduce;
  • have a metabolism and breathe;
  • maintain homeostasis;
  • being made of cells; and.
  • passing traits onto offspring.

Viruses do not do most of that. Their sole existence is to reproduce (really replicate). They do not eat, grow (individually), etc.; they just replicate. Viruses are parasites. They cannot reproduce (their sole purpose of existence) outside of a host. That is also good for us. It means they are relatively easy to kill and will die on their own in a relatively short period of time anyway when exposed to an environment outside of their designated host. There are exceptions I will admit, but luckily most are not subject to infecting humans. Some examples: certain types of cold viruses are known to "live" (remember a virus is not actually alive by definition) on certain surfaces for up to a week or so. This is the exception, but helps explain why colds are so prevalent and so resistant to any "cure". The flu virus is thought to be active for no more than 24 hours in most cases on most surfaces. The SARS-CoV-2 virus is still being studied but it appears to be somewhere closer to the flu than the cold in at least that respect.

Viruses are a "sack" of DNA or RNA. They can be a single strand of either, or a double strand of either. Both types are encased in a protein sheath (sack). There is no inlet or outlet, no reproductive organ, no mitochondria for metabolism, no nucleus, just a sack of DNA or RNA. There are viruses that are simple enough to encode only 4 proteins and some complex ones that can encode 100 to 200 proteins. ( a refresher: DNA and RNA carry genes that can reproduce an entire organism - DNA; or just proteins - RNA. The D in DNA is for deoxy a prefix that means remove oxygen. The difference in the two is this fact. The D and R have different simple sugars, with  different structures (remember, this is NOT meant to be a scientific article! I know I oversimplified that!!) Although not a reason for the name, you can also say that the "D" in DNA is for double, as it is a double helix and RNA is not.

There are two large classes of DNA viruses (brilliantly called Class 1 or Class 2) and four large classes of RNA viruses (you can talk among yourselves for figuring out their Class names). Type 6 of RNA viruses (the 4th type - they are consecutively named with the DNA virus classes - did you get it right above?) are called "retro-viruses for reasons I will not get into here for simplicity. Suffice to say their structure is different than standard viruses. If you want to do research on your own, here is a graph showing an example of the six types:  

from one of the sources I used for this. FYI, this is now considered an obsolete way of classifying viruses. However, it is the one I studied in the past and am more comfortable with. It is more common now to use a molecular analysis of their replicative cycle. Using this system there are seven classes:

  As mentioned above, there are many, many viruses (219 species) of viruses that can infect humans. Rather than me type out a LOT more "stuff" here is a link to a page that shows the types:

 On that page is an embedded link to a similar chart that shows the diseases associated with each virus. Also, almost every virus has a link embedded within its name for additional information.

In the chart you can see that the corona viruses, of which SARS-CoV-2 virus is one, are single stranded positive RNA viruses. 

Once in a population and causing illnesses, can be classified in another way, by the R0 factor (pronounced R null, or R naught). This is an indication of the number of people that are likely to be infected by a patient with the infection. For example, if the R0 factor is less than R1, each infected person will infect less than one other person. This means the disease will die out. (and is somewhat used to warrant "social distancing") With a new disease, the R0 factor generally assumes no prior infections (no antibodies) and no drugs/vaccines for the disease. If any of these variables exist, the R0 factor will be much lower. If the R0 factor is R1, each patient will infect one other. The disease will sustain but not reach an outbreak or epidemic.

If the R0 factor is greater than R1 that is where the disease causes great infections in the population. Hepatitis and Ebola are both R2 diseases - 2 people infected per patient. This means it can grow rapidly and needs to be aggressively attacked. HIV and SARS have a R4 rating. Now HIV and SARS are both under relative control now. That shows the R0 factor can be mitigated and controlled, at least somewhat, with medical/societal activities. Mumps and Measles are much more virulent with a R10 for Mumps and a R18 for measles. This means without extreme measures or vaccinations both of these can go through a population very quickly. Luckily we have vaccines for both. It just requires a very large percentage of the population to take them to be effective.

To give you some examples, seasonal influenza is put at 1.2 to 1.4 with that average being used for most purposes - 1.3. H1N1 or swine flu has been pegged at 1.4 - 1.6. You may have seen Covid-19 specified as a "novel" coronavirus early on when it was mostly in China. That means it had not been seen in human populations and no information was known on it. Care was limited to treating symptoms. The R0 value at that time was placed at R1.5 to one clinician in China saying he thought it was a R4 or so. Although the "true" number is hard to determine on a moving target most of the figures I can find now put it at a R1.8 - R2.5 or so. That makes this more virulent than H1N1/swine flu but less than SARS. 

One other rating of a disease is the Case Fatality Rate or CFR. This is a percentage of patients diagnosed that die from the disease. This is a moving target somewhat like the R0. The more that is learned about the disease the more treatments can be structured to care for patients. A lot of patients died early on in China as the speed with which the disease progressed, especially in the elderly and/or those that already had other medical issues that the medical staffs were overwhelmed. They were running tests to determine what was wrong not knowing that in severe pneumonia was setting in. The CFR during this period was estimated to be 2.3% overall with a 14.8% for those 80-89 years of age and 8% in those 70-79. Those that were already in critical condition had a CFR of 49%. Now that there is some information and history of the disease as well as knowledge in the population of what symptoms to look for, most expert opinions I could find say they think the CFR will end up at 1.5 to 2.5 when this is over. All commented that it will probably be artificially high as such a large number of infected patients are asymptomatic thus do not report to or seek medical care. (then there are outliers like Italy - that could change things or be a mutation - see more later)

One final comment about CFR and R0. A disease with a high CFR and R0 typically does not make it. What do I mean? Well, if the virus acts quickly and infects a large portion of the population and then kills the hosts/patients it cannot efficiently spread as needed to keep growing. These viruses drop from the population or mutate to come back later. Which is my next subject.

One other factor on viruses that can make them both more deadly and worrisome and less of an issue; the fact that they mutate and change. There was a great quote that I saw a few days ago from an epidemiologist that said (paraphrasing as I did not write it down and cannot find it now) "Only in movies do viruses mutate to become more deadly!" Most viruses actually mutate to do less damage to their hosts for the reasons above. The only purpose of a virus is to make other viruses. As a parasite that can only take place in a host, if the viral disease and symptoms caused kills too many of the hosts too quickly their whole mission is foiled and they die out. There is already one mutation that has been identified in the SARS-CoV-2 virus. It has proven to cause less death in those infected. That is a good thing!

I hope you find this informative. I find those little critters that can infect us to be fascinating. They exist just to exist and make more of themselves. They bear us no ill will; in fact, they need us to exist in a lot of cases.                                                                                           


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