This past week it was reported that was a new COVID-19 mutation had taken over and that this strain was more infectious than the prior circulating strain.  Depending on your source for this information, the implications of a more infectious strain may or may not have been clear.  Today will provide a little primer on what is the prime directive for a virus, what a mutation is, how a mutation affects the viral prime directive and why that does not always correlate to increased severity of disease.

This weeks listening recommendations were selected based on the theme mutation.  First up, Pastime Paradise by Stevie Wonder.  Released in 1976 on the album Songs in the Key of Life (a must listen), it resonates today as much as ever.  While the song ties in based on use of the word “mutation,” it was my way to get you to eat your musical veggies.  This album should be a staple of any music library.  Second listening suggestion for the week is Beck’s album “Mutation.”  Great album from an artist that just doesn’t get enough credit in general.

What is The Viral Prime Directive?

Viruses have a singular goal, and that goal is to propagate theirselves.  In the case of COVID-19, that involves the need to accomplish several tasks: gain access to a host, be able to replicate itself, assemble itself, and exit the cell to seek out another to infect.  Wash, rinse, repeat.

Viruses are essentially common criminals.  They begin their lifecycle with a demonstration of lock picking skills.  In the case of COVID-19, it means that the virus attaches to the ACE2 receptor that is found on the surfaces of cells throughout much of the human body (lungs, heart, blood vessels, kidneys, liver, and GI tract to list a few).   The ACE2 receptor does not exist to permit COVID-19 entry, but rather is part of the system that regulates your body’s blood pressure and prevents organ damage.   The “spike” protein you have come to know and love is the “key” that COVID-19 uses to pick the lock.

Once the key is in the lock, the key is turned and the lock opens.  For COVID-19 this means that the envelope that surrounds the virus becomes one with that of the cell, resulting in the release of its genetic material (composed of RNA) and some protein into the cell.  As this is starting to read in a manner where it will require a PG-13 rating, please refer to the picture below for a visual of this process.

So far, COVID-19 is guilty of only a misdemeanor for breaking and entering.  What it does next to achieve its prime directive is most definitively felonious.

Once the COVID-19 genetic material and proteins gain access to the cell, they hijack typical cellular machinery to replicate themselves.   It’s akin to breaking into the NY Times factory and directing the printing press to make copies of your own manifesto. Once replication has occurred, the new viral particles are assembled within the host cell prior to their escape to look for new victims.  Viruses are about as considerate as many rock stars in a hotel room.   They steal part of the cells membranes and generally are blasting holes through them on their way out.  The process is called exocytosis.

How To Make a Mutant

Replicating genetic material is a process not unlike copying a passage in a book by typing it on your word processor of choice.  Mistakes are made, and they are called mutations.  Some mutations are called base substitutions.  They are the equivalent of hitting a wrong key on the typewriter.  Others are called deletions and are what they sound like – essentially forgetting an entire sentence.  Lastly, there are insertions, and are also what they sound like – adding additional sentences that were not present in the original document.

So what happens when a mutation occurs?  Sometimes nothing changes.   Other times, the mutation results in a change in the proteins that genetic material codes for.  This can alter the abilities of that protein in ways that can render it useless, give it superpowers, or anything in between.

Learn a smidge more about they types of mutations that occur

Remember that the viral prime directive is to propagate itself.  A successful mutation from a viral perspective therefore is one that permits improvement in meeting its prime directive of propagation.  This could be by developing a better key to pick the entry lock into the cell.  It could be learning ways to crank up the speed of the printing press to make more of itself.  Lastly, it could be learning how to escape just a bit faster.  Notice, none of these has anything to do with causing disease.  It is not part of the viral agenda to make you sick.

COVID-19 Mutants

Circling back to the news…

A study published last week in the journal Cell describes demonstrated that over the last several months a strain of COVID-19 (G614 SARS-CoV-2) has replaced the previously predominant strain (D614 SARS-CoV-2) worldwide.   A single base pair copying error resulted in a spike protein that has a slightly different shape and appears to make it easier for the viral and cell membranes to fuse after binding to the ACE2 receptor.

At this time there is no evidence that this change has any significant effect on those infected.  To reiterate, the prime directive of the virus is propagating itself.  It achieves no additional benefits through making you ill.  In fact, making you ill too quickly and/or too severely is disadvantageous to its prime directive as it limits the ability to permit spread of the virus.  In some cases, we can get lucky and the virus will propagate faster though have less ability to make you ill.  Fingers crossed on this one.

General COVID-19 Update

At this time the trend in the country as a whole is clear (screen capture below from WHO website).  The number of cases are escalating.  As has been mentioned in prior posts, it is tough to decipher how much of an effect increased testing impacts this number.  More alarming is that the number of deaths in the country has been steadily increasing again for about one month.  Each of the last four days there have been over 1000 deaths reported nationwide.  That has not occurred since the end of May.  New York currently is holding tight, though if the nationwide trend continues, there is little chance of a state escaping the collective fate while remaining open for business.

School Openings Update

School districts are actively planning for how to reopen in the fall.  Guidance from the state level is due over the next few weeks.  The CDC has already been providing some guidance.  There are many issues pertaining to the decision to open schools and to date not a tremendous amount of data to assist.  The journal Science printed a nice summary of how many other nations have handled the situation to date.   

If all remains status quo here in New York with respect to hospitalization rates, which have been at least stable if not declining, let’s hope for a return to school at least part-time for all students.  Depending of district capabilities, maybe closer to full time for our younger and special needs students that need in school services and education the most.

I will close today with answering some frequently asked questions.  Hope everyone stays safe and gets to enjoy some sunshine this week.

Can I get a medical exemption for my child to not be required to wear a mask in school?

No.  The CDC guidelines are clear as to what would qualify as an exemption.  They exemptions mentioned are being younger than 2 years, having trouble breathing, or being unconscious, incapacitated or otherwise unable to remove the face covering without assistance.  Trouble breathing means the type of difficulty by which you would be heading to your local emergency room, not “I can’t breathe with this thing on.”  These guidelines include those with special needs.  If you have children with sensory issues (such as autism), it is best to start desensitizing them now.  Schools may on their own permit such children to go without a mask, but there is no medical reason to base that on.  Remember, this is not a case where it may cause a teacher inconvenience, the student could be the direct cause for infecting and killing their teacher, and they have the right to be protected from such.  I have two step-children on the autism spectrum.  They have both been able to comply with wearing masks when required.

Can I get a letter clearing my recently ill child for school?

Of course you can.  This is of course once you meet the following criteria:

  1. At least 10 days have passed since the onset of symptoms
  2. At least 24 hours have past since the resolution of fevers WITHOUT using medication to keep fevers at bay (ie: acetaminophen or ibuprofen)
  3. Other symptoms have improved

Note, these are the criteria for home isolation for a person with COVID-19.  If there are symptoms consistent with even mild COVID-19 infection, these are the criteria we will follow.  Getting a negative test will not alleviate these directions as the false negative rate for the tests remain very high.  In addition, most of the labs that are performing PCR testing have a one week lag on getting results which is essentially the same duration of the instructions we are providing.

I require a test prior to going to college/work/my mother’s house, can you assist?

Yes.  We will have rapid tests in the office – we already have the tests, just waiting on the machine to run them to be delivered.  Hopefully we will have the technology in the next couple of weeks.  Until then, we can provide scripts for testing in these cases.  I do not believe that this strategy is effective due to the false negative rates of those without symptoms, but would rather perform the test than send folks to a lab to do same.   

What if a household contact has COVID-19?

If you have a household member who tests positive for COVID-19, you bought yourself a 14 day stint at home, Willy Wonka style – nobody comes in, nobody goes out.

What constitutes exposure to COVID-19?

Any individual who has had close contact (defined as less than six feet apart for at least 15 minutes) with someone with COVID-19 symptoms or someone who tests positive for COVID-19 with or without symptoms two days prior to testing or until they have met criteria for discontinuing home isolation (see above question regarding school clearance).