Thursday, December 31, 2020

The Virus that Stopped Time

In November 2019 an unknown species of coronavirus left a bat reservoir and by way of an intermediate host, possibly a Malayan Pangolin, entered the lungs of a human being living in Wuhan, China[1]. This species was zoonotic, meaning it could infect and spread within a human host. The invading virus had one objective: create more virus particles by hijacking the host cells' genetic protein building machinery. It was a parasite[2], like all viruses, that could not replicate itself on its own.

Shannon Stapleton/Reuters Shannon Stapleton/Reuters
A coyote stands by the roadside, as the spread of the coronavirus pandemic continues, at Golden Gate Bridge View Vista Point across from San Francisco, April 7, 2020.[3]

The microscopic virus particles, or virions, of this new species had protein shells, or nucleocapsids, and lipid envelopes that were spherical in shape and coated with spikes that looked like a crown (hence the name coronavirus). Inside each envelope was RNA genetic material having about 30,000 nucleotides. After entering the body by either the nose or mouth, the particles landed on cells in the host's respiratory tract and latched onto ACE-2[4] cell membrane receptors with their protein spikes. Molecular deception employed to unlock the ACE-2 receptors allowed the particles' envelopes to fuse with cell membranes.

Once a particle's membrane merged with the cell its genetic material was released into the cell's cytoplasm. This positive-sense RNA material was free to hijack the host cell's Ribosome (the yellow organelle in Figure 1). The Ribosome, the organelle that builds the proteins instructed by messenger RNA emitted from the cell's nucleus, treated the foreign invader RNA as messenger RNA and proceeded to build multiple coronavirus particle copies.

HepC replication

Virus protein parts were repeatedly synthesized within the connected sacs of the cell's rough endoplasmic reticulum and sent, along with copies of the original particle's RNA genome, to the Golgi apparatus. Within the Golgi apparatus the proteins and RNA copies assembled[6] into new virus particles. These virus progeny secreted to the cell's outer membrane and budded out one after the other to infect neighboring host cells.

Millions of particles were manufactured, upwards of 1,000 per cell, as the virus spread within the host's body. By coughing, sneezing, or just talking the host released water droplets into the air carrying a multitude of virus particles. Anyone close enough to the host to breathe in these droplets became another infected host. One infected host infected two to four others and each of these hosts infected a few others, and so on. The virus exploded exponentially throughout the community. Thus the COVID-19 pandemic began, a highly contagious pneumonia caused by the SARS-CoV-2 virus.

Travelers from Wuhan, China to distant corners of the world brought the SARS-CoV-2 virus with them. In every country where there was an outbreak the number of COVID-19 cases grew exponentially until the authorities realized something had to be done. There were only four cases in the world outside China on January 20, 2020. With an infection rate initially of about 20% that number grew to 44,900 cases 51 days later on March 11th.

NdThe number of cases on a given day
EThe average number of people someone who is infected is exposed on a given day
pThe probablility each person exposed to an infected person becomes infected
∆NdThe number of new cases on a given day

∆Nd = E ∗ p ∗ Nd
Nd+1 = Nd + E * p * Nd
Nd+1 = (1 + E * p) * Nd
. . .
Nd = (1 + E * p)d * N0

E * p = 0.2 (0.20065),
N0 = 4 cases on January 20, 2020,
d = 51 days,
Nd = (1 + 0.2)5 * 4 ≈ 44,900 cases on March 11, 2020.[7]

Infographic: The Spread of the Coronavirus Outside China | Statista You will find more infographics at Statista

In March, 2020, countries around the world locked down. Business offices and factories closed, employees worked from home, and doctors and nurses in hospitals were overwhelmed by the disease. Workers not considered essential were laid off or fired. Former restaurant, bar, and hotel employees soon ran out of money to pay for food and rent. Airplanes languished in hangers, cruise ships remained moored to docks, and foot and car traffic quieted. The pulse of civilization slowed until for a moment it stopped.

The environment got better. Air and water pollution levels dropped. Global energy-related CO2 emissions dropped by two billion metric tons as energy demand fell by 25%. The drop in nitrogen dioxide levels over China could be seen from space. Waterways like the Venice canals were clear. The Alps and the Himalayas could be seen from a distance in the daytime. At night, the stars and nearby planets shone bright in the sky.

The streets were empty, it was a lot less noisy, and the animals noticed. Goats and wild boar came down from the hills to forage in towns. Deer roamed in London, coyotes in San Francisco, otters in Singapore, and penguins in Cape Town. Alligators window-shopped in Myrtle Beach, dolphins played in city sea ports, whales sang in seas the cruise ships had sailed, and birdsong was loud. This was a reprieve from the sixth extinction[8] that couldn't last. Human industrial activity had to return.

We are leveling the wild places. One consequence are the animals we come into contact with have reservoirs of unknown viruses. Some of these will cause zoonotic outbreaks. Outbreaks occur all the time all over the world. One of these will turn into another pandemic. Until we find a new vaccine we'll be culled like the animals we find lurking in the forests and wetlands we knock down. Either that or some lab somewhere will invent a virus that will wipe us all out.

Scale

Viruses exist in an invisible ubiquitous cloud around us and inside us. They are found everywhere there is cellular life, in the air, soil, water, and on and inside plants and animals. They are found near volcanic vents on the ocean floor, under the polar ice caps, and high in the atmosphere swept up by sea spray and wind currents. Electron microscope measurements of soil and ocean water samples determined that there are ten times more viruses than bacteria. In ocean water their number is calculated to be 107 virus particles per milliliter. That is 49.3 million in a single teaspoon. Most viruses in the ocean are bacteriophages that infect bacteria, but there are about 100 million virus species and most haven't been identified. Given these numbers, the number of virus particles in all the oceans is estimated to be ~1031.

107The number of virus particles per milliliter of ocean water
321,003,271Cubic miles of water in all the oceans
4.168182 * 1012Number of liters in a cubic mile of water
13.38 * 1023Number of milliliters of water in all the oceans
1.338 * 1031Number of virus particles in all the oceans

The number of virus particles everywhere on Earth at any one time is about the same order of magnitude as tne number in all the oceans.[9] A single virus particle generally varies in size between 20 to 300 nanometers[10], although very large viruses, on the order of 500-1000 nanometers, have been discovered[11] (the coronavirus particle's average size is in the middle at 120 nanometers). If the average size of a virus particle is assumed to be close to an average T7 bacteriophage, or 60 * 10-9 meters, what would be the length of a row of 1031 virus particles on earth if they could be laid end-to-end? The answer is the length of ~60 Milky Way galaxies laid end-to-end.

60 * 10-9Approximate diameter of a virus particle in meters
9.461 * 1015Length of one light year in meters
1031Estimated total number of virus particles on earth
105,700The diameter of the milky way in light years

60 * 10-9 * 1031 = 60 * 1022 meters
60 * 1022 / 9.461 * 1015 = 6.34 * 107 light years
6.34 * 107 = 63.4 million light years = length of 1031 virus particles laid end-to-end
63.4 * 106 ≈ 600 Milky Way galaxies laid end-to-end[12]

Viruses are an example of how something can have more than one perspective of scale. From one perspective viruses are very small and from another they are very large.

Statistics

COVID-19 Fatality Rate by Condition
Cardiovascular disease 13.2%
High blood sugar 9.2%
High blood pressure 8.4%
Chronic respiratory diseases 8.0%
Cancer 7.6%
COVID-19 Fatality Rate by Age
0 - 9 0%
10 - 19 0.2%
20 - 29 0.2%
30 - 39 0.2%
40 - 49 0.4%
50 - 59 1.3%
60 - 69 3.6%
70 - 79 8.0%
80+ 14.8%
US COVID-19 Fatality Rate by Race Age Adjusted
Pacific Islander 0.197%
Indigenous 0.173%
Latino 0.193%
Black 0.182%
White 0.079%
Asian 0.073%
All with known race 0.100%

Notes

  1. I'm describing my basic understanding. It may not be a coincidence that a lab dedicated to the study of viruses was also in Wuhan. It's suspicious, if true, that the coronavirus was not found in any of the animals at the wet market where the outbreak officially originated.
  2. "A virus is an obligate intracellular parasite." What is a virus?
    Virology Lectures 2020, Prof. Vincent Racaniello, Columbia University, ©Principles of Virology, ASM Press
  3. Photo licensed from Reuters Pictures according to their Terms and Conditions.
  4. The ACE-2 receptor resides on cells lining the gastrointestinal and respiratory tracts, blood vessels, kidneys, and lungs. This receptor protein pokes out from the cell membrane's outer surface and extends to its inner surface. When the body's blood pressure needs to be lowered, an enzyme called shaddase cleaves away that part of the receptor that's outside the membrane. The cleaved portion enters the circulation to counteract the effects of the angiotensin-2 hormone. The cell's protein building machinery rebuilds the external part of the receptor.
  5. GrahamColm at English Wikipedia - Transferred from en.wikipedia to Commons by Leptictidium using CommonsHelper, Public Domain, https://commons.wikimedia.org/w/index.php?curid=4783979
  6. "And yet, under the right conditions, basic viral components can accomplish what many natural phenomena cannot: a process called self-assembly, combining their bits into neat, structured particles without any external forces to guide them, like cake ingredients mixing themselves into batter or snowflakes sprouting spontaneously out of room-temperature water."
    If You Squeeze the Coronavirus, Does It Shatter? By Katherine J. Wu, New York Times, Jan. 26, 2021.

    Logically, viruses can't be older than cells because viruses need cells to replicate. But it's possible a proto-virus particle bootstrapped itself from a set of protein parts before the beginning of cellular life.
  7. There are many curves describing natural phenomenon that start out as exponential but ultimately they're all logistical curves. An inflection point is reached and the curve begins to level off. Even if no precautions were taken and a vaccine never arrived the spread of the virus would level off when it began to run out of humans to infect.
  8. The Sixth Extinction: An Unnatural History By Elizabeth Kolbert, Copyright © 2014, Henry Holt and Co., New York.
  9. Are There 1031 Virus Particles on Earth, or More, or Fewer?, A. R. Mushegian, William Margolin, Editor, American Society for Microbiology Journal of Bacteriology, Published: 2020-02-18
  10. Size and Shape of Viruses Microbiology (Kaiser), Biology LibreTexts, January 3, 2021.
  11. How big are viruses? Cell Biology by the Numbers, Book, BioNumbers.org.
  12. A length of 63.4 * 106 light years is conservative. On-line articles and videos generally quote 250 million light years. I read one article that quoted 100 and another that quoted 200. The "Introduction to Virus Ecology and Evolution" video by Dr. Paul Turner, quotes 250 million light years as the length of the unraveled genetic material of each virus laid end-to-end. The idea that a teaspoon of salt water has enough virus particles that if laid end-to-end would extend about three meters makes more sense after considering that this contigurous stack of particles would have s width about 1/1,000 of a human hair.

References

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