Saturday, June 20, 2020

On The Origin Of The Home Of COVID-19 - 5

Earth's Most Abundant Entities
I. Background

This series is a follow-up of previous posts based on early blogging events that I experienced.

When anyone researches the impact of civilization on the Earth's ecosystems there will be times of concern.

Some years I back became concerned about the impact that current civilization was having on microbes / viruses.

One expected result from the impact of current societies was change we should not believe in or want:
"If we consider that certain types of viruses and microbes require or are naturally inclined to operate in or on specific plants and specific animals but not in or on others, we can hypothesize that as times get desperate for them, and then become catastrophic for them, they will radically morph (genetically and behaviourally)."
(The Real Dangers With Microbes & Viruses). Like humans, viruses in and on microbes that are being destroyed by antibiotics and other toxic chemicals have a life changing experience during humanity-induced ecosystem catastrophes.

As in times past, some of the victim microbes/viruses become no longer mutualists, morphing instead into pathogens, and perhaps back again (What Did The Mass Extinctions Do To Viruses and Microbes?).

In the first post I pointed out that we were given a notable clue as to places to begin our search:
"This lesson introduces students to the microbial world and provides insight on the function of microbes by examining bacteria that both help and harm cows. Although multiple bacteria inhabit the cow’s rumen, this lesson focuses on two harmless microbes, Ruminococcus and Selenomonas, which break down cellulose and starch in plant matter, respectively. These bacteria obtain nutrients from the cow’s diet, and the cow gains energy from the products of bacterial metabolism. Therefore, these bacterial species are in a symbiotic relationship with the cow. Other bacterial species can harm cows. Such is the case with Escherichia coli, a non-ruminant bacterium that can cause the udder infection known as mastitis."
(On The Origin Of The Home Of COVID-19). Thanks to the microbiologists who set us out on the right path.

Special thanks to those who point out that the beneficial virus realm in gut microbiota is not limited to ruminants (Move Over, Bacteria! Viruses Make Their Mark as Mutualistic Microbial Symbionts).

At times it is more than we can fathom:
"If not for a virus, none of us [placental human mammals] would ever be born.

In 2000, a team of Boston scientists discovered a peculiar gene in the human genome. It encoded a protein made only by cells in the placenta. They called it syncytin.

The cells that made syncytin were located only where the placenta made contact with the uterus. They fuse together to create a single cellular layer, called the syncytiotrophoblast, which is essential to a fetus for drawing nutrients from its mother. The scientists discovered that in order to fuse together, the cells must first make syncytin.

What made syncytin peculiar was that it was not a human gene. It bore all the hallmarks of a gene from a virus."
(The Uncertain Gene - 5). But I digress.

II. Ongoing Events In This Series

Recently, I have studied an interesting paper that deals with some of the issues related to the hypothesized 'home of microbes' where the coronavirus realm originated (Nature, Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery).

One of those 'homes of microbes' would be the microbes in the rumen of ruminants.

I mean ruminants that are "mass produced" ('unnaturally' produced) by "the meat industry" (factory animal meat producers).

I processed the nucleobases/nucleic acid sequences in some of those rumen with data that was linked-to in that paper.

Lo and behold I found sections of human-infected coronavirus nucleobases/nucleic acid sequences in the "rumen metagenome-assembled genomes" of the cows that were the subject of that study (the data in coronavirus nucleobases/nucleic acid sequences files were previously discussed in this series).

In other words, the cattle rumen (stomach) material contained a number of coronavirus nucleobases/nucleic acid sequences pattern matches (see Appendix - A , then review On The Origin Of The Home Of COVID-19, 2, 3, 4).

Appendix - A gives a very 'short' (but long) list of the scaffold_0 section of the compendium of files presented in the aforesaid paper published in Nature.

Note that the list in the appendix is a very small percent (some files not detailed in the appendix have a couple hundred scaffolds ... e.g. scaffold_0 thru scaffold_200), nevertheless you can get the idea from Appendix A that plentiful amounts of coronavirus base sections are found in the rumen of the studied cows.

Note that a 'section' in this case is ten 'ACGTU' contiguous base elements in a spaceless (no gaps) row ... (see the examples in the previous post and this nomenclature).

Note also that there will be many more examples in the coming days of this research.

III. Closing Comments

I had intended to cover bats, first, but when I ran across the article and the data I thought I had better post this right away ... after searching and having found evidence supporting the current hypothesis.

The next post in this series is here, the previous post in this series is here.

Nobel Prize For Literature winner says:


  1. "It’s spreading like wildfire across fur farms!

    THOUSANDS of minks at this Denmark fur farm will be killed after minks were found to be infected with #COVID19. Fur farms need to SHUT DOWN immediately!"

  2. US too ... "At least 12,000 mink dead as coronavirus spreads among fur farms in Utah and Wisconsin" (link).

  3. Dredd Blog hypothesises that it's because of what they are fed. “A major reason is that the Western farmers have access to large amounts of offal, including chicken heads, viscera and other waste parts of butchered animals, that go into their feed" (US Fur Commission).