Saturday, July 18, 2020

On The Origin Of The Home Of COVID-19 - 10

Fig. 1 Lineage
I. Preface

I have found high percentage matches for virus RNA/DNA ("Most viruses have either RNA or DNA as their genetic material" - NCIB) in a wide variety of creatures.

I am a software engineer, so my study of viruses is primarily composed of reading scientific papers for the nuts and bolts of their concepts of DNA/RNA, but it does not stop there, because I make software tools that very quickly analyze millions of nucleotides, by comparing, organizing, and finally writing reports about them.

The bulk of research scientists have to explain what they want to a software engineer at some corporate location, which involves two nomenclatures (Nomenclature).

Conversations in two "languages" (computer Latin & science Latin) can lead to misunderstandings or weakened understandings.

Further, the bulk of research scientists have management constraints.

Since I don't have to be told what to research or explain what I want to a programmer, then wait to see if the software produced is what I wanted, I have more freedom to explore what I want to explore, and make the tools with which to do it.

So, my analysis result is "gray/grey literature" that is free from the constraints of corporate management and politics:
"That which is produced on all levels of government, academics, business and industry in print and electronic formats, but which is not controlled by commercial publishers."
(Fourth International Conference on Grey Literature). Corporate politics can cover up what is really happening during funded research projects, rather than uncover what is really happening (The Ghost-Water Constant - 9, quoting Dr. James Hansen describing "The Mercer Effect").

II. Hypotheticals

I have, in previous posts in this series, hypothesized that the SARS-CoV-2 virus found in humans came from microbes that are being killed by various means.

This, I postulated, is happening in the realm of mass-produced animal meat in mass production farms and factories, a.k.a. "the whole process of rearing animals for slaughter" (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6, 7, 8, 9).

While reading articles in the commentariat,  I have been wondering if the saying "opposites attract" applies in the ongoing Covid-19 mystery.

I say that because I read "we still don’t have enough evidence to write an origin story for the cause of the coronavirus disease of 2019" according to (Virology Down Under).

Then, in another place I read "to date, the coronaviruses in livestock are not considered reportable diseases ... the most common coronaviruses found in production animals ... have not yet infected humans" (Feedstuffs).

Oh? What about:
"However, it remains unanswered whether the infection of SARS-CoV-2 could occur via ingestion and whether the virus can survive passage through the stomach."
(On the Coronaviruses and Their Associations with the Aquatic Environment and Wastewater, p.4, emphasis added).

I wondered why the location of one of the conglomerations of coronavirus populations (meat mass-producer factories) is not suspect, while obscure markets are:
"So what is it about these places that makes them such dangerous incubators for the novel coronavirus? It’s a question that urgently needs answers, especially now that concerns over food shortages and an order given on April 28 by President Donald Trump classifying meat processors as critical infrastructure are already forcing workers back to the production line. Like most aspects of the pandemic, this one, too, is complicated by a dearth of data. Figuring out how exactly the disease is spreading between workers and which slaughterhouse practices are to blame is going to take time and lots of epidemiological legwork."
(The Workers Did It). They go on to point out that the suspects are not the meats because we do ... er ... don't ... er... do ... er ... do or don't ... know that coronavirus specimens are in the animals (they are there, see On The Origin Of The Home Of COVID-19).

So the suspects are the workers? ... yep, they did it, those Covid-19 card carrying workers did it, exclaim the Ignorati.

The idiotic reaction of politicians was to order the meat-factory workers to keep doing it (Trump orders meat processing plants to stay open).

The government had to order them to stay open because the Covid-19 pandemic was making the employees sick and/or killing them (ibid).

III. Big Slaughter Economy

Agriculture is "the science, art, or practice of cultivating the soil, producing crops, and raising livestock and in varying degrees the preparation and marketing of the resulting products" (Merriam-Webster).

The current Secretary of Agriculture is a climate change denier who seeks to remove or weaken various regulations on corporate agriculture (Sonny Perdue).

Perdue supported the presidential order for meat production plant workers to stay put (USDA To Implement President Trump’s Executive Order On Meat and Poultry Processors).

So, is this agricultural slaughtering of animals a "big business"?

Here is a look at one player:
"Tyson Foods, Inc. is an American multinational corporation based in Springdale, Arkansas, that operates in the food industry. The company is the world's second largest processor and marketer of chicken, beef, and pork after JBS S.A. and annually exports the largest percentage of beef out of the United States. Together with its subsidiaries, it operates major food brands, including Jimmy Dean, Hillshire Farm, Ball Park, Wright Brand, Aidells, and State Fair. Tyson Foods ranked No. 80 in the 2018 Fortune 500 list of the largest United States corporations by total revenue."
(Wikipedia). "The industry" is a significant part of the US economy, and much more than only an ongoing mass slaughter of animals:
"'The U.S. food system is a complex network of farmers and the industries that link to them. Those links include makers of farm equipment and chemicals as well as firms that provide services to agribusinesses, such as providers of transportation and financial services. The system also includes the food marketing industries that link farms to consumers, and which include food and fiber processors, wholesalers, retailers, and food service establishments'.

The term food industries covers a series of industrial activities directed at the processing, conversion, preparation, preservation and packaging of foodstuffs. The food industry today has become highly diversified, with manufacturing ranging from small, traditional, family-run activities that are highly labor intensive, to large, capital-intensive and highly mechanized industrial processes. Many food industries depend almost entirely on local agriculture or fishing."
(Wikipedia). That is big enough to require special interest attention to control advertising and research by managing "how to tell us the truth as we should see it ... for our own good."

Speaking of "big", I found a big source of circumstantial evidence in the DNA/RNA records in GenBank, and have prepared many of them for the perusal by Dredd Blog readers.

It so happens that one of the major agricultural businesses in Europe has been destroyed by SARS-CoV-2, which is linked to a part of US Agribusiness, in that, offal food from the US "feeds" that European agribusiness.

Yes, that source of SARS-CoV-2 production, which the president ordered to stay busy (meat industry), exports its offal to Europe (and other countries).

More on that below.

The Appendices to today's post have HTML tables containing the results of one of my typical grey/gray literature analyses.

One interesting factor is that the SARS-CoV-2 viruses found in mink (raised on US offal) on the Netherlands fur farms is crippling:
"The Netherlands is one of 24 countries where mink farming is still legal. In a historic move, the Dutch parliament has voted to permanently close the mink fur farms shut down by COVID-19.
...
The spread of COVID-19 among mink across multiple farms since April resulted in at least two workers catching the virus from the animals and triggered calls for the government to rapidly shut down the industry. “Waiting until 2024 for the mink ban to take effect would have been unjustifiable and irresponsible,” says Sandra Schoenmakers, director of Dutch anti-fur organizations Bont voor Dieren. The latest available figures show that nearly 600,000 mink across 13 farms had been killed by gassing with carbon monoxide on the orders of the Dutch government, but many more are likely to be killed in the coming weeks.

Factory farms and slaughterhouses across the world have become coronavirus hotbeds due to cramped and unsafe working conditions, endangering the lives of workers who have been given inadequate protection by the companies that employ them. While transmission between workers on the Dutch mink farms has not reached the levels seen on agricultural farms, it presents the first case in which humans passed the virus to the farmed animals who then transmitted it back to humans.
...
The intensive breeding of animals on fur farms is an incredibly cruel practice that not only causes immense suffering to animals, but can also serve as a reservoir for coronaviruses
".
(Dutch Parliament Votes to Close Mink Fur Farms Following COVID-19 Outbreaks, emphasis added). The mink SARS-CoV-2 viruses match the human SARS-CoV-2 viruses on the CruiseA-18 cruise ship 99% in the segments comparisons, and about 30% in the sequences comparisons (the implication is that mass-produced meats are suspect as the origin of the virus).

Yes, the bustling mink industry was destroyed by the same virus found on the CruiseA-18 cruise ship, and the courts agreed to their demise (Dutch court confirms ban on mink farming in the Netherlands).

It is interesting that the feed for those mink is primarily cow, pork, and poultry offal (offal is the 'guts'):
"35,000 tons of fish (herring and sprat) catch are used for fur feed
160,000 tons of beef, pork and poultry offal used for fur feed
(Netherlands Fur Industry). That diet would be about 78% offal from beef, pork, and poultry.

The US food industry (Section III above) sells lots of offal to Europe (et al.) where it is fed to both animals and humans:
"Rarely found on menus in the U.S., variety meat – also called offal or fancy meat – takes many forms: kidneys, livers, stomachs, tendons, aortas, cheek meat, oxtails and more. And because it's highly sought after in key export markets of Egypt, Japan, Peru and Mexico, variety meat [offal] is gold to the U.S. beef industry.

According to the U.S. Meat Export Federation, total U.S. beef exports in 2012 set a new record at $5.51 billion. Beef offal represented $703.1 million, or about 12% of that. It also accounted for 28.4% of the total volume of beef exports.

And, virtually 100% of the U.S. livestock herd is represented in variety meat exports [offal] – some part of every animal is sold to international customers.

'Demand for both large and small intestines would tank without the international market,' says Jerry Wiggs, export salesman for Greater Omaha Packing Company Inc. (OPC). 'We are selling large intestines to South Korea or Koreans who recently moved to the U.S.'

Wiggs says OPC just recently resumed selling small intestines to Mexico, where they had been banned since BSE was found in the U.S. in late 2003."
(Offal Meats As Good As Gold For U.S. Beef Market). Exporting offal with SARS-CoV-2 viruses in it is a big business:
"Edible offal products, which are made from an animal’s intestines, internal organs, and other parts, rarely end up on American plates. Does that mean it simply goes to waste?

Thanks in large part to international trade, the answer is no. Culinary traditions in countries around the world call for the use offal in a wide variety of dishes ... In many places, certain offal products are even considered a delicacy. By looking beyond America’s borders, meat processors have been able to uncover lucrative markets and reach new consumers hungry for American food products.

Consider the case of Mexico, a country that consistently ranks as one of the leading importers of U.S. offal products, also known as “variety meats”. One of the most popular products is tripe, an offal made from a cow’s stomach."
(An Offal Lot of Exports: The Trade in Variety Meats, emphasis added). The offal food business is 'big', including sales to mink fur farms in many countries.

The fur farming nations list includes the USA (The Fur Trade).

IV. Appendices

In the appendices readers will find a "taxo" (taxonomy id) and a "lineage" designation within braces ("[]").

The "taxo" designation is the technical name of the virus being scanned by the Dredd Blog software.

The "lineage" designation is the historical lineage or pathway of the virus (see Fig. 1).

That pathway description will sometimes begin with "Coronaviridae->" then "betacoronavirus->" then "Severe acute respiratory syndrome-related coronavirus" or the like as depicted in Fig. 1 (See "Coronaviridae" and "Betacoronavirus").

As I indicated earlier, I want to now focus on the percentages of segments and individual nucleotide bases:
"A nucleotide is one of the structural components, or building blocks, of DNA and RNA. A nucleotide consists of a base (one of four chemicals: adenine, thymine, guanine, and cytosine) plus a molecule of sugar and one of phosphoric acid"
(NCBI, emphasis added). The (ACGT) matches in today's appendices compare the nucleotides taken from a person on board a cruise ship:
"SARS coronavirus 2 isolate 2019-nCoV
USA-CruiseA-18
2020"
to virus specimens that were found in various animal virus genomes (marked as "vAN") and various human genomes (marked as "vHS*").

Fig. 2 HTML table percentage locations
It is quite interesting that a cruise ship (CruiseA-18) way out in the ocean, which had not been to port for a couple of weeks, had several Covid-19 episodes.

I matched the virus nucleotides from that ship (data from GenBank) with many other nucleotide bases in GenBank.

I then made HTML tables for showing the results.

A lot of animals and other humans had about 99% match resulting from a comparison of vHS segments to vAN* and vHS* segments, and about 20-30% matches in terms of nucleotide alignment (see here for an explanation of nucleotide alignment, see here for an explanation of segment matches, that is, number of segments in the vHS genome that are also found in vAN or vHS* genomes).

The graphic at Fig. 2 shows where those percentages are positioned in the HTML tables (if you think Fig. 2 is difficult to discern or difficult to follow, check out this where CruiseA-18 is in it at about 4 o' clock, in the "big circle of tiny words").

Anyway, here are links to today's appendices so that you can take a look at the hundreds of DNA/RNA matches in them:

Nucleobase
Comparison
Appendix
Location
humanAppendix HS-1-99
humanAppendix HS-2-99
animalsAppendix AN-1-99

I am going to do a much more comprehensive report in future posts with appendices sorted by country and percentage.

V. The "Circumstantial" Coronaviruses

In my analysis of thousands of DNA & RNA from GenBank, where hundreds of thousands of nucleotides (DNA ACGT "genetic maps") are stored, I found that some SARS-CoV-2 virus DNA/RNA in animals matches ~99% with SARS-CoV-2 virus DNA from humans (humans on the CruiseA-18 cruise ship that was quarantined and in the news).

I will expand upon that evidence in future posts.

VI. Meanwhile

The news media influenced by big business has not focused much on the origin of SARS-CoV-2, but some of them say "China did it", others say "we don't know".

The focus of others in the media is on the proper reaction to the pandemic, which they say is "learn to live with it".

The structure of media news is an old one, in that, for about a century since the 1918 Pandemic caused by another coronavirus, big business in general is in it to deceive the public:
"Noam Chomsky: One of the most important comments on deceit, I think, was made by Adam Smith. He pointed out that a major goal of business is to deceive and oppress the public.

And one of the striking features of the modern period is the institutionalization of that process, so that we now have huge industries deceiving the public — and they're very conscious about it, the public relations industry. Interestingly, this developed in the freest countries—in Britain and the US — roughly around time of WWI, when it was recognized that enough freedom had been won that people could no longer be controlled by force. So modes of deception and manipulation had to be developed in order to keep them under control
"
(The Deceit Business). The American author of the book "Propaganda", also called the father of PR or spin, explains how that deceit is done "properly":
Ok, so now it is probably a safe time to pull back the curtain to reveal the wizard of odds, the father of MOMCOM DNA:
THE conscious and intelligent manipulation of the organized habits and opinions of the masses is an important element in democratic society. Those who manipulate this unseen mechanism of society constitute an invisible government which is the true ruling power of our country. We are governed, our minds are molded, our tastes formed, our ideas suggested, largely by men we have never heard of. This is a logical result of the way in which our democratic society is organized. Vast numbers of human beings must cooperate in this manner if they are to live together as a smoothly functioning society.
Edward L. Bernays

Our invisible governors are, in many cases, unaware of the identity of their fellow members in the inner cabinet.

They govern us by their qualities of natural leadership, their ability to supply needed ideas and by their key position in the social structure. Whatever attitude one chooses to take toward this condition, it remains a fact that in almost every act of our daily lives, whether in the sphere of politics or business, in our social conduct or our ethical thinking, we are dominated by the relatively small number of persons — a trifling fraction of our hundred and twenty [now 320] million — who understand the mental processes and social patterns of the masses. It is they who pull the wires which control the public mind, who harness old social forces and contrive new ways to bind and guide the world.
...
It is the purpose of this book to explain the structure of the mechanism which controls the public mind, and to tell how it is manipulated by the special pleader who seeks to create public acceptance for a particular idea or commodity. It will attempt at the same time to find the due place in the modern democratic scheme for this new propaganda and to suggest its gradually evolving code of ethics and practice.
(Propaganda, by Edward L. Bernays, emphasis added). Old Fast Eddie totally believed in propaganda, and was not all "don't ask don't tell" in the closet about it.
(A Closer Look At MOMCOM's DNA - 4). So, for those who want to know the origin, in addition to the proper way to react to a pandemic, read widely.

VII. Closing Comments

The appendices include a column ("vAN Information") that often includes a "lineage" item which shows how the current SARS-CoV-2 sequentially descended from previous viruses.

That is, how the microbe host of the virus changed it during that host's reproduction of that virus's RNA or DNA.

In future posts I want to analyze more closely the possibility that US beef, pork, and poultry are the location of the microbe homes of SARS-CoV-2 and its ancestors.

This has been done in less dramatic contexts:
"Recent advances in our ability to characterize the gut microbiota have led to tremendous interest in identifying organisms associated with different human diseases. Two general categories of disease that have attracted widespread interest are obesity, diabetes and metabolic syndrome, and inflammatory bowel disease including Crohn’s disease and ulcerative colitis. In both cases, significant associations with disease have been reported by different studies."
(Meta-analyses of human gut microbes, emphasis added). The current context of a pandemic would seem to be a candidate for that type of research.

Note that the meta-task must begin with an understanding that beef, swine, and poultry are meta-hosts, not originating hosts.

They are meta-hosts to the originating microbes that were in a symbiotic relationship with ancestors of coronaviruses (they became pathogens when their host microbes were killed with chemicals).

So, we have to analyze this "ugly all the way to the bone" scenario by searching all the way to the originating host microbe.

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

Offal is just another word for "Leftovers":



5 comments:

  1. "the possibility that US beef, port, and poultry" - Don't blame the wine! ~Survival Acres~

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  2. Good eye! Thanks. Corrected.

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  3. How did they get Covid-19? "The American Triumph has been at sea since June 27, when the vessel left hake fishing and headed to Alaska to fish for Wild Alaska Pollock. All crew members quarantined for a minimum of 14 days and passed all public health protocols in order to board the vessel." (American Seafoods)

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  4. It is not likely that the crew on the American Triumph got Covid-19 from "hake fishing":

    "... the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes COVID-19 in humans and the general societal concern of potential contamination of aquatic animals used as food or their products with the virus. SARS-CoV-2 belongs to the family Coronaviridae and genus Betacoronavirus. Betacoronaviruses are only reported to infect mammals. Currently, there is no evidence to suggest that SARS-CoV-2 can infect aquatic food animals (e.g. finfish, crustaceans, molluscs, amphibians) and therefore these animals do not play an epidemiological role in spreading COVID-19 to humans"

    (Asian Fisheries Science)

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  5. Randy ... gotta ring them bells link

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