A Blast From The Past

Quixote Virus

I. Background

As reported in previous posts, the "1918 Pandemic virus" has been charged and booked:

>gb:AF116575|Organism:Influenza A virus
(A/Brevig Mission/1/1918(H1N1))
|Strain Name:A/Brevig Mission/1/1918|
Segment:4|Subtype:H1N1|Host:Human
ATGGAGGCAA GACTACTGGT CTTGTTATGT GCATTTGCAG CTACAAATGC
AGACACAATA TGTATAGGCT ACCATGCGAA TAACTCAACC GACACTGTTG
ACACAGTACT CGAAAAGAAT GTGACCGTGA CACACTCTGT TAACCTGCTC
GAAGACAGCC ACAACGGAAA ACTATGTAAA TTAAAAGGAA TAGCCCCATT
ACAATTGGGG AAATGTAATA TCGCCGGATG GCTCTTGGGA AACCCGGAAT
GCGATTTACT GCTCACAGCG AGCTCATGGT CCTATATTGT AGAAACATCG
AACTCAGAGA ATGGAACATG TTACCCAGGA GATTTCATCG ACTATGAAGA
ACTGAGGGAG CAATTGAGCT CAGTGTCATC GTTCGAAAAA TTCGAAATAT
TTCCCAAGAC AAGCTCGTGG CCCAATCATG AAACAACCAA AGGTGTAACG
GCAGCATGCT CCTATGCGGG AGCAAGCAGT TTTTACAGAA ATTTGCTGTG
GCTGACAAAG AAGGGAAGCT CATACCCAAA GCTTAGCAAG TCCTATGTGA
ACAATAAAGG GAAAGAAGTC CTTGTACTAT GGGGTGTTCA TCATCCGCCT
ACCGGTACTG ATCAACAGAG TCTCTATCAG AATGCAGATG CTTATGTCTC
TGTAGGGTCA TCAAAATATA ACAGGAGATT CACCCCGGAA ATAGCAGCGA
GACCCAAAGT AAGAGATCAA GCTGGGAGGA TGAACTATTA CTGGACATTA
CTAGAACCCG GAGACACAAT AACATTTGAG GCAACTGGAA ATCTAATAGC
ACCATGGTAT GCTTTCGCAC TGAATAGAGG TTCTGGATCC GGTATCATCA
CTTCAGACGC ACCAGTGCAT GATTGTAACA CGAAGTGTCA AACACCCCAT
GGTGCTATAA ACAGCAGTCT CCCTTTCCAG AATATACATC CAGTCACAAT
AGGAGAGTGC CCAAAATACG TCAGGAGTAC CAAATTGAGG ATGGCTACAG
GACTAAGAAA CATTCCATCT ATTCAATCCA GGGGTCTATT TGGAGCCATT
GCCGGTTTTA TTGAGGGGGG ATGGACTGGA ATGATAGATG GATGGTATGG
TTATCATCAT CAGAATGAAC AGGGATCAGG CTATGCAGCG GATCAAAAAA
GCACACAAAA TGCCATTGAC GGGATTACAA ACAAGGTGAA TTCTGTTATC
GAGAAAATGA ACACCCAATT

(1918 Virus in FASTA format, bold added to show segments found in both the 1918 Pandemic virus and the Sars-Cov-2 virus).

The next thing to do was searching for all 122 of the segments in that 1918 genome to see which ones are also in the current SARS-CoV-2 virus that causes COVID-19 infections.

II. Groupies

The three sequences of the 1918 viruses that are in bold in Section I above are in fact found at various locations within the SARS-CoV-2 virus.

Therefore, I have grouped the genomes by location, that is, where the locations of both the 1918 virus and the SARS-CoV-2 virus are repeated (in different people and different geographical locations).

An example of a matched group, for example, would be a list of genomes that have this match-up: "350:28650 480:1921 1020:26829".

There are three matches in that example, separated by spaces, the first being "350:28650".

The "350" means that the 1918 virus location of the 10-letter segment "ACTATGAAGA" begins at location 350 in the 1918 virus genome.

The colon separates the 1918 virus location from the SARS-CoV-2 virus location, so  the "28650" means that the same "ACTATGAAGA" segment begins at location 28650 in the SARS-CoV-2 virus.

The grouping is determined by changes in the SARS-CoV-2 virus location, since the 1918 virus locations are constant throughout (350, 480, and 1020).

Those three 1918 virus segments ("ACTATGAAGA", "AGCAAGCAGT", "CATTCCATCT") are the only ones found in the 8,218 SARS-CoV-2 virus samples scanned (note that all three are found in all 8,218 of the SARS-CoV-2 virus genomes).

The appendices are linked to in the menu table in Section III below:

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III. Menu of Links To Appendices

Matches By Group	Appendix Location
Group I	Appendix 1
Group II	Appendix 2
Group III	Appendix 3
Group IV	Appendix 4
Group V	Appendix 5

IV. Group Changes

An example of a group change is:

7674	MT641524.1	29845	350:28650 480:1921 1020:26829	USA WA S801 2020
0304	MT198652.2	29782	350:28621 480:1892 1020:26800	ESP Valencia003 2020

Each group file (Group I - Group V) has one or more groups of this sort.

The changes that rows are grouped by are changes to the location of the 1918 virus segments within the SARS-CoV-2 virus genome.

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V. Closing Comments

The significance of the fact that virus segments from the previous pandemic in 1918 are found in people around the world today is multifaceted.

For example, some other ancient virus segments in female humans is essential for giving birth:

"Consider placental mammals for example:

"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, cf. Retroviruses turned egg-layers into live-bearers, The placenta goes viral: Retroviruses control gene expression in pregnancy). What? Virus nucleobases in humans, virus genes that give us a start at life so to speak?"

(On The Origin Of The Home Of COVID-19 - 6). In that case, did all placental mammals, including female humans, get that virus merely by sneezing or coughing on one another?

Note that I am not yet commenting on these factors in terms of Virology or Genetics, rather, I am deducing what it can teach us statistically, logically, and logistically.

For example, in the groups shown in the appendices, the length of the virus can and does change from time to time, even when the locations of the segments do not change (in that group).

This indicates that the SARS-CoV-2 virus has been changed into either a recombinant virus or a reassortment virus, indicated by an addition of genetic material to the end of the genome (if it had happened at the front end of the SARS-CoV-2 virus, the locations of the three search-segments would have changed from 350, 480, and 1020 to something else).

This change to the SARS-CoV-2 virus happens during the host microbe ribosome's copying of the genetic material within the cell during the cell's reproduction of itself, that is one cell becoming two (normally identical) cells (On the Origin of the Genes of Viruses - 2 ).

So, when you peruse the groups and notice how many geographical areas around the globe have the same virus with the same segments of a century-old pandemic virus, and how many changed in length.

Then ask yourself "did all these millions of people thousands of miles apart, who have Covid-19 get it only by contact with other people IN JUST THE PAST SIX MONTHS?" ... (little wonder that "we don't completely know" is the answer to the question "how did the pandemic spread so fast").

Or, as an Oxford Professor suspects, do we have this virus in us due to food consumption, because our internal cellular-microbes were "mutualists" or "symbionts" with the now pathogenic SARS-CoV-2 virus, and have they been there harmlessly for a long time?

Did relatively recent events over a long span of time cause a change in their nature:

"We know that microbial life has flip-flopped from time to time, from pathogen to mutualist, which is in accord with life changing stressful events:

Like pretty much all multi-cellular organisms, humans enjoy the benefits of helpful bacteria. (As you may have heard, there are more bacteria in the human body than cells.) These mutualistic microbes live within the body of a larger organism, and, like any good long-term house guest, help out their hosts, while making a successful life for themselves. It’s a win-win situation for both parties.

Scientists still don’t understand exactly how these relationships began, however. To find out, a team of researchers from the University of California, Riverside, used protein markers to create a detailed phylogenic tree of life for 405 taxa from the Proteobacteria phylum—a diverse group that includes pathogens such as salmonella as well as both mutualistic and free-living species.

Those analyses revealed that mutualism in Proteobacteria independently evolved between 34 to 39 times, the researchers report in the journal Proceedings of the Royal Society B.  The team was a bit surprised to find that this happened so frequently, inferring that evolution apparently views this lifestyle quite favorably.

Their results also show that mutualism most often arises in species that were originally parasites and pathogens.

(Communicating With The Underworld). Humans are the same way, in the sense that they will become cannibals or worse in some stressful situations...

(If Cosmology Is "Off," How Can Biology Be "On?" - 2). There are some things we have to analyze more closely to find out.

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The following video will inform readers about the homes of Sars-CoV-2 (cellular mircrobes). It is very much worth your time:

Microbes

Video Index (time - subject)

00:21 - microbes are oldest life forms on Earth
01:03 - 10 times more microbes than human cells in us
01:31 - 100 times more microbial genes than human genes in us
02:00 - microbes are 99% of our make-up; they keep us alive
02:20 - microbes are vital for keeping us alive and healthy
04:20 - microbes talk with a molecular language
07:50 - quorum sensing (like a census) to know population count
08:20 - Intra species communication (shape of words) dialects
10:50 - microbes communicate with other microbes (multi-lingual)
11:20 - they take a census of all other microbes around them
12:30 - synthetic molecules-words interrupt communication
13:50 - synthetic molecules-words confuse the microbes
15:00 - they have collective, community behaviors
15:20 - microbes made the rules for multi-cellular development
16:00 - microbes invented multi-cellular behavior inside us
17:15 - the team

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Dr. Bonnie L. Bassler, Princeton University:

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