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Sunday, July 5, 2020

On The Origin Of The Home Of COVID-19 - 9

T4 backteriophage
I. Spooky

In the previous post I quoted from a researcher who pointed out that a virus in the dead flesh of a victim of the 1918 pandemic was reactivated in a lab circa 1997-98 (How long can viruses survive in a dead body?).

Some indicated that the dead flesh came from permafrost in the vast Alaska wilderness of that time, or in laboratories that had saved some of the flesh of victims here and there.

Wow, who woulda thunk it?

Other sources indicated that the viruses nucleotide sequence had been revealed, so I looked it up (The Deadliest Flu: The Complete Story of the Discovery and Reconstruction of the 1918 Pandemic Virus).

Not only that, I found a copy of the nucleotide sequence in fasta format, so, I just had to show it to Dredd Blog readers:

>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
ATGGAGGCAAGACTACTGGTCTTGTTATGTGCATTTGCAGCTACAAATGCAGACACAATATGTATAGGCT
ACCATGCGAATAACTCAACCGACACTGTTGACACAGTACTCGAAAAGAATGTGACCGTGACACACTCTGT
TAACCTGCTCGAAGACAGCCACAACGGAAAACTATGTAAATTAAAAGGAATAGCCCCATTACAATTGGGG
AAATGTAATATCGCCGGATGGCTCTTGGGAAACCCGGAATGCGATTTACTGCTCACAGCGAGCTCATGGT
CCTATATTGTAGAAACATCGAACTCAGAGAATGGAACATGTTACCCAGGAGATTTCATCGACTATGAAGA
ACTGAGGGAGCAATTGAGCTCAGTGTCATCGTTCGAAAAATTCGAAATATTTCCCAAGACAAGCTCGTGG
CCCAATCATGAAACAACCAAAGGTGTAACGGCAGCATGCTCCTATGCGGGAGCAAGCAGTTTTTACAGAA
ATTTGCTGTGGCTGACAAAGAAGGGAAGCTCATACCCAAAGCTTAGCAAGTCCTATGTGAACAATAAAGG
GAAAGAAGTCCTTGTACTATGGGGTGTTCATCATCCGCCTACCGGTACTGATCAACAGAGTCTCTATCAG
AATGCAGATGCTTATGTCTCTGTAGGGTCATCAAAATATAACAGGAGATTCACCCCGGAAATAGCAGCGA
GACCCAAAGTAAGAGATCAAGCTGGGAGGATGAACTATTACTGGACATTACTAGAACCCGGAGACACAAT
AACATTTGAGGCAACTGGAAATCTAATAGCACCATGGTATGCTTTCGCACTGAATAGAGGTTCTGGATCC
GGTATCATCACTTCAGACGCACCAGTGCATGATTGTAACACGAAGTGTCAAACACCCCATGGTGCTATAA
ACAGCAGTCTCCCTTTCCAGAATATACATCCAGTCACAATAGGAGAGTGCCCAAAATACGTCAGGAGTAC
CAAATTGAGGATGGCTACAGGACTAAGAAACATTCCATCTATTCAATCCAGGGGTCTATTTGGAGCCATT
GCCGGTTTTATTGAGGGGGGATGGACTGGAATGATAGATGGATGGTATGGTTATCATCATCAGAATGAAC
AGGGATCAGGCTATGCAGCGGATCAAAAAAGCACACAAAATGCCATTGACGGGATTACAAACAAGGTGAA
TTCTGTTATCGAGAAAATGAACACCCAATT

(Genome of the 1918 Pandemic causing virus, bold added). Having done that I decided to search for matches of genome segments of that virus in cow rumen.

The process is to search for a 10 segment sequence (the bold at the beginning of the sequence above shows the first one) of that 1918 pandemic virus.

It is the same process I had used with Sars-CoV-2 in cow rumen, poultry, swine, and bats (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6, 7, 8).

The bold section of ten bases is searched for first, a count is kept, then we move to the next ten bases, and so forth, keeping a tally as shown in Section II below.

The purpose is to see if any segments of that 1918 virus are in our current 'virusphere'.

If so, then we are talking about reassortment/recombinant viruses (RNA Virus Reassortment, Recombinant).

II. Searchin' Searchin' Searchin'

My software module searched hundreds of thousands of cow rumen nucleotide/genome datasets in files in the GenBank, and reported:

1918 Virus Bases ID: AF116575
(Organism: Influenza A virus
A/Brevig Mission/1/1918
Strain Name: A/Brevig Mission/1/1918
Host: Human virus type: H1N1)

Target bases to search:
Cow Rumen

Comparison Type:
1918 Virus segment = Rumen segment?

Search Results:
GenBank
File Id
Segments in
1918 Virus
Genomes in
Rumen File
1918 Virus Segments
Found in Genomes
1918 Segments
per Genome
10676_0040 122 295,166 10,983 26.8748
10676_0039 122 128,519 6,266 20.5105
10676_0010 122 787 855 0.920468
10676_0003 122 1,088 937 1.16115
10676_0011 122 176 282 0.624113
10676_0036 122 6,630 2,553 2.59694
10676_0046 122 42,643 5,391 7.91004
10676_0012 122 296 473 0.625793
10676_0022 122 87 186 0.467742
10676_0038 122 364,399 13,241 27.5205
10676_0049 122 64,980 6,150 10.5659
10676_0045 122 187,633 8592 21.8381
10676_0005 122 220,342 8,575 25.6959
10676_0037 122 117,147 7,505 15.6092
10676_0015 122 568 700 0.811429
10676_0002 122 245 424 0.57783
10676_0030 122 1,793 1,264 1.41851
10676_0041 122 53,535 5,979 8.95384
10676_0009 122 355,497 14,134 25.1519
10676_0019 122 138,641 6,497 21.3392
10676_0051 122 44,327 5,808 7.63206
10676_0029 122 7,539 2,376 3.17298
10676_0028 122 2,366 1,770 1.33672
10676_0018 122 9,976 3,092 3.22639
10676_0042 122 66,725 6,840 9.75512
10676_0021 122 437 627 0.69697
10676_0032 122 15,691 4,193 3.74219
10676_0013 122 192,309 9,732 19.7605
10676_0035 122 1,408 1,054 1.33586
10676_0001 122 119 215 0.553488
10676_0034 122 1,091 986 1.10649
10676_0004 122 772 827 0.933495
10676_0023 122 320,673 11,944 26.848
10676_0050 122 121,778 6,336 19.22
10676_0033 122 33,440 5,181 6.45435
10676_0014 122 230,170 9,615 23.9386
10676_0006 122 1,662 1,311 1.26773
10676_0024 122 405,094 14,710 27.5387
10676_0025 122 2,617 1,618 1.61743
10676_0048 122 38,609 6,462 5.97478
10676_0016 122 144,629 6,531 22.145
10676_0020 122 3,295 1,720 1.9157
10676_0031 122 36,897 4,728 7.80393
10676_0047 122 118,461 6,913 17.136
10676_0043 122 45,438 5,880 7.72755
10676_0027 122 103,080 5,830 17.681
10676_0017 122 10,564 2,882 3.66551

Per-file Average (47 files):

Genomes in Rumen File: 83,815.7
1918 Virus Segments Found in Genomes: 4,897.19
1918 Segments per Genome: 9.90128

III. Closing Comments

That report in Section II above is a perusal of a vast amount of data freely available at GenBank.

It is quite a story that a century-old virus could be reactivated, then put through the paces so that the genome could be captured for further scientific use.

And, so that Dredd Blog could go looking for it with modern software in the rumen of modern cattle.

A quote from one researcher caught my eye:

"The lessons we're learning today from COVID-19 build on the lessons we learned from the 1918 influenza. We aren't the apex predator we think we are. An organism 750 times smaller than the width of human hair can wreak havoc on us to rival most wars..."

(How long can viruses survive in a dead body?, bold added). The Sars-CoV-2 that causes COVID-19 has already rivaled WW1 and two Vietnam's.

The count in those wars took years to accumulate, in the case of Vietnam ten years.

This COVID-19 war-like landscape of dead bodies has only begun.

It is halfway through its first year.

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

1 comment:

  1. "The explanation for this could only be that these agents don’t come or go anywhere. They are always here and something ignites them, maybe human density or environmental conditions, and this is what we should be looking for" (Telegraph).

    ReplyDelete