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| 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
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:
| 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.