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Thursday, June 25, 2020

On The Origin Of The Home Of COVID-19 - 7

Why can't we all get along?
I. Background

Regular readers are aware that I have been expecting the news we see in newspapers and on TV for about six years (What Did The Mass Extinctions Do To Viruses and Microbes?, The Real Dangers With Microbes & Viruses).

So, this will be the last Sars-Cov-2 (COVID-19) post in this series for awhile (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6).

The current spike in the first wave has been caused by the denial of the GOP, just as the first spike was (different geographical states, same state of mind).

I want to point out the results of checking out the nucleobases/nucleic acid sequences of bats as I indicated in the previous post of this series.

It is interesting mostly because of what was not found rather than what was found as in the analysis of cattle.

To sum it up, only about 6% of bat genomes had significant segments of coronavirus in them (94% had no segments or 1-2 segments).

This is a stark result, because much of the historical scientific papers indicated that bats were the prime suspect.

It further supports the hypothesis that our food mass production methods, practices, and techniques generate pathogenic viruses and pathogenic single celled microbes, in the sense that bats are not part of that industry.

The research into viruses is embryonic but moving fast:
"Virologist Jemma Geoghegan at the University of Otago, New Zealand, says that before researchers can use viral traits to predict the next spillover event, many more viruses need to be sampled and characterized to reveal the true diversity of viruses in nature. Until then, she thinks surveillance efforts are better directed towards genomic surveillance at the ‘fault lines’ where people and animals interact, such as live animal markets [and industries where animals are being mass produced and drugged]. 'That way, we can quickly recognize any viruses that spill over,' she says."
(Bats are a key source of human viruses — but they’re not special).

II. The Search

The results of the search of bat genomes/nucleic acid sequences can be seen below:
Covid Bases ID:MT641485.1
(sars coronavirus 2 isolate 
SARS-CoV-2 human USA WA-S709 2020
complete genome virus type: SC-HS-CG-DN) 
Target bases to search: bats 
Bat File Type: nucleic acid sequences/base_pairs_bats
 Search Results:
Bats File
Section Id		 Bats Virus
Type		 Covid-19
Segments Found
NC_048212.1 CO-AN-CC-DN 211
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III. Closing Comments

I am currently updating all of my World Ocean Database files (over 5.5 billion in situ measurements) and will be posting updates on seaports, ghost plumes, ghost photons, and general world ocean subjects.

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

at 1 comment:

Tuesday, June 23, 2020

On The Origin Of The Home Of COVID-19 - 6

Microbe Whisperers
I. Introduction

In today's post we will take a look at a SARS-CoV-2 (a.k.a. Covid-19) nucleobase/nucleic acid sequences 'map' from a human in the state of Washington, U.S.A.

It will be compared to about 500 samples of nucleobase/nucleic acid sequences 'maps' taken from the rumen (first stomach) of cows in the U.S.A. and elsewhere.

Many such nucleotide maps are stored at Genbank, and are available for downloading.

A nucleotide in fasta format map looks like:
[description]
GTTTTTTTGTGTTGCCGGTCAAAACGCGATGACGTTCCCGCCTCTTCCCGTTCCCGGCAC
AGAGCCCTAAGCGTCACCACGGCGACGGTCAGCGACATGGGAAGGCGCAGGTAACCGCCC
CCTAAGAGGGAGTCACTGTTAAAACAGCGGCTCCCTCGTTTTTTTGTTGCCGGTCAAAGC
GCGATGACGTTCCCGCCTTTTCCCGTTCCTGGCACAGAGCCCTAAGCATCACCACGGCGA
CGGTCAGCGACATGGGAAGGCGTAGGTAACCGCCCCCTAAGAGAGGTGATGTCAGCAATG
ATGTCGCCTCTCGTTTTTTTGTTGCCGGTCAAAACGCGATGACGTTCCCGCCTCTTCCCG
TTCCTGGCACAGAGCCCTAAGCGTCACCACGGCGACGGTCAGCGACATGGGAAGGCGCAG
GTAACCGCCCCCTAAGAGGGAGTCACTGGTAAAACAGCGGCTCCCTCGTTTTTTTGTGTC
CTGTAGAAGCTATAGTTTTTATAACTACTATAGGGTGTCATGGTTGTGGGTTGTTTTTGC
TTTGAGATTGGCGTTGTTTGTTTTTTTTTAGTAATTTAGCATCGTTATCATTCGTAATTA
ATAACCAGAATTAAGATAAAATATTAAAAATGAAGCATTTAATATCTATCTTGCTGTTGC
...
(see fasta format). Human and microbe nucleotide maps "look the same" in one sense, however, the sequences are different even though there may be 'segments' or 'sections' that match between species.

This can happen in recombinant emergence situations, and it can cause major changes in the hosts in which such changes take place.

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?

As it turns out, one of the likely homes of Covid-19 is going to be a surprise (Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery).

II. The Comparison Experiment

So, as I said, we are going to look for human Covid-19 nucleotide segments in cow nucleotide/nucleic acid sequences maps.

This is important because cattle are a big part of our food production system.

The report of what I found in the search via software modules I developed is contained in Appendices A-F as follows:

Nucleobase
Comparison		Appendix
Location
1 - 6Appendix A
9 - 15Appendix B
16 - 22Appendix C
23 - 30Appendix D
31 - 37Appendix E
38 - 51Appendix F

The number of matches between segments of SARS-CoV-2 and segments of microbes in cow rumens might surprise you as it did me.

III. How The Results Were Derived

After downloading SARS-CoV-2 and bovine nucleobases/nucleic acid sequences I wrote software to iterate through the SARS-CoV-2 human nucleobase/nucleic acid sequences example from Washington, one ten-base-segment at a time.

The comparisons then take place while searching through ten bovine nucleobases/nucleic acid sequences (0000 - 0009) per bovine data file.

The search is for that particular SARS-CoV-2 segment in those bovine rumen nucleobases/nucleic acid sequences in each bovine data file.

The results in Appendices A-F give rise to some interesting inferences (got comments? got questions?).

IV. Closing Comments

I think that the hypothesis of this series is bolstered by the results of this SARS-CoV-2 vs. Bovine nucleobase/nucleic acid sequences comparison experiment.

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

at 1 comment:

Appendix A

This is an appendix to: On The Origin Of The Home Of COVID-19 - 6
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0001 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 107
0001 127
0002 75
0003 118
0004 97
0005 47
0006 66
0007 130
0008 75
0009 65
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0002 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 55
0001 59
0002 103
0003 93
0004 54
0005 210
0006 136
0007 139
0008 78
0009 108
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0003 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 140
0001 131
0002 99
0003 51
0004 32
0005 83
0006 92
0007 136
0008 69
0009 57
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0004 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 460
0001 228
0002 106
0003 147
0004 81
0005 104
0006 80
0007 93
0008 284
0009 69
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0005 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 238
0001 70
0002 70
0003 71
0004 67
0005 81
0006 79
0007 48
0008 65
0009 53
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0006 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 157
0001 66
0002 126
0003 95
0004 88
0005 53
0006 46
0007 89
0008 32
0009 64





at No comments:

Appendix B

This is an appendix to: On The Origin Of The Home Of COVID-19 - 6
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0009 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 150
0001 51
0002 232
0003 92
0004 79
0005 125
0006 82
0007 82
0008 80
0009 91
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0010 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 148
0001 126
0002 74
0003 118
0004 46
0005 88
0006 59
0007 139
0008 47
0009 88
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0011 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 210
0001 86
0002 74
0003 68
0004 152
0005 55
0006 89
0007 135
0008 116
0009 71
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0012 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 166
0001 119
0002 136
0003 86
0004 123
0005 127
0006 55
0007 70
0008 88
0009 60
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0013 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 82
0001 212
0002 200
0003 202
0004 65
0005 232
0006 66
0007 133
0008 74
0009 84
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0014 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 302
0001 119
0002 218
0003 92
0004 121
0005 112
0006 71
0007 58
0008 144
0009 66
Covid Bases ID: MT641485.1
(sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome
virus type: SC-HS-CG-DN)

Target bases to search: cattle rumen

Rumen File Type 10676_0015
Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 176
0001 77
0002 81
0003 226
0004 178
0005 107
0006 52
0007 141
0008 46
0009 101


at No comments:

Appendix C

This is an appendix to: On The Origin Of The Home Of COVID-19 - 6
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0016 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 265
0001 133
0002 90
0003 96
0004 151
0005 88
0006 130
0007 102
0008 51
0009 68
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0017 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 118
0001 185
0002 87
0003 68
0004 68
0005 90
0006 125
0007 88
0008 49
0009 147
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0018 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 153
0001 155
0002 285
0003 154
0004 122
0005 132
0006 146
0007 172
0008 148
0009 88
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0019 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 98
0001 162
0002 103
0003 119
0004 43
0005 77
0006 70
0007 88
0008 65
0009 68
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0020 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 153
0001 79
0002 126
0003 88
0004 52
0005 46
0006 29
0007 88
0008 37
0009 61
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0021 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 151
0001 110
0002 139
0003 136
0004 204
0005 115
0006 77
0007 181
0008 51
0009 141
Covid Bases ID: MT641485.1
(sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome
virus type: SC-HS-CG-DN)

Target bases to search: cattle rumen

Rumen File Type 10676_0022
Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 171
0001 132
0002 82
0003 105
0004 88
0005 151
0006 69
0007 57
0008 109
0009 85


at No comments:

Appendix D

This is an appendix to: On The Origin Of The Home Of COVID-19 - 6
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0023 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 141
0001 159
0002 98
0003 110
0004 167
0005 200
0006 129
0007 108
0008 78
0009 79
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0024 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 117
0001 221
0002 83
0003 96
0004 105
0005 114
0006 86
0007 66
0008 70
0009 97
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0025 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 154
0001 149
0002 144
0003 119
0004 111
0005 103
0006 97
0007 41
0008 88
0009 101
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0027 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 149
0001 142
0002 104
0003 144
0004 140
0005 79
0006 61
0007 67
0008 95
0009 88
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0028 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 117
0001 171
0002 116
0003 124
0004 186
0005 82
0006 80
0007 105
0008 165
0009 60
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0028 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 117
0001 171
0002 116
0003 124
0004 186
0005 82
0006 80
0007 105
0008 165
0009 60
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0029 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 122
0001 35
0002 110
0003 140
0004 61
0005 43
0006 53
0007 42
0008 88
0009 88
Covid Bases ID: MT641485.1
(sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome
virus type: SC-HS-CG-DN)

Target bases to search: cattle rumen

Rumen File Type 10676_0030
Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 173
0001 269
0002 131
0003 271
0004 232
0005 166
0006 136
0007 69
0008 74
0009 85


at No comments:

Appendix E

This is an appendix to: On The Origin Of The Home Of COVID-19 - 6
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0031 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 167
0001 192
0002 103
0003 96
0004 149
0005 63
0006 98
0007 36
0008 27
0009 74
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0032 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 212
0001 180
0002 180
0003 251
0004 186
0005 43
0006 67
0007 63
0008 76
0009 46
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0033 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 136
0001 139
0002 84
0003 67
0004 74
0005 69
0006 73
0007 54
0008 87
0009 71
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0033 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 136
0001 139
0002 84
0003 67
0004 74
0005 69
0006 73
0007 54
0008 87
0009 71
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0034 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 153
0001 262
0002 156
0003 111
0004 79
0005 57
0006 46
0007 39
0008 39
0009 109
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0035 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 232
0001 137
0002 209
0003 61
0004 70
0005 127
0006 149
0007 155
0008 69
0009 130
Covid Bases ID: MT641485.1 (sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome virus type: SC-HS-CG-DN) Target bases to search: cattle rumen Rumen File Type 10676_0036 Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 270
0001 87
0002 54
0003 87
0004 80
0005 91
0006 98
0007 87
0008 59
0009 65
Covid Bases ID: MT641485.1
(sars coronavirus 2 isolate SARS-CoV-2 human USA WA-S709 2020 complete genome
virus type: SC-HS-CG-DN)

Target bases to search: cattle rumen

Rumen File Type 10676_0037
Search Results:
Rumen File
Section Number		 Covid-19
Segments Found
0000 70
0001 247
0002 120
0003 121
0004 181
0005 200
0006 54
0007 95
0008 142
0009 99


at No comments: