Brilliant stack per usual, Christine, w/all these invaluable, additional resources that have continued to debunk the non-existent "boogey-man Cov19 virus"as well as the "consensus" on ALL so-called viruses.
You are simply one of the best investigators out there & we are deeply appreciative of your hard work.
<3
And btw - I posted your article link here over on MCrispinMiller's stack just now w/my comment >
I think Joshua Quick was right when he said that there's an assembly error in the first version of Wuhan-Hu-1 and that they fixed the 3' tail in the third version by doing RACE. In the first version of Wuhan-Hu-1 at GenBank, they accidentally included a 618-base segment of human DNA at the 3' end, where the first 20 of the 618 bases are actually part of the real genome of SARS 2. In the second version they removed the last 598 bases from the 3' end, but they ended up missing a part of the real tail of SARS 2 which was added in the third version. Another assembly error was that in the first and second versions, they accidentally included a wrong 27-base segment at the 5' end, where the last 24 bases of the segment are identical to a segment near the 3' end of Wuhan-Hu-1. I have found similar assembly errors in other SARS-like viruses, like RfGB02, SoD, Sin3408, Rs7907, Rs7931, and Ra7909. I described it in more detail in this HTML file, where I also addressed some of the other questions that Quick was asked: https://output.jsbin.com/suwuxoy.
You always have so much to say about these meaningless, fraudulent, assembled "genomes", but never any science showing that there is a "virus" to "sequence" in the first place.
Well I'm an amateur in human population genetics but I don't have any other background in biology, so I try to focus on what I know about. And I don't have access to lab equipment so I can't do benchwork like isolating viruses, but the only equipment I need to do bioinformatics is my iMac.
BTW as a control for the metagenomic assembly of Wuhan-Hu-1, you can use any human lung metagenome published before 2020. You won't be able to use it to assemble contigs of SARS 2. For example I searched the NCBI's sequence read archive for "human lung metagenome pneumonia 2000:2019[dp]": https://www.ncbi.nlm.nih.gov/sra/?term=human+lung+metagenome+pneumonia+2000%3A2019%5Bdp%5D. The first few pages were filled with rRNA sequences, and viruses don't have ribosomes, so I picked a result from page 10 titled "Human Lung Microbiome from patients with pneumonia": https://www.ncbi.nlm.nih.gov/sra/SRX682954%5baccn%5d. When I ran MEGAHIT with the default settings, I got a total of about 34,000 contigs with a maximum length of about 15,000. When I aligned the contigs against a file of about 15,000 virus reference sequences, I got only 12 aligned contigs, and they all aligned against human endogenous retrovirus K113 which ended up having about 60% of the bases of its genome covered by at least one of my contigs:
brew install megahit -s # `-s` compiles from source because the bottle was compiled against GCC 9 so it gave me the error `dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/9/libgomp.1.dylib`
When I simply aligned the raw reads without generating contigs, I additionally got about 15% coverage for escherichia phage phiX174, and I got hundreds of covered bases for some herpes viruses.
virologists are never dealing with something as simple as just some lung tissue (and since when do all men and women have the exact some "genome" anyways?).
it doesn't matter anyways, because to sequence a "virus" you need a "virus" to exist first
Actually in my previous example, the reads which matched the human endogenous retrovirus K113 probably just matched a part of the human genome. When I did a BLAST search for one one 99-base read which was 100% identical to the K113 refseq, it was also 100% identical to a part of the human genome and to some endogenous retroviruses of non-human apes. And when I did a BLAST search for the whole genome of K113, it was about 98.7% identical with 100% query coverage to a region of human chromosome 8. About 8% of the human genome consists of regions which code for endogenous retroviruses.
I downloaded another human lung metagenome sample from a patient with pneumonia: https://www.ncbi.nlm.nih.gov/sra/SRX18162393%5baccn%5d. When I aligned its reads against the viral refseqs, I again got by far the highest number of covered bases for "Human endogenous retrovirus K113" (7,881). It was followed by "Enterobacteria phage P7" (1,682), "Haemophilus phage HP2" (267), "BeAn 58058 virus" (240), "Haemophilus phage HP1 strain HP1c1" (209), and finally "Escherichia phage RCS47" (124).
The hemophilus phages may have been phages of Haemophilus influenzae, which is a common cause of bacterial pneumonia, and which was erroneously thought to cause influenza in the 1800s when it was named. In the STAT analysis, the lung metagenome sample had 952 reads which matched Haemophilus influenzae, which was the 6th most abundant leaf node in the STAT tree:
Thanks for your help and efforts. Be sure to have a week off or a month, now and again. I subscribed just to attempt a moderate support of your past work. Which for me, was enough. So now I hope you can live into the macobe humor of our foibled human and institutional tendancies.
Somehow I hope we can live into the cure of placebo and no-ceebo effects and affects. And we can deprogram the "in silico virus" back out of our human fears and froughts.
Carl Smythe has a new twitter account (last one was suspended).
He is extraordinarily rude. There are dozens of reasons why you might not be able to find the response, or maybe never got one from U of Sheffield. He just jumps to the conclusion that you are lying. How rude.
I tried engaging with him for a while, but it's all ad hom, so I blocked him.
Brilliant stack per usual, Christine, w/all these invaluable, additional resources that have continued to debunk the non-existent "boogey-man Cov19 virus"as well as the "consensus" on ALL so-called viruses.
You are simply one of the best investigators out there & we are deeply appreciative of your hard work.
<3
And btw - I posted your article link here over on MCrispinMiller's stack just now w/my comment >
https://markcrispinmiller.substack.com/p/as-german-study-finds-that-vaccination/comment/16617347
Thanks so much Lucinda :)
I think Joshua Quick was right when he said that there's an assembly error in the first version of Wuhan-Hu-1 and that they fixed the 3' tail in the third version by doing RACE. In the first version of Wuhan-Hu-1 at GenBank, they accidentally included a 618-base segment of human DNA at the 3' end, where the first 20 of the 618 bases are actually part of the real genome of SARS 2. In the second version they removed the last 598 bases from the 3' end, but they ended up missing a part of the real tail of SARS 2 which was added in the third version. Another assembly error was that in the first and second versions, they accidentally included a wrong 27-base segment at the 5' end, where the last 24 bases of the segment are identical to a segment near the 3' end of Wuhan-Hu-1. I have found similar assembly errors in other SARS-like viruses, like RfGB02, SoD, Sin3408, Rs7907, Rs7931, and Ra7909. I described it in more detail in this HTML file, where I also addressed some of the other questions that Quick was asked: https://output.jsbin.com/suwuxoy.
All "virus genomes" ARE assembly errors lol.
You always have so much to say about these meaningless, fraudulent, assembled "genomes", but never any science showing that there is a "virus" to "sequence" in the first place.
Well I'm an amateur in human population genetics but I don't have any other background in biology, so I try to focus on what I know about. And I don't have access to lab equipment so I can't do benchwork like isolating viruses, but the only equipment I need to do bioinformatics is my iMac.
BTW as a control for the metagenomic assembly of Wuhan-Hu-1, you can use any human lung metagenome published before 2020. You won't be able to use it to assemble contigs of SARS 2. For example I searched the NCBI's sequence read archive for "human lung metagenome pneumonia 2000:2019[dp]": https://www.ncbi.nlm.nih.gov/sra/?term=human+lung+metagenome+pneumonia+2000%3A2019%5Bdp%5D. The first few pages were filled with rRNA sequences, and viruses don't have ribosomes, so I picked a result from page 10 titled "Human Lung Microbiome from patients with pneumonia": https://www.ncbi.nlm.nih.gov/sra/SRX682954%5baccn%5d. When I ran MEGAHIT with the default settings, I got a total of about 34,000 contigs with a maximum length of about 15,000. When I aligned the contigs against a file of about 15,000 virus reference sequences, I got only 12 aligned contigs, and they all aligned against human endogenous retrovirus K113 which ended up having about 60% of the bases of its genome covered by at least one of my contigs:
wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR155/009/SRR1553689/SRR1553689.fastq.gz
brew install megahit -s # `-s` compiles from source because the bottle was compiled against GCC 9 so it gave me the error `dyld: Library not loaded: /usr/local/opt/gcc/lib/gcc/9/libgomp.1.dylib`
megahit -r SRR1553689.fastq.gz -o megacontrol
brew install bowtie2 seqkit gnu-sed
wget -q https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.1.genomic.fna.gz
seqkit fx2tab viral.1.1.genomic.fna.gz|sed $'s/A*\t$//'|seqkit tab2fx>viral.fa
bowtie2-build viral.fa{,}
bowtie2 -p3 -x viral.fa -fU megacontrol/final.contigs.fa --no-unal|samtools sort ->megacontrol.bam
samtools coverage megacontrol.bam|awk -F\\t 'NR==FNR{a[$1]=$2;next}$4{print$0"\t"a[$1]}' <(seqkit seq -n viral.fa.gz|sed $'s/ /\t/;s/, .*//') -|(gsed -u 1q;sort -rnk6)|cut -f1,3-6,10|column -ts$'\t'
When I simply aligned the raw reads without generating contigs, I additionally got about 15% coverage for escherichia phage phiX174, and I got hundreds of covered bases for some herpes viruses.
virologists are never dealing with something as simple as just some lung tissue (and since when do all men and women have the exact some "genome" anyways?).
it doesn't matter anyways, because to sequence a "virus" you need a "virus" to exist first
Actually in my previous example, the reads which matched the human endogenous retrovirus K113 probably just matched a part of the human genome. When I did a BLAST search for one one 99-base read which was 100% identical to the K113 refseq, it was also 100% identical to a part of the human genome and to some endogenous retroviruses of non-human apes. And when I did a BLAST search for the whole genome of K113, it was about 98.7% identical with 100% query coverage to a region of human chromosome 8. About 8% of the human genome consists of regions which code for endogenous retroviruses.
I downloaded another human lung metagenome sample from a patient with pneumonia: https://www.ncbi.nlm.nih.gov/sra/SRX18162393%5baccn%5d. When I aligned its reads against the viral refseqs, I again got by far the highest number of covered bases for "Human endogenous retrovirus K113" (7,881). It was followed by "Enterobacteria phage P7" (1,682), "Haemophilus phage HP2" (267), "BeAn 58058 virus" (240), "Haemophilus phage HP1 strain HP1c1" (209), and finally "Escherichia phage RCS47" (124).
The hemophilus phages may have been phages of Haemophilus influenzae, which is a common cause of bacterial pneumonia, and which was erroneously thought to cause influenza in the 1800s when it was named. In the STAT analysis, the lung metagenome sample had 952 reads which matched Haemophilus influenzae, which was the 6th most abundant leaf node in the STAT tree:
$ curl 'https://trace.ncbi.nlm.nih.gov/Traces/sra-db-be/run_taxonomy?acc=SRR22183690&cluster_name=public'>SRR22183690.stat
$ jq -r '[.[]|.tax_table[]|.parent]as$par|[.[]|.tax_table[]|select(.tax_id as$x|$par|index($x)|not)]|sort_by(-.total_count)[]|((.total_count|tostring)+";"+.org)' SRR22183690.stat|head
327514;Homo sapiens
2534;Gorilla gorilla gorilla
1597;Pongo abelii
1363;Pan paniscus
1329;Pan troglodytes
952;Haemophilus influenzae
853;Bacillus thuringiensis
649;Nomascus leucogenys
593;Colobinae
586;Hylobates moloch
whew. Looks like i have some reading ahead of me. Thanks for all this.
What happened to Kevin Corbett kn the meantime? His recent Substack post is just a rant about “divisiveness,” and he deletes critical comments.
No idea!
Thanks for your help and efforts. Be sure to have a week off or a month, now and again. I subscribed just to attempt a moderate support of your past work. Which for me, was enough. So now I hope you can live into the macobe humor of our foibled human and institutional tendancies.
Somehow I hope we can live into the cure of placebo and no-ceebo effects and affects. And we can deprogram the "in silico virus" back out of our human fears and froughts.
Thanks Bradley, and yes indeed we need to de-program :)
I love Tom Cowan.
Great post, per usual!!! xo Thanks, CM. ^_^
in vitro, veritas...
;)
👊🏻
Just Quick's quick admission by itself is ...HUGE! Thanks, Christine, i am so sharing this!!
Carl Smythe has a new twitter account (last one was suspended).
He is extraordinarily rude. There are dozens of reasons why you might not be able to find the response, or maybe never got one from U of Sheffield. He just jumps to the conclusion that you are lying. How rude.
I tried engaging with him for a while, but it's all ad hom, so I blocked him.
https://twitter.com/search?q=CarlSmythe%20OR%20CarlSmytheCells%20podcastbill%20OR%20williamahuston%20massey%20OR%20christine&src=typed_query&f=live
.
If You Are Vaccinated
It Is Too Bad That You
Hate Speech.
Because As We Have Been Saying
All Along
“Boy Does That Vaccine Hate You”
.
evil who is shedding wef
@ the weevil's wedding, chef...!
Great article Christine, and thanks for all your work in this time of lies and murder.
to Joshua Quick and Carl Smythe, I am happy to call you two, liars, crooks and frauds. If you want to sue me, please, please, do so.
Contact me via my substack - :Carl-david: