He knows, but is convinced some dead Chinaman created Covid, when it was Fauci's own biodefense lab in Montana. Rand is literally carrying Fauci's water.
Another factor that can affect the distance percentages is whether you're ignoring positions where either sequence has a gap or not. They are often ignored because it's common for sequences to be missing parts from the UTRs which would artificially inflate the distance if gaps are not ignored, or because sometimes people are comparing a partial sequence to a full sequence but they're only interested in the similarity of the overlapping regions. Tor2 and Wuhan-Hu-1 have about 20.0% nucleotide distance if you ignore positions where either sequence has a gap or about 21.1% if you don't:
And another factor which can affect the distances is whether you're looking at a multiple sequence alignment or a pairwise alignment. In my multiple sequence alignment of sarbecoviruses, Wuhan-Hu-1 and Tor2 have about 20.3% distance when gaps are ignored, so it's about 0.3 percentage points higher than in the pairwise alignment:
But anyway, viral genomes don't exist in 1D space where you could calculate distances so that a virus which is 20% away from SARS1 would always be 0.4% away from a virus that is 20.4% away from SARS1. Distances don't even work that way on a 2D map.
For example the sarbecovirus Rc-kw8 is about 21.1% away from Tor2 but it's also about 19.7% away from Wuhan-Hu-1 (when you ignore positions where either sequence has a gap and when you're looking at a multiple sequence alignment of sarbecoviruses):
When the DARPA meeting notes said that HKU3 was about 20% different from Tor2, it may have meant either amino acid distance or nucleotide distance in the spike protein. When gaps are ignored, HKU3 has about 19.9% aa distance to Tor2 in the spike protein and about 21.9% aa distance to Wuhan-Hu-1:
Complicated but understood. Like the 1D vs 2D vs 3D analogy. But the bigger picture is that UNC lied in their 2020 paper? No way to get SARS2 "22% different" than SARS1?
The first version of Wuhan-Hu-1 had an assembly error where a 597-base piece of the human genome was accidentally included at the 3' end of the sequence. So if you compare the first version of Wuhan-Hu-1 to Tor2 and you don't ignore positions where either sequence has a gap, the distance is about 22.6%:
Or another way you might get a 22% distance between SARS1 and SARS2 is if you have a multiple sequence alignment which doesn't only include sarbecoviruses but also merbecoviruses or other betacoronaviruses.
Great work. Very diligent. Love the map at the end. :D
It started as meme on Twit but more truth than fiction
Incredible piece of work. Please get this to Rand Paul ASAP!
He knows, but is convinced some dead Chinaman created Covid, when it was Fauci's own biodefense lab in Montana. Rand is literally carrying Fauci's water.
https://jimhaslam.substack.com/p/my-open-letter-to-senator-rand-paul
Another factor that can affect the distance percentages is whether you're ignoring positions where either sequence has a gap or not. They are often ignored because it's common for sequences to be missing parts from the UTRs which would artificially inflate the distance if gaps are not ignored, or because sometimes people are comparing a partial sequence to a full sequence but they're only interested in the similarity of the overlapping regions. Tor2 and Wuhan-Hu-1 have about 20.0% nucleotide distance if you ignore positions where either sequence has a gap or about 21.1% if you don't:
curl -Ls sars2.net/f/sarbe.fa.xz|xz -dc>sarbe.fa
seqkit grep -nrp 'Tor2|Hu-1' sarbe.fa|mafft --quiet --thread 4 -|seqkit seq -s|awk 'NR==1{split($0,a,"");l=length;next}{split($0,b,"");for(i=1;i<=l;i++){if(a[i]!="-"&&b[i]!="-"){n++;if(a[i]!=b[i])d++};if(a[i]!=b[i])d2++}print d/n,d2/l}'
And another factor which can affect the distances is whether you're looking at a multiple sequence alignment or a pairwise alignment. In my multiple sequence alignment of sarbecoviruses, Wuhan-Hu-1 and Tor2 have about 20.3% distance when gaps are ignored, so it's about 0.3 percentage points higher than in the pairwise alignment:
curl -Ls sars2.net/f/sarbe.pid|awk -F\\t 'NR==1{for(i=2;i<=NF;i++)if($i~/Hu-1/)break;next}$1!=x{print$i,$1}'|grep Tor2
---
But anyway, viral genomes don't exist in 1D space where you could calculate distances so that a virus which is 20% away from SARS1 would always be 0.4% away from a virus that is 20.4% away from SARS1. Distances don't even work that way on a 2D map.
For example the sarbecovirus Rc-kw8 is about 21.1% away from Tor2 but it's also about 19.7% away from Wuhan-Hu-1 (when you ignore positions where either sequence has a gap and when you're looking at a multiple sequence alignment of sarbecoviruses):
cut -f1 sarbe.pid|egrep -n 'Tor2|Hu-1'|cut -d: -f1|csvtk -t cut -f`paste -sd, -`,1 sarbe.pid|awk '$1>78&&$1<82&&$2>78&&$2<82'
When the DARPA meeting notes said that HKU3 was about 20% different from Tor2, it may have meant either amino acid distance or nucleotide distance in the spike protein. When gaps are ignored, HKU3 has about 19.9% aa distance to Tor2 in the spike protein and about 21.9% aa distance to Wuhan-Hu-1:
curl -Ls sars2.net/f/pid.cpp>pid.cpp;g++ pid.cpp -O3 -o pid
seqkit grep -nrp 'HKU3-2|Tor2|Wuhan-Hu-1' sarbe.fa|seqkit seq -ni|curl -sd id=`paste -sd, -` "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=fasta_cds_aa"|seqkit grep -nrp surface\|spike|mafft --quiet --thread 4 -|sed 's/lcl|//;s/_prot_.*//'|seqkit fx2tab|awk -F\\t 'NR==FNR{a[$1]=$2;next}{print">"$1" "a[$1]"\n"$2}' <(seqkit seq -n sarbe.fa|sed $'s/ /\t/'|cut -d, -f1) -|./pid
Complicated but understood. Like the 1D vs 2D vs 3D analogy. But the bigger picture is that UNC lied in their 2020 paper? No way to get SARS2 "22% different" than SARS1?
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7207110/
The first version of Wuhan-Hu-1 had an assembly error where a 597-base piece of the human genome was accidentally included at the 3' end of the sequence. So if you compare the first version of Wuhan-Hu-1 to Tor2 and you don't ignore positions where either sequence has a gap, the distance is about 22.6%:
curl 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=fasta&id=MN908947.1,NC_004718.3'|mafft --quiet --thread 4 -|seqkit seq -s|awk 'NR==1{split($0,a,"");l=length;next}{split($0,b,"");for(i=1;i<=l;i++){if(a[i]!="-"&&b[i]!="-"){n++;if(a[i]!=b[i])d++};if(a[i]!=b[i])d2++}print d/n,d2/l}'
Or another way you might get a 22% distance between SARS1 and SARS2 is if you have a multiple sequence alignment which doesn't only include sarbecoviruses but also merbecoviruses or other betacoronaviruses.
Interesting, but that doesn't like a mistake UNC would make?
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Our Human Bodies Are Water Based.
Nothing Derived From Manufactured Metals Or Petroleum Should Be Injected Into Them.
Nothing. Not A Goddamn Particle.
Next Question ...
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