Anyhow, I would not agree with the opinion that sequencing can prove that a virus or this particular virus exists.
For me, the whole hanta-story lacks logic.
If this "virus" is related to mice or rat feces: Why are these particles which some call "virus" are not phages of a typical gut bacteria of these species?
And then: Why are these bacteria not the actually pathogenic items?
Oh, I see ... because some have developed a vaccine ....
Not only would they need to rule out the possibility that a sequence was human, wouldn't they also have to rule out sequences from other organisms hosted in the human body?
It would take years to fully understand all the implications. And those who have spent years and decades studying the subject could come to a conclusion that has a near certainty of being a summary of the situation with the Hanta virus, be it Swiss or from Swaziland.
Everything we read from official sources will be a part of a scam to disempower and harm ordinary human beings.
Seems everyone is barking up the wrong tree- even the supposedly "in the know" alt-doctors/dissidents."
It's chemical poisoning of a few people who wandered into an ultra toxic superfund waste site to find some rare birds, and the genomic tests can "find" sequences in anyone once the lab is told what to "find" with the eyes of the world on them.
All they have to do was get some media people placed, demand asymptomatic testing to generate "positives" (2% guaranteed with an allegedly 98% specific test), and the process snowballs and become self-sustaining.
The genome of a hantavirus does not consist of a single molecule, because hantaviruses have a segmented genome with 3 segments, so there are 3 molecules and not 1.
If the de-novo assembler would've accidentally inserted a piece of foregin genetic material to the end of some segment, you would be able to spot it if you aligned the segment against other hantavirus sequences, and the segment had a piece at the end that was missing from the other sequences.
But for example if you compare the L segment of the new genome against earlier hantavirus refseqs, you can see that there's no extra crap at the ends of the segment:
You’re right that hantaviruses are segmented, so strictly speaking the issue is three genome segments, not one single molecule.
You’re also right that alignment to related hantavirus references can rule out obvious junk at the ends, but only if those are considered valid to begin with. And that only shows the assembly looks plausible and hantavirus-like. It still does not prove that the exact segment was directly present in the sample as a complete biological molecule(s), or that the short-read assembly uniquely established it.
Thank you very much!
Anyhow, I would not agree with the opinion that sequencing can prove that a virus or this particular virus exists.
For me, the whole hanta-story lacks logic.
If this "virus" is related to mice or rat feces: Why are these particles which some call "virus" are not phages of a typical gut bacteria of these species?
And then: Why are these bacteria not the actually pathogenic items?
Oh, I see ... because some have developed a vaccine ....
Maybe I missed, it but where did I say that sequencing can prove that?
The current push is likely to keep the mRNA pipeline warm and/or keep WHO relevant.
And it's appearing in random places all over the world in a very non viral manner
Yes, b/c its likely of human origin.
Or the tests are fraudulent.
Not only would they need to rule out the possibility that a sequence was human, wouldn't they also have to rule out sequences from other organisms hosted in the human body?
Exactly!
It would take years to fully understand all the implications. And those who have spent years and decades studying the subject could come to a conclusion that has a near certainty of being a summary of the situation with the Hanta virus, be it Swiss or from Swaziland.
Everything we read from official sources will be a part of a scam to disempower and harm ordinary human beings.
Seems everyone is barking up the wrong tree- even the supposedly "in the know" alt-doctors/dissidents."
It's chemical poisoning of a few people who wandered into an ultra toxic superfund waste site to find some rare birds, and the genomic tests can "find" sequences in anyone once the lab is told what to "find" with the eyes of the world on them.
All they have to do was get some media people placed, demand asymptomatic testing to generate "positives" (2% guaranteed with an allegedly 98% specific test), and the process snowballs and become self-sustaining.
So, in other words, mostly BS modeling. Ugh.
We have symptoms, antibodies , PCR, and full genomic sequencing all telling the same story, but carryon
Like flu like illness?
Pfft
The genome of a hantavirus does not consist of a single molecule, because hantaviruses have a segmented genome with 3 segments, so there are 3 molecules and not 1.
If the de-novo assembler would've accidentally inserted a piece of foregin genetic material to the end of some segment, you would be able to spot it if you aligned the segment against other hantavirus sequences, and the segment had a piece at the end that was missing from the other sequences.
But for example if you compare the L segment of the new genome against earlier hantavirus refseqs, you can see that there's no extra crap at the ends of the segment:
curl https://virological.org/uploads/short-url/jklVP5qLw930YK9f5BmseNDu3Bs.gz|gzip -dc>hanta.fa
wget https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/viral.1.1.genomic.fna.gz
seqdif()(seqkit fx2tab|gawk -F\\t '{name[NR]=$1;split($2,z,"");for(i in z)seq[NR][i]=z[i];if(length($1)>max1)max1=length($1);if(length($2)>max2)max2=length($2)}END{for(i=1;i<=max2;i+=width){printf("%"(max1+1)"s","");for(pos=i;pos<i+width&&pos<=max2;pos+=10)printf(pos-i>width-10?"%s":"%-10s",pos);print"";for(j in seq){out=sprintf("%"max1"s ",name[j]);for(k=i;k<=max2&&k<i+width;k++)out=out (seq[j][k]==seq[1][k]?seq[j][k]:"\033[31m"seq[j][k]"\033[0m");print out}}}' "width=${1-60}")
seqkit grep -nrip hantavirus viral.1.1.genomic.fna.gz|seqkit seq -m6000|cat <(seqkit grep -nrp _L hanta.fa) -|mafft --thread 7 -|seqdif
You’re right that hantaviruses are segmented, so strictly speaking the issue is three genome segments, not one single molecule.
You’re also right that alignment to related hantavirus references can rule out obvious junk at the ends, but only if those are considered valid to begin with. And that only shows the assembly looks plausible and hantavirus-like. It still does not prove that the exact segment was directly present in the sample as a complete biological molecule(s), or that the short-read assembly uniquely established it.
How is this determined (that it is segmented), if the sequence is essentially a guess?