Share this page!

Kevin McKernan 🙂 Profile picture
Twitter logo
18 Dec 21, 9 tweets, 3 min read
A few folks raised valid geopolitical concerns over this paper firing shots at the Venter Institute/Institut Pasteur SARs-Cov-1 lableak.

This is Beijing claiming one of the premier US genome centers is leaking SARs-CoV-1.

Let's reproduce it.
sciencedirect.com/science/articl…
If you want to follow along you will need a Ubuntu instance with a few free software tools installed.
1)Fasterq-dump (Free from NCBI)
2)trim_galore (bioinformatics.babraham.ac.uk/projects/trim_…)
3)samtools (samtools.sourceforge.net)
4)BWA (bio-bwa.sourceforge.net)
5)IGV (Broad Institute)
First we download the reads they mention in the paper using Fasterq-dump

fasterq-dump ERR1091914

This will download one of the samples in the paper that is listed as being contaminated with SARs-CoV-1.
This sample will be downloaded as a fastq file. This raw sequencing still has illumina primer sequences on them and these need to be trimmed with trim galore. /tools/TrimGalore/trim_galore ERR1091914.fastq
Once you have trimmed reads you can map them to a reference genome or assemble them. Lets stick with read mapping for the moment as assembly requires a bit more software downloads like megahit.
You'll want to download the reference they mention in the paper from NCBI. Image
Click on the genome tab in blue and you will get a .fna file. This will need to indexed with bwa.
bwa mem index SARs-CoV-2_GCF_000864885.1_ViralProj15500_genomic.fna
Next step is to map these reads with bwa mem on 4 threads and to pipe this into samtools so you get a .bam file out of the mapping.

bwa mem -t 4 SARs-CoV-2_GCF_000864885.1_ViralProj15500_genomic.fna ERR1091914_trimmed.fq | samtools view -Sb - > ERR1091914.bam
This bam file just needs to be sorted and indexed and you are ready to load the BAM file into IGV for viewing.

samtools sort ERR1091914.bam -o ERR1091914_sort.bam

samtools index ERR1091914_sort.bam

Copy both of these files to a local drive that has IGV installed.
Bingo... There are indeed SARs-CoV-1 sequences in the listed samples in the paper. While it may be from heavily censored China, it is reproducible. ncbi.nlm.nih.gov/sra/?term=ERR1… Image

• • •

Missing some Tweet in this thread? You can try to force a refresh
　

Keep Current with Kevin McKernan 🙂

Kevin McKernan 🙂 Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @Kevin_McKernan

Kevin McKernan 🙂 Profile picture
1 Jan
I like mice…
So does some lab that derived Omicron.

Very good read.
You’ll see how Molnupiravir could not have done this alone.
Random C->U mutations are not elevated in omicron but GC-AT are different in early omicron Vs post outbreak.
Mice host!

sciencedirect.com/science/articl…
GC-AT mutations are a signature of ROS damage that makes 8-OxoG.
ROS is elevated in febrile viral infections.

These authors looked at early omicron Vs post outbreak omicron and see a difference here suggesting omicron had a different host at some point.
Mice fit the bill.
Another kind cat sent me this paper.
Another important point is the Ka/Ks analysis they do (dN/dS).
This shows 6.6X higher selective pressure on spike but not on the rest of the SARs genome.
Mice + selection against spike (vax of MAbs) could do this.

Lab derived.
Read 6 tweets
Kevin McKernan 🙂 Profile picture
29 Dec 21
Can't Find a C19 test?
Low supply, Fiat Demand...

I am shocked at how expensive these C19 tests are ($100-$300).

And no...The free ones are not free!

They are printing money, diluting yours and paying a heavy price you just can't see.

Diagnostic PCR is usually $30.
Even with 10X higher margins on C19 PCR, there are still droughts after 2 years?

Why?

This is the story of central planning where the market gets run by whimsical gov diktat and pricing signals are destroyed.

When pricing signals are destroyed companies dont know how to plan
Will Biden have an aneurism or an epiphany today and order 500M tests they fumble?

Will schools panic on Omicron and order more school testing of asympto kids who don't get sick?

When you run the market by Fiat, you create artificial demand but you don't create supply.
Read 5 tweets
Kevin McKernan 🙂 Profile picture
29 Dec 21
I’m in the process of updating this for submission (2,000 downloads before submission)
Several details people have brought up in support of this.

Will walk through them.

osf.io/bcsa6/
1)Some folks at NIH reached out pointed out the work on ribosomal pausing that we missed.
It’s very relevant.

Just the codon change in the FCS is enough to pause the ribosomes and alter 3D structure of spike.
Just 2 codons!

mdpi.com/1422-0067/22/1…
They changed many codons.

2)pseudouridine and N1-methyl should be better spelled out. Xia et al conflates the two and we will spell this out more.
PseudoU wobbles more the methylpseudoU but both significantly alter Tm and thus are ‘stickier’ bases than disrupt translation.
Read 11 tweets
Kevin McKernan 🙂 Profile picture
22 Dec 21
230 days RNA positive post infection.

Turn off the asymptomatic PCR pipeline or we’ll never get out of this.
Tissue specific viral heteroplasmy.
That’s wild.
Very thorough.
Not only applied a live-dead like PCR looking at sgRNA, they also cultured the virus and looked for immune histochemistry confirmation of proteins.
Read 8 tweets
Kevin McKernan 🙂 Profile picture
22 Dec 21
Great chat with @jjcouey
I have some errors to confess to as I spoke to fast.
1)I was enrolled in a PhD program at UW but dropped out to focus on my job when the HGP starting racing with Craig Venter. So No PhD.

twitch.tv/videos/1239989…
2)nsp13 should be nsp3. It interacts with quadruplex G
academic.oup.com/nar/article/49…
3)The vaccines have N1-Methyl Pseudouridine and I shouldn't shorthand this to Pseudouridine as the former has less wobble than the latter. N1-Methyl does alter the Tm and increase base stacking in RNA but its methyl group steals one potential H-bond.

ncbi.nlm.nih.gov/labs/pmc/artic…
Read 9 tweets
Kevin McKernan 🙂 Profile picture
16 Dec 21
Here we can see honest virologists being confronted by ones that might have been named in Fauci’s email.

The later amplify flawed preprints from Drosten.

The reads are not out yet (of course), so there is not much to say about this headline whore print.
Let’s have a look at the methods section of the paper.

2 rounds of 45 cycles of PCR?

This is what you do if you want to make polymerase slippage errors near GC rich triplet repeats.

People this library illiterate shouldn’t have the keys to $20K NovaSeq runs.
Having engineered very accurate sequencers, to address PCR polymerase error, you must utilize DNA barcodes that get attached to your PCR products in the first cycle of PCR. Any barcode that over amplifies through the PCR process is discounted.

For rare variants
This is the way
Read 6 tweets

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Too expensive? Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us on Twitter!

Like this author's thread?

Get emails when @Kevin_McKernan has new unrolls!

Check out other threads from @Kevin_McKernan!

Read all threads by @Kevin_McKernan

:(