Thread by @BillyBostickson

3. This was proposed by @stuartjdneil after @PhilippMarkolin posted a flawed claim concerning filter use

However if we examine the quoted method used carefully here:
ncbi.nlm.nih.gov/labs/pmc/artic…
some points can be clarified.

This procedure would be expected to remove eukaryotic and bacterial reads, and to highly enrich reads from viral capsids.

That is not what is observed.

70.62% of reads are identified, of which 70.61% are cellular organisms, only 0.01% are viruses.

There is no logical reason that this procedure would skew the ratio so heavily towards eukaryotic reads.

This cannot be the procedure that produced the data, as the stated protocol does not adequately explain the data.

A desperate zoonati may propose the unlikely scenario:

1. WIV Lysed the eukaryotic cells but not the bacterial ones

2. WIV failed to adequately digest with DNase & RNase, which resulted in massive amounts of remaining extracellular eukaryotic nucleic acids

Still not a solution

The best explanation for the anomalies is, of course as @stevenemassey proposes, that it was not a fecal swab.

Let's now invite @stuartjdneil and @PhilippMarkolin to show us any other “fecal swab” data that has a read profile like this?

Thus, the findings by @stevenemassey @Daoyu15 @MonaRahalkar @BahulikarRahul on anomalies of RaTG13 data are upheld despite spurious attempts to explain it away as a "purification procedure"

The different findings can be found in this thread:

An Unanswered Question

Why would this purification procedure be applied to RaTG13’s sample but not any of the other samples of the same type and uploaded around the same time?

2. Mutations in the Spike protein of RaTG13

This recent paper argues that mutation from T to R at position 403 in RaTG13’s spike is essential for allowing it to infect human cells:

Spike residue 403 affects binding of coronavirus spikes to human ACE2

nature.com/articles/s4146…

Notably, SARS-CoV-2 has an R at the corresponding position, and mutation back to T (as in RaTG13) diminishes its ability to infect human cells.

Supplementary figure 7 is the interesting part here, from:

Supplementary information for Spike residue 403

static-content.springer.com/esm/art%3A10.1…

Logically therefore, were "they" to generate a consensus sequence virus (even within the RsYN06-RaTG13 clade) as has been suggested by some, it would surely have an R at that position...

Position 403

Without knowing what "they" have (or "had") in their dearly missed database, which may have been used to generate a consensus sequence, we can’t know what sequence it would produce.

but we can be reasonably sure that it would have an R, not a T at position 403...