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Beware the Peptides of SARS
More evidence pointing towards a lab origin for SARS-CoV-2
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A paper recently published in Taylor & Francis - Communicative & Integrative Biology, places further doubt on the zoonotic origins of Covid. Whilst using a new method to find the original host of the ancestor of SARS-CoV-2, the authors found that the virus had been adapted to bats, BUT the spike was adapted to humans. Furthermore, they concluded that the coronavirus had been passaged in treeshrews, whilst the spike had been passaged in rats before recombination.
The zoonosis origin theory suggests that SARS-CoV-2 originated in bats which then transmitted to humans via an intermediate animal. The problem with this theory is that the spike protein is so well suited to humans but not to bats.
To be successful, a virus must not only infect a host’s cells but also outmanoeuvre its immune system. A host’s T-cells play a huge part in recognising and eliminating new viruses. They do this by identifying peptides that are present in the proteins of the virus but not in the proteins of the host. Peptides are short chains of amino acids linked together by peptide bonds.
More often than not, mature T-cells only recognise peptides that are not present in the host itself. It does this by carrying a population of identical molecules on its receptors with affinity to a particular peptide or small group of peptides. It is therefore advantageous for T-cells to have a narrow peptide vocabulary because it then recognises the broadest spectrum of peptides in a virus. The virus also wants a small peptide vocabulary because it means fewer targets for T-cells to recognise.
The virus also eliminates unnecessary peptides from its own proteins, i.e. ones that are not in the host. Over time, peptide vocabularies of the host and the virus become increasingly similar. The number of peptides present in the virus but not the host is called the immunological T-distance. The smaller this distance, the better adapted the virus is to the host species. Therefore, the species with the smallest T-distance should be the natural host for a particular virus.
So, the authors analysed the T-distances for SARS-CoV-2 and 38 representatives of all major clades of mammals. As a control, they did the same analysis with ten other animals and human coronaviruses, including RaTG13 which is supposedly from samples taken from bats in a Chinese mine and is the closest ancestor to SARS-CoV-2. However, many speculate that RaTG13 was just made up to cover tracks.
They found that for SARS-CoV-2 WITHOUT the spike protein, the closest match was to the greater horseshoe bat. This goes along with the zoonosis origin theory. However, this was the virus without the spike.
When the spike alone was analysed, the closest match was to humans.
The analysis above was done by looking at peptides with five amino acids. When you look at peptides with six amino acids, the evolution of the peptide vocabulary is faster so you can find out more about its history.
When the analysis was done with peptides with six amino acids, it revealed that SARS-CoV-2 without the spike was closest to a treeshrew. The spike in SARS-CoV-2 was closest to a black rat and in RaTG13 a house mouse. This suggests that the virus and spike were passaged in these animals before recombining.
The authors conclude that the “results therefore do not answer the question whether the new virus is the product of a natural recombination of two viruses or the outcome of deliberate insertion of the gene for the spike protein into the genome of other coronavirus species. Of course, the probability of two ancestors of SARS-CoV-2 – one adapted to horseshoe bats and one to humans – being briefly passaged in two different species of laboratory animals before a natural recombination event does not seem high.”
Overall they suggest that whilst not proving it, the analysis strongly supports the artificial origin of SARS-CoV-2.
As is to be expected, there are many critics of this new article. Some claim the jump to rats happened in the Chinese mine. Others question why the authors focused on peptides with five or six amino acids. However, if the analysis turns out to be correct, it is further evidence showing the lab origin of SARS-CoV-2.
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