I did a BLAST search limited to eukaryotes and there were 3 hits with 100% match over the full length. One was from Saprolegnia, a protozoan, 2 were from the sea birds found by geo12the. Based on the combined results, it looks like “The absence of CTCCTCGGCGGGCACGTAG from any eukaryotic or viral genome in the BLAST database” is incorrect.
Geo12the is right to mock the notion that “Fauci had a secret program to make killer Chimney Swifts”, but the absurdity of that notion does not support the conclusion that he seems to think. Of course nobody would have a rational reason to pull a short sequence from these organisms and put it into a bat virus genome. But then, what natural process would bring a bat virus in contact with these genomes to enable recombination and arrive at SARS-Cov2? So even though the sequence can be found by chance in some organisms, I think the conclusion “recombination in an intermediate host an unlikely explanation for its presence in SARS-CoV-2” still stands.
I agree that the presence of the 19 base sequence in the Moderna patent may not be all that significant. SARS-Cov2 differs from its nearest relative by the insertion of the four amino acids that make up the furin site; the flanking amino acids on both sides are identical (see Fig. 1 at https://www.ncbi.nlm...les/PMC7095063/ ) . So, the 12 nucleotides that encode the furin cleavage sequence are within the 19 base sequence, the other nucleotides that make up the 19 bases were present in the bat virus. Therefore one has to account for the introduction of 12 bases , not 19. Those 12 bases had to come from somewhere and they just happened to land at the boundary of the S1 and S2 domains. Given that we know that people were contemplating the introduction of a furin cleavage site (the grant proposal), and the codons happened to coincide with those that would be picked from the human codon optimization tables, deliberate engineering seems more likely than chance selection in the wild.
When you compare sequences from closely related organisms you can see all kinds of changes -deletions, insertions, etc. I don't find a 12 base pair insertion into a coding sequence that unusual that I would hypothesize it's more likely to have been deliberately engineered vs. just happened by natural mutation processes. This paper looks at the cleave site in related viruses. I underlined the key sentences in one of the results sections. First as we have already established here: "SARS-CoV-2 is the only virus in subgenus Sarbecovirus having this feature, while even its closest relatives, bat coronavirus RaTG13 (sequence identity 97.7%) and pangolin coronaviruses (92.9%–90.7%), do not have furin site" . But there is a related virus (belongs to a siter clade) that does although no other viruses in the clade do: "However, in Hibecovirus, the sister clade of Sarbecovirus, a Hipposideros bat coronavirus collected in 2013 at Zhejiang Province in China has furin site at S1/S2. Interestingly, the other member in Hibecovirus lacks such site, similar to the situation of SARS-CoV-2 and its close relatives."
My personal view: From the beginning I have been been uncertain if SARS-CoV-2 escaped from a lab by accident or came from nature. If you asked me now to bet $1 million dollars if it is natural origin or lab escape I would be on the fence, but if forced to choose I would bet natural origin. But I am afraid we will never know for certain. I have worked in enough labs to know that some lab workers are meticulous about safety issues while others may be caviler and/or sloppy. And sterile hoods have leaks and are much less foolproof than people imagine. And the Chinese government has a record at covering up embarrassing things. So while I think the origin probably was natural I would not be surprised if it was an accidental release that was covered up.
"We mapped the furin recognition motif RXXR at both S1/S2 and S2′ positions in phylogenetic trees of spike protein sequences (Fig. 3, Fig. 4, Fig. 5 and S2, S3). In the Sarbecovirus + Hibecovirus + Nobecovirus clade (Fig. 3), furin cleavage sites at either position occur only in limited ranges. Strains of SARS-CoV-2 (we also added sequences from the GISAID database) have furin cleavage sites at spike S1/S2. Moreover, SARS-CoV-2 is the only virus in subgenus Sarbecovirus having this feature, while even its closest relatives, bat coronavirus RaTG13 (sequence identity 97.7%) and pangolin coronaviruses (92.9%–90.7%), do not have furin site. However, in Hibecovirus, the sister clade of Sarbecovirus, a Hipposideros bat coronavirus collected in 2013 at Zhejiang Province in China has furin site at S1/S2. Interestingly, the other member in Hibecovirus lacks such site, similar to the situation of SARS-CoV-2 and its close relatives. The SARS-CoV-2 strains and Hipposideros bat coronavirus (Zhejiang 2013) are not sister groups, in agreement with the distinct sequence patterns of their furin cleavage sites at spike S1/S2 (Fig. 6A). Besides, two strains of bat coronavirus HKU9, belonging to Nobecovirus, are the only members in the Sarbecovirus + Hibecovirus + Nobecovirus clade having furin cleavage site at spike S2′."
Edited by geo12the, 27 February 2022 - 06:17 PM.
