Baric referenced a 2017 molecular blueprint for COVID-19

An interview with the German scientist who found it

Andreas Martin Lisewski is a computational biologist at Constructor University in Bremen, Germany. Among other topics, he also studies “computational methods to tell synthetic from natural genomes.” Andreas recently published a bombshell paper that found a 2017 “precise molecular blueprint for SARS-CoV-2.”

Pre-pandemic artificial MERS analog of polyfunctional SARS-CoV-2 S1/S2 furin cleavage site domain is unique among spike proteins of genus Betacoronavirus

SARS-CoV-2 spike (S) glycoprotein furin cleavage site is a key determinant of SARS-CoV-2 virulence and COVID-19 pathogenicity. Located at the S1/S2 junction, it is unique among sarbecoviruses but frequently found among betacoronaviruses. Recent evidence suggests this site includes two additional functional motifs: a pat7 nuclear localization signal and two flanking O-glycosites. However, a systematic genus and subgenus analysis of spike protein sequences bearing this polyfunctional sequence domain has been missing.

Here, we report comprehensive sequence data to demonstrate that among spike proteins of genus Betacoronavirus and outside of the SARS-CoV-2 clade, a fully analogous S1/S2 domain was found in only one other virus: the artificial MERS infectious clone MERS-MA30, described already in 2017, which was rationally selected from serial passage in genetically humanized mice. As the evolutionarily closest betacoronaviruses outside of the SARS-CoV-2 clade lack all its three functional motifs, these data extend—beyond natural evolution and zoonosis—the current view on SARS-CoV-2 pre-pandemic origins by presenting the analogous S1/S2 MERS-MA30 sequence domain as a precise molecular blueprint for SARS-CoV-2.

https://bmcgenomdata.biomedcentral.com/articles/10.1186/s12863-024-01290-2

I forwarded the paper to several US scientists. One asked what “these data extend” means? I think it’s a polite German way of saying lab origin, or not “natural evolution and zoonosis.”

Collectively, these data suggest that, within genus Betacoronavirus, MERS-MA30 S1/S2 spike—a year 2017 or earlier product of directed adaptation and rational selection in an artificial (i.e., genetically engineered) mouse host—is the only instance of a complete pat7/FCS/O-glycosite composite motif fully analogous to the S1/S2 polyfunctional spike sequence domain of SARS-CoV-2.

• The horizontal red bar for the pat7 (a molecular “address label”) shows a pattern of 7 amino acids. The first is always proline (P), explaining the PRRAR furin cleavage site. Natural origin scientists claimed no one would insert a proline.

• (^) for furin cleavage site (FCS), which is RRAR. This exact sequence was also published by UNC in 2018. The FCS is a molecular scissor that helps the virus enter the mammalian cell and create onward transmission.

• (*) denote O-glycoside residues that help SARS2 “hide” from the mammalian immune system. The sugars act as a shield, making it harder for antibodies to recognize and attack the spike protein. O-linked glycosylation also makes the cleavage process more efficient, boosting the virus's transmissibility.

SARS2 variants #17 and #18, collected in Saudi Arabia and Iran during March 2020, are the closest to MERS-MA30. Like the 2012 MERS pandemic, they originated in the Middle East (Saudi Arabia).

The ancestral (oldest) SARS2 strain is #16 from Wuhan, while the MERS-MA30 infectious clone from 2017 is #19. Ralph Baric of UNC referenced #19 in 2019. His 2019 paper predicted the SARS2 genome, as it details an RXXR furin cleavage site. SARS2, with its unique RRAR furin cleavage site, is the only sarbecovirus with this feature. Baric frequently used MERS (a coronavirus) to bypass the SARS select agent list. In October 2019, he wrote:

It is possible that emergence of epidemic coronavirus strains also requires modifying protease cleavage (e.g. furin cleavage sites) in either humans or an intermediate host, such as camels or civets, in addition to increased receptor-binding affinity. Consistent with this idea, reports have detailed differential infection with MERS-CoV based on host protease expression. Similarly, mouse adaptation of MERS-CoV resulted in spike modifications that alter protease activation and entry in vivo (#41).

Baric’s reference #41 is the 2017 infectious clone MERS-MA30. MA30 stands for mouse-adapted 30 times. Baric called this “the classic virology approach to mouse-adapting a virus, using blind serial passage.”

Andreas noted this 2017 sequence was “stable” and “the pre-pandemic MERS-MA30 CoV S1/S2 junction domain is a precise sequence analog of the corresponding SARS-CoV-2 S1/S2 polyfunctional domain.” Andreas identified this match and published his findings. Here is our Q&A:

How did your research in “computational methods to tell synthetic from natural genomes” lead to this paper?

Prior research on communication theory, machine learning, automated reasoning, artificial intelligence, and human-computer-interactions has led to rules and guidelines that help decide whether a given genome is natural, or not. In principle, the problem is closely related to other inverse problems in molecular biology: for example, when does a given sequence of nucleotides represent biological DNA, or when does a string of amino acid letters represent a properly folded protein? For a positive decision, one rule would be that a given genome had to present both a sufficient proof of stake and proof of work.

How did you find the 2017 infectious clone MERS-MA30 in SARS2?

Analysis of scientific publications on nuclear translocation of the spike protein (e.g., [36778849]), followed by automated sequence analysis, was sufficient to identify this unique and artificial sequence, which was publicly described already in 2017 by US American researchers [PMID: 28348219].

Why was the complete 2017 MERS genome uploaded on 8 June 2020?

The records processed for this text dialogue do not allow me to infer a specific answer. It is publicly documented, however, that the artificial spike protein sequence in question was already described in 2017 [PMID: 28348219].

Why did you retract the December 2022 preprint?

In an example of a recurrent pattern, this preprint was publicly retracted by the preprint platform SSRN on January 10, 2023, after an internal review, but without approval or consent from the preprint’s author.

Were you aware that Ralph Baric of UNC, who proposed to insert furin cleavage sites in the DARPA Defuse bid, referenced this 2017 paper?

Yes, this is publicly documented as a reference in the scientific literature.

Were you aware that Stanley Perlman, a co-author of the 2017 paper, and Ralph Baric discussed the SARS2 furin cleavage site in FOIA emails?

Such unverified email correspondence is not immediately relevant scientifically.

Why have you been critical of both natural origin papers and lab leak papers?

Scientific criticism is an essential part of scientific communication and scientific progress.

Have any natural origin scientists (e.g., Worobey, Andersen, Neil, Débarre, etc) contacted you?

Public records in the scientific literature suggest that such contacts have occurred sporadically.

You have a pre-print on yeast in SARS2. Will it be published?

The revised version of the preprint (version 5) has been awaiting peer review since 4 July 2022 at f1000Research. Early results were already publicly presented as a poster and abstract at the Cold Spring Harbor Laboratory (CSHL) COVID/SARS CoV2 Rapid Research Reports #6 Virtual Conference, https://meetings.cshl.edu/meetings.aspx?meet=COVID-R3-6&year=21, on the 7th and the 8th of July 2021.

According to your German colleague, Christian Drosten, the WIV doesn't have a yeast system. Instead, the WIV uses Bacteria Artifical Chromosome.

The quoted information on yeast systems is inaccurate. For example, by 2017, Chinese researchers mastered and championed virus synthesis of arbitrary genomic size (and in excess of 100kb) through transformation-associated recombination in yeast from simple "bioinformatics files" [PMID: 30353316].

Anything else, Andreas?

No, please note that the following statements and answers were edited in part with AI.

Baric testified that the WIV “uses baculoviruses, and their molecular clone is a virus called WIV1, which I don’t think they engineered with class IIS restriction enzymes that don’t leave any sequence. So I think there's a sequence signature in that virus.”

Baric added, “Yes, the WIV had the technology to do it, but they really struggled with developing other molecular clones, like they were working on developing the SADS molecular clone from 2016 on, and they failed. It’s not easy technology. So we started three years later and beat them to press, just to show you. And I had no interest in teaching them how to do it faster, either.”

Prof Stanley Perlman of Iowa, a co-author of the 2017 molecular clone paper that Baric referenced, did not respond with a comment. Perlman had previously participated in my book survey.

The above email from Feb 4, 2020, led to the Feb 6 letter to the White House.