Beware of the false claims: The pandemic coronavirus spike protein furin cleavage site was not deliberately engineered in a laboratory

Thread on Twitter today plus key cited reports

SARS-CoV-2 furin cleavage site was not engineered

Robert F. Garry

Carolina (UNC) and the Wuhan Institute of Virology (WIV) based on an eight-amino-acid sequence similarity between the furin cleavage site (FCS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike and one of the FCSs of human amiloride-sensitive epithelial sodium channel α subunit (ENaC) (2). Both proteins have the sequence RRARSVAS (Fig. 1A). Harrison and Sachs cite work on rat ENaC from UNC (3, 4) and suggest that the UNC and WIV coronavirologists may have mimicked human ENaC FCS to make SARS-CoV-2 more infectious for lung epithelia.

Numerous features of SARS-CoV-2 FCS demonstrate that it was not engineered to mimic human ENaC:

• Alignment of the nucleotide sequence of the SARS-CoV-2 Spike gene with the closest known coronavirus Spike gene from Laotian bat coronavirus BANAL-20-52 (5) clearly shows that four extra amino acids (PRRA), not eight, were added to the SARS-CoV-2 Spike protein (Fig. 1B).
• There was an insertion of 12 nucleotides into the Spike gene (Fig. 1B, box) (6). This nucleotide insertion is out of frame (6, 7).
• The insertion adds a proline not present in ENaC.
• Except for one codon (cgu that encodes arginine 685), each of the codons for RRARSVAS is different in human ENaC and SARS-CoV-2 (Fig. 1B).
• Five of eight amino acids (RSVAS; underlined in Fig. 1A, red box in Fig. 1C) in or near the ENaC FCS sequence shared with SARS-Cov-2 Spike are present in Spikes of sarbecoviruses, such as BANAL-20-52. It would be illogical to use the FCS from ENac rather than from a FCS of another coronavirus.

Harrison and Sachs’s (1) claim that alignment of sarbecovirus Spike amino acid sequences illustrates “the unusual nature of the [SARS-CoV-2] FCS” is misleading. FCSs are common in coronaviruses, and present in representatives of four out of five betacoronavirus subgenuses (8). The highly variable nature of the S1/S2 junction is easily ascertained by inspecting a precise alignment of sarbecovirus Spikes (Fig. 1C).

After commenting about the “unusual nature” of the SARS-CoV-2 FCS, Harrison and Sachs (1) then argue the opposite. With regard to our earlier publication (7), they write, “In fact, the assertion that the FCS in SARS-CoV-2 has an unusual, nonstandard amino acid sequence is false.” We made no such assertion. Rather, we noted that the SARS-CoV-2 FCS is “suboptimal.” We also noted, correctly, that placing the insertion out of frame would be “an unusual and needlessly complex feat of genetic engineering.”

The immediate proximal ancestor of SARS-CoV-2 did not come directly from a bat to a human, but first evolved in an intermediate host. Two related lineages of SARS-CoV-2—lineage A and lineage B—first infected humans via the wildlife trade at the Huanan Market in Wuhan (9, 10). For the ENaC hypothesis to be true, UNC or WIV researchers would have had to possess the direct SARS-CoV-2 progenitor isolated from another animal—not a bat.

Harrison and Sachs (1) allege that scientists at NIH and elsewhere, including myself and colleagues, conspired to suppress theories of a laboratory origin of SARS-CoV-2. This is false. A possible laboratory origin of SARS-CoV-2 was discussed in our earlier publications (6, 7). 

References

1. N. L. Harrison, J. D. Sachs, A call for an independent inquiry into the origin of the SARS-CoV-2 virus. Proc. Natl. Acad. Sci. U.S.A. 119, e2202769119 (2022).
2. P. Anand, A. Puranik, M. Aravamudan, A. J. Venkatakrishnan, V. Soundararajan, SARS-CoV-2 strategically mimics proteolytic activation of human ENaC. eLife 9, e58603 (2020).
3. A. García-Caballero, Y. Dang, H. He, M. J. Stutts, ENaC proteolytic regulation by channel-activating protease 2. J. Gen. Physiol. 132, 521–535 (2008).
4. P. Kota, M. Gentzsch, Y. L. Dang, R. C. Boucher, M. J. Stutts, The N terminus of α-ENaC mediates ENaC cleavage and activation by furin. J. Gen. Physiol. 150, 1179–1187 (2018).
5. S. Temmam et al., Bat coronaviruses related to SARS-CoV-2 and infectious for human cells. Nature 604, 330–336 (2022).
6. K. G. Andersen, A. Rambaut, W. I. Lipkin, E. C. Holmes, R. F. Garry, The proximal origin of SARS-CoV-2. Nat. Med. 26, 450–452 (2020).
7. E. C. Holmes et al., The origins of SARS-CoV-2: A critical review. Cell 184, 4848–4856 (2021).
8. Y. Wu, S. Zhao, Furin cleavage sites naturally occur in coronaviruses. Stem Cell Res.50, 102115 (2020).
9. J. E. Pekar et al., The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science 377, 960–966 (2022).
10. M. Worobey et al., The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic. Science 377, 951–959 (2022).

https://orcid.org/0000-0002-5683-3250

[email protected]

September 29, 2022 PNAS USA 119 (40) e2211107119

https://doi.org/10.1073/pnas.2211107119

Continuation of thread:

Sander, AL., Moreira-Soto, A., Yordanov, S. et al. Genomic determinants of Furin cleavage in diverse European SARS-related bat coronaviruses. Commun Biol 5, 491 (2022). https://doi.org/10.1038/s42003-022-03421-w

Summary

The furin cleavage site (FCS) in SARS-CoV-2 is unique within the Severe acute respiratory syndrome–related coronavirus (SrC) species. We re-assessed diverse SrC from European horseshoe bats and analyzed the spike-encoding genomic region harboring the FCS in SARS-CoV-2. We reveal molecular features in SrC such as purine richness and RNA secondary structures that resemble those required for FCS acquisition in avian influenza viruses. We discuss the potential acquisition of FCS through molecular mechanisms such as nucleotide substitution, insertion, or recombination, and show that a single nucleotide exchange in two European bat-associated SrC may suffice to enable furin cleavage. Furthermore, we show that FCS occurrence is variable in bat- and rodent-borne counterparts of human coronaviruses. Our results suggest that furin cleavage sites can be acquired in SrC via conserved molecular mechanisms known in other reservoir-bound RNA viruses and thus support a natural origin of SARS-CoV-2.