randombio.com | Science Dies in Unblogginess | Believe All Science | Follow The Science
Thursday, July 22, 2021 | Science

Fauci is in error about NIAID funding of gain-of-function experiments

The National Library of Medicine's own Pubmed finds thirteen papers from Shi Zhengli funded by NIAID, including gain of function experiments

F irst of all, let's define the term. A “gain of function” experiment is one in which a researcher genetically manipulates a virus to add a new function. This could include adding a new restriction site or mutating the virus to change its tropism, receptor affinity, or pathogenicity. Some of these are routinely done in science and don't necessarily indicate sinister intent. Even changing the DNA/RNA sequence isn't necessarily a major risk, provided that the product is expressed in a pseudovirus.

Things that aren't gain-of-function experiments are natural phenomena (which aren't experiments) or adding an expression tag such as green fluorescent protein, which doesn't change what the virus does.

I mention this because people are already sending me newsclips from the media claiming that upregulation of protein expression and mRNA editing that happens normally in cells are gain-of-function. Apparently the media's new party line will be that gain of function is a nothingburger. Dr Anthony Fauci of NIAID and Senator Rand Paul got into a nasty disagreement this week as to whether NIAID funded gain-of-function research at the Wuhan Institute of Virology. Fauci became indignant and said Paul didn't know what he was talking about.

This sort of politicizing of science by scientist/administrators is unimaginably harmful because it induces suspicion. The evidence shows that Paul is correct and Fauci is wrong.

The PLoS Pathogens paper

The 2017 paper “Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus” in PLoS Pathog.[1] contains the following paragraph:

In the current study, we successfully cultured an additional novel SARSr-CoV Rs4874 from a single fecal sample using an optimized protocol and Vero E6 cells [17]. . . . Using the reverse genetics technique we previously developed for WIV1 [23], we constructed a group of infectious bacterial artificial chromosome (BAC) clones with the backbone of WIV1 and variants of S genes from 8 different bat SARSr-CoVs. Only the infectious clones for Rs4231 and Rs7327 led to cytopathic effects in Vero E6 cells after transfection (S7 Fig). . . . In contrast, when Vero E6 cells were respectively infected with the two successfully rescued chimeric SARSr-CoVs, WIV1-Rs4231S and WIV1-Rs7327S, and the newly isolated Rs4874, efficient virus replication was detected in all infections (Fig 7). To assess whether the three novel SARSr-CoVs can use human ACE2 as a cellular entry receptor, we conducted virus infectivity studies using HeLa cells with or without the expression of human ACE2. All viruses replicated efficiently in the human ACE2-expressing cells. [emphasis added]

This paragraph says the WIV researchers took SARS-related coronavirus SARSr-CoV Rs4874 and artificially recombined it with variants from eight other viruses. The word ‘chimeric’ means that the product is a combination of two or more other DNA segments. They then used the new viruses to infect Vero E6 cells, which are kidney cells from African Green monkey often used to study SARS-CoV-2.[2] Finally they tested them on human HeLa cells, which are immortalized cancer cells taken from a cervical cancer patient.

HeLa cells containing human ACE2, which is the receptor for SARS coronaviruses, are widely available and often used to study the infectivity of pathogenic coronaviruses.

Under “Funding”, the authors write

Funding: This work was jointly funded by National Natural Science Foundation of China (81290341, 31621061) to ZLS, China Mega-Project for Infectious Disease (2014ZX10004001-003) to ZLS, Scientific and technological basis special project (2013FY113500) to YZZ and ZLS from the Ministry of Science and Technology of China, the Strategic Priority Research Program of the Chinese Academy of Sciences (XDPB0301) to ZLS, the National Institutes of Health (NIAID R01AI110964), the USAID Emerging Pandemic Threats (EPT) PREDICT program to PD and ZLS, CAS Pioneer Hundred Talents Program to JC, NRF-CRP grant (NRF-CRP10-2012-05) to LFW and WIV “One-Three-Five” Strategic Program (WIV-135-TP1) to JC and ZLS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

The Journal of Virology paper

Reference 23 in the paper is Zeng et al. [3], published in the Journal of Virology, in which the authors developed a “fast and cost-effective method for reverse genetics of coronaviruses.” They write:

Our method allows the genomes of coronaviruses to be split into multiple fragments and inserted into a BAC plasmid with a single step. . . . As the genomes can be divided into multiple short fragments, mutations can be introduced into individual fragments easily.

They took SARS-like coronaviruses named WIV1 and WIV16 and showed that a mutant form in which one segment called ORFX was deleted was still infectious. By doing further cloning experiments, they found that this ORFX segment inhibits interferon production, which means that it blocks the cell's immune response to the virus. The authors write:

Besides three naturally occurring BglI sites (GCCNNNN↓NGGC), four BglI sites were successfully introduced by synonymous mutations in the genome (Fig. 1B). Different asymmetric 3-nt overhangs at the junctions of each two contiguous fragments were created by these BglI sites. The eight fragments were then linked in one direction. A SacII site was added to the 5' terminus of fragment A. A poly(A) sequence (25 nt) and an AscI site were added to the 3' terminus of fragment G. A naturally occurring BglI site at nucleotide 1571 was removed by the synonymous mutation C1575A (Fig. 1B). Other unexpected synonymous mutations also occurred, including T1422C, T12984C, T14213C, T17130C, C17934T, and T26068G.

The plasmid pBAC-CMV was constructed by inserting the cytomegalovirus (CMV) promoter, hepatitis delta virus (HDV) ribozyme, and bovine growth hormone (BGH) transcription terminal signal sequences into pBeloBAC11, along with the introduction of the SacII and AscI sites between the CMV promoter and HDV ribozyme (Fig. 1C). The eight genomic fragments were inserted into pBAC-CMV in one step. Recombinant viruses could be rescued by direct transfection with the BAC constructs. . . .

The constructed clone (pBAC-CMV-rWIV1) was transfected into Vero E6 cells. A cytopathic effect was observed at 72h posttransfection.

This is all scientifically interesting and valuable research, but it cannot be denied that here too the authors are doing gain-of-function experiments, specifically adding new restriction sites and promoter sites, and inserting them into a plasmid, putting them into mammalian cells, and measuring the viral replication efficiencies. This too was funded by NIAID.

This work was jointly funded by the National Natural Science Foundation of China (81290341, 31321001, and 81401672) and the National Institutes of Health (NIAID R01AI110964).


The National Library of Medicine's own Pubmed search finds thirteen articles using the simple search term shi zl[au] and niaid. Not all of these, of course, will be gain of function experiments, but there's no doubt the WIV is using NIH funding.

Also, we don't want to leave out Peter Daszak, the zoologist and president of EcoHealth Alliance, who helped WIV get funding on this topic [4]. In case anyone still reads The Lancet, Daszak wrote an editorial there on July 5 2021 defending the idea that SARS-CoV-2 evolved in nature. Perhaps reflecting the controversy surrounding him, the importance of this article is that it may be the first editorial where the disclaimer is longer than the article itself.

The question is: why is the government lying about this? Again, there is nothing necessarily sinister about what the WIV was doing. The million-yuan question is whether they did gain-of-function on SARS-CoV-2, specifically on the RBD and furin site. The reason is they want you to get vaxxed. But there's a very good reason why the US gov't has started pouring money into antiviral drugs. They know that vaccines against slowly mutating viruses like poliovirus and smallpox are very effective, while vaccines against rapidly mutating viruses rapidly become ineffective. This is why those of us who work in hospitals are forced to get influenza shots every year, regardless of how well they work. As wonderful as vaccines may be, only a small molecule that acts to inhibit how a virus functions, rather than an antibody that binds to a structural feature, has a chance of blocking every mutant.

There may be good reasons to get vaccinated now, or to wait until the really scary Omega variant comes along. You could take all the vaccines as they come out, as long as you recognize a ‘booster’ will always be necessary. The virus has nasty effects and it can screw up your brain, and the vaccine also has risks that are probably smaller. It is your choice. But you'd be a fool to take advice from somebody who demonstrably issues false statements.

But the point is these arguments about shouldn't even be happening at all, least of all on the Senate floor. In science, we try to avoid insulting each other by carefully defining our terms and calmly evaluating the facts. This is an issue about rules and that's what committee meetings are for.

Note: I downloaded these articles on July 22, 2021 at 4:23 am. If you want to read it, you might want to grab a copy of the PLoS Pathogens paper soon, as the PDF is stored on the Google cloud, and clouds have a wonderful habit of disappearing when the weather gets hot.

1. Hu B, Zeng LP, Yang XL, Ge XY, Zhang W, Li B, Xie JZ, Shen XR, Zhang YZ, Wang N, Luo DS, Zheng XS, Wang MN, Daszak P, Wang LF, Cui J, Shi ZL. Discovery of a rich gene pool of bat SARS-related coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathog. 2017 Nov 30;13(11):e1006698. doi: 10.1371/journal.ppat.1006698. PMID: 29190287; PMCID: PMC5708621.

2 Ogando NS, Dalebout TJ, Zevenhoven-Dobbe JC, Limpens RWAL, van der Meer Y, Caly L, Druce J, de Vries JJC, Kikkert M, Bárcena M, Sidorov I, Snijder EJ. SARS-coronavirus-2 replication in Vero E6 cells: replication kinetics, rapid adaptation and cytopathology. J Gen Virol. 2020 Sep;101(9):925-940. doi: 10.1099/jgv.0.001453. PMID: 32568027; PMCID: PMC7654748.

3. Zeng LP, Gao YT, Ge XY, Zhang Q, Peng C, Yang XL, Tan B, Chen J, Chmura AA, Daszak P, Shi ZL. Bat Severe Acute Respiratory Syndrome-Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response. J Virol. 2016 Jun 24;90(14):6573-6582. doi: 10.1128/JVI.03079-15. PMID: 27170748; PMCID: PMC4936131.

4. Ge XY, Li JL, Yang XL, Chmura AA, Zhu G, Epstein JH, Mazet JK, Hu B, Zhang W, Peng C, Zhang YJ, Luo CM, Tan B, Wang N, Zhu Y, Crameri G, Zhang SY, Wang LF, Daszak P, Shi ZL. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013 Nov 28;503(7477):535-8. doi: 10.1038/nature12711. Epub 2013 Oct 30. PMID: 24172901; PMCID: PMC5389864.

july 22 2021, 6:50 am

Related Articles

The hidden debate about the SARS-CoV-2 furin cleavage site
The most important scientific discussion of our time going on within obscure scientific journals

Strange things started happening to me after I got vaccinated
I finally got around to getting a Covid vaccine. Now forks are sticking to my head, drones crash around me, and I can no longer get Wi-Fi

What does furin do when it's not trying to kill us?
Furin is involved in AIDS, cancer, and anthrax. It helps deadly viruses like SARS-CoV-2 and Ebola enter the cell. But what is furin, and why does it hate us?

A discussion of Li-Meng Yan's paper on SARS-CoV-2
Three dissident virologists claim to have proof that SARS-CoV-2 was artificially created. What is their evidence? (Updated)

On the Internet, no one can tell whether you're a dolphin or a porpoise

book reviews