Molecular Biology Clues Portray SARS-CoV-2 as a Gain-of-Function Laboratory Manipulation of Bat CoV RaTG13

The origin of SARS-CoV-2, the causative agent of the COVID-19 pandemic, is highly controversial.¹⁻³ Many researchers steadfastly support a natural origin,² but a recent report by journalist Nicholas Wade¹ upholds the view that SARS-CoV-2 is the outcome of genetic manipulation of a bat coronavirus intended to promote transmissibility to humans.³

Genomic analyses³ show that SARS-CoV-2 is a chimera, with most of its sequence identical to that of the bat CoV RaTG13, except for the receptor binding domain (RBD), which is almost identical to that of a pangolin (Manis javanica) CoV and has been optimized to bind the ACE2 receptor in human cells.³ Such gain-of-function chimeras can in principle arise via natural recombination, but that would be unlikely in this case. The natural recombination would require that the viruses from bat and pangolin infected the same cell in the same organism simultaneously, a rather improbable event considering the low population density of pangolins, the dearth of CoV-infected specimens in their natural populations, and the fact that CoV RATG13 does not have significant affinity for the pangolin ACE2,³ and therefore is unlikely to penetrate the infected pangolin cell.

Gain-of-function recombinations of coronaviruses have been ongoing in the laboratory for more than a decade.¹ As early as 2007, the group headed by Zheng-li Shi from the Wuhan Institute of Virology (WIV) created a series of “bat-man” CoV chimeric spike proteins^1,4 to enable CoVs to jump from one species to another and model “spillover effects” that could trigger a pandemic. Shi’s goal was to turn the bat CoVs into huACE2-binding molecules, that is, to design promoters of human infection.^1,3,4

With regard to the recent history of these gain-of-function manipulations of coronaviruses, a U.S. NIH funded $3.7 million grant was approved by Trump’s COVID-19 advisor Anthony Fauci in 2015. The gain-of-function research was outsourced to the WIV, which remains at the center of scrutiny with regard to the COVID-19 pandemic.⁵

An indicator that the NIH-funded research had gone too far arose when the tinkered CoV-RaTG13 became endowed at the spike protein with a “detonator”, that is, a cleavage site recognized and activated by the host-cell enzyme furin (Figure 1).⁶ This site has not been identified in other CoVs from the same lineage. The way this cleavage site is incorporated attests to the artificial origin of SARS-CoV-2. The furin-associated cleavage site was created by incorporation of the 12-nucleotide insert TCCTCGGCGGGC coding for the PRRA amino acid sequence at the S1/S2 junction in the spike monomer. Strikingly, the two adjacent arginines are coded by two consecutive CGG codons. Only about 5% of arginines in SARS-CoV-2 or RaTG13 are coded by CGG.³ This implies that the CGGCGG in the inset would have an estimated 0.25% probability to “naturally” occur as an encoder of the RR motif. Other suspicious aspects pertain to the way in which the encoding cassette was inserted to create the cleavage site. The insertion causes a split in the original codon for serine (TCA) in RaTG13,³ so the TC portion becomes now part of a new codon for serine (TCT), while the terminal adenosine (A) becomes part of a codon for alanine (GCA), yielding the following sequence: TC[TCCTCGGCGGGC]A. This is very odd, clearly pointing to an artificial origin.

Figure 1.

Two gain-of-function modifications of bat CoV RaTG13 promoting transmission to humans.

Clues from molecular biology uphold the artificial origin of SARS-CoV-2, reinforcing the recent investigation by journalist Nicholas Wade.¹ The gain-of function insertions of human-adapted pangolin CoV RBD and furin-associated cleavage site are likely the result of genetic manipulations conducted in a laboratory. Such manipulations may have been carried out without leaving a trace. A thorough investigation of the research records at WIV is needed, notwithstanding the recent deletion of their internet database.