A Lab Sped Up Coronavirus Evolution to Find What Mutation Might Emerge and Potential Drug

Shin

A 50-fold more infectious SARS-CoV-2 is possible if the Q498R mutation arises.

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The coronavirus (SARS-CoV-2) is actively evolving as it spreads among us. With the recent advent of multiple strains — i.e., variants or mutants with slightly different viral properties — SARS-CoV-2 has become even better apt at surviving amidst humans. This is thanks to the three mutations arriving sequentially:

  1. The D614G mutation — change of amino acid at position 614 from D to G —dominated the globe last year. D614G helps the virus infect cells more easily and become more contagious, at least in animals.
  2. The more recent N501Y mutation is found in the U.K., South Africa, and Brazil SARS-CoV-2 mutants. N501Y helps SARS-CoV-2 binds and infects human cells more easily.
  3. The most current E484K mutation is present in South Africa, Brazil, and, more recently, the U.K. E484K helps the virus evade human antibodies — contributing to vaccine resistance. But the vaccines are still effective for now; only with reduced efficacy.
  4. Q498R?

(For scientific names, the U.K. mutant is called B.1.1.7 or 501Y.V1; the South African one is B.1.351 or 501Y.V2; the Brazil one is B1.1.28 or 501.V3.)

What’s the next mutation? This is rather an unsettling question but must be considered as SARS-CoV-2 continues to circulate at a large scale in human populations. It will not be surprising if the SARS-CoV-2 evolution takes another step forward.

The lab-accelerated emergence of Q498R mutation

To this end, researchers at the Weizmann Institute of Science, Israel — one of the world-leading research institutions — sought to predict what mutations in SARS-CoV-2 might come. Gideon Schreiber, professor and laboratory head with over 150 published academic papers on biochemistry, molecular biology, and related topics, led the study.

Last week, they released their results as a preprint, titled “SARS-CoV-2 RBD in vitro evolution follows contagious mutation spread, yet generates an able infection inhibitor,” so the paper should be interpreted more cautiously. But at least the study authors and institution have a great record of published papers in quality journals. Failing peer-review is, thus, unlikely.

Herein, researchers used a well-established yeast surface display method to screen groups of SARS-CoV-2’s receptor-binding domain (RBD) in lab dishes that contain ACE2. Yeasts expressing (or displaying) the RBD that bound more strongly to ACE2 were isolated and cultured again in another lab dish. This process was repeated many times to discard non-beneficial mutations and to keep propagating beneficial mutations in the RBD — mimicking natural evolution.

Why RBD? The RBD of SARS-CoV-2 is what binds to the ACE2 receptor on the human cell surface to initiate infection. Thus, the SARS-CoV-2’s RBD is always under constant evolutionary pressure. And most, if not all, clinically meaningful mutations occur in the RBD.

They found that the N501Y and E484K mutations emerged independently in their screening — showing that their lab settings successfully emulated natural evolution, leading to the actual real-life scenario we are witnessing now. “It is expected that in vitro [lab dish] selection follows affinity gain, but it is surprising to see that natural SARS-CoV-2 selection follows the same path,” the study authors wrote.

(In biology, affinity means how strongly two molecules interact. In virology, affinity then means how strongly the virus binds to a receptor.)

After a few more rounds of evolution, something dangerous emerged. The Q498R mutation alongside N501Y and E484K increases the RBD’s binding capacity to the ACE2 receptor by 50-fold. “The synergism of Q498R with N501Y and E484K increases ACE2 binding by ~50-fold relative to WT [wild-type],” stated the authors. Wild-type means the prevalent type (species, virus strain, or gene), at least before the emergence of never types.

Surprisingly, the researchers also found an RBD with a 600-fold greater binding capacity to the ACE2 receptor. But this RBD has 9 mutations in the virus’s spike protein — I358F, V445K, N460K, I468T, T470M, S477N, E484K, Q498R, and N501Y — making it unlikely to arise in SARS-CoV-2 anytime soon. But the simple thought of this possibility is scary.

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Possibly more infectious and antibody-resistant

For reference, the N510Y and E484K+N501Y RBDs exhibited a 5- and 13-fold greater binding capacity to the ACE2 receptor, respectively. Yet, the E484K+N501Y mutant present in South Africa, Brazil, and, more recently, the U.K. is already spreading rapidly. Notably, a more contagious virus is more dangerous than a more lethal one because it would lead to more cases and death counts over time.

One could only imagine what the Q498R+N501Y+E484K mutant could do. Perhaps this mutant could infect people with 50-times fewer viral particles or 50-times greater transmissibility, but this is just speculation for now.

Biochemically speaking, the N501Y mutation docks on the ACE2 receptor. This then allows the Q498R mutation to form a robust hydrogen bond and salt bridge to strengthen binding to the ACE2 receptor, the study found.

The study also noted evidence of antibody resistance of the lab-cultured RBD of SARS-CoV-2, wherein human antibodies were less effective at binding and neutralizing the RBD. Apparently, “E484K and Q498R caused most of the observed effects,” the authors stated.

Indeed, many previous studies have found that the E484K mutation makes SARS-CoV-2 strongly resistant to antibodies. The E484K mutation is likely also the primary driver of the current vaccine resistance. (Note that vaccines still work but with lower efficacy) Thus, it’s possible that the Q498R mutation (if it emerges) would exacerbate the threat of E484K mutation.

“The rapid spread of N501Y in the population increases the likelihood for the emergence of the Q498R mutant, which will probably have even higher infectivity,” the authors wrote. “This suggests that with the spread of the “British”, “Brazilian”, and “South African” variants, we project that the Q498R mutation will appear in the future, on top of these mutations.”

Turning it around as a promising drug

As mentioned above, the researcher managed to accelerate the SARS-CoV-2’s RBD evolution to the point where it gains 9 mutations that confer a 600-fold increase in binding capacity to the ACE2 receptor.

The researchers then thought of an interesting idea to exploit this highly infectious RBD mutant as a potential treatment for Covid-19. Since this RBD evolved to bind the ACE2 receptor so strongly, it could also be used as an ACE2 receptor blocker to prevent SARS-CoV-2 infection.

So, they decoded and purified this RBD mutant to derive a harmless molecular binder of ACE2. Applying this ACE2 binder to cells, the researchers showed that it occupied the ACE2 receptor — without disrupting the cell’s normal functions — and completely blocked SARS-CoV-2 entry into the cell.

As the authors explained, “RBD-62 [the ACE2 molecular binder] blocked >99% of viral entry and replication…The complete blockage of viral replication…makes it a promising drug candidate.” Experiments are underway to investigate this potential drug, the researchers stated. “Despite the high hopes that vaccines will eradicate COVID-19, realistically, the development of a working drug stays high on the agenda.”

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Short abstract

To see what future SARS-CoV-2 might look like, researchers accelerated its receptor-binding domain (RBD) evolution in the lab. Initial results gave rise to the N501Y and E484K mutations, consistent with what has happened in the real world. After further evolution, the researchers derived the Q498R mutation that increases the RBD’s binding capacity to the ACE2 receptor by 50-fold and confers antibody resistance. More fast-paced evolution led to an RBD harboring 9 mutations that bind the ACE2 receptor with 600-fold greater intensity. While the possible reality of SARS-CoV-2 actually evolving this RBD is indeed frightening, the RBD could also be a promising ACE2 receptor blocker treatment for Covid-19.

But, of course, lab settings do not always translate accurately to real-world settings. Still, the possibility is a wake-up call to prevent the further spread of SARS-CoV-2 in the world today. After all, every infected person provides an opportunity for SARS-CoV-2 to mutate and evolve the Q498R mutation or other unexpected mutations.

This article was previously published in Microbial Instincts with minor modifications.

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