New mechanism; new pathway

SANTA CLARA, Calif.—A pair of antibody discovery companies— Antibody Solutions and Single Cell Technology (SCT)—is sharing research into the rise and dominance of a mutant SARS-CoV-2 virus that identifies a new mechanism which might indicate a competitive advantage for the mutation.

The predictions coming out of this research, if they hold up, could have a serious impact on the direction of future work on vaccines and therapeutics to deal with infection with the SARS-CoV-2 virus and COVID-19, the disease such infection brings about. The researchers hope that their findings could help biopharma scientists more effectively target their research efforts on specific regions of the SARS-CoV-2 virus that may contribute to its infectivity power and speed the discovery of an effective vaccine or therapy.

The researchers predict that the mutation they were studying may very well induce a structural change in the spike protein of the virus that would enhance virus entry. The study by the two companies is available on Preprints.org at https://www.preprints.org/manuscript/202005.0407/v1 but had not yet been peer-reviewed when this issue of DDN went to press.

According to Dr. John Kenney, president and co-founder of Antibody Solutions, the advanced molecular modeling used in the research for the study may have revealed how D614G, the dominant mutation isolated from a majority of patients in Europe and the eastern United States, gained a competitive advantage over the earlier isolates of SARS-CoV-2 found in China.

“Our results from gene sequencing clearly show the D614G mutation is more common as the pandemic unfolds,” Kenney said. “Our homology modeling identifies a mechanism whereby the D614G mutation favors the orientation of critical residues in the furin cleavage domain. You can think of the recently discovered furin domain as an activation sequence or ‘trigger.’ A better orientation of this domain for cleavage would be expected to enhance infectivity.”

In work on treatments to intervene in COVID-19, one of the primary targets has been the spike protein of the novel coronavirus. As Kenney and colleagues note, cleavage of the spike protein by furin is a key mechanism distinguishing SARS-CoV-2 from SARS-CoV and non-pathogenic coronaviruses.

“Our findings of the competitive and mechanistic advantages arising from the D614G mutation strengthen the rationale for targeting the furin cleavage domain of the spike protein with vaccines or neutralizing antibodies to inhibit COVID-19 progression,” Kenney said.

Dr. Chun-nan Chen, chief science officer and CEO of SCT, used his company’s informatics platform to mine worldwide SARS-CoV-2 genome data to learn more about how the mutants’ efficiency and geography may be correlated. Through genetic sequencing analysis of 11,542 viral genome records collected through April 28, 2020, Chen said his team was able to compute the frequency of different mutations.

“By examining amino acid changes in each case, we identified mutations along the Spike, or ‘S,’ protein at 103 positions,” Chen said, “And D614G was, put simply, the dominant mutation, occurring in 56 percent of all sequences—far more than all of the other identified mutations combined.

“When we examined the geographical distribution of G614-containing viral genomes,” he continued, “distribution patterns emerged that show the G614 mutant as the dominant SARS-CoV-2 mutant in Europe and large swathes of the U.S. But viral sequences from Chinese and South Korean patients and those from the West Coast of the U.S. were mainly found to be carrying the Wuhan Spike or ‘S’ protein genotype.”

The team modeled a three-dimensional protein domain of SARS-CoV-2 Spike protein with the goal of creating a prediction of the secondary structure of the region that contains both the site of mutation and the furin cleavage site that is believed to impart enhanced infectivity onto the virus.

“We created two models and observed a provocative result in which the only significant changes in structure are seen at the furin binding site,” Kenney explained. “Essentially, the D614G mutation changes the orientation of critical residues in the furin cleavage domain and is more favorably aligned within the active site of furin. If furin cleavage is rate-determining in the membrane fusion process, such an increase in protein cleavage would lead to more rapid membrane fusion and entry into cells that serve as hosts for the virus.

“So, our modeling predicts a conformational change in a specific cleavage site induced by the D614G mutation that may reduce the required activation energy and translate into an advantage in infectivity.”

Kenney, Chen and the other members of the team emphasize that understanding of whether this advantage is conferred by infectivity, immune evasion or pathogenicity—or some combination of these—is incomplete right now. And they caution that their research is not intended to draw specific conclusions about the D614G mutation’s transmissibility, sequelae influence or other broad immunological dynamics relating to the SARS-CoV-2 pandemic.

As Kenney noted, even if their findings hold up, they would not preclude other mechanisms that could act in concert with the one they have identified. To that end, the team is continuing to push toward a fuller understanding of the biology of the virus and why the D614G mutation seems to be so central to greater infectivity.

“This is a case where sequencing and molecular modeling working hand-in-hand can help build a greater understanding about the key mechanisms in the pathogenesis of SARS-CoV-2,” Kenney said. “Most mutations either fade from view or, if they stick, don’t have deleterious effects. We believe that the D614G mutation represents one of those instances where there’s a clear case of it increasing the pathogenesis of this virus, which points to the site we identified as an important target for therapeutic antibodies, vaccines and other modalities.”

“We hope this research provides an ideal engagement point for researchers working on SARS-CoV-2,” he continued. “This wasn’t an ‘obvious find,’ and it took both of our teams working closely together to reveal it. It was a unique insight that we hope will inspire the scientific community to continue exploring. Genuinely, we want to know what we have right and wrong, and we intend to explore therapeutic angles ourselves.”

Kenney said that in addition to its most recent collaboration with SCT, the company is working on multiple SARS-CoV-2 research initiatives on its own and on behalf of clients pursuing vaccines and therapies for the virus.