In 2020 I was invited by Chris Conway to write an Op-ed Piece for the New York Times. I was thrilled. However, I work for a government lab and the process of getting it cleared took long enough that it was no longer timely when approval was given, so it got tucked away and was never published. My sister Dorothy thought it would be of interest to put up here for the history, a sense of where we were at then. So here it is.
One thing that struck me when I was re-reading it today was that I wrote it in the hardest of COVID-19 lockdown times so the portrait of bustling Madrid would have been stark contrast to what we were living at the moment. Also, sadly, the Imokodu HIV-1 vaccine trail failed to protect -- onward.
Identifying a new form of the COVID-19 virus helps the vaccine effort
By Bette Korber, 2020
This is a personal story about being part of a team of scientists working to keep COVID-19 vaccine research stay one step ahead of the virus as it evolves. Like any good mystery, there are red herrings, dead ends, worrisome facts and, towards the end, some hopeful discoveries.
I’m a computational biologist, working in the Theory Division of Los Alamos National Laboratory. I don’t work at a lab bench – I spend my days staring at a computer screen. I study how viruses evolve and use that information to guide vaccine design and testing, to optimize therapeutics, and to understand the biology of viral transmission.
My usual turf is the AIDS virus, HIV. I designed the HIV mosaic vaccine currently being tested in southern Africa, in the “Imbokodu” clinical trial. We will know if it shows promise in people (or not) when the trial is completed finally in 2021. Of note, we first published the concept for the mosaic vaccine way back in 2007. It has taken years of slow but steady progress, led by Dr. Dan Barouch of Harvard, to finally get the design to the clinic. Vaccine work is not for the impatient. But HIV is a highly variable virus, which is basically why an effective HIV vaccine has eluded us to date. In contrast, SARS-CoV-2, the virus that causes COVID-19, mutates much more slowly and is very similar across the pandemic, giving us a much better chance at a faster solution.
For me, the coronavirus story began with a trip to an HIV meeting in Spain in late February 2020. I took an afternoon off to walk around Madrid with a colleague (Rick Koup -- bk). It was a gorgeous sunny day. We sat in a lively plaza and enjoyed people-watching at a packed outdoor café. There was animated conversation and rippling laughter on all sides of us. I had no clue at the time that this was to be my last day off for the next five months. On the long flight home to New Mexico, I started reading coronavirus scientific papers, trying to get my head around the new outbreak.
In Madrid a few weeks later, 120,000 Women’s Day marchers filled the streets, 60,000 soccerfans turned out for a big match, and 9,000 people came together at a political rally. Within days, Spain was plunged into a full-scale epidemic, at that time second only to Italy’s. People went home, and closed their doors. The world changed in the blink of an eye.
As the seriousness of the COVID-19 pandemic became ever clearer, many scientists around the globe felt the same call I did: Was there something, anything, we could do to help?
SARS-CoV-2 Origins
My first opportunity came by joining a team of scientists trying to learn how SARS-CoV-2 wasable to jump species and infect humans. No coronavirus yet found in an animal is related closely enough to the pandemic strain to be identified as its source. But we can piece together some of the story of its ancestry through its genetic sequences.
Wild bats are a natural reservoir of coronaviruses, but most bat viruses cannot infect human cells. SARS-CoV-2 was found to be most closely related to a bat virus that was sampled in China in 2013, though a small part of it was closer to a virus isolated from a pangolin. This kind of genetic mixing, called recombination, is common in coronavirus evolution.
Pangolins are remarkable little anteaters, covered with scales. Though endangered, their meat is eaten in some parts of Asia, and their scales are used in Chinese folk medicine. The part of SARS-CoV-2 related to the pangolin’s virus is in the Spike protein, an essential bit for enabling human infection. In micrographs, Spike proteins project out from the surface of the virus like the spikes in a crown (“corona” in Latin), which gives coronaviruses their name.
The SARS-CoV-2 Spike can bind to a human protein called ACE2. Spike binding to ACE2 triggers a series of molecular changes including a cleavage step that allow the virus to enter our cells. Infected cells then become virus factories. Our immune system responds by clearing out the infected cells and by making antibodies that block Spike and ACE2 interactions in the first place. Thus, Spike is an incredibly important protein in terms of the pandemic. Yes, it causes the infection of our cells — but it is also the major target for antibody-based COVID-19 vaccines.
New Collaborations Emerge to Fight COVID-19
Many scientists working on other vaccines have now refocused their efforts on COVID-19.
Because I’ve worked for years at the interface of viral evolution and vaccines, some of these people are dear friends and colleagues. That’s why, very soon after I got back from Madrid, calls started pouring in from immunologists, always with the same questions: “Is Spike evolving in the pandemic? Are there any particular Spike mutations in the virus I should be testing?”
At that time, the consensus view was that the virus was evolving so slowly that variation would not be a concern for vaccines. Still, I wanted to be sure. I changed my focus from where the virus had come from to where the virus was headed.
Meanwhile, something remarkable was happening. The urgency of the pandemic had fueled a new collaborative spirit. Thousands of scientists and clinicians from all over the world were sequencing the genetic material of the virus, and freely sharing their data in real time. This pooling of information made it possible to tackle the questions the immunologists were asking.
This global data sharing was enabled by GISAID, a database designed for influenza sequence data and retooled in response to the pandemic. New sequences, along with the date and place they were sampled, are easily uploaded into GISAID, rapidly processed, and offered back out to the scientific community as an integrated part of the global data.
Sequences representing the pandemic were streaming in from all over the world. As of this writing (August 6, 2020), there are over 78,000 sequences in the GISAID COVID-19 data set. Unlike HIV, new mutations in SARS-CoV-2 naturally arise slowly, but the vast number of infections offers the virus many opportunities to vary. The few mutations that do arise allow scientists to track the virus as it moves across the globe and also to drill down into local epidemics.
Keeping up with the daily GISAID updates felt like trying to stand in a firehose of data. But our small team at Los Alamos linked metaphoric elbows (actually, we tucked into our own work-from-home quarantine worlds, and we “zoomed” and emailed a lot) and together we managed to keep standing. At Los Alamos, we built a data pipeline to harness and analyze the new GISAID data each day, to monitor mutations over time and by geographic regions, and to look for early indicators of an emerging viral variants that adapting to the human host — and perhaps becoming more dangerous.
A Mutation Beyond Random Chance
There was (and so far still is) only one Spike mutation relative to the original strain from Wuhan that is common among pandemic sequences. It causes a single amino acid change from an Aspartic Acid (abbreviated as D) to a Glycine (a G) at Spike position 614. It almost always tracks with 3 other mutations in other places in the viral genome; this means it arose once in a single ancestor and usually propagates by being passed from person to person. This new “clade” (from the Greek word for branch) was first sampled in Italy in late February. By early March, it was spreading throughout Europe. GISAID started tracking this variant, dubbing it the G clade.
In my April 3rd review of GISAID data, I noticed that when both the D and G forms were found circulating together in a local population, the G clade would rapidly increase in frequency, within a few weeks. This pattern of a shift towards the G clade was repeated at every geo/political level: country, state, county, and city.
Chance events might spark a shift from D to G in a particular location, but if such events were random and both forms were equally likely to propagate, they would not be expected to always go in the same direction. That was the essence of the matter. If you keep flipping a coin and it keeps coming up heads, maybe something besides random chance is afoot.
I immediately discussed this with Dr. David Montefiori, a close colleague at Duke University, who was working on a pseudovirus assay to enable his lab to test COVID-19 vaccine responses as vaccine research progressed. We’d been brainstorming about criteria for selecting Spike variants to be put into the queue for experimental testing. I remember telling David, “This is not a drill.”
We knew that comparing the two forms of the virus experimentally could take months; the kinks were still being worked out in the new SARS-CoV-2 experimental systems. Since time was of the essence, called other experimentalists who were working on Spike and laid out the data. Some were intrigued and set out to compare the two viruses.
A More Transmissible Form of the Virus Emerges
At the time we had two plausible hypotheses regarding how the D-to-G mutation might give rise to a more transmittable form of virus. Either (1) the G form of the Spike protein was more infectious, or (2) it could evade or even be enhanced by the antibodies that come up during natural SARS-CoV-2 infections.
We were concerned that if the G clade virus was more transmissible, it might also cause more severe disease. We partnered with Dr. Thushan de Silva at the University of Sheffield in England to look into this. To our tremendous relief, he found that hospitalization rates did not increase for people infected with the G form. Thushan did find, however, that people infected with the G form had significantly more viral RNA in their upper respiratory tract, which was consistent with the possibility that the G form was more infectious.
By the end of April, the Los Alamos team had automated the computational tools needed to track mutations, developed graphics to map the transition to the G form globally, and made a public website (cov.lanl.gov) with tools and analytics to explore Sars-CoV-2 mutations. We identified several dozen geographic locations where the local epidemic had rapidly shifted from predominantly D to G forms, and almost no exceptions to this pattern. In the spirit of data sharing, we published our epidemiological and clinical findings in a preprint, simultaneously submitting the paper for peer review to the journal Cell.
We did not anticipate the controversy the preprint would engender – our paper was soon downloaded over 200,000 times. There were some days it felt like all 200,000 of those people were trying to contact me. While we got much positive feedback from colleagues, others disagreed with our interpretation.
Some critics thought our findings could have resulted from random factors — a super-spreader event, say, or repeated introductions from travelers (“founder effects”). But this objection missed the central point of our analysis: if such events were indeed random, they would not always go in one direction; instead this “coin” was continually coming up heads.
Global prevalence of the newer G variant
Throughout May, our case kept getting stronger. First, the G form was becoming the most prevalent form globally. Second, we devised statistical strategies to systematically explore all GISAID data, enabling us to identify every single geographic region were the D/G frequencies were changing. In the first figure in our paper, we identified 48 geographic regions with significant shifts in frequency towards the G clade, and only 2 exceptions towards D. We could readily explain both exceptions.
Thushan now had nearly 1,000 patients in his Sheffield study, and the data still pointed toward higher viral RNA levels in people infected with G viruses. Meanwhile two other groups had independently repeated his result and published their findings in preprints.
But the most critical new data were provided by our co-authors, David and Dr. Erica Ollmann Saphire of the La Jolla Institute of Immunology. Erica and David each independently showed that Spike proteins with the G mutation were more infectious in their laboratory assays. A third laboratory also confirmed their findings, and published in a preprint.
Armed with our new data and analysis, as well as the supporting evidence from other laboratories, we responded to the reviews in Cell, and our revised paper was accepted and e-published in Cell on July 3, 2020.
Recently a series of experiments that were initiated by others back in April came to completion, and were also published in a preprint server. These experiments fill out many missing aspects of the story. And the end result is hopeful, indeed.
We had worried that vaccines aimed at the D form of the virus might be less effective against the now globally dominant G form. To our complete surprise, the opposite was true! The G form is even more sensitive to antibodies elicited by vaccines. Also, new protein structure studies have revealed that the G form of the Spike tends to open up and better expose the ACE2 binding site and antibody binding sites, which could explain both its greater infectivity and its greater sensitivity to antibodies. Thus, this the G614 mutation likely fuels the rapid spread of the COVID pandemic -- but it may help hasten the end of it, as well.
This remembrance of events of the spring of 2020 is not complete without thanking my Los Alamos colleagues: Will Fischer, Hyejin Yoon, James Theiler, Werner Abfalterer, Nick Hengartner, Gnana Gnanakaran, Tanmoy Bhattacharya, and Elena Giorgi.
Bette Korber is a theoretical biologist at Los Alamos National Laboratory whose research is focused on developing an HIV vaccine. She was named Scientist of the Year 2018 by R&D magazine for her innovative “mosaic” vaccine designed using Los Alamos’ extensive HIV genome database. That vaccine is now in human trials.
Relevant Research Korber has worked on:
1) Korber et al., Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 182, 1–16 (2020)
2) Li et al., Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection. Science Advances 6:27 eabb9153 (2020)
3) Mansbach et al., The SARS-CoV-2 Spike Variant D614G Favors an Open Conformational State, bioRxiv 2020 (doi: https://doi.org/10.1101/2020.07.26.219741)
4) Weissman et al., D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. medRxiv (doi: https://doi.org/10.1101/2020.07.22.20159905)
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