Brianna Bibel, CSHL School of Biological Sciences
The COVID/SARS CoV2 Rapid Research Reports is a series of meetings organized by Cold Spring Harbor Laboratory (CSHL) that brings together scientists from around the world to discuss the very latest research on the novel coronavirus SARS-CoV-2 and the disease it causes, COVID-19. The series began in June 2020 and continues with the fifth installment this week.
Brianna “Bri” Bibel is a fifth-year graduate student in the CSHL School of Biological Sciences studying biochemistry and structural biology in Leemor Joshua-Tor’s lab. Bri is the scientist behind the popular blog, The Bumbling Biochemist and Instagram account @thebumblingbiochemist. Her style of explaining basic biochemical experiments is approachable, and appreciated by science teachers and young students alike. Here she guest writes for us, reflecting on the first three installments of the CSHL COVID meeting series.
Do you remember where you were when you first heard about the novel coronavirus SARS-CoV-2? I do – vividly. I was at the gym and I saw a trending story on Twitter about a strange cluster of pneumonia cases in Wuhan, China. For the next couple of months I’d hear about it sporadically and then, wham! It was here. It was everywhere. And we had a lot of catching up to do.
So I was excited when I learned about a series of virtual meetings being set up by Cold Spring Harbor Laboratory (CSHL). Titled “COVID/SARS CoV2 Rapid Research Reports,” these meetings would feature experts from around the world filling us all in on the very latest research on the virus SARS-CoV-2 and the disease it causes, COVID-19. The first meeting was held June 16-17, 2020, and featured close to 30 talks. I don’t have space to go into every one of them, but I’d like to share some of the highlights.
A short history of coronavirus biology
Susan Weiss, University of Pennsylvania
The meeting was kicked off by a talk I know I needed – a lecture on the history and basic biology of coronaviruses by University of Pennsylvania’s Susan Weiss. Coronaviruses may have been new to many of us, but not to Weiss – SARS-Cov-2 was, of course, but Weiss has years of experience working on other, related, coronaviruses, so was well positioned to get us all up to speed. She told us about how coronaviruses have a single-stranded RNA genome that, although very small compared to our genome, is able to pack in a lot of tools to efficiently hijack our cells and bodies. For example, it makes an RNA-dependent RNA polymerase that it uses to make more copies of its RNA. Some of the copies it makes are full-length copies, which it can package up and ship out to infect more cells, whereas others are shorter “subgenomic” copies that it can use to make proteins from.
Some of these proteins are ones you’ve probably heard a lot about, such as the Spike protein, the protein that juts out from the viral membrane like a crown or halo, giving coronaviruses their name and giving them a way to dock onto our cells by binding to cellular receptors (a membrane protein called ACE2 in the case of SARS-CoV-2). But what fascinated me the most were the “Nsps” (non-structural proteins) she told us about that I’d never heard of. They don’t get that much attention, but many of them have the job of making sure our bodies don’t pay the virus much attention! For example, nsp13, nsp14 & nsp16 help with capping the viral RNAs so that they look like our own RNAs and thus don’t trigger an interferon-mediated immune response.
“When confronted with something “foreign,” an animal’s immune system has to decide what to do about it and how “paranoid” to be. Instead of focusing on host defense...bats err on the side of tolerance.”
Bats as reservoirs
Speaking of immune response, next up we heard from Linfa Wang from the University of Singapore about how bats are able to serve as reservoirs for viruses like SARS-CoV-2 because they have better balanced immune responses than us. When confronted with something “foreign,” an animal’s immune system has to decide what to do about it and how “paranoid” to be. Instead of focusing on host defense, which risks potentially over-reacting and causing autoimmune-related disorders and/or excessive inflammation, bats err on the side of tolerance. Wang explained his work showing that bats actually have a different way to control inflammation than other mammals, so they’re able to harbor viruses and allow those viruses to replicate within their bodies (and potentially go on to infect others) without getting sick themselves. Consistent with Wang’s findings, the University of Hong Kong’s Leo Poon told us that, since 2005 when he discovered the first bat coronavirus, he, and other labs around the world, have found many, many more (including ones closely related to SARS-CoV-2), stressing the importance of continuous surveillance in case they develop the capacity to infect other species.
Spike proteins
Figure 5 from Model for structural rearrangements of SARS-Cov-2 S protein. Image source.
As a graduate student in a structural biology lab, I know I’m biased, but some of my favorite talks came during the “molecular biology” session, where we got to hear about early work solving the structure of the coronavirus Spike protein. This protein is a bit like a molecular Transformer; after docking to ACE2 receptors on cell surfaces and getting cleaved by protease(s), it’s able to undergo a dramatic conformational change that enables it to fuse the viral membrane with the cell membrane, thereby releasing the viral genome into our cells.
I remember how surprised I was when the first SARS-CoV-2 Spike structure was published so quickly back in March, and at the meeting I got to learn more about how that was possible. Similar to Weiss, Jason McLellan from the University of Texas had a history of work on other coronaviruses – he had already solved the structures of the Spike proteins from SARS-CoV and MERS. So as soon as he received the sequence for the Spike protein, he cloned it and stuck it into cells to have them make Spike protein he could purify and take “molecular pictures” of. Thanks to his prior work on the “original” SARS-CoV & MERS Spike proteins, he knew that this Spike likely wouldn’t want to sit still for its photo-op. But he also knew a couple of changes he could make to the protein to help stabilize it in the pre-fusion conformation. By switching out a couple of amino acids (protein letters) in part of the protein, he was able to “freeze” it and then literally freeze it in a thin sea of vitreous ice (glasslike water) and use cryo-electron microscopy to solve its structure.
Overall, McLellan found that it looked very similar to the SARS-CoV Spike protein, but he was able to identify key differences in the part of the Spike responsible for binding the ACE2 receptor (the receptor binding domain). The structure was great, but McClellan and his lab weren’t satisfied – there were missing regions in their model and they were getting poor expression of their original construct, so McClellan told us about ongoing work in his lab trying to engineer a more stable, better-expressing version.
Neutralizing antibodies
David Veesler, University of Washington
One of the reasons it’s so valuable to know the structure of the SARS-CoV-2 Spike protein is because pre-fusion Spike can be used to look for neutralizing antibodies, as we got to hear about in a talk by David Veesler of the University of Washington. Antibodies are small proteins made by the immune system that bind specifically to foreign molecules (aka antigens) such as viral proteins; neutralizing antibodies are a subclass of antibodies that bind to a virus in such a way that they prevent the virus from infecting cells, thus “neutralizing” their threat. The search for neutralizing antibodies for SARS-CoV-2 has been focused on the Spike protein because, if antibodies bind to the Spike protein in the right places, they can prevent it from binding ACE2 and/or undergoing fusion, and thus prevent the virus from getting in.
Veesler developed a pseudovirus assay he could use to test for neutralizing antibodies. In these experiments, he used a different virus, MLV, to make “fake” SARS-CoV-2 viral particles that express the SARS-CoV-2 Spike protein and a fluorescence reporter, and then added this pseudovirus to cells. If the virus can infect cells, those cells will start glowing. But if the virus can’t get in because neutralizing antibodies are present, the cells won’t glow. Veesler and his collaborators used this assay to look for antibodies in the blood of SARS patients, hoping to find cross-reactive neutralizing antibodies (thanks to the high similarity between the Spike proteins of SARS and SARS-CoV-2). And they found some – Veesler used cryo-EM to solve the structure of one of them bound to SARS-CoV-2, and is now taking it into clinical development for use as a therapeutic.
“...if you use multiple antibodies you can prevent “viral escape,” a scenario whereby rare mutations in the Spike protein prevent the antibody from binding and therefore allow the virus in. ”
Later in the meeting we heard from Christos Kyratsous from Regeneron Pharmaceuticals about their development of neutralizing monoclonal antibody cocktails. Kyratsous explained that if you use multiple antibodies you can prevent “viral escape,” a scenario whereby rare mutations in the Spike protein prevent the antibody from binding and therefore allow the virus in. While some versions of the virus might have one of those mutations, it’s much less likely that a virus would have mutations that prevent binding of both antibodies. To find the antibodies to put in their cocktail, Kyratsous and his team immunized mice which had been genetically altered to produce human antibodies, and screened the mice’s blood along with blood from patients who had recovered from COVID-19 for the presence of neutralizing antibodies, choosing the most promising ones to take into clinical development. Kyratsous’ talk came just days after Regeneron had announced their first clinical trial, so it was especially exciting to hear about.
Antivirals and vaccines
Last but definitely not least was the session on “Antivirals and Vaccines,” where talks featured experts from Moderna and Gilead (among others), companies I’d heard so much about in the news but mostly in soundbytes and short pieces aimed at a more general audience. Here I got to hear about the science of Moderna’s mRNA vaccine and Gilead’s RNA dependent RNA polymerase (RdRp) inhibitor remdesivir, at a deeper, geekier, level.
Remdesivir is a nucleotide analog – essentially a “fake” RNA letter that the viral RdRp gets tricked into using, resulting in RdRp getting stuck and being unable to successfully copy the viral RNA. As we heard from Gilead’s Danielle Porter, it’s actually a repurposed drug. It was initially found by Gilead in a screen for hepatitis C drugs, and was later provided to the CDC and U.S. Army Medical Research Institute of Infectious Diseases as part of a library of molecules the government agencies could screen for effectiveness against various infectious diseases. The government scientists found it potentially useful against Ebola, but it was put aside after a different treatment (monoclonal antibodies) worked better. Since remdesivir had the potential to target viruses that depend on viral RdRps, scientists tested it against SARS-CoV-2 and got some promising early results that led to larger clinical trials. Because Gilead had already taken remdesivir fairly far along in the testing process for the Ebola trials, scientists knew a lot about its safety profile - and they knew how to make it – enabling it to come to market quickly.
Matthew Hall, National Center for Advancing Translational Sciences
The story of remdesivir highlights the potential of drug repurposing and, if there are other existing drugs that could be repurposed to treat COVID-19, Matthew Hall wants to find them! He told us how he and his team at the NIH are running high-throughput screens of various SARS-CoV-2-related assays against all approved drugs, and sharing the data freely through their OpenData Portal, which they also use to host data from similar assays run around the world, allowing for the most people possible to benefit.
This meeting was an amazing opportunity, especially as a graduate student. I got to hear directly from the scientists whose names graced the papers I’d been poring over as I tried to make sense of what was going on. If I had to sum up the spirit of the first meeting in one word, it’d be “unity.” Despite the fact that we were coming from all over the world, despite the fact that attendees were of all training levels and most of us were completely outside of the virology field, there was a strong sense that we were all in this together. That those with the knowledge were willing to share it freely, with unprecedented speed and scale. That labs from different institutions and even different countries were teaming up in the fight. Coming away from the meeting, not only did I have hope about tackling the disease, but I also had hope that the future of science – all science – will be much more collaborative and open.
“Despite the fact that we were coming from all over the world, despite the fact that attendees were of all training levels and most of us were completely outside of the virology field, there was a strong sense that we were all in this together.”