HOW the CORONAVIRUS INFECTS OUR CELLS Scientists Are Unpicking SARS-Cov-2’S Life Cycle

Feature JANET IWASA, UNIV. UTAH UNIV. IWASA, JANET A computer simulation of the structure of the coronavirus SARS-CoV-2. HOW THE CORONAVIRUS INFECTS OUR CELLS Scientists are unpicking SARS-CoV-2’s life cycle. By Megan Scudellari

he coronavirus sports a luxurious tools that have enabled the virus to spread so 2–4 times more strongly4, because several sugar coat. “It’s striking,” thought quickly and claim millions of lives. “That’s why changes in the RBD stabilize its virus-binding Rommie Amaro, staring at her com- it’s so difficult to control,” says Wendy Barclay, hotspots5. puter simulation of one of the trade- a virologist at Imperial College London. Worrying variants of SARS-CoV-2 tend to mark spike proteins of SARS-CoV-2, have mutations in the S1 subunit of the spike which stick out from the virus’s Barbed and ready protein, which hosts the RBDs and is responsi- surface. It was swathed in sugar It starts with the spikes. Each SARS-CoV-2 ble for binding to the ACE2 receptor. (A second molecules, known as glycans. virion (virus particle) has an outer surface spike subunit, S2, prompts viral fusion with the T“When you see it with all the glycans, it’s peppered with 24–40 haphazardly arranged host cell’s membrane.) almost unrecognizable,” says Amaro, a compu- spike proteins that are its key to fusing with The Alpha variant, for example, includes tational biophysical chemist at the University human cells2. For other types of virus, such ten changes in the spike-protein sequence, of California, San Diego. as influenza, external fusion proteins are which result in RBDs being more likely to stay Many viruses have glycans covering their relatively rigid. SARS-CoV-2 spikes, however, in the ‘up’ position6. “It is helping the virus outer proteins, camouflaging them from the are wildly flexible and hinge at three points, along by making it easier to enter into cells,” human immune system like a wolf in sheep’s according to work published in August 2020 says Priyamvada Acharya, a structural biolo- clothing. But last year, Amaro’s laboratory by biochemist Martin Beck at the Max Planck gist at the Duke Human Vaccine Institute in group and collaborators created the most Institute of Biophysics in Frankfurt, Germany, Durham, North Carolina, who is studying the detailed visualization yet of this coat, based and his colleagues3. spike mutations. on structural and genetic data and rendered That allows the spikes to flop around, sway The Delta variant, which is now spreading atom-by-atom by a supercomputer. On and rotate, which could make it easier for them around the world, hosts multiple mutations 22 March 2020, she posted the simulation to to scan the cell surface and for multiple spikes in the S1 subunit, including three in the RBD Twitter. Within an hour, one researcher asked to bind to a human cell. There are no similar that seem to improve the RBD’s ability to bind in a comment: what was the naked, uncoated experimental data for other coronaviruses, to ACE2 and evade the immune system7. loop sticking out of the top of the protein? but because spike-protein sequences are Amaro had no idea. But ten minutes later, highly evolutionarily conserved, it is fair to Restricted entry structural biologist Jason McLellan at the assume the trait is shared, says Beck. Once the viral spikes bind to ACE2, other University of Texas at Austin chimed in: the Early in the pandemic, researchers con- proteins on the host cell’s surface initiate a uncoated loop was a receptor binding domain firmed that the RBDs of SARS-CoV-2 spike process that leads to the merging of viral and (RBD), one of three sections of the spike that proteins attach to a familiar protein called the cell membranes. bind to receptors on human cells (see ‘A ACE2 receptor, which adorns the outside of The virus that causes SARS, SARS-CoV, uses hidden spike’). most human throat and lung cells. This recep- either of two host protease enzymes to break In Amaro’s simulation, when the RBD tor is also the docking point for SARS-CoV, the in: TMPRSS2 (pronounced ‘tempress two’) or lifted up above the glycan cloud, two glycans virus that causes severe acute respiratory cathepsin L. TMPRSS2 is the faster route in, swooped in to lock it into place, like a kickstand syndrome (SARS). But compared with SARS- but SARS-CoV often enters instead through on a bicycle. When Amaro mutated the glycans CoV, SARS-CoV-2 binds to ACE2 an estimated an endosome — a lipid-surrounded bubble — in the computer model, the RBD collapsed. which relies on cathepsin L. When virions enter McLellan’s team built a way to try the same A HIDDEN SPIKE cells by this route, however, antiviral proteins experiment in the lab, and by June 2020, the The spike protein of SARS-CoV-2 is coated in can trap them. collaborators had reported that mutating the sugar molecules, or glycans, which disguise it SARS-CoV-2 differs from SARS-CoV because two glycans reduced the ability of the spike from the immune system. It can hinge at three it efficiently uses TMPRSS2, an enzyme found points on the stalk, giving it flexibility. protein to bind to a human cell receptor1 — a in high amounts on the outside of respiratory

role that no one has previously recognized in Receptor-binding cells. First, TMPRSS2 cuts a site on the spike’s 8 coronaviruses, McLellan says. It’s possible that domain S2 subunit . That cut exposes a run of hydro- snipping out those two sugars could reduce phobic amino acids that rapidly buries itself in the virus’s infectivity, says Amaro, although Glycan the closest membrane — that of the host cell. researchers don’t yet have a way to do this. Next, the extended spike folds back onto itself, Since the start of the COVID-19 pandemic, S1 like a zipper, forcing the viral and cell mem- scientists have been developing a detailed subunit branes to fuse (see ‘Viral entry up close’). understanding of how SARS-CoV-2 infects The virus then ejects its genome directly cells. By picking apart the infection process, into the cell. By invading in this spring- they hope to find better ways to interrupt it loaded manner, SARS-CoV-2 infects faster through improved treatments and vaccines, than SARS-CoV and avoids being trapped in

NATURE and learn why the latest strains, such as the endosomes, according to work published in Delta variant, are more transmissible. April by Barclay and her colleagues at Imperial 9 What has emerged from 19 months of work, S2 Hip College London . backed by decades of coronavirus research, is subunit The virus’s speedy entry using TMPRSS2 a blow-by-blow account of how SARS-CoV-2 Knee explains why the malaria drug chloroquine invades human cells (see ‘Life cycle of the pan- Stalk didn’t work in clinical trials as a COVID-19 treat- demic coronavirus’). Scientists have discov- ment, despite early promising studies in the ered key adaptations that help the virus to grab lab10. Those turned out to have used cells that Ankle on to human cells with surprising strength and rely exclusively on cathepsins for endosomal then hide itself once inside. Later, as it leaves entry. “When the virus transmits and replicates cells, SARS-CoV-2 executes a crucial process- in the human airway, it doesn’t use endosomes, ing step to prepare its particles for infecting so chloroquine, which is an endosomal disrupt-

SOURCE: STRUCTURAL IMAGE FROM LORENZO CASALINO, UNIV. UNIV. CASALINO, LORENZO FROM IMAGE STRUCTURAL SOURCE: 1); GRAPHIC: NIK SPENCER/ (REF. DIEGO SAN CALIFORNIA, even more human cells. These are some of the ing dr