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Coronavirus – tracking its deadly tactics inside our cells

We know alarmingly little about the biological tricks that make this coronavirus so deadly. But scientists are beginning to piece together how the virus works once it has invaded our cells. Understanding this process could reveal new ways to tackle the infection and give us a head start against future coronavirus strains.

Viewed under a powerful electron microscope this latest coronavirus, named SARS-CoV-2, doesn’t look unusual. Its distinctive appearance, with large projections resembling a solar corona, led to its name when human coronaviruses were first discovered in the 1960s.

Yet underneath its spiky coat lies a biological toolkit that really packs a punch – with a complex genome double the size of influenza virus. Lying within this vast genetic code are the instructions that are the keys to its success.

Understanding how the virus’s genes work inside our cells is the aim of David Tollervey’s research group at the Wellcome Centre for Cell Biology. By delving deep into the virus’s biology the team hope to reveal the sophisticated strategies that allow it to hijack our cells and turn them into virus factories.

This work, in collaboration with Roslin Institute, could also provide a vital first step in the path to future therapies, by revealing weak spots in the virus’s tactics.

Despite previous SARS and MERS epidemics, coronavirus biology was a largely neglected field before the current pandemic took hold. Now huge effort is, understandably, going into vaccine development, but less attention is being paid to the fundamental interactions between the virus and the human cells that are subverted to become viral production lines.

Virus Biology

Buried within the virus genome are instructions to make 20 major proteins, yet only four are proteins that make up parts of its structure – the membrane, spike projections and packaging for its genetic material.

The rest, known as non-structural proteins, are biological keys that coordinate the virus’s heist after it has invaded the cell. They take over the cell’s machinery, forcing it to make multiple copies of the virus. For many viruses this process is so effective that a single virus infecting a cell can trigger production of over 1 million copies of itself.

It is these non-structural proteins that are the focus of the team’s attention. Together they hijack one of the cell’s most fundamental processes – the production of proteins.

Often described as the workhorses of the cell, proteins have a role in almost every aspect of our biology and make up everything from the structures in our cells, muscles and bones to the enzymes that help us digest our food.

Hijacking Protein Production

Instead of making human proteins, SARS-CoV-2 tricks cells into making viral proteins – the first step in replicating the virus. The team’s challenge will be to pinpoint exactly how the virus does this and which parts of the cell’s vast protein production system are targeted. What they already know from previous work is that, like other viruses, SARS-CoV-2 takes over the cell with remarkable sophistication. Its genetic material is a biological doppelganger for a key component in the cell’s protein production process.

The instructions to make proteins are embedded in our genome, which is protected inside a structure known as the nucleus. RNA, a close molecular cousin of DNA, acts as a go-between; it reads and makes a short-lived copy of the string of chemical letters that make up the DNA sequence of protein genes.

This RNA copy then leaves the nucleus and carries the instructions to the cell’s protein-making factories, small particles known as ribosomes.

But RNA is not just an intermediary, it is an early ancestor to DNA. Many viruses, including SARS-CoV-2, still use it as their genome. Once the virus enters the cell it sheds its coat and the viral RNA, almost indistinguishable from human RNA, begins its hijack.

Ribosomes read the foreign RNA’s instructions and are tricked into making viral proteins. First in the pipeline are the non-structural proteins. The team are interested in the way they behave as it triggers the rest of the hijack.

Making New Viruses

Some of these proteins stick together to form a larger protein complex, that help a molecule known as RNA polymerase, to read and make multiple copies of the virus’s entire genome – ready to make new viruses.

A suite of non-structural proteins improve the speed and accuracy of the viral RNA polymerase and modify the resulting RNAs, disguising them to resemble human RNAs – important for avoiding detection by the immune system.

But RNA polymerase not only copies the entire viral genome, it also skips along the genome to makes copies of specific genes. This allows it to trick human ribosomes into making very high amounts of the virus’s structural proteins.

The genome must have the full-length RNA, but most proteins are made using shorter fragments of RNA. To make these shorter RNAs, the polymerase is able to hop and slide along the genome - skipping thousands of chemical letters at a time to locate these protein genes.

Preventing the Hijack

Ribosomes are attached to an internal network of tubes that process, package and export proteins from the cell. All the new virus parts, including the genome, join this pipeline and are assembled into new viruses that spread the infection.

Stopping the process of viral protein production once it’s in action would be risky – the ability of other uninfected cells to manufacture proteins essential for our health might be hampered by drugs that have a broad action. Instead, it would be better to prevent ribosomes from getting hijacked in the first place.

To do this the team need to understand how RNA polymerase makes copies of the genes that contain the instructions to make new virus parts.

They know that virus’s genome must contain instructions that mark out these structural protein genes – indicating when RNA polymerase should start and stop reading. But the virus cannot copy its genome, and make proteins, via ribosomes, at the same time. So there must be sophisticated systems for first prioritising viral protein production before replication of the viral genome.

Identifying and understanding these interactions is the first step to finding drugs that could help to stop the virus’s structural proteins from being made and being assembled into new viruses.

Competition Inside the Cell

The virus’s manipulations do not end there. It also needs to compete with the cell’s own RNA for access to the protein-making machinery. Based on previous work on other coronaviruses, the team suspects that the virus’s non–structural proteins have several clever tactics designed to elbow out the competition.

There are many different types of RNA in our cells that could be targeted, including those that help to switch the cell’s protein genes on and off, process human RNA so it is ready to leave the nucleus, form the structure of ribosomes and transport the building blocks that make proteins. As an example the virus may give itself the upper hand by preventing human protein genes from being switched on.

To add to the complexity, the RNA in our cells does not act alone. It is always helped by other proteins, which form complexes with human RNAs at different stages of this lifecycle. They help to control RNA production and packaging, stabilise it, transport it through the cell and finally degrade it after its task is complete.

The team predict that the virus’s non-structural proteins will interfere with many parts of the complex RNA lifecycle within human cells - including RNA-protein complexes, individual RNAs and key proteins – in order free up the cell’s machinery. The question is which ones?

Compared with other RNA viruses SARS-CoV-2 has more proteins that alter RNA metabolism. These may protect the virus’s own RNA from being destroyed, and help viral RNAs to compete with human RNAs for access to the cell’s protein-making machinery. This may involve degrading human RNAs and/or proteins and blocking production of human proteins.

Understanding the Virus’s Interactions

To unravel these interactions the team are analysing how 14 of the virus’s non-structural proteins behave inside human cells. The cell line they use makes it easy to add individual genes for specific viral proteins, so their effects can be isolated. UV light is then used to freeze the interactions in place, so they can be isolated and analysed.

Once the team has pinpointed the virus’s targets, their next step is to find the exact binding sites for the interactions on the surface of these large molecules. Blocking the parts hijacked by the virus could offer an attractive target for new therapies. Equally, protecting parts of the cell that are inhibited by the virus could potentially thwart its attack.

Evading the Immune System

These analyses could also shed light on other tactics triggered by the virus’s non-structural proteins. To be successful the virus must evade detection by the immune system. Analysis of other coronaviruses indicate that some non-structural proteins may help the virus to fly under the radar by interfering with the cell’s early warning system.

One non-structural protein is thought to destroy stray RNA strands, produced whilst the virus is copying its genome. These foreign RNA strands are normally detected as a threat by cells. Others add “caps” and “tails” to the ends of the virus’s RNA strands, which tricks the cell into treating them like human RNA strands.

Even if the cell’s early warning signal is triggered another protein is thought to have a role in blocking the RNA that contains instructions to make interferon – a key signalling molecule that warns nearby cells of an impending attack.

Preparing for the Future

These insights could form a vital safety net for the future. Whilst vaccines are the gold standard in long-term control of the virus, we don’t know how long the protective antibodies will last and future coronavirus variants might pose new challenges. If the most vulnerable people in society are still at risk, then we will also need drugs that can tackle an established infection.

Understanding the virus’s tactics offers fresh routes to develop new drugs or indicate which existing drugs might be successful. Whilst the path from biological insight to new therapy is painstakingly slow and fraught with uncertainty, there is a good reason to start now.

Our pathway out of this pandemic not only involves living with this coronavirus for some time, but accepting this is likely not the end of the road. In the past 20 years we have seen three deadly coronavirus outbreaks. Insights into the biology of SARS-CoV-2 is the foundation that will ultimately help us to understand and combat future coronavirus strains.

With thanks to the COVID Team in the Tollervey lab - Stefan Bresson, Alexandra Helwak, Nic Robertson, Emanuela Sani, Tomasz W. Turowski, Vadim Shchepachev, Michaela Kompauerova and Laura Milligan

Images - ttsz, TefiM, sabelskya, PenWin, BlackJack3D, narvikk, Hakat, traffic_analyzer, selvanegra, Jose Luis Calvo Martin & Jose Enrique Garcia-Maurino Muzquiz via Getty Images

Words - Marie-Anne Robertson, Science Communications Manager, School of Biological Sciences, The University of Edinburgh

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Marie-Anne Robertson
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