Four ways researchers are responding to the COVID-19 outbreak

How did researchers react so quickly to the SARS-CoV-2 epidemic? Nature Medicine has asked some key experts.
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“The reason we were able to go so fast this time is we've been working on solutions for coronaviruses for several years now,” says Barney Graham, Deputy Director of the Vaccine Research Center at the US National Institute of Allergy and Infectious Diseases (NIAID) in Bethesda, Maryland, who is overseeing the development of a vaccine candidate.

Weeks before the World Health Organization (WHO) declared the novel coronavirus, also called ‘2019-nCoV’ or SARS-CoV-2’, a public-health emergency of international concern, research groups around the globe had already swept into action, sequencing and sharing the viral genome and studying how the virus infects human cells.

The similarity of SARS-CoV-2 to the coronaviruses that cause the respiratory syndromes MERS and SARS, which both broke out in the past two decades, has enabled rapid studies of diagnostic tests, antiviral strategies and vaccine candidates, many of which will reach phase 1 clinical trials by mid-2020.

How was a diagnostic test released so quickly?

By the time Shanghai Public Health Clinical Center & School of Public Health released the first genome sequence for SARS-CoV-2, work was already underway to develop a diagnostic test.

Along with researchers at the University of Hong Kong, virologist Christian Drosten and his team at the German Center for Infection Research at Charité in Berlin developed an assay that accurately detects SARS-CoV-2 in samples from nose and throat swabs or sputum of hospitalized patients. Their protocol was quickly distributed to public-health authorities around the world.

Because they did not have access to samples of the virus, Drosten’s team worked from their knowledge of SARS-CoV-2’s close relative, the SARS coronavirus (SARS-CoV). They put together genetic sequences for a PCR test based on a SARS-CoV genome, and when the SARS-CoV-2 sequence was released, they picked the two closest matches: genes encoding the envelope protein and RNA-dependent RNA polymerase. The test is built so that sequences from SARS-CoV can serve as positive controls. To avoid cross-reactivity with SARS-CoV or other coronaviruses, the test detects a region of the gene encoding RNA-dependent RNA polymerase that is unique to SARS-CoV-2.

BGI Genomics, a sequencing company based in Shenzhen, China, has developed a detection kit for SARS-CoV-2. It was distributed under an emergency authorization from China’s National Medical Products Administration.

BGI is collaborating with European companies to manufacture the test in Europe; at least a dozen other companies are developing their own commercial versions of the PCR test; and the US Centers for Disease Control and Prevention has begun distributing its own kit to approved labs under and emergency use authorization granted by the US Food and Drug Administration.

If used properly, the diagnostic test should remain reliable, says NIAID virologist Vincent Muster. The genes used for the diagnostic test are not prone to mutation, he says, and according to an analysis of 24 full-length genomes posted on on 24 January 2020, of viral isolates released on 23 January, there is very limited genetic diversity between isolates. Analyses done since then have continued to find limited diversity.

Credit: JEFF PACHOUD/Contributor/AFP/Getty

How similar is SARS-CoV-2 to SARS CoV, and how many isolates do we have?

SARS-CoV-2 was initially grown in cells and isolated at the Wuhan Institute of Virology. Virologist Zheng-Li Shi and her team found that the viral genome is 79.5% identical to that of SARS-CoV.

Using an infection challenge on cell lines exogenously expressing the protein, her team also found that the virus enters cells through the receptor ACE-2—the same receptor used by SARS-CoV—via a spike protein that SARS-CoV-2 shares with other coronaviruses. Therefore, therapies that interfere with this interaction may be effective against the new virus.

In late January, a lab at The Peter Doherty Institute for Infection and Immunity in Melbourne, Australia, became the first group to grow the virus outside of China. Samples from that lab were distributed to others via the World Health Organization. Isolates are now also available through the European Viral Archive and the NIAID.

Tim Sheahan, a virologist at the University of North Carolina at Chapel Hill, is also working with the Centers for Disease Control and Prevention’s isolate and plans to infect human lung cells grown in a system that accurately models the lung environment by exposing cells to air on one side and fluid on the other. This system will help reveal which subtypes of lung cells are most susceptible to infection by SARS-CoV-2and which drugs are best at entering those cells.

A single-cell level analysis of human lung cells recently released as a preprint on bioRxiv suggests that ACE-2 is most highly concentrated in a type of epithelial cell responsible for producing surfactant, but more studies will be needed to find out if it is also the cell type most affected by infection.

How can existing therapeutics be used against SARS-CoV-2?

A combination of two human immunodeficiency virus (HIV) antivirals, lopinavir and ritonavir, has been taking center stage as a potential therapeutic for COVID-19, the name given to the syndrome associated with SARS-CoV-2.

China’s National Health Commission has recommended this combination for patients infected with SARS-CoV-2 and, in early February, physicians at the Rajavithi Hospital in Bangkok reported success in treating patients with lopinavir–ritonavir plus the influenza drug oseltamivir. One patient, a 70-year-old woman from Wuhan, reportedly tested negative for the virus after 48 hours on the therapy.

Sheahan says there is precedent for using HIV antivirals to treat coronavirus. In a retrospective study from 2003, patients with SARS who received lopinavir–ritonavir were more likely to survive infection or avoid advanced disease.

However, Sheahan says he would be surprised if HIV antivirals have a big benefit against SARS-CoV-2. He argues that their design is tailored specifically to block the activity of HIV proteases to avoid off-target effects on human cells, which makes them less likely to bind coronavirus proteases as well. “You may need to use drug at levels that are never achievable in a person,” Sheahan says. “It’s unrealistic.”

“This happened for SARS, where clinicians were giving any approved drug that they could to try to improve a patient outcome or save their lives,” he says.

There are at least three registered randomized clinical trial testing the lopinavir–ritonavir combination in Chinese patients infected with SARS-CoV-2 (NCT04255017, NCT04252885 and NCT04251871). A handful of other HIV antivirals are currently in clinical testing against SARS-CoV-2, including darunavir–cobicistat, donated by the US pharmaceutical company Johnson & Johnson to the Shanghai Public Health Clinical Center.

SARS-CoV-2 does have its own proteases, including its main protease, Mpro, which shares features with proteases found in enteroviruses, such as norovirus. A team from ShanghaiTech University compared Mpro’s structural analysis against a worldwide protein databank and found 30 small molecules known to inhibit similar structures. Researchers at the Chinese Academy of Sciences are screening these drugs for antiviral activity in cells.

Sheahan’s team is testing another class of drugs against 2019nCoV: nucleoside analogs, including one nucleoside analog from Drug Innovation Ventures at Emory University in Atlanta, Georgia, and another called remdesivir, an experimental Ebola therapy made by Gilead Sciences in Foster City, California. Remdesivir was used to treat the first US patient infected with SARS-CoV-2, who recovered, and is in phase 3 trials in Wuhan patients infected with SARS-CoV-2, overseen by the China-Japan Friendship Hospital in Beijing (NCT04252664 and NCT04257656).

How can we develop a vaccine within 3 months?

Several MERS vaccines were already in clinical trials when word of the new outbreak spread.

Moderna, based in Cambridge, Massachusetts, has already created an mRNA vaccine against SARS-CoV-2 that encodes a version of the viral spike protein designed by Kizzmekia Corbett, a virologist on Graham’s team at the Vaccine Research Center.

The spike protein shape is pliable and, as it interacts with ACE-2, the areas of the protein most important for that interaction can become hidden from the immune system. Corbett made mutations to the spike-encoding gene so that the protein it encodes stays in a stable, ‘open’ form.

In animal studies, the stabilized form of the MERS spike protein elicits a stronger immune reaction than does the native form. Corbett says she will have the initial data on the mouse immune response to SARS-CoV-2 stabilized spike protein around the end of March.

With financial support from the Coalition for Epidemic Preparedness Innovations (CEPI), Moderna has begun producing their vaccine according to good manufacturing practices, and a phase 1 study should start in April.

CEPI is funding another mRNA vaccine made by Curevac, in Tubingen, Germany; a DNA vaccine made by Inovio Pharmaceuticals in Plymouth Meeting, Pennsylvania; and a protein vaccine developed by a group at the University of Queensland in Australia. Seeking to diversify their collection of vaccine options even further, CEPI released a call for applications that remains open until mid-February.

Laurent Humeau, Inovio’s chief scientific officer, says multiple players will have to be involved to meet the demand. “I don’t think there is one that will cover the millions of doses that are requested.”

Some groups and companies have touted their ability to have a vaccine ready for clinical testing in 3 months or less. “Despite all the claims about how quickly you can move RNA and DNA vaccines into getting to licensure, you still need to do the phase 1 safety studies. That’s the bottleneck,” says Peter Hotez, a microbiologist at Baylor College of Medicine in Houston, Texas. From there, phase 2 studies cannot begin without sufficient data on a vaccine’s safety and ability to stimulate immunity in animal models.

Hotez and fellow Baylor microbiologist Maria Bottazzi have submitted a vaccine plan to CEPI that uses the ACE-2-binding region of the SARS-CoV spike protein to elicit immunity. That area of the protein is more than 80% identical between SARS-CoV and SARS-CoV-2, and they have already tested the vaccine in animals and found it is very safe, Bottazzi says.

As vaccine researchers work through that bottleneck, groups like Sheahan’s will continue to study SARS-CoV-2 and test antiviral approaches. “There’s space for all of this to be done concurrently,” he says. “There’s going to be this explosion of information over the next 6 months to 5 years, and we’re going to be in a better place for the next emergence.”

Amanda Keener

doi: 10.1038/d41591-020-00002-4

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