Two vaccines made using messenger RNA (mRNA) have proved spectacularly successful at warding off COVID-19, but a third mRNA-based candidate has flopped in a final-stage trial, according to an initial report released this week. Researchers are now asking why — and some think that choices about the type of mRNA chemistry used might be to blame. Any insight could help to guide the future design of mRNA vaccines against COVID-19 or other diseases.

The company behind the beleaguered trial, CureVac, based in Tübingen, Germany, announced preliminary data on 16 June from a 40,000-person trial, which showed that its two-dose vaccine was just 47% effective at preventing disease.

CureVac’s mRNA vaccine was expected to be cheaper and to last longer in refrigerated storage than the earlier mRNA vaccines made by Pfizer–BioNTech and Moderna. Many had hoped that it could help to expand the reach of mRNA-based vaccines in lower-income countries, and European countries were expecting to order hundreds of millions of doses.

“I’m definitely surprised — and also disappointed,” says Philip Santangelo, a biomedical engineer at the Georgia Institute of Technology in Atlanta who has worked with many mRNA-focused companies, including CureVac.

He and others suspect that CureVac’s decision not to tweak the biochemical make-up of its mRNA, as Pfizer–BioNTech and Moderna did, might be behind its poor performance — although it is too early to know for sure.

Variant problem

CureVac executives put the poor results down to the high number of coronavirus variants — including emerging ones such as the Lambda variant first detected in Peru — circulating in the ten countries across Europe and Latin America where the company is running its trial. Of 124 COVID-19 cases for which scientists obtained a genetic sequence, only one was caused by the original version of SARS-CoV-2.

But the other mRNA vaccines have fared much better in the face of variants.

Researchers in the United Kingdom have reported, for instance, that the Pfizer–BioNTech shot offered 92% protection against symptomatic cases of COVID-19 caused by the Alpha variant (first identified in the United Kingdom) and 83% protection against the Delta variant (initially reported in India). A study in Qatar similarly found the vaccine to be around 90% effective against the Alpha strain and 75% effective against the Beta variant that emerged in South Africa.

Those differences in efficacy have led trial investigators and other scientists to suggest that the problem is with the vaccine itself.

Dose of reality

“My best take is that the dose is the culprit,” says Peter Kremsner, an infectious-disease specialist at Tübingen University Hospital who is leading CureVac’s clinical studies.

In phase I testing, Kremsner and his colleagues evaluated doses ranging from 2 to 20 micrograms of mRNA per injection. At the higher dose levels, the vaccine caused too many side effects, with trial participants frequently complaining of problems such as severe headaches, fatigue, chills and injection-site pain.

At 12 micrograms, the vaccine proved more tolerable, and all recipients developed antibodies that blocked the virus from entering cells. But the levels of those ‘neutralizing’ antibodies were relatively low — on a par with the amounts found in people who have recovered from SARS-CoV-2 infections, but well below the levels seen in recipients of the Moderna and Pfizer–BioNTech vaccines, which are both given at higher doses.

Perhaps it’s no surprise, then, that CureVac’s shot came up short, says Nathaniel Wang, the chief executive of Replicate Bioscience, an RNA-focused biotech start-up based in San Diego, California. Those low antibody titres in early testing were “already a red flag”, he says.

Some researchers wonder why the vaccine couldn’t be administered at higher doses without inducing side effects.

The tiny bubbles made of lipids that mRNA vaccines are encapsulated in — to help deliver their genetic payloads into cells — can trigger side effects such as those documented by the CureVac trial. But Santangelo says that the CureVac and the Pfizer–BioNTech vaccines use practically indistiguishable, if not identical, lipid bubbles.

He and others think that the problem might lie in the mRNA sequence.

Modified RNA

All three mRNA vaccines encode a form of the coronavirus spike protein, which helps virus particles to penetrate human cells. But the Moderna and Pfizer–BioNTech vaccines use modified RNA, incorporating an mRNA nucleotide called pseudouridine — which is similar to uridine but contains a natural modification — in place of uridine itself. This is thought to circumvent the body’s inflammatory reactions to foreign mRNA. CureVac’s vaccine uses normal uridine and relies on altering the sequence of RNA letters in a way that does not affect the protein it codes for, but helps the vaccine to evade immune detection.

Proponents of modified mRNA have long argued that the chemical adjustment is integral to the success of the vaccine technology. Drew Weissman, an immunologist at the University of Pennsylvania in Philadelphia who co-discovered the importance of pseudouridine in this context in the mid-2000s4, describes it as the “best platform for antibody and neutralization levels”. In light of the new CureVac data, many scientists who spoke to Nature agree.

“Modified mRNA has won this game,” says Rein Verbeke, an mRNA-vaccine researcher at Ghent University in Belgium.

There are a few other possible explanations for CureVac’s tolerability problems. Structural differences in the non-coding regions of the CureVac sequence could play a part. Alternatively, the higher storage temperature of CureVac’s jab might have accelerated the breakdown of mRNA in the vial, yielding pieces of genetic code that would raise immune hackles. And if any impurities were introduced during the company’s manufacturing process, these would, in principle, have the same effect.

So for some scientists it remains too early to draw conclusions. “The jury is still out on which of these is a better technology,” says Jeffrey Ulmer, a former pharmaceutical executive who now consults on vaccine research issues. He predicts that both modified and unmodified mRNA will be useful in different contexts. “It could be that there’s not a one-size-fits-all solution to everything.”

CureVac hopes that its vaccine — or at least its unmodified mRNA technology — might yet deliver. The company is continuing its trial and expects a final analysis in the next few weeks. On a public health level, even if the vaccine fails, “I don’t think it’s going to set the world back much”, says Jacob Kirkegaard, a vaccine-supply expert at the Peterson Institute for International Economics, a think-tank in Washington DC.

He points out that another second-generation vaccine that offers many of the same logistical selling points as CureVac’s, such as long-term refrigerator storage, has stood up to the variant challenge well. Earlier this week, Novavax in Gaithersburg, Maryland, reported that its protein-based vaccine was more than 90% effective at preventing COVID-19 in a large US trial, run at a time that the Alpha variant was prevalent.

The scale of production of other vaccines more than makes up for the lack of CureVac’s product, Kirkegaard says.

CureVac, in collaboration with London-based GlaxoSmithKline, also has a second-generation COVID-19 vaccine in the works that, like its predecessor, uses unmodified mRNA, but has been fine-tuned so that it elicits levels of neutralizing antibodies that are around ten times higher, according to data from rat and monkey studies. “Our optimization has never stopped,” says CureVac’s chief technology officer Mariola Fotin-Mleczek. “It’s too early to say unmodified, natural messenger RNA is not an option.” Human trials are due to launch later this year.

This article is reproduced with permission and was first published on June 18 2021.