News 31 October 2022

Gain-of-function research and the origins of Omicron

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Authored by
Cate Swannell
IN her new book, Dark Winter, renowned global biosecurity expert Professor Raina MacIntyre hides what would be called “easter eggs” in video games – nuggets of knowledge that leave the readers with plenty to think about.

Released tomorrow, Dark Winter: an insider's guide to pandemics and biosecurity is a history of pandemics, a warning about the state of the world’s virus holdings, and a primer for what we need to do to protect ourselves from future pandemics. One such easter egg leaps off the page ahead of all the others.

Was the Omicron variant of SARS-CoV-2 manufactured?

A major discussion point in the book is the ethics of gain-of-function research.

“Gain-of-function research is a subset of dual use research of concern,” Professor MacIntyre told InSight+ in an exclusive podcast.

“To begin with, dual use research of concern applies to any technology that can be used for benefit, but also for harm. It might be robotics or artificial intelligence or biological technology, where the primary purpose is to benefit humanity, whether it’s for medicines, vaccines for agriculture, for defence or for other types of purposes,” she said.

“The same technology can also be used to harm humanity. So, gain-of-function research is where you engineer a pathogen to confer on it properties it didn’t gain naturally.”

The controversy began to hit the headlines in 2012, when two groups of scientists did gain-of-function research on avian influenza viruses, which are not naturally contagious between humans.

“Humans can die from avian influenza – usually they’re people who’ve been poultry handlers or otherwise working in very close contact with sick or dead birds,” Professor MacIntyre told InSight+.

“These research groups took these avian flu viruses and repeatedly passaged them through ferrets, which are a good human proxy, because they have the same makeup of the respiratory tract receptors.

“When you passage a virus repeatedly through a species, you help it to adapt to that species.

“In this case, the virus was conferred with properties that made it suitable for human-to-human transmission. When the virus picked up those characteristics, it became easily transmissible from humans to humans.

“They’ve taken an avian flu virus that is not transmissible easily between humans and conferred on it pandemic potential,” she said.

Big question: why?

“Their arguments were that it helps with making vaccines against a pandemic, should it arise, and should it be the same virus as the one they engineered,” said Professor MacIntyre. “As we know you can never predict what virus is going to naturally emerge. There’s no way you could predict the virus and make a vaccine for it.”

The avian flu gain-of-function research polarised the scientific community. One group was adamant gain-of-function research was essential and that the future of humanity was at stake. Another group, including Donald Henderson, who was one of the leaders of smallpox eradication, cautioned against it and against publishing the methodologies in scientific journals where anyone could access them.

“For a period of time, there was a moratorium on that kind of research, initially in 2011, but there was a lot of pressure after that,” Professor MacIntyre told InSight+.

“There was so much pressure that by about May 2012, that [moratorium] was overturned, and the papers were published. And that was it – the gates were open. Hundreds, if not thousands of [gain-of-function] papers, have been published since.”

Has gain-of-function research been done on coronaviruses?

“Oh, absolutely,” said Professor MacIntyre.

“Ever since SARS first occurred, scientists have been fascinated with the virus and, since 2014, plenty of groups were doing that kind of research and on other viruses too.”

In September 2021 Professor Paul Bieniasz and colleagues from Rockefeller University in New York published a paper in Nature. Here’s what Professor MacIntyre wrote about that research:
“As Bieniasz told NPR, ‘the goal was to answer the question: Is it possible for SARS-CoV-2 to completely evade neutralizing antibodies?’ In order to explore this question, Bieniasz and his team engineered a mutant version of the SARS-CoV-2 spike protein to make it resistant to vaccines. They took about 20 mutations that occurred already around the world, but never together, and engineered a ‘polymutant spike mutant’ – in other words, they showed how to make SARS-CoV-2 resistant to vaccines. Two months later, by November 2021, the Omicron variant had emerged, which had most of the 20 mutations Bieniasz and team published with open access methods, plus more.”

Dark Winter, page 77
Can we conclude that Omicron was manufactured?

Professor MacIntyre does not say so specifically in Dark Winter, but she told InSight+:

“In the book, there are some things that I don’t say. I’ll just call it easter eggs – there are easter eggs in the book and people who are switched on, following the topics, can read between the lines.

“That’s all I’ll say.”

Dark winter: an insiders’ guide to pandemics and biosecurity by Raina MacIntyre is published by NewSouth Publishing and will be released tomorrow, 1 November 2022.

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