Bird flu DGOF research debunked by flu folks

"On reading," by Simon Wain-Hobson, is a weekly discussion of scientific papers and news articles around gain of function research in virology.

Since January 2024, Dr. Wain-Hobson has written weekly essays for Biosafety Now discussing risky research in virology. You can read his entire series here.

Saint Eustache church, Paris, 2^nd arrondissement

On rereading Gain-of-function experiments on H7N9 by Ron Fouchier, Yoshihiro Kawaoka and 20 others, Science 2013; 341:612-3

The same piece was published in Nature 2013 500:150-1

Limited airborne transmission of H7N9 influenza A virus between ferrets, by Mathilde Richard and 16 colleagues. Nature 2013; 501:560-3.

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Lookback can be useful. Some of the unknowns are now known while much of the angst has subsided. In the case of disease, some threats have come and gone. So let’s look at bird flu viruses again, albeit another strain.

Since the end of March 2013, avian A influenza viruses of the H7N9 subtype have caused more than 130 human cases of infection in China, many of which were severe, resulting in 43 fatalities.

The specter of a novel human flu pandemic galvanized public health specialists the world over. We’ve been here, done that. H5N1 bird flu they felt would go pandemic, one day, yet we’re still waiting. But H7N9? The above lines are from an appeal for DGOF experiments on this novel H7N9 virus to see if it could indeed be efficiently transmitted between ferrets by the aerosol route, a trait synonymous with human-to-human respiratory transmission of flu viruses.

They propose to perform the following experiments that may result in GOF (emphasis added):

(i) Immunogenicity. To develop more effective vaccines… We’ve seen this before; fold vaccines into the discussion to neuter dissent. Anyway, a DGOF outcome is very unlikely.

(ii) Adaptation. To assist with risk assessment of the pandemic potential of field strains and evaluate the potential of A(H7N9), viruses to become better adapted to mammals. Pandemic potential is very hard to assess and even harder to quantify. If these viruses are not passaged extensively on human cells and in large volumes, the experiments may yield qualitative results that are worth having.

(iii) Drug resistance. Another red herring. Move on.

(iv) Transmission. To assess the pandemic potential of circulating strains and perform transmission studies to identify mutations and gene combinations that confer enhanced transmissibility in mammalian model systems (such as ferrets and/or guinea pigs). A DGOF outcome is certain. The word enhanced says it all.

(v) Pathogenicity. To aid risk assessment and identify mechanisms, including reassortment and changes to the hemagglutinin cleavage site, that would enable circulating A(H7N9) viruses to become more pathogenic. Emphasis added. Ring a bell? (Cleavage sites in the SARS2 Spike protein as per the DEFUSE project). Will result in some DGOF outcomes.

They close with The risk of a pandemic caused by an avian influenza virus exists in nature. As members of the influenza research community, we believe that the avian A(H7N9) virus outbreak requires focused fundamental and applied research conducted by responsible investigators with appropriate facilities and risk-mitigation plans in place. To answer key questions important to public health, research that may result in GOF is necessary and should be done.

The difficulties of designing lab experiments To answer key questions important to public health have been addressed in many essays. But one of them will be mentioned here (Limits to lab simulated virus evolution).

For the record, the same appeal was published simultaneously in Nature (August 7, 2013) and Science (August 9, 2013), the top two journals who compete for the best papers from around the world. Most unusual.

Readers will have spotted that the lead authors are none other than Drs. Fouchier and Kawaoka of H5N1 bird flu fame. Yep, the ones who ignited the DGOF controversy back in 2011. They want more novel human respiratory viruses morphed from bird flu strains. Here, they are supported by 20 top flu researchers from around the world. Perhaps the logic was safety in numbers next time round.

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Let’s turn to the Nature paper describing DGOF research on the bird flu H7N9 virus. Its title Limited airborne transmission of H7N9 influenza A virus between ferrets, is a good resumé. Its outcome didn’t follow the DGOF H5N1 work.

But look at the precision emerging from this study: Here we report that airborne transmission of Anhui/1, as for A/Shanghai/2/2013, [both H7N9 flu strains] can occur between ferrets. Keeping in mind that quantifying transmission in our current experimental model is difficult, and that any transmission may not be directly extrapolated to transmission between humans… Note the added bold type. What can any public health official anywhere do with such remarks? Nothing.

Two points:

• For the record This work was financed through NIAID-NIH contract HHSN266200700010C and EU FP7 programs EMPERIE and ANTIGONE. There has been much discussion in the US about NIH funded DGOF research, but in Europe? Ten times less, if not more. Where’s the European discussion and transparency intrinsic to science? The UK and Germany did a little yet still under par, France and The Netherlands a soupçon, nothing from the Scandinavian countries, Switzerland, Austria, Italy or Spain. Where’s the European oversight?

• The appeal in Nature was dated August 7, 2013, with the Science version coming out the next day. The Fouchier paper on H7N9 dangerous GOFing came online on August 7. Neither of the appeals mentioned that the work they were calling for had already been published the same day in Nature! Words like collusion, connivence and capricious come to mind along with others. The appeal was a veneer trying to justify more dangerous GOF research, trying to ram it down our throats without engaging public concerns. The authors and journals knew the ropes. They had done it the year before. With the H5N1 bird flu virus.

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Fast forward a decade. Between February 2013 and February 2019 there were 1,568 confirmed human cases and 616 deaths associated with the outbreak in China. …The outbreak in China has been partially contained by a program of poultry vaccination which commenced in 2017. It’s not reared its head since 2019 in part due to a campaign of vaccinating birds against the virus.

Dr. Kawaoka published a paper in 2023 on H7N9. Although wild-type H7N9 AIVs [avian influenza viruses] can be transmitted by respiratory droplets in ferrets, they have not yet caused widespread outbreaks in humans. Yes, we had spotted that. Through growth in ferrets We show that three main factors—purifying selection, stochasticity, and very narrow transmission bottlenecks— combine to severely constrain the ability of H7N9 AIV to effectively adapt to mammalian hosts in isolated, acute spillover events. Stochasticity refers to the randomness observed in physical systems. Hence, predicting pandemics, the original claim of the H5N1 DGOF research, and preparing for pandemics is fraught with a degree of randomness. Good to hear, but we did know this from work on other viruses years before.

We conclude that human-adapted H7N9 viruses are unlikely to emerge during typical spillover infections. Our findings are instead consistent with a model in which the emergence of a human-transmissible virus would be a rare and unpredictable, though highly consequential, ‘jackpot’ event. Strategies to control the total number of spillover infections will limit opportunities for the virus to win this evolutionary lottery. Emphasis added.

Reducing spillover infections will lower the chance of a virus going bigtime. That makes perfect sense for once inside humans the virus can adapt. Note that the above words show that the H7N9 virus wasn’t ‘pre-adapted’, a concept we encountered in the last essay (Natural COVID crowd miss target again).

A viral pandemic is a rare though highly consequential, ‘jackpot’ event. Yep. So, all those claims for DGOF work on H7N9 a decade earlier meant what? Clearly, nobody had a sixth or seventh sense for the avian flu viruses despite all 22 authors being topflight flu researchers. But we’re not finished.

Another of the signatories to the 2013 appeal for DGOF on H7N9 is Dr. Garcia-Sastre of the Ichan School of Medicine at Mount Sinai, New York. He published a paper just a year later. We learn that it has recently been noted that some circulating H5N1 strains are only three amino acid substitutions away from achieving airborne transmission in ferrets [The Fouchier and Kawaoka DGOF papers]. These mutations were predicted to have the ability to arise concurrently in an infected mammalian host, but only at proportions ranging from 10-7 to 10-11. Our findings indicate that dissemination of viruses at these levels is unlikely and offers an explanation as to why, despite significant numbers of human infections, a mammalian transmissible H5N1 has not yet emerged.

Yet we were told it was a matter of time before these viruses would pick up the DGOF generated mutations and go pandemic. All hands to the pumps and more financing were needed to prevent this.

Lastly, our data illustrate that in order for a virus like H5N1 to develop into a pandemic it must pass through two distinct bottlenecks. As demonstrated previously, the virus must first acquire a specific set of mutations and/or reassortments to adapt and allow for optimal replication in the new host. Obvious but see above. Second, the virus must also overcome the sequence independent bottlenecks we have defined that occur during transmission between susceptible hosts. Infections following direct contact with the host are more efficient and maintain a greater proportion of the original virus population when compared to airborne transmission events. Given these results, preventative measures such as avoiding direct contact with infected individuals may help curb the emergence of future pandemics.

Sequence independent phenomena! This will put the cat among the pigeons for the computer jocks who attempt to explain away virus evolution and emergence by looking at genomes. Stochastic events were evident from HIV replication in vivo years before these papers by Drs. Kawaoka and Garcia-Sastre. Transmission bottlenecks can go down to a single infecting virus – that too from HIV research but also from HBV research years before.

To a retired HIV evolution gent peering into flu there is something missing. Flu A is treated with a single drug called oseltamivir. When taken early in infection it is very efficient. The emergence of resistance… was detected in 43/1207 (3.56%) oseltamivir-treated influenza A- infected patient. The vast majority of mutations conferring resistance are single amino acid residue substitutions in the neuraminidase enzyme, the target of oseltamivir. In short, oseltamivir resistance is rare. The frequency of a single mutation in a pool of flu genomes is of the order of 7x10^-5 (1/influenza genome size). At this level a resistance conferring mutant is present in any stock of virus in lab culture.

Why then isn’t oseltamivir resistance rampant? Today it would be criminal to treat an HIV patient with a single drug. It was the combination of several drugs, tri-therapy, that ushered in efficient HIV treatment in 1995. Something isn’t right. Sense can only be had if flu replication is curtailed to fewer than 13,600 cells (1/7x10^-5) at any one moment which is small.

Looking back, we saw multiple themes:

• Vocal flu pandemic drum beating no doubt designed to garner research funding, H7N9 being the case in point here.

• Self-serving and disingenuous calls for DGOF work on H7N9 in Nature and Science never mentioned that the work had been done and published online in Nature. The two journals were complicit. No wonder trust is an issue.

• More predictions that did not hold up - the Fouchier and Kawaoka experiments predicting the next pandemic.

• The genesis of novel human viruses carried pandemic potential and with them inherent risks – lab accidents, crazies and rogue states – which could rise to catastrophic risks threatening millions to billions (You couldn’t make body bags fast enough) and the world economy.

• As little as two years after the controversy erupted, flu virologists were learning of stochastic events and sequence independent bottlenecks. The H5N1 DGOF research didn’t yield anything. Virologists quickly learnt that that noisy DGOF research feeding in to beating the grant funding drum, was unsound.

• Yet virologists didn’t change their tune, dixit the position of the American Society for Microbiology who continued to laud the claims of dGOF research years after. (Deconstructing the portrait; Going places; Flights from reason; Perilous posturing. Let’s stop there).

Have we heard any apologies, or even a simple admission like ‘we goofed’? No. It not even like a page 1 news story with the correction, no matter how important, showing up on page 7 or beyond. Just nudnik.

Conclusions

With the failure to confront DGOF and COVID origins head on it’s a rough time for virology in particular, and science in general.

‘Could do better’ is out by a couple of orders of magnitude.

The Europeans just can’t discuss hot scientific issues where questioning and discussion is everything. Pathetic.

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Simon Wain-Hobson is an emeritus professor at the Institute Pasteur, Paris, from which he retired in 2021. He and his colleagues were the first to sequence the genome of HIV, and Wain-Hobson has published more than 230 papers on virology and cancer.