Monday, November 25, 2024

Microorganisms: The Growing Phenomenon of ‘Frozen’ Virus Genome Sequences and Their Likely Origin in Research Facility Escapes


Yes, that’s me in 1976, giving Swine Flu Shots
Helping to make Guillain-Barré a household name

#18,443

Forty-eight years ago, as an impossibly young paramedic (see photo above) I played a very minor role in the ill-fated response to an H1N1 `swine flu' pandemic that never materialized. For those who are interested in ancient public health history, I gave my account of those events 15 years ago, in Deja Flu, All Over Again

While the predicted pandemic virus of 1976 was a no-show, quite unexpectedly the following year an H1N1 virus did emerge, after an absence of 2 decades.   

H1N1 - which had reigned supreme for nearly 4 decades was supplanted by an H2N2 virus with the 1957 pandemic, and that gave way to an H3N2 virus in the 1968 pandemic. 

Both of these pandemics were the result of an avian flu virus reassorting with seasonal flu. 

The return of H1N1 in 1977 was unique, a) because it mainly affected those under the age of 25, and b) because it did not supplant the existing H3N2 virus.  As a result we've had an H3 and an H1 influenza virus co-circulating for nearly 50 years.

For years scientists have tried to explain how a virus – gone from the wild for 20 years – could just suddenly reappear. Particularly one that was practically identical to a strain last seen more than a quarter of a century before.

Nine years ago, in mBio: The Reemergence Of H1N1 in 1977 and The GOF Debate, the authors of a review of 1977's return of the H1N1 virus examined 3 plausible scenarios, writing:

Given the importance of this historical epidemic to ongoing policy debates, we revisit the evidence that the 1977 epidemic was not natural and examine three potential origins: a laboratory accident, a live-vaccine trial escape, or deliberate release as a biological weapon.
Based on available evidence, the 1977 strain was indeed too closely matched to decades-old strains to likely be a natural occurrence. While the origin of the outbreak cannot be conclusively determined without additional evidence, there are very plausible alternatives to the laboratory accident hypothesis, diminishing the relevance of the 1977 experience to the modern GOF debate.

Of the three hypotheses, given the timing (just after the 1976 swine flu scare) a live-vaccine trial escape in either China or Russia seemed most likely.  Other reviews have concluded that the emergence of H1N1 in 1977 was likely not a natural occurrence, although we may never know the particulars. 

The return of H1N1 in 1977 is the best known, and arguably the most impactful example, but there are a number of other incidents where a virus has mysteriously re-appeared after many years.

Which brings us to a review, published in the journal Microorganisms - of 5 unexplained viral resurrections over the past 5 decades:
  • 1977 ‘ Russian’ H1N1 Flu
  • 1995 Venezuelan Equine Encephalitis Virus in Venezuela
  • 2007–2009 Hand, Foot and Mouth Disease in Beijing, China
  • 2014 Polio in Anhui, China
  • 2021 Guinea Ebola Outbreak
It's a fascinating read, and while the mechanisms behind the abrupt return of these viruses remains a subject of considerable debate, the author cautions that these are likely just the tip of the iceberg.  

I've only reproduced the abstract, so click the link to read it in its entirety.  I'll have a postscript after the break.

The Growing Phenomenon of ‘Frozen’ Virus Genome Sequences and Their Likely Origin in Research Facility Escapes

by 

Biology Department, University of Puerto Rico-Rio Piedras, San Juan 00931, Puerto Rico
Microorganisms 202412(12), 2412; https://doi.org/10.3390/microorganisms12122412 (registering DOI)
Submission received: 4 November 2024 / Revised: 20 November 2024 / Accepted: 21 November 2024 / Published: 24 November 2024
Abstract

‘Frozen’ virus genome sequences are sampled from outbreaks and have unusually low sequence divergence when compared to genome sequences from historical strains. A growing number of ‘frozen’ virus genome sequences are being reported as virus genome sequencing becomes more common. Examples of ‘frozen’ sequences include the 1977 H1N1 ‘Russian’ flu; Venezuelan Equine Encephalitis Virus from Venezuela and Colombia in 1995; E71 sequences from a Hand, Foot and Mouth outbreak in 2007–2009 in China; and a polio strain isolated in 2014 from Anhui, China.
The origin of these ‘frozen’ sequences has been attributed to escapes from research facilities and often appears to be associated with vaccine work. Consequently, a new paradigm for pathogen emergence appears in operation, that involves laboratory research or vaccine production which utilizes ‘live’ virus isolates of historical strains.
The accidental release and re-emergence of such strains are straightforward to detect from their genome sequences and should spur the routine sequencing and publication of all known pathogenic viral strains undergoing experimentation, or being used for vaccine manufacture, in order to facilitate tracing.
However, it is noted that novel pathogenic viruses accidentally released into the population from research facilities are harder to detect if their sequence has first not been made public, which should prompt the routine sequencing and reporting of all novel pathogenic viruses before experimentation.

          (Continue . . . ) 


Over the years we've devoted a fair amount of coverage of GOF (Gain of Function) research and to  laboratory accidents (see CIDRAP News report Report: 395 mishaps at US labs risked releasing select agents). 

Ten years ago the U.S. laboratories (CDC, FDA, DOD, NIH) suffered an embarrassing series of lab accidents involving select agents including H5N1, Ebola, and Anthrax.
CDC Statement On Possible Lab Exposure To Anthrax

CDC Media Statement on Newly Discovered Smallpox Specimens

CDC Announces Another Serious Biosecurity Incident  (H5N1)

While reports like this are rare, the reality is that many such events likely go unreported or deliberately covered up, all around the globe.  

Others, like China's 2019 Outbreak Of Brucellosis Reported At Veterinary Research Institute - Gansu Province - which we looked at just weeks before the news broke on the COVID outbreak in Wuhan, simply fade from memory.

According to a preliminary report by the Gansu Province health commission, a bio-pharmaceutical company which was producing a Brucellosis vaccine - and which sits in close proximity to the Lanzhou Veterinary Research Institute - allowed prolonged, unintentional release of the bacteria into the environment, apparently due to the use of expired disinfectants.

The number of infected was reported to be roughly 200, but a year later a report (see The Lanzhou Brucella Leak: The Largest Laboratory Accident in the History of Infectious Diseases?) put the number of people infected as > 10,000.

While there is obviously a need for vaccine production, and in some rare cases GOF experimentation, history has shown repeatedly that there are genuine risks involved. 

And as the availability and affordability of the tools required to dabble in synthetic biology increase, so do biosecurity concerns. 


While we rightfully worry about the natural evolution of pathogens, sometimes - through ignorance, neglect, and sometimes malice - we can be our own worst enemy.