Gain of function

Jayant Radhakrishnan
Darien, Illinois, United States

 

It is no good to try to stop knowledge from going forward. Ignorance is never better than knowledge.
– Enrico Fermi (1901–1954)

 

Virus with spike protein (mostly external raised part), small envelope protein (small part sticking up out of the envelope to interior and exterior of virus), envelope (covering or wall of virus), nucleocapsid protein (dot on RNA), RNA (ribbon-like structure inside of virus, protected by envelope), and membrane protein (another small part sticking up out of the envelope) labeled
SARS-CoV-2 virus anatomy with proteins labeled. Created by Maya Peters Kostman for the Innovative Genomics Institute. CC BY-NC-SA 4.0.

“Gain of Function” (GoF) burst into the general lexicon in 2021 during two shouting matches in the US Senate between the Junior Senator from Kentucky and the Director of the National Institute of Allergy and Infectious Diseases (NIAID). Both claimed the other was lying. The senator implied that the SARS-CoV-2 virus was created in a Chinese laboratory and was financed by the National Institutes of Health (NIH). Actually, the virus seems to have mutated spontaneously from bats. According to the evidence so far, it is unlikely to have escaped from a laboratory or to have been created by GoF.

Organisms adapt and evolve to survive. In 1864, Herbert Spencer (1820–1903) called this phenomenon “survival of the fittest” after reading Charles Darwin’s On the Origin of Species.1 Genetic mutations in cells alter the nucleotide sequence of deoxyribonucleic acid, permitting cells to adapt and respond to changing conditions. In microorganisms and viruses, mutations sometimes help them jump from a reservoir species to another for their own survival. However, they can be injurious to the new species they inhabit. Some examples of viruses that jumped to humans with devastating consequences include: Ebola from African fruit bats in 1976, Human Immunodeficiency Virus (HIV) from chimpanzees in 1981, Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) from Chinese horseshoe bats in 2002, Middle East Respiratory Syndrome CoV (MERS CoV) from bats via camels in 2012, and now the Severe Acute Respiratory Syndrome-related coronavirus 2 (SARS-CoV-2) from bats in 2019. In addition, influenza viruses continually trade genes with other flu viruses. Due to this property of “antigenic drift,” antibodies that developed in response to a previous flu infection cannot neutralize the new variant.

A virus is a submicroscopic infectious agent consisting of a nucleic acid molecule within a protein coating. It is not a functional body; hence it must enter living cells and commandeer the cell’s workings to obtain energy to replicate rapidly and repeatedly. Viral genomes are composed either of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA) but not both. Mutations are the result of incorrect pairings during replication. The DNA synthesis mechanism can autocorrect an incorrect pairing but such a mechanism does not exist for many RNA viruses. Some RNA viruses, such as the coronavirus, do have a special enzyme to help it autocorrect and keep the mutation rate down. Because viruses replicate repeatedly, the chance of replication error is high. Mutation is inevitable but when and where cannot be predicted. Nor is it possible to know whether the new virus will attack human beings and if it does, we cannot foretell the severity of illness or its transmissibility.

Preventive measures, vaccines, and therapeutic agents can only be developed when the structure and behavior of a virus is known. Hence, certain laboratory maneuvers have been developed to test scientific hypotheses, to try to predict events, and if necessary, develop vaccines and therapeutic agents rapidly. One such technique is GoF. Gain of Function occurs when an organism gains a new property or an existing property is enhanced. Farmers and gardeners have used it since time immemorial by harvesting and preserving the largest seeds or the healthiest plants to sow the next year to obtain a better yield.

Credit for the first use of GoF in medicine should go to Louis Pasteur. In 1879 he observed that a chicken injected with few drops of a fresh culture of Pasteurella developed “fowl cholera” and died. Injection of an old culture, on the other hand, did not kill them and it even protected them from subsequent inoculations of a virulent culture. This discovery may have been inadvertent, but Pasteur had created a live attenuated vaccine. In 1881 he followed up by successfully vaccinating sheep against anthrax. Next, he turned his attention to rabies. This was particularly challenging as he could not see or cultivate the infective agent. However, he knew it had to be present in a nervous system attacked by the disease. Therefore, he transferred the organism from one rabbit to another by intracerebral injection and then desiccated the spinal cord of the infected rabbit. He intended to attenuate the virus, but in reality he had killed it during preparation. This time he had created an inactivated vaccine. In 1881 Pasteur also recognized that attenuation could weaken or enhance virulence depending upon the conditions.2

In time it was realized that Gain of Function Research (GoFR), in which a mutation is introduced to alter a gene’s function, could be used to render pathogens harmless and even beneficial to humanity. Some examples are the engineering of Escherichia coli to tackle consumer-generated plastic waste by converting it into vanillin, which can be used to flavor foods and also in cosmetics.3 Two devastating diseases, dengue fever and malaria, can be controlled by rendering their respective vector mosquitoes incapable of transmitting the causative organisms.4,5 Viruses, being high-risk to humans for reasons mentioned above, were also subjected to this form of research. Two viruses of particular concern to humans are influenza viruses (Orthomyxoviridae) and the coronavirus subfamily (Orthocoronavirinae).

Avian influenza, or bird flu, is caused by a group of viruses. The majority of these infections fall under the category of Low Pathogenic Avian Influenza (LPAI) with infected birds demonstrating few, if any, symptoms. However, H5 and H7 are two LPAI viruses that can mutate into Highly Pathogenic Avian Influenza (HPAI), which has a 100% mortality in chickens. Bird flu is usually transmitted through contact with feces of infected water birds and its chance of infecting humans is low. However, in May of 1997 the tracheal aspirate of a three-year-old boy who died in Hong Kong demonstrated the H5N1 virus.6 From then on, information on this virus was collected7 and its transmissibility and virulence studied. Two groups of researchers, one led by Yoshihiro Kawaoka at the University of Wisconsin and another led by Ron Fouchier at Erasmus University Medical Center, Rotterdam, repeatedly transferred the virus from ferret to ferret until the virus was able to replicate in mammalian lungs and could be transferred by respiratory droplets when infected ferrets coughed or sneezed.8,9 These researchers demonstrated that only a few mutations were required for the virus to become a human pathogen. Their studies are valuable because monitoring for critical mutations in nature could warn us to take preventive action. In addition, vaccines and therapeutic drugs could be developed by using the mutants developed in the laboratory prior to an epidemic taking hold.

However, some scientists were troubled that human pathogens were being created in the laboratory. Further concern was raised in 2013 by several studies carried out at the Harbin Veterinary Research Institute in China.10 Some experts praised the work while others considered it irresponsible. They were especially bothered that proper precautions to prevent accidents were not taken in this laboratory. Scientists who were alarmed by the nature of this research believe that GoFR is of limited beneficial value and could potentially result in a catastrophe if the mutated virus escaped from the laboratory. GoFR could also be used to create dangerous viruses if the technique fell into the wrong hands.11 Consequently, Kawaoka and Fouchier voluntarily suspended further work until GoFR could be regulated.12 The European Union issued regulations to control such research in the future and the United States Government issued a moratorium on it from 2014-2017. Eventually the moratorium was lifted for some projects, provided they were carried out under strict regulations and oversight. In addition, Potential Pandemic Pathogens (PPP) and GoFR were carefully re-defined. It was clarified that the term enhanced PPP only applied to organisms that had their transmissibility and/or virulence enhanced. It did not apply to wild-type pathogens circulating or recovered from nature, regardless of their pandemic potential.13

Arguably, the COVID-19 pandemic has validated the need to plan for dangerous viral mutations occurring in nature. National and international organizations responsible for our collective health seemed to have been caught flat-footed when the pandemic struck, despite there being a World Health Organization (WHO) plan in place since 2017.14 On the other hand, laboratories that had been cooperatively researching coronaviruses for three decades or more were prepared and sprang into action. The first patient was admitted to hospital in Wuhan, China on December 12, 2019, and by January 7, 2020, the genetic sequence had been identified and shared.15 Within two months, four vaccines were ready for human evaluation. By the end of the year, the US Food and Drug Administration (FDA) had given two messenger RNA (mRNA) vaccines Emergency Use Authorization (EUA). In December 2021, nirmatrelvir/ritonavir (PaxlovidTM), which reduces the risk of hospitalization and death in COVID-19 by 88%, also received EUA.16 The ultra-rapid development of mRNA vaccines and the anti-COVID-19 oral drug are due in part to prior research on the coronavirus by Drs. Baric and Shi.17 A pan-coronavirus vaccine is also being developed on the basis of the same science. To date it has been 100% effective in non-human primates.18

Unfortunately, the term “Gain of Function” has been weaponized and international cooperation is frowned upon. Regardless of how this pandemic started, all pertinent information is now out there and the only safe approach is to continue to study pathogens and potential pathogens. Rigorous oversight of the facilities conducting GoFR, preapproval of the research methodology by independent experts in the field, and uncompromising maintenance of the greatest safety precautions should be prerequisites, while minimal interference from governments would be beneficial.

 

Notes

  1. H. Spencer, Principles of Biology, (Charleston: Bibliobazaar, 1864), released October 2015.
  2. M. Schwartz, “The life and works of Louis Pasteur,” J Applied Microbiol 91, (2001): 597-601.
  3. J. Sadler and S. Wallace, “Microbiol synthesis of vanillin from waste poly (ethylene terephthalate),” Green Chem 23, no.13 (2021): 4665-4672.
  4. A. Buchman et al., “Broad dengue neutralization in mosquitoes expressing an engineered antibody,” PLOS Pathogens 16, no.1 (2020).
  5. Y. Dong, M. Simões, and G. Dimopoulos, “Versatile transgenic multistage effector-gene combinations of Plasmodium falciparum suppression in Anopheles, Science Advances 6, no. 20 (2020).
  6. E. Claas et al., “Human influenza A H5N1 virus related to a highly pathogenic avian influenza virus,” Lancet 351, no. 9101 (1998): 472-477. Erratum in Lancet 351, no. 9111: 1292.
  7. S. Lai, et al., “Global epidemiology of Avian influenza A H5N1 virus infections in humans, 1997-2015: a systematic review of individual case data,” Lancet Infect Dis 16, no. 7 (2016): e108-e118.
  8. M. Imai et al., “Experimental adaptation of an influenza H5HA confers respiratory droplet transmission to a reassortant H5HA/H1N1 virus in ferrets,” Nature 486, no. 7403 (2012): 420-428.
  9. E. Schrauwen et al., “The multibasic cleavage site in H5N1 virus is critical for systemic spread along the olfactory and hematogenous routes in ferrets,” J Virol 86, no.7 (2012): 3975-3984.
  10. Y. Zhang et al., “H5N1 Hybrid Viruses Bearing 2009/H1N1 Virus Genes Transmit in Guinea Pigs by Respiratory Droplet,” Science 340, no. 6139 (2013): 1459-1463.
  11. M. Lipsitch, “Why do exceptionally dangerous gain-of-function experiments in influenza?” Methods Mol Biol 1836 (2018): 589-608.
  12. R. Fouchier, A. García-Sastre, and Y. Kawaoka, “Pause on avian flu transmission studies,” Nature Correspondence 481 (2012): 443.
  13. U.S. Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, “Recommended Policy Guidance for Departmental Development of Review Mechanisms for Potential Pandemic Pathogen Care and Oversight (P3CO),” 9 January 2017.
  14. J. Radhakrishnan, “The wonderful world of vaccines,” Hektoen International, Spring 2021.
  15. F. Wu et al., “A new coronavirus associated with human respiratory disease in China,” Nature 579 (2020): 265-269.
  16. US Food and Drug Administration, News Release Coronavirus (COVID-19) Update, “FDA authorizes first oral antiviral for treatment of COVID-19,” December 22, 2021.
  17. V. Menachery et al., “A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence, Nature Medicine (letters) 21, no.12 (2015):1508-1513. Correction 20 November 2015.
  18. B. Ferreri, “Researchers discuss new vaccine that could prevent future pandemics,” Duke Today, May 17, 2021.

 


 

JAYANT RADHAKRISHNAN, MB, BS, MS (Surg), FACS, FAAP, completed a Pediatric Urology Fellowship at the Massachusetts General Hospital, Boston following a Surgery Residency and Fellowship in Pediatric Surgery at the Cook County Hospital. He returned to the County Hospital and worked as an attending pediatric surgeon and served as the Chief of Pediatric Urology. Later he worked at the University of Illinois, Chicago from where he retired as Professor of Surgery & Urology, and the Chief of Pediatric Surgery & Pediatric Urology. He has been an Emeritus Professor of Surgery and Urology at the University of Illinois since 2000.

 

Summer 2022  |  Sections  |  Infectious Diseases