The Soviet biological warfare program and its uncertain legacy.
Past Soviet secrecy when linked with a promise by Putin raise nagging questions about Russian BW-related intentionsRaymond A. Zilinskas
Microbe, 2014. 9, 191-197.
RZ is Director of Chemical & Biological Weapons Nonproliferation Program at the Monterey Institute of International Studies, Monterey, California
The paper is interesting and relevant for two reasons. The first is that some of the work undertaken during the second generation of Russian biological warfare (1972-94) is the equivalent of gain of function virus research.
“The Soviet second-generation BW program had two components, codenamed Ferment and Ekology. Ferment was mandated to weaponize pathogens for use against humans, while Ekology weaponized animal and plant pathogens. Both components were set up to apply genetic engineering techniques to enhance the ability of pathogens to cause infections, to increase the virulence of pathogens, to endow them with new capabilities for circumventing or defeating defenses against them, including vaccines, antibiotics, and detection techniques, and to develop new genetic constructs that caused unique symptoms. It bears noting that in today’s parlance these kinds of experiments are termed “gain of function” experiments.”
Reversing the argument based on cold war logic leads to the conclusion that contemporary GOF influenza virus experiments are de facto the equivalent of biological warfare research. Accordingly, if this work had been performed in some military lab in the West and had been leaked to the press, it is probable that there would have been uproar with headlines like “Weaponizing avian flu”.
The second reason why this article is worth reading is the suggestion that Russia might engage on a new round of biological warfare research.
Thursday, May 1, 2014
Friday, April 11, 2014
April 11, 2014
Dr. Kawaoka gave a talk at the Institut Pasteur as part of the 9th Louis Pasteur conference on Emerging Infectious Diseases. No title or abstract were provided. Lots of data were flashed up; not easy to keep up with the tempo.
• Started with pandemic 2009 influenza A virus (pH1N1) and selected escape mutants with polyclonal sera. Classic. There was little diversity and was disappointed.
• Took gene segment corresponding to amino acid residues 71-270 of the hemagglutinin (HA), performed error prone PCR, re-expressed as mutant library in H1N1 backbone by reverse genetics.
• Took 14 convalescent sera and isolated 50 escape mutants. Found 9 amino acid sites of variation.
• Factored in a few other sites (didn’t catch how) and ended up with 15 key sites in the HA sequence
• Performed saturation codon mutagenesis on these sites in the gene and ended up with 2 amino acid site, 3 site, 4 site and 5 site virus variants that were further refined by mutagenesis. 4 and 5 site mutants completely escaped vaccine-induced antibodies.
They worked hard to get a vaccine resistant virus. Apparently the work was performed at biosafety level 2 (BSL2).
• Started with pandemic 2009 influenza A virus (pH1N1) and selected escape mutants with polyclonal sera. Classic. There was little diversity and was disappointed.
• Took gene segment corresponding to amino acid residues 71-270 of the hemagglutinin (HA), performed error prone PCR, re-expressed as mutant library in H1N1 backbone by reverse genetics.
• Took 14 convalescent sera and isolated 50 escape mutants. Found 9 amino acid sites of variation.
• Factored in a few other sites (didn’t catch how) and ended up with 15 key sites in the HA sequence
• Performed saturation codon mutagenesis on these sites in the gene and ended up with 2 amino acid site, 3 site, 4 site and 5 site virus variants that were further refined by mutagenesis. 4 and 5 site mutants completely escaped vaccine-induced antibodies.
They worked hard to get a vaccine resistant virus. Apparently the work was performed at biosafety level 2 (BSL2).
Thursday, April 10, 2014
April 10, 2014
Linster M, van Boheemen S, de Graaf M, Schrauwen EJ, Lexmond P, Mänz B, Bestebroer TM, Baumann J, van Riel D, Rimmelzwaan GF, Osterhaus AD, Matrosovich M, Fouchier RA, Herfst S.
Identification, characterization, and natural selection of mutations driving airborne transmission of A/H5N1 virus.
Cell. 2014 Apr 10;157(2):329-39. doi: 10.1016/j.cell.2014.02.040.
Identification, characterization, and natural selection of mutations driving airborne transmission of A/H5N1 virus.
Cell. 2014 Apr 10;157(2):329-39. doi: 10.1016/j.cell.2014.02.040.
Wednesday, January 15, 2014
January 15, 2014
A new strain of Clostridium botulinum encoding a novel toxin, BoNT/H the eight such toxin, has been described, the first such toxin to be described in >40 years (Barash et al., 2014; Dover et al., 2014).
The authors referred their concerns up the line. Journal editors and US security agencies were involved resulting in the publication of the work without description of the toxin itself. The original paper was published accompanied by a letter from the editors describing the review process and decision (Hooper & Hirsch, 2014), a historical overview of botulinum toxins (Popoff, 2014) and a comment from David Relman, former member of the NSABB and one who handled the original Kawaoka and Fouchier papers (Relman, 2014).
While the efficiency and merits of redacting essential data from a paper can be debated, the example is well worth reading for the authors flagged up their concerns and shared their observations and difficulties with other stakeholders. It shows that complex and worrying biological issues can be shared and acted upon. The accompanying review papers make for good reading.
A note at the end of the editor’s letter (Hooper & Hirsch, 2014) lists the large number of committees that were involved in commenting on the larger dimensions of theses findings.
“A committee representing various branches of the US government reviewed and approved submission of the manuscripts. Represented on this committee were the Drug Development Section, Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); the Enteric and Hepatic Diseases Branch, NIAID, NIH; the Bacteriology and Mycology Branch, NIAID, NIH; the Office of Biotechnology Activities, Office of Science Policy, NIH; the National Counterproliferation Center, Office of the Director of National Intelligence; the Office of the Assistant Secretary for Preparedness and Response, Department of Health and Human Services (DHHS); the Biomedical Advanced Research and Development Authority, Office of the Assistant Secretary for Preparedness and Response, DHHS; the Threat Characterization and Attribution Branch, Chemical and Biological Defense Division, Science and Technology Directorate, Department of Homeland Security; the US Army Medical Research Institute of Infectious Diseases; the Division of Select Agents and Toxins, Office of Public Health Preparedness and Response, Centers for Disease Control and Prevention, DHHS; and the Biological Countermeasures Unit, Federal Bureau of Investigation Weapons of Mass Destruction Directorate, Department of Justice.”
The last paragraph from Relman’s letter is worth reading.
“Finally, for voluntary controls to play a useful role in the management of problematic information in the “gray area,” scientists will first need to recognize their ethical and moral responsibilities to society in the pursuit of knowledge. Scientists have obligations to society that involve more than blind pursuit of information. Like clinicians, scientists have an obligation to do no harm.”
References
A novel strain of Clostridium botulinum that produces type B and type H botulinum toxins.
Barash JR, Arnon SS.
J Infect Dis. 2014 Jan 15;209(2):183-91. doi: 10.1093/infdis/jit449. Epub 2013 Oct 7.
Molecular characterization of a novel botulinum neurotoxin type H gene.
Dover N, Barash JR, Hill KK, Xie G, Arnon SS.
J Infect Dis. 2014 Jan 15;209(2):192-202. doi: 10.1093/infdis/jit450. Epub 2013 Oct 7.
Novel clostridium botulinum toxin and dual use research of concern issues.
Hooper DC, Hirsch MS.
J Infect Dis. 2014 Jan 15;209(2):167. doi: 10.1093/infdis/jit528. Epub 2013 Oct 7.
Botulinum neurotoxins: more and more diverse and fascinating toxic proteins.
Popoff MR.
J Infect Dis. 2014 Jan 15;209(2):168-9. doi: 10.1093/infdis/jit505. Epub 2013 Oct 7.
"Inconvenient truths" in the pursuit of scientific knowledge and public health.
Relman DA.
J Infect Dis. 2014 Jan 15;209(2):170-2. doi: 10.1093/infdis/jit529. Epub 2013 Oct 7.
The authors referred their concerns up the line. Journal editors and US security agencies were involved resulting in the publication of the work without description of the toxin itself. The original paper was published accompanied by a letter from the editors describing the review process and decision (Hooper & Hirsch, 2014), a historical overview of botulinum toxins (Popoff, 2014) and a comment from David Relman, former member of the NSABB and one who handled the original Kawaoka and Fouchier papers (Relman, 2014).
While the efficiency and merits of redacting essential data from a paper can be debated, the example is well worth reading for the authors flagged up their concerns and shared their observations and difficulties with other stakeholders. It shows that complex and worrying biological issues can be shared and acted upon. The accompanying review papers make for good reading.
A note at the end of the editor’s letter (Hooper & Hirsch, 2014) lists the large number of committees that were involved in commenting on the larger dimensions of theses findings.
“A committee representing various branches of the US government reviewed and approved submission of the manuscripts. Represented on this committee were the Drug Development Section, Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH); the Enteric and Hepatic Diseases Branch, NIAID, NIH; the Bacteriology and Mycology Branch, NIAID, NIH; the Office of Biotechnology Activities, Office of Science Policy, NIH; the National Counterproliferation Center, Office of the Director of National Intelligence; the Office of the Assistant Secretary for Preparedness and Response, Department of Health and Human Services (DHHS); the Biomedical Advanced Research and Development Authority, Office of the Assistant Secretary for Preparedness and Response, DHHS; the Threat Characterization and Attribution Branch, Chemical and Biological Defense Division, Science and Technology Directorate, Department of Homeland Security; the US Army Medical Research Institute of Infectious Diseases; the Division of Select Agents and Toxins, Office of Public Health Preparedness and Response, Centers for Disease Control and Prevention, DHHS; and the Biological Countermeasures Unit, Federal Bureau of Investigation Weapons of Mass Destruction Directorate, Department of Justice.”
The last paragraph from Relman’s letter is worth reading.
“Finally, for voluntary controls to play a useful role in the management of problematic information in the “gray area,” scientists will first need to recognize their ethical and moral responsibilities to society in the pursuit of knowledge. Scientists have obligations to society that involve more than blind pursuit of information. Like clinicians, scientists have an obligation to do no harm.”
References
A novel strain of Clostridium botulinum that produces type B and type H botulinum toxins.
Barash JR, Arnon SS.
J Infect Dis. 2014 Jan 15;209(2):183-91. doi: 10.1093/infdis/jit449. Epub 2013 Oct 7.
Molecular characterization of a novel botulinum neurotoxin type H gene.
Dover N, Barash JR, Hill KK, Xie G, Arnon SS.
J Infect Dis. 2014 Jan 15;209(2):192-202. doi: 10.1093/infdis/jit450. Epub 2013 Oct 7.
Novel clostridium botulinum toxin and dual use research of concern issues.
Hooper DC, Hirsch MS.
J Infect Dis. 2014 Jan 15;209(2):167. doi: 10.1093/infdis/jit528. Epub 2013 Oct 7.
Botulinum neurotoxins: more and more diverse and fascinating toxic proteins.
Popoff MR.
J Infect Dis. 2014 Jan 15;209(2):168-9. doi: 10.1093/infdis/jit505. Epub 2013 Oct 7.
"Inconvenient truths" in the pursuit of scientific knowledge and public health.
Relman DA.
J Infect Dis. 2014 Jan 15;209(2):170-2. doi: 10.1093/infdis/jit529. Epub 2013 Oct 7.
Wednesday, January 1, 2014
January 2014
Alternative reassortment events leading to transmissible H9N1 influenza viruses in the ferret model.
Kimble JB, Angel M, Wan H, Sutton TC, Finch C, Perez DR.
J Virol. 2014 Jan;88(1):66-71. doi: 10.1128/JVI.02677-13. Epub 2013 Oct 16.
Kimble et al., describe inoculation of ferrets with MDCK (dog) cells transfected by 15 plasmids for avian H9N2 flu strain and human pandemic 2009 H1N1 (minus the H1 hemagglutinin). Theoretically 128 reassortant viruses can be made. Two of three animals so inoculated became infected giving rise to what were called lineage A and B viruses. Within 4 days of transfection, the dye was cast and one combination quickly dominated in each infected animal. This contrasts to the findings for tissue culture that once again highlights the need for animal studies.
At the end of 4 manual passages (P1-P4 virus) a fifth passage by aerosol transmission with P4 virus was attempted for three infected animals and it worked (RCP5 virus, RC=respiratory contact). P1 and RCP5 viruses were sequenced. There were 4 non-synonymous nucleotide changes (i.e. resulting in amino acid changes) for lineage A virus and 6 (5 non-synonymous, 1 synonymous, or silent change) for lineage B virus. None of the mutations overlapped. None were in the HA receptor binding pocket. This shows that there are many constellations that compatible with aerosol transmission using 6 common genes (PB2, PA, HA, NP, NA, and NS, Table 1). 2/4 and 5/5 mutations were of unknown phenotype indicating once again the wide gap in correlating genotype and phenotype.
The authors did not sequence the P4 virus used to initiate the aerosol transmission experiment hence we cannot work out which mutations arose during serial mechanical passage and which resulted from selection via transmission. It is unlikely that all 4 and 6 mutations arose during the single aerosol transmission passage, hence the numbers so acquired must be <4 and <5 for lineage A and B. Sequencing the P4 virus would have established the precise number involved.
Their interest in GOF is shown by the last sentence: “A similar approach can be implemented to ascertain the gene constellation that would most likely lead to more effective respiratory-droplet transmission of other avian influenza viruses in mammals.” Sequencing the P4 virus would have helped.
Kimble JB, Angel M, Wan H, Sutton TC, Finch C, Perez DR.
J Virol. 2014 Jan;88(1):66-71. doi: 10.1128/JVI.02677-13. Epub 2013 Oct 16.
Kimble et al., describe inoculation of ferrets with MDCK (dog) cells transfected by 15 plasmids for avian H9N2 flu strain and human pandemic 2009 H1N1 (minus the H1 hemagglutinin). Theoretically 128 reassortant viruses can be made. Two of three animals so inoculated became infected giving rise to what were called lineage A and B viruses. Within 4 days of transfection, the dye was cast and one combination quickly dominated in each infected animal. This contrasts to the findings for tissue culture that once again highlights the need for animal studies.
At the end of 4 manual passages (P1-P4 virus) a fifth passage by aerosol transmission with P4 virus was attempted for three infected animals and it worked (RCP5 virus, RC=respiratory contact). P1 and RCP5 viruses were sequenced. There were 4 non-synonymous nucleotide changes (i.e. resulting in amino acid changes) for lineage A virus and 6 (5 non-synonymous, 1 synonymous, or silent change) for lineage B virus. None of the mutations overlapped. None were in the HA receptor binding pocket. This shows that there are many constellations that compatible with aerosol transmission using 6 common genes (PB2, PA, HA, NP, NA, and NS, Table 1). 2/4 and 5/5 mutations were of unknown phenotype indicating once again the wide gap in correlating genotype and phenotype.
The authors did not sequence the P4 virus used to initiate the aerosol transmission experiment hence we cannot work out which mutations arose during serial mechanical passage and which resulted from selection via transmission. It is unlikely that all 4 and 6 mutations arose during the single aerosol transmission passage, hence the numbers so acquired must be <4 and <5 for lineage A and B. Sequencing the P4 virus would have established the precise number involved.
Their interest in GOF is shown by the last sentence: “A similar approach can be implemented to ascertain the gene constellation that would most likely lead to more effective respiratory-droplet transmission of other avian influenza viruses in mammals.” Sequencing the P4 virus would have helped.
Tuesday, December 31, 2013
2013
Evolution and control of H5N1: A better understanding of the evolution and diversity of H5N1 flu virus and its host species in endemic areas could inform more efficient vaccination and control strategies
Watanabe Y, Ibrahim MS, Ikuta K.
EMBO Rep. 2013 Feb;14(2):117-22. doi: 10.1038/embor.2012.212. Epub 2013 Jan 11.
A readily readable paper on the state of H5N1 virus infection in poultry with particular attention given to Egypt.
“Unfortunately, it is unlikely that science will ever produce a clear answer as to when, where and how the next pandemic influenza virus will emerge.”
Yet another group of authors coming to the same conclusion.
Watanabe Y, Ibrahim MS, Ikuta K.
EMBO Rep. 2013 Feb;14(2):117-22. doi: 10.1038/embor.2012.212. Epub 2013 Jan 11.
A readily readable paper on the state of H5N1 virus infection in poultry with particular attention given to Egypt.
“Unfortunately, it is unlikely that science will ever produce a clear answer as to when, where and how the next pandemic influenza virus will emerge.”
Yet another group of authors coming to the same conclusion.
Sunday, December 1, 2013
December 2013
Human infection with avian influenza A H6N1 virus: an epidemiological analysis.
Wei SH, Yang JR, Wu HS, Chang MC, Lin JS, Lin CY, Liu YL, Lo YC, Yang CH, Chuang JH, Lin MC, Chung WC, Liao CH, Lee MS, Huang WT, Chen PJ, Liu MT, Chang FY.
Lancet Respir Med. 2013 Dec;1(10):771-8. doi: 10.1016/S2213-2600(13)70221-2. Epub 2013 Nov 14.
A 20 year old woman with respiratory distress presented to a hospital in Taiwan. An unusual influenza virus subtype was isolated, H6N1 making it the first recorded case. Molecular analysis of the virus identified a G228S mutation in the hemagglutinin (H) surface protein which is generally considered to help hemagglutinin binding to human a2-6 linked sialic acid receptors, although it was not proven here. As a unique clade of H6N1 viruses with a G228S substitution of hemagglutinin have circulated persistently in poultry in Taiwan the case represents another example of a zoonosis, and probably a dead-end infection.
The article concludes with “Our report highlights the continuous need for preparedness for a pandemic of unpredictable and complex avian influenza.” This is an impossible conclusion. Extrapolation from a single point is not possible. Furthermore the “unpredictable and complex nature of avian influenza” has been highlighted before and our ability to predict the next pandemic has been found wanting.
Nonetheless, it represents an important case report.
Wei SH, Yang JR, Wu HS, Chang MC, Lin JS, Lin CY, Liu YL, Lo YC, Yang CH, Chuang JH, Lin MC, Chung WC, Liao CH, Lee MS, Huang WT, Chen PJ, Liu MT, Chang FY.
Lancet Respir Med. 2013 Dec;1(10):771-8. doi: 10.1016/S2213-2600(13)70221-2. Epub 2013 Nov 14.
A 20 year old woman with respiratory distress presented to a hospital in Taiwan. An unusual influenza virus subtype was isolated, H6N1 making it the first recorded case. Molecular analysis of the virus identified a G228S mutation in the hemagglutinin (H) surface protein which is generally considered to help hemagglutinin binding to human a2-6 linked sialic acid receptors, although it was not proven here. As a unique clade of H6N1 viruses with a G228S substitution of hemagglutinin have circulated persistently in poultry in Taiwan the case represents another example of a zoonosis, and probably a dead-end infection.
The article concludes with “Our report highlights the continuous need for preparedness for a pandemic of unpredictable and complex avian influenza.” This is an impossible conclusion. Extrapolation from a single point is not possible. Furthermore the “unpredictable and complex nature of avian influenza” has been highlighted before and our ability to predict the next pandemic has been found wanting.
Nonetheless, it represents an important case report.
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