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Record W2895049133 · doi:10.1371/journal.ppat.1007025

Synthetic horsepox viruses and the continuing debate about dual use research

2018· article· en· W2895049133 on OpenAlexaff
Ryan S. Noyce, David H. Evans

Bibliographic record

VenuePLoS Pathogens · 2018
Typearticle
Languageen
FieldImmunology and Microbiology
TopicPoxvirus research and outbreaks
Canadian institutionsUniversity of Alberta
Fundersnot available
KeywordsDual (grammatical number)VirologyPolitical scienceBiologyPhilosophy

Abstract

fetched live from OpenAlex

On January 19, 2018, a paper describing the complete synthesis of a horsepox virus was published in PLOS ONE [1].This is the largest virus assembled to date, and it shows that no viral pathogen is likely beyond the reach of synthetic biology.The paper and reports of its contents have attracted much comment [2][3][4].As the two authors who conducted these experiments, we thank PLOS Pathogens for giving us the opportunity to address some of the issues arising from this work.At the heart of the discussion lies the fact that this is dual use research of concern (DURC) [5] because any method that can be used to assemble horsepox virus could be used to construct variola, the virus that causes smallpox.This renders our work of special relevance for the agencies tasked with ensuring that smallpox remains a disease of history.Although the world's known variola stocks are securely stored in Russia and the United States, synthetic biology compromises this approach for securing any agent.This was shown by the reconstruction of poliovirus in 2002 [6] and has been discussed within WHO [7].Whether secret or lost [8] stocks of variola virus still exist is unknown, but countermeasures are still stockpiled because of this recognized threat.If one looks at the opinions that have been expressed about our work, an important point concerns the possibility that it provides instructions for making variola.For good or ill, the world is full of talented scientists who do not need a blueprint to extract knowledge well described in published works [7,[9][10][11].This includes papers showing how to assemble a bacmid encoding herpes simplex virus [12] and how to recover vaccinia virus (VACV) from a bacmid [13].This does not mean this technology is still easily implemented.It is not.All modern "methods" sections omit details familiar to experts.Although variola virus DNA has been recovered from historical specimens [14,15], it is not accessible by "mail order" [16].The design work is tricky, 30 kbp plasmids are unstable, and the assembly reactions are inefficient.The skill set needed to do this work requires advanced scientific training, insider knowledge, and infrastructure that is not widely accessible.Our interest in testing horsepox virus as a potentially safer vaccine was prompted by phylogenetic [17][18][19] and historical [20][21][22][23][24] evidence suggesting that smallpox vaccines might have originated in horses.Considering the evidence of actual efficacy [22,24], could a horsepox virus still serve this purpose?Gene synthesis offered a route for obtaining the virus while also providing commercial freedom to operate.But do we still need another smallpox vaccine?There is no short or simple answer to that question, although the Russian and American collaborating centers have reported to WHO that their variola stocks are still being used for ongoing vaccine research [25].Given this lack of consensus, it seems reasonable to explore other options when considering how best to periodically replenish vaccine stockpiles.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

How this classification was reachedexpand

Full frame machine prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.

metaresearch head score (Codex)0.065
metaresearch head score (Gemma)0.043
Version: metacan-v3-hybrid-931329e0061cValidation status: machine_predicted_unvalidated
Candidate categoriesResearch integrity
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Not applicable · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: none
Teacher disagreement score0.989
Threshold uncertainty score0.342

Distilled classifier scores by category (both heads)

CategoryCodexGemma
Metaresearch0.0650.043
Meta-epidemiology (narrow)0.0010.001
Meta-epidemiology (broad)0.0010.001
Bibliometrics0.0010.001
Science and technology studies0.0020.022
Scholarly communication0.0060.017
Open science0.0030.005
Research integrity0.0110.015
Insufficient payload (model declined to judge)0.0070.002

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.070
GPT teacher head0.320
Teacher spread0.251 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it

Classification

machine, unvalidated

Machine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.

Study designNot applicable
Domainnot available
GenreEmpirical

How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".

Quick stats

Citations35
Published2018
Admission routes1
Has abstractyes

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