Synthetic Genomics

Applicability of the Select Agent Regulations to Issues of Synthetic Genomics

The Federal Select Agent Program is providing guidance regarding the application of the current select agent regulations (published October 5, 2012) to those who create and use synthetic genomic products.

In a December 2006 report entitled "Addressing Biosecurity Concerns Related to the Synthesis of Select Agents" ( www.biosecurityboard.gov/links.asp), the National Science Advisory Board on Biosecurity recommended that the Federal government take steps to "increase awareness among providers and users of synthetic genomic materials regarding compliance with the select regulations; and provide a list of genomic materials explicitly covered by the regulations."

The following genetic elements, recombinant and/or synthetic nucleic acids, and recombinant and/or synthetic organisms are select agents (See section 3(c) of 42 CFR Part 73, 9 CFR Part 121, and 7 CFR Part 331):

• Nucleic acids that can produce infectious forms of any of the select agent viruses.
• Recombinant and/or synthetic nucleic acids that encode for the functional form(s) of select agent toxins if the nucleic acids:
  • Can be expressed in vivo or in vitro or,
  • Are in a vector or recombinant host genome and can be expressed in vivo or in vitro.
• Select agents and toxins that have been genetically modified.

Some select agent genomes are not covered under the select agent regulations. The select agent regulations currently regulates nucleic acids encoding select agent genomes only when the nucleic acids are inherently infectious (i.e., the nucleic acids are capable of generating infectious forms of a regulated virus by utilizing host polymerases but without the need for any additional exogenous factors (proteins, nucleic acids, etc.) or encode for the functional form(s) of any of the select agent toxins.) The purpose of this guidance is to address advances in molecular biology that may influence the production of infectious forms of select agent viruses, or the active forms of select agent toxins from recombinant and/or synthetic nucleic acids. It has been demonstrated, for example, that positive strand RNA viruses and certain double strand DNA viruses that utilize host polymerases contain nucleic acids that can produce infectious forms of the viruses. Such nucleic acids are subject to the select agent regulations.

Genetic elements

Genetic elements are sequences of nucleic acids. Genetic elements from select agents are regulated if they encode for a functional form of a select agent toxin and can be expressed in vivo or in vitro or are in a vector or recombinant host genome and can be expressed in vivo or in vitro , or if the nucleic acids (RNA) are inherently infectious as discussed above.

Recombinant and/or synthetic nucleic acids

Provided below is the list of select agents whose nucleic acids (including recombinant and/or synthetic nucleic acids) are regulated. Regulation is limited to those nucleic acids that are the immediate precursors to virus production. For the viruses listed below, regulation is limited to positive strand RNA forms of the viral genome which can be translated into protein precursors for virus production. A cDNA copy of the viral genomes listed below would not be regulated because they would first need to be transcribed into RNA then translated into protein and therefore would not be an immediate precursor to virus.

• Classical Swine Fever Virus
• Eastern Equine Encephalitis virus (except South American type)
• Foot-And-Mouth Disease Virus
• Kyasanur Forest disease virus
• Omsk hemorrhagic fever virus
• SARS-associated coronavirus (SARS-CoV)
• Swine vesicular disease virus
• Tickborne encephalitis complex (flavi) viruses:
  • Far Eastern subtype
  • Siberian subtype
• Venezuelan Equine Encephalitis virus subtypes IAB and IC
• Recombinant and/or synthetic nucleic acids that encode for the functional form(s) of the regulated toxins, if the nucleic acids can be expressed in vivo or in vitro or, are in a vector or recombinant host genome and can be expressed in vivo or in vitro .

Under the current select agent regulations the following are examples of materials that would not be regulated as a select agent:

• Nucleic acids that cannot produce infectious forms of any of the regulated select agent viruses
• cDNA made from regulated select agent nucleic acids (only the positive strand RNA forms of the viral genome is regulated)
• Genetic elements from select agents (unless they encode for a functional form of a select agent toxin)
• Nucleic acids encoding complete genomes of single-stranded negative strand RNA viruses, double stranded RNA viruses, and double-stranded DNA viruses that require a unique polymerase (Variola virus*, Monkeypox virus (except West African clade), African swine fever virus, Goat pox virus, Lumpy skin disease virus, and Sheep pox virus)
• Nucleic acids that encode for the genomes of select agent bacteria or fungi
• Nucleic acids that encode for toxins not subject to the select agent regulations but derived from regulated select agents
• Nucleic acids that encode for the genomes of select agent strains that have been excluded from regulation under section 3(e) of the select agent regulations
• Select agent nucleic acid sequence information

* Section 175c of Title 18, United States Code, provides that, except for conduct approved under the authority of the Secretary of Health and Human Services, it shall be unlawful for any person to knowingly produce, engineer, synthesize, acquire, transfer directly or indirectly, receive, possess, import, export, or use, or possess and threaten to use, variola virus. Section 175c defines the term "variola virus" to mean "a virus that can cause human smallpox or any derivative of the variola major virus that contains more than 85 percent of the gene sequence of the variola major virus or the variola minor virus". Resolutions adopted by the World Health Organization (WHO) provide that institutions other than the two currently recognized WHO collaborating centers are also prohibited from possessing genetic fragments exceeding 20% of the Variola virus genome. For additional information on WHO Guidelines for Variola virus research, please see http://www.who.int/csr/disease/smallpox/research/en/index.html, and the report, also published in the Weekly Epidemiologic Record in 2008, on permissible use of Variola genetic material ( http://www.who.int/csr/disease/smallpox/SummaryrecommendationsMay08.pdf ).

Organisms containing regulated recombinant and/or synthetic nucleic acids
Any organisms that contain regulated recombinant or synthetic nucleic acids are subject to the regulations unless the organisms or nucleic acids are excluded as a non-viable select agent or toxin, an attenuated strain, or inactive toxin. Please see Select Agents Exclusion for further guidance. If currently regulated select agent recombinant and/or synthetic nucleic acids (see above) are introduced into either a select agent organism or an organism used for molecular cloning (e.g., E. coli ), the resulting recombinant and/or synthetic organism would be subject to the regulations.

The following examples, Example scenarios involving synthetic genomic select agent materials, while not inclusive of all potential scenarios, illustrate the application of the current select agent regulations to activities involving synthetic genomics or synthetic biology.

The Department of Health and Human Services' Screening Framework Guidance for Providers of Synthetic Double-Stranded DNA sets forth recommended baseline standards for the gene and genome synthesis industry and other providers of synthetic double-stranded DNA products regarding the screening of orders so that they are filled in compliance with current U.S. regulations. The Guidance also encourages best practices in addressing biosecurity concerns associated with the potential misuse of their products to bypass existing regulatory controls. Even when the double-stranded DNA sequence being processed does not fall under the current select agent regulations, providers are advised to refer to this policy for additional guidance on screening such orders.