Biosafety Manual

Updated: April 2016


Chapter 1 - Introduction to Biosafety

Chapter 2 - Biological Safety Program Administration

Chapter 3 - Who Needs a Biological Use Authorization (BUA) Approval?

Chapter 4 - The BUA Process

Chapter 5 - Human Gene Transfer Research

Chapter 6 - Laboratory Design and Biosafety Cabinets

Chapter 7 - Medical (Biohazardous) Waste Management

Chapter 8 - Responding to Emergencies Involving Biohazardous Materials

Chapter 9 - Biological Safety Training

Chapter 10 - Animal Biosafety

Chapter 11 - Shipping and Transport of Biohazardous Materials

Chapter 12 - Importation and Exportation Permits for Biological Materials

Chapter 13 - Biological Toxins

Chapter 14 - Select Agents

Chapter 15 - Working with Aerosol Transmissible Diseases

Chapter 16 - Health Surveillance Program

Chapter 17 - Audits and Inspections


The purpose of this manual is to define the biological safety policies and procedures for the University of California, San Francisco (UCSF). These policies and procedures were designed to safeguard personnel and the environment from biologically hazardous materials and to comply with federal and state regulatory requirements without unduly intruding on research.  All UCSF Principal Investigators (PIs) and laboratory workers must adhere to these biological safety policies and procedures in the conduct of their research and in the management of their laboratories.

For information about specific biological safety programs or operations not covered in this manual, contact your Environment, Health and Safety Specialist (EH&S Specialist), the Biosafety Officer (BSO) or Assistant Biosafety Officers (ABSOs), or the Institutional Biosafety Committee (IBC) office, at the UCSF Environment Health and Safety (EH&S).


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Chapter 1

Introduction to Biological Safety

The goals of the Biological Safety (or Biosafety) Program are to protect laboratory workers, the public and the environment from potentially hazardous biological materials. Compliance with State and Federal regulations is essential if experiments are to be done safely, although excessive interference would hinder research unnecessarily. The University of California, San Francisco (UCSF) Institutional Biosafety Committee (IBC) provides guidance in determining the use of biological safety precautions that effectively reduce or eliminate the risk of exposure to potentially hazardous biological materials used in research.  The other essential goal of the Committee, and by extension, the Biosafety Officers (BSOs), is to protect the University from punitive sanctions by Federal or State agencies as a result of compliance failures on the part of the research community.  It is a difficult balance to maintain, and full cooperation and dialog between the research community and the IBC is essential to successfully achieve this balance.

Biological research laboratories are special work environments that pose potential exposure risks to infectious diseases, genetically modified organisms (GMOs) or toxins by persons working in these laboratories or entering them.  There is a clear historical record of laboratory-acquired infections; more than 4,000 laboratory-acquired infections have been reported and many others have certainly occurred.  Incidents such as a splash to mucous membranes, needle stick, contamination of open wounds or skin lesions, ingestion or inhalation of an aerosolized infectious agent or toxin have all produced laboratory-acquired disease.

There are two documents that provide key guidance to the UCSF Biosafety Program. The CDC-NIH document Biosafety in Microbiological and Biomedical Laboratories 5th Edition (BMBL-US Government Printing Office, Washington D. C., December 2009) recommends a tiered system of laboratory practices for protection of laboratory workers, depending on anticipated risks of exposure to infectious agents and toxins. Agents themselves are assigned to Risk Groups (RGs) based upon the extent of hazard they pose to a healthy adult.  Requirements for laboratory facilities and operations for working with these agents are divided into Biosafety Levels (BSLs).  The criteria are cumulative; BSL2 criteria include all of the criteria for BSL1 adding additional criteria as listed.  BSL3 is layered upon BSL1 and BSL2 and so on. There are also separate sets of criteria designed either for work without or with experimental animals, grouped under Biosafety Levels (BSL), and Animal Biosafety Levels (ABSL) 1, 2, 3 and 4.

The second and largely dominant document that governs much of the research work at UCSF is the NIH document Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules (March 2013).  It is essential that Principal Investigators (PIs) understand that all recombinant genetic work, regardless of species, falls under this document.  While there are categories of exempt experiments, it is critical that the PI file a Biological Use Authorization (BUA) with the IBC for all recombinant work.  The BSOs will review the BUA and determine if the work is exempt.  Some of the exemption criteria are straightforward while others are not, and this area of regulation is rapidly changing.

In addition, there are state and federal regulations that the Biosafety Program is responsible for enforcing.  At the state level, the Bloodborne Pathogens standard, the California Medical Waste Regulations, and the Aerosol Transmissible Disease Standard are the regulations that impact the campus.  At the Federal level, the Biosafety Program is responsible for assisting the campus in complying with the Select Agent Program, the Federal Department of Transportation shipping and packaging regulations governing the shipment of biohazardous materials, and the highly complex import and export regulations as well as other regulations that have more limited impact.

The essential component of evaluating and controlling exposure to biohazardous materials is the process called “Risk Assessment.”  The most straightforward component of risk is evaluating the possibility that a researcher could become infected with an agent they are handling.  However, protection of the environment and community against an accidental release of biohazardous materials and/or genetically modified materials or animals is also essential.  In order for the Biosafety Officers and the Institutional Biosafety Committee to do their analysis, researchers must provide complete and comprehensive information.  It is therefore essential when completing applications, such as a Biological Use Authorization (BUA), for descriptions of the work and materials to be written so that a layperson can understand.  This will be described in more detail in chapter 3.

A comprehensive description of the Risk Assessment process from the BMBL may be found here:

The tools used during risk assessment include identifying an agent’s Risk Group, and determining the appropriate Biosafety Level (BSL) required for adequate containment.  The characteristics of Risk Groups and BSLs are described in the tables at the end of the chapter.  Note that Risk Groups are only based upon the potential for an agent causing disease in healthy adults, not children or those who may be at increased risk due to immunocompromised conditions.  Also note that the Biosafety Level often corresponds to the Risk Group, but not always.  There are many cases where an agent poses little or no risk to a person but could do serious harm to agriculture or the environment if released.  The Biosafety Level will be higher than the risk group would indicate.  The BSL may also be increased for working with large quantities of culture (greater than 10 liters) or if laboratory manipulations dictate higher containment conditions (i.e. generating aerosols).

It is important to understand that the Risk Group for an agent is assigned by entities external to UCSF, such as the National Institutes of Health (NIH) or the World Health Organization (WHO).  It is the practice of the UCSF IBC to use the most conservative reasonable RG assignment for an agent in their risk assessment.  However, it is entirely the UCSF IBC’s responsibility to assign the appropriate BSL for the work being done.

Biosafety Information by Biosafety Level:


Risk Groups Summary

Biosafety Level Summary

Based upon the CDC/NIH Document “Biosafety in Microbiological and Biomedical Laboratories” (“BMBL”), 5th edition, December 2009.

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Chapter 2

Biological Safety Program Administration

The essential objectives set forth in the Biological Safety (Biosafety) Manual and associated biosafety-related trainings are:

  • To protect University of California, San Francisco (UCSF) patients, students, and employees against unnecessary and potentially harmful exposures to biological materials.
  • To protect the human and animal populations outside of our facilities from the release of any potentially hazardous agent whether wild-type or especially if genetically modified.
  • To ensure compliance with international, national, state, and local regulations that impact biological research, thereby protecting both the researcher and the institution from harm.

For these rules and procedures to be effective each involved person or administrative office must have their roles and responsibilities clearly defined.


The Chancellor is ultimately responsible for assuring that comprehensive campus-wide programs are in place for the safe handling of all hazardous materials at UCSF. The Institutional Biological Safety Committee (IBC) and the Office of Environment Health and Safety (EH&S) have been charged with the planning and implementation of the campus Biological Safety Program whose purpose is to ensure the health and safety of all personnel working with biohazardous or infectious agents, toxins, and materials and agents containing recombinant DNA or other genetic alterations.


Federal law requires the establishment of an Institutional Biosafety Committee (IBC) at institutions where recombinant biological materials are used in research. At UCSF, the IBC is appointed by the Vice Chancellor for Research and consists of a Chair, Vice Chair, and members selected to represent the UCSF faculty, staff, and public interests, and to provide expertise in a wide variety of biological disciplines. At least two community members with no UCSF affiliation (other than membership on the IBC) are required, and are responsible for representing the surrounding community’s interests regarding health and environmental protection. Ex Officio members include the Director of EH&S, the Biosafety Officer (BSO), the Director of the Animal Care Facility, and the Public Health Officer, or their designated representative. The IBC membership represents collective expertise and research experience in recombinant DNA, infectious agents, biological toxins, and animal research which are applied to the evaluation of appropriate safety measures needed for experiments that may pose potential risks to health or the environment.

The IBC is also specifically authorized by the Chancellor to limit or suspend any research that is not in compliance with UCSF biosafety policies and procedures. The IBC advises and works with EH&S in administering the various aspects of the campus Biosafety Program.

The IBC is responsible for 1) ensuring that research conducted at UCSF is in compliance with the NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules (“Guidelines”); 2) drafting campus biosafety policies and procedures; and 3) reviewing individual research proposals for biosafety concerns. The IBC meets monthly to review proposals from faculty at all UCSF campuses and affiliated Institutes (Gladstone, Gallo, Howard Hughes Medical Institute, and others), and faculty members who work off-campus.  Veterans Administration-funded projects are specifically excluded from the IBC's charge. The IBC does not oversee biosafety policies for the hospitals and clinics, but does provide consultation when requested.  Biosafety policies for hospitals and clinics are the responsibility of the respective Hospital Epidemiology and Infection Control Committees.

Principal Investigators (PIs) who wish to perform research using biological materials must submit a Biological Use Authorization (BUA) application to the IBC for approval prior to beginning work.  The Committee generally reviews applications that involve work at Biosafety Level 2 or 3 and the BSO and Assistant Biosafety Officers (collectively “BSOs”) review Biosafety Level 1 research applications.  BSL 1 applications are usually considered exempt from committee review unless a BSO has specific concerns that warrant full Committee involvement, or if the work involves certain types of recombinant genetic work. IBC review includes an independent assessment of the containment levels required by the NIH Guidelines for the proposed research, an assessment of the laboratory facilities, procedures and practices, and a review of the training and expertise of personnel.

While the IBC cannot alter the Risk Group of an organism, it is within the IBC’s authority to raise or lower containment for the work involving the organism based upon a full risk assessment of the work being done.  Recommendations for the biosafety level (BSL) of laboratory operation are often modified according to the number of infectious particles encountered in the project and the usual route of infection.



The Office of Environment Health and Safety (EH&S) administers the Biological Safety Program as well as other campus safety programs such as radiation and chemical safety. As designated by the Director of EH&S, the Biological Safety Officer is primarily responsible for implementing and overseeing the campus Biological Safety Program.

             1. BIOSAFETY OFFICER (BSO)

UCSF has one Biosafety Officer (BSO) and one or more Assistant Biosafety Officers (ABSOs).  The BSO has overall responsibility for the operation of the UCSF Biosafety Program, and provides supervision to the ABSOs. In general the BSOs’ duties include, but are not necessarily limited to, providing technical advice to the IBC and researchers on laboratory containment and safety procedures, conducting pre-reviews of authorization applications and interacting with Principal Investigators to ensure that the applications are complete and understandable, overseeing or conducting periodic inspections to ensure that laboratory standards are rigorously maintained, and developing emergency plans for handling spills and personnel contamination. The BSO regularly reports on the status of the Biological Safety Program to the IBC, particularly if any significant problems or violations of the NIH Guidelines or any research-related accidents or illnesses have occurred.  The BSO is also responsible for overseeing all phases of operations for all BSL3 laboratories, and is the Responsible Official for Select Agents. The ABSOs review and approve Biosafety Level 1 applications and work closely with the Environment, Health and Safety Specialists on all aspects of the Biological Safety Program.  One ABSO provides specialized safety consultations to the vivarium staff.

            2. EH&S SPECIALISTS

Environment, Health and Safety Specialists (EH&S Specialists) are the primary contact persons regarding all EH&S activities for their assigned departments. The EH&S Specialist is responsible for conducting laboratory inspections, reviewing proper operation of safety equipment such as biosafety cabinets and autoclaves, and ensuring that laboratory personnel are current on required trainings. EH&S Specialists also help researchers complete their Biological Use Authorization (BUA) application and maintain an accurate and up-to-date Biological Safety Logbook.


The Public Health Officer (PHO) is an employee of EH&S who interacts with the Occupational Health Program and works closely with researchers to ensure that medical surveillance, such as screening and vaccinations, are completed. The PHO also ensures biohazardous material exposure reports are managed and investigated, as necessary. The PHO works with the BSOs and IBC to investigate laboratory exposures and laboratory-acquired infections, advises the IBC regarding new developments in regulatory medical surveillance programs, and is an ex officio member of the IBC.



The Occupational Health Program (OHP) provides general occupational health services to all UCSF staff. The director of the OHP serves as an ex officio member of the IBC and provides recommendations for appropriate medical surveillance and preventive programs for personnel using biohazardous materials.


Each Department Chair is responsible for providing adequate support to researchers in their unit or department to ensure that appropriate facilities are available to contain and control biological hazards, as well as to enable PIs to comply with applicable regulations and campus policies. Chairs are also responsible for assuring that the PI and all personnel listed on a Biological Use Authorization (BUA) application have both technical ability and safety training that is commensurate with the proposed project, and that the project’s design and monitoring methods meet UCSF safety standards. Department Chairs, or their designated safety representatives, are responsible for correcting work errors and conditions that may result in personal injury, exposure to, or release of biohazardous agents or materials.


The Principal Investigator (PI) is directly and primarily responsible for the safe operation of their laboratory, and for compliance by all their laboratory personnel with all UCSF biosafety policies and procedures. The PI’s knowledge and judgment are critical in assessing risks and appropriately applying campus biosafety guidelines.         

  • they will not initiate research using infectious agents, human blood or tissues, toxins, or recombinant DNA (rDNA) unless all the applicable requirements outlined in this manual are met.
  • they will consult Chapter 1’s tables and the appropriate references (web links) to determine the appropriate Risk Group classification of the microorganisms to be used, and that they will use the prescribed microbiological practices and laboratory techniques required by the Biosafety Level assigned to their work by the IBC.
  • they will report immediately to the BSO all violations of the policies and procedures and all significant research-related accidents (spills, needle-sticks, exposures, injuries, etc.) which result in overt or potential exposure to infectious materials, or their release into the environment, whether contained within the laboratory or not.
  • they are prepared to implement methods for dealing with accidental spills and personnel contamination.
  • appropriate permits required by the United States Department of Agriculture (USDA), the Centers for Disease Control (CDC), Food and Drug Administration (FDA), and any state or local permits for work with certain animal and plant pathogens are obtained prior to beginning work.
  • they will follow all appropriate importation, exportation and interstate shipping requirements for certain biological materials. See Chapter 19.
  • receive appropriate IBC or BSO approval for all research projects.
  • determine, in consultation with the BSO (415-514-2824) and Public Health Officer (415-514-3531), the usefulness of serological screening, the requirements of medical surveillance, and the availability of vaccination for Risk Group 2 and 3 agents.  They shall inform the laboratory staff of the reasons and provisions for any precautionary medical practices advised or requested, such as vaccination or antibody titers. Where appropriate, the hepatitis B vaccination series must be offered free of charge to the employee. The PI is responsible for ensuring that records of HBV immunizations and/or declination statements for his or her staff are sent to the Occupational Health Program for filing.  The PI must not keep these documents themselves.
  • communicate in writing to the IBC any protocol changes that modify the research procedures or alter the list of biohazards, upon which approval was originally based. Other modifications, such as changes in personnel or laboratory sites, should be submitted online via the Research Information Online (RIO) system.
  • assure that personnel working with infectious agents or biohazardous materials are appropriately trained so that they are aware of the hazards,  and are proficient in the practices and techniques required for the safe handling of such materials. Instruction in proper laboratory procedures, bloodborne pathogens, Herpes B and Q-fever training is available through EH&S. For more information, contact the department’s EH&S Specialist.


  • appropriately supervise the performance of their staff to ensure that the required safety practices and techniques are employed.
  • investigate and report in writing to the IBC via the BSO any significant biosafety problems pertaining to the pursuit of the research goals, specifically, new information which was not available at the time of the application. The PI is responsible for correcting any conditions that might expose their personnel or release biohazardous materials into the environment.
  • implement the procedures prescribed for dealing with laboratory accidents.
  • assure that the biological characteristics of the microorganisms used in experiments haven’t undergone adverse change.  Periodic assessment should include the purity and phenotype of the strain. Special restrictive characteristics such as attenuation or replication deficiency require regular surveillance.  Strain verification should be performed periodically on all replication-defective microorganisms.


Safety in activities involving biohazardous agents ultimately depends on the individual conducting these activities. Motivation and good judgment are essential in the protection of health and the environment. The NIH Guidelines are intended to help the institution, the IBC, EH&S, and the PI determine the safeguards that should be implemented. These guidelines will never be complete or final in that all conceivable experiments involving rDNA and other biohazardous agents cannot be foreseen. Therefore, it is the responsibility of each individual employee to adhere to the intent of the NIH Guidelines as well as to specific procedures.

Personnel who work with RG 1 agents must have standard training in microbiological practices to ensure proper handling of the agent. Those personnel working with RG 2 or 3 agents must also have specific training in handling pathogenic microorganisms, and those individuals working with Risk Group 3 agents must have specific training in handling potentially lethal agents. Annual Bloodborne Pathogen training is required for all UCSF employees with potential occupational exposure to HIV/HBV/bloodborne pathogens and Q-fever training is required for personnel working with sheep, goats or their tissue. Herpes B virus training is required for those working with Old World Primates, their tissues or body fluids.

Immunocompromised persons should contact the Occupational Health Program, whose practitioners can provide medical advice regarding possible work restrictions. This includes individuals under systemic corticosteroid therapy, chemotherapy for malignancies, radiation therapy, and those who have certain diseases (e.g., lymphomas, leukemia, AIDS) which induce severe impairment of immune competence.

Researchers who are pregnant, or anticipate becoming pregnant are encouraged to contact the Occupational Health program.  Amended work practices can be identified by OHP practitioners who can then guide the researcher and the PI towards establishing safe working conditions.  Certain microbes such as Listeria monocytogenes, Toxoplasma gondii, LCMV, Rubella virus, cytomegalovirus, and vesicular stomatitis virus pose a specific hazard to pregnant women, who should carefully evaluate the risk of working with or near these agents.  The Public Health Officer and OHP should also evaluate special hazards and exceptions (e.g., individuals vaccinated against rubella virus) so that appropriate guidance can be given to the individual and the PI.

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Chapter 3

Who Needs a Biological Use Authorization Approval?

University of California, San Francisco (UCSF) Principal Investigators (PIs) planning to carry out research which may involve biological hazards should submit a Biological Use Authorization (BUA) application form to the Institutional Biosafety Committee (IBC) for review and approval.

The BUA application is available electronically at Research Information Online ( Researchers using any of the following should complete and submit a BUA application form for review and approval (Orientation and Reference Guide for Online BUA Application in RIO):

  • Recombinant DNA materials or technology
  • Human source material (including established or primary cell lines, blood, body fluids, organs, and tissues)
  • Infectious agents (including Risk Group 1 agents that are infectious to vertebrates other than humans).
  • Toxins of biological origin
  • Transgenic plants or animals in which the genome will be altered by stable introduction of recombinant DNA into the germ-line (e.g. making founder lines and breeding existing lines to create new genetic lines, but NOT including purchasing or maintaining already established lines)
  • Human gene transfer
  • Sheep or primates or their source material
  • Wild caught animals
  • Animals or their source material requiring permits to use or bring in to the State of California

If you are uncertain whether your research falls into any of the above categories, contact the Biosafety Officer (BSO) at 415-514-2824.

The IBC has delegated authority to the Biosafety Officer (BSO) to approve the following types of research without Committee review:

  • Bloodborne pathogen only applications (e.g., human blood, body fluids, or cell lines, fixed human tissue).  Work with human or some primate blood or tissues known to harbor pathogens may require full IBC approval.
  • Infectious agent work limited entirely to RG1 agents
  • rDNA work where hosts and vectors are restricted to RG1, or human cell lines are used as hosts, unless oncogenes or other toxic genes are inserted
  • Toxin usage where the LD50 value of the toxin >25 ug/kg (including non-hazardous subunits)
  • Modifications to BUAs that are either administrative (adding rooms or staff), or involve adding any materials listed above, even if the overall BUA is designated for Committee review

If you are working with potentially infectious agents, recombinant materials, or toxins and human subjects or experimental animals, IBC review is necessary in addition to review by the Committee on Human Research (CHR) and/or the Institutional Animal Care and Use Committee (IACUC), respectively.

Note: The IACUC and the CHR do not consider biosafety issues during their respective reviews.

PIs whose research comes under the governance of any of the following campus rules or governmental regulations are required to complete a BUA, and where applicable, maintain a medical surveillance program for laboratory employees:

  • NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules
  • Cal-OSHA Bloodborne Pathogens Standard
  • Cal-OSHA Aerosol Transmissible Diseases Standard
  • Cal-OSHA Special Orders for Q-Fever
  • Medical Waste Management Act (generation of medical [red bag] or sharps waste)
  • International, Federal, and State Transport, Import, or Export Regulations

For additional information, call the Technical Committees Coordinator at 415-476-2198 or contact your Environment, Health and Safety Specialist (EH&S Specialist). For more detailed information about the BUA review process, see Chapter 4.

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Chapter 4

The Biological Use Authorization (BUA) Process

New BUA applications and renewals are done online in RIO (  If you are new to UCSF, request a new RIO Account by completing the online form at the above link. Instructions for completing the online BUA are detailed in the Orientation and Reference Guide for Online BUA Application in RIO.


PI status is required to obtain a BUA.  Request PI status for RIO by contacting the BSO at 415-514-2824 or via email at  You will be notified when you have PI status in RIO.  To start a new BUA Application, log into RIO using the same username and password you use for MyAccess and click on “Portfolio List.” Populate your portfolio with locations, personnel, and equipment. To create your BUA application, scroll up to the Authorizations and Protocols section of your portfolio. Start a BUA application using the “Create New Application(s)” link. Click the box for “Biological Use Authorization (BUA) Application”. Press the “Create Application(s)” button.


BUAs must be renewed every three years, with the exception of BUAs covering work conducted at Biosafety Level 3, which are renewed annually. Renewal reminder notices are sent approximately 90 days prior to the expiration date of each application.  If the PI does not respond within the prescribed period, the IBC will be notified and the BUA terminated.  To renew your BUA, log into RIO using the same username and password as MyAccess and click on “Portfolio List” on the RIO Home PageFind your portfolio and follow the “Click Here” link under Details to open the portfolio.  Read the instructions and then scroll down to see the authorizations, personnel, locations and equipment that are listed in your portfolio.  Check the contents of each list and update as needed.  Scroll up to the Authorizations and Protocols section of your portfolio and read the instructions.  Press “Click Here” to open the BUA you want to renew.  Click the “Create Renewal or Modification” button and select the “Renewal” option.

The renewal application will have the same BUXXXXX number, but with an -02, -03, etc. extender, depending on how many times the BUA has been renewed.  “Demographic” information on your BUA application is on the Main page, i.e., type / sub-type, PI name, BUA title, PI department (or location), assigned EH&S Specialist, approval date (blank until approved), expiration date (of currently approved BUA), approval status (of BUA renewal application).


It is important that the IBC and EH&S maintain accurate records of all ongoing experiments utilizing biological materials.  Therefore, PIs should submit a modification request for changes in personnel, research locations, biomaterials and/or experimental procedures which may impact the biosafety requirements. This modification must include a narrative describing proposed changes when adding biomaterials or procedures.

To submit a modification, open up the BUA you wish to modify and press the “Create Renewal or Modification” button.  Select the “Modification” option.


If a PI terminate a BUA, EH&S must be notified in writing via a Principal Investigator BUA Termination Form. This notification will ensure that the inspection, training and surveillance programs instituted for the BUA are appropriately included, that all research materials are accounted for, and that items which are no longer to be used are appropriately decontaminated and/or disposed. EH&S provides assistance in the disposal or transfer of any biological materials which are no longer needed and all biohazard warning signs will be removed from the facility.


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Chapter 5

Instructions for Human Gene Transfer Research Submission to IBC at UCSF

Human gene transfer is the process of transferring genetic material (DNA or RNA) into a person. At present, human gene transfer is experimental and is being studied to determine whether or not it can treat certain health problems by compensating for defective genes, producing a potentially therapeutic substance, or triggering the immune system to fight disease.

Human gene transfer research falls under the federal NIH Guidelines for Research Involving Recombinant or Synthetic Nucleic Acid Molecules (NIH Guildelines). The NIHGuidelines for Research Involving Recombinant or Synthetic Nucleic Acid Moleculesspecify practices for constructing and handling rDNA molecules, organisms and viruses containing rDNA molecules. For experiments involving human gene transfer, no research participant shall be enrolled until the Recombinant DNA Advisory Committee (RAC) review process has been completed and approvals obtained from the Institutional Biosafety Committee (IBC) (from the clinical trial site), the Institutional Review Board approval (IRB), and any additional applicable regulatory authorization(s).


Please note that although the information below is extensive, PIs should not consider it to be a complete list of all requirements; please refer to the NIH Guidelines for additional information. It is the PI’s responsibility to ensure that ALL regulations and requirements are met.

Below are UCSF’s procedures for assisting Principal Investigators (PIs) in complying with the NIH Guidelines.


Submit a BUA application for IBC review and approval via the online system Research Information Online (RIO).

Provide the following documents by uploading electronic copies to the BUA document library ('Documents' link in the left menu).




Completed Appendix M submitted to the NIH RAC

Explain if not applicable


Copy of RAC Review and Relevant Correspondence with RAC

If pending, provide date when submitted for RAC review.


Clinical Protocol

Explain if not applicable


Investigator’s Brochure

Explain if not applicable


FDA IND Correspondence

Explain if not applicable


Informed Consent Forms

Must be site-specific



Biosafety Officer must conduct a site inspection


BUA modification is required for:

  • Serious Adverse Event (SAE) submission
  • Changes in location
  • Title change (in some instances)
  • Changes to the investigational drug (at a minimum requires an amendment but may require a new BUA)


A. If clinical trial is initiated at UCSF, the Principal Investigator(s) shall submit the following documentation to the IBC and NIH/OBA within 20-working days after enrollment of first trial participant:
  1. copy of the informed consent document approved by the IRB;
  2. copy of the protocol approved by the IBC and IRB;
  3. copy of the final IBC approval from the clinical trial site;
  4. copy of the final IRB approval;
  5. applicable NIH grant number(s);
  6. the FDA IND number; and
  7. the date of the initiation of the trial.
  8. brief written report that includes the following information:
  • how the investigator(s) responded to each of the RAC’s recommendations on the protocol (if applicable); and
  • any modifications to the protocol as required by FDA
B. Annual Reports:  Although the BUA does not expire annually, the annual report is subject to verification requirements:

1) Within 60 days after the one year anniversary of the date on which the IND application went into effect, and after each subsequent anniversary until the trial is completed, the PI (or delegate) shall submit to the NIH/OBA and IBC the information set forth in the NIH recombinant DNA guidelines (see below)

2) To submit the report to the IBC, log on to RIO to access the BUA application. Upload the “Annual Report” to the BUA document library and provide a brief, non-technical summary of the study.

3) The following items must be included in each annual report:

(a) Clinical Trial Information:  A brief summary of the status of each trial in progress and each trial completed during the previous year.  The summary must include the following information for each trial:

  1. the title and purpose of the trial;
  2. clinical site;
  3. the Principal Investigator;
  4. clinical protocol identifiers, including the NIH OBA protocol number, NIH grant number(s) (if applicable), and the FDA IND application number;
  5. participant population;
  6. the total number of participants planned for inclusion in the trial; the number entered into the trial to date; the number whose participation in the trial was completed; and the number who dropped out of the trial with a brief description of the reasons;
  7. the status of the trial, i.e. open to accrual of subjects, closed but data collection ongoing, or fully completed, and
  8. if the trial has been completed, a brief description of any study results.

(b) Progress Report and Data Analysis.  Information obtained during the previous year's clinical and non-clinical investigations, including: 

  1. a narrative or tabular summary showing the most frequent and most serious adverse experiences by body system;
  2. a summary of all serious adverse events submitted during the past year;
  3. a summary of serious adverse events that were expected or considered to have causes not associated with the use of the gene transfer product such as disease progression or concurrent medications;
  4. if any deaths have occurred, the number of participants who died during participation in the investigation and causes of death; and
  5. a brief description of any information obtained that is pertinent to an understanding of the gene transfer product’s actions, including, for example, information about dose-response, information from controlled trials, and information about bioavailability.

(c) A copy of the updated clinical protocol including a technical and non-technical abstract.

C. Safety Reporting:

1) Principal Investigators must submit a written report clearly labeled as a “Safety Report” to the NIH/OBA and the IBC (via BUA amendment) in the following instances:

a) Any SAE that is both unexpected and associated with the use of the gene transfer product (i.e., there is reasonable possibility that the event may have been caused by the use of the product; investigators should not await definitive proof of association before reporting such events); and

  • Any SAE that is fatal or life-threatening, that is unexpected, and associated with the use of the gene transfer product must be reported to the NIH OBA as soon as possible, but not later than 7 calendar days after the sponsor’s initial receipt of the information (i.e., at the same time the event must be reported to the FDA).
  • Any SAE that is unexpected and associated with the use of the gene transfer product, but are not fatal or life-threatening, must be reported to the NIH OBA as soon as possible, but not later than 15 calendar days after the sponsor’s initial receipt of the information (i.e., at the same time the event must be reported to the FDA).

2) Safety Reporting: Content and Format

a) The SAE report must include, but need not be limited to:

  1. the date of the event;
  2. designation of the report as an initial report or a follow-up report, identification of all safety reports previously filed for the clinical protocol concerning a similar adverse event, and an analysis of the significance of the adverse event in light of previous similar reports;
  3. clinical site;
  4. the Principal Investigator;
  5. NIH Protocol number;
  6. FDA’s IND Application number;
  7. vector type and subtype;
  8. gene delivery method;
  9. route of administration;
  10. dosing schedule;
  11. a complete description of the event;
  12. relevant clinical observations;
  13. relevant clinical history;
  14. relevant tests that were or are planned to be conducted;
  15. date of any treatment of the event; and
  16. the suspected cause of the event.

3) The items above may be reported by using the NIH OBA’s Adverse Event Reporting Template or other means provided that all of the above elements are specifically included.


EH&S Biosafety Staff      

Peili Zhu

Biosafety Officer

(415) 514-2824

Jonathan Koolpe

Assist. Biosafety Officer

(415) 502-1799

Mei-Chuan Huang

Assist. Biosafety Officer

(415) 476-2097

Sean Umamoto Assist Biosafety Officer (415) 514-2665



Office of Biotechnology Activities

National Institutes of Health, MSC 7985

6705 Rockledge Drive, Suite 750

Bethesda, Maryland  20892-7985


Fax:  301-496-9839

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Chapter 6

Laboratory Design and Biosafety Cabinets

Laboratory Design must follow:

BSO must attend Plans Review meetings for all new and/or renovation projects.

Biosafety Cabinet Characteristics Comparison

Biological Safety Cabinets (BSCs) are designed to provide personnel, environmental and product protection when appropriate practices and procedures are followed. Three kinds of BSCs, designated as Class I, II and III, have been developed to meet varying research and clinical needs.


From “Primary Containment for Biohazards, Selection, Installation and Use of Biological Safety Cabinets, 5th edition, September 2009 

Installation may require a special duct to the outside; an in-line charcoal filter; and a spark-proof, explosion-proof motor and other electrical components in the cabinet.  Discharge of a Class I or Class II, A2 cabinet into a room should not occur if volatile chemicals are used.

  •  The chemical concentration in the cabinet should never approach the lower explosive limit (LEL) of any compound.


Click to enlarge

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Chapter 7

Medical (Biohazardous) Waste Management


Research with biological and in particular with biohazardous materials generate waste that cannot be discarded in the regular trash. At UCSF, the large majority of this waste is accumulated in red “Medical Waste” bags, which are picked up by EH&S to be transferred to waste disposal vendor, and depending on the nature of the contents, are either autoclaved  or incinerated. The storage and disposal procedures are described below. For A/BSL3 laboratories only, wastes are autoclaved out of the laboratories. The autoclaved waste is then picked up and transferred to the vendor for incineration.


Medical (Red Bag) Waste Accumulation Policy & Procedure
  • Only red bags are legal in California, ALL other colorsare prohibited.
  • Anything contained in red bag labeled “Biohazardous” MUST be managed as medical waste. 
  • Do NOT use red bags for storing non-waste or as an equipment cover. These may be picked up.
  • All solid medical waste must be picked up by EH&S..
  • For pick up at Parnassus, Mt. Zion, Mission Bay, Laurel Hts. call 476-0546 SFGH Call 206-8076.
If you work in a Biosafety Level 1 (BSL1) laboratory
  • Microbiological solid waste such as petri dishes can be discarded in regular trash, in closed clear or white bags to contain odors prior to pickup by janitorial staff.
  • Drain dispose liquid waste if not mixed with chemicals or radioisotopes.
  • Discard sharps in sharps containers. 

NOTE:  Waste generated from Recombinant DNA procedures involving RG1 materials are disposed of as biohazardous waste.  See detailed information here.


If you work in a BSL2 or BSL3 laboratory

Discarding Liquid Biohazardous Waste
  • Decontaminate liquid biohazardous waste by mixing one volume of undiluted bleach with nine volumes of liquid biohazardous waste (final dilution of 1:10), and mix thoroughly but carefully to avoid any spill or aerosol.  Allow to stand for 30 minutes (prion waste has other requirements; contact a BSO for more information.) This can be drain-disposed if not mixed with chemical or radioactive material.  Liquid biohazardous waste must be decontaminated.

The following types of BSL1 rDNA waste are EXEMPT from the NIH Guidelines and can be disposed of as non-biohazardous waste (in regular trash), in closed clear or white bags to contain odors prior to pickup by janitorial staff. **

  1. BSL1 rDNA waste which is not in organisms or viruses (e.g., DNA, RNA, oligos waste, PCR waste, Microarrays, etc.).
  2. BSL1 rDNA waste from experiments which use Escherichia coli K-12 host-vector systems. The system uses only non-conjugative plasmids as vectors (e.g., pBR322, pBR313) and does not contain conjugation proficient plasmids or generalized transducing phages.
  3. BSL1 rDNA waste from experiments involving Saccharomyces cerevisiae and Saccharomyces uvarum host-vector systems.
  4. BSL1 rDNA waste that contains less than one-half of any eukaryotic viral genome that is propagated and maintained in cells in tissue culture.
* Examples of liquid biohazardous waste include:
  • Risk Group 2 (RG2) or Risk Group 3 (RG3) vacuum trap contents, decanted tissue culture media, microbial cultures,
  • human or primate blood, serum, or other body fluids


Discarding Solid Medical Waste:


Pathological Waste is:

Biohazardous Waste is:


All solid waste from BSL3 labs after autoclaving, human surgery specimens, tissue, or human body waste > 1 cubic inch but not needing mortuary disposal, animal tissues > 1 cubic inch, animal carcasses


Solid waste from BSL2 laboratories known or thought to be contaminated with RG2 agents such as: diagnostic specimens, sharps, cultures from human or animal specimens, RG2 bacterial or viral culture or spore production,  live or attenuated vaccines used in research, fluid blood or blood products, or containers or equipment containing fluid, blood


Segregate pathological and biohazardous wastes into separate clearly labeled containers.


Medical Waste Container Labeling:
  • Both liquid and solid medical waste must be labeled with the biohazard symbol and "Biohazard" on all sides and lid.
  • Pathological waste containers must be labeled with “Pathology Waste” or “PATH” or “for incineration” on all sides and on the lid, in addition to the biohazard symbol.
  • Bags containing medical waste must be inside a medical waste container with a tight-fitting lid at all times. The lid must be in place when container is not in active use.  DO NOT store red bags containing waste on floors or carts.
  • DO NOT overfill bags.  Ensure that they are securely fastened for transport with no tearing or leaking. If needed, use double bags.
What must NOT go into a red bag?
  • Sharps such as needles, syringes, scalpels, razors or Pasteur pipettes (these must be placed in rigid sharps containers)
  • Chemical or radioactive waste, or mixed waste (bio+chem., bio+rad, chem+rad). Contact your EH&S Specialist before creating any mixed-waste to ensure proper disposal.
  • Uncontaminated waste, except in BSL3 laboratories.
What laboratory waste must not be autoclaved?
  • BSL1 & 2 labs should never autoclave sharps waste containers.

Never autoclave chemical or radioactive or mixed waste as these materials may become volatile in an autoclave. Autoclaved waste must not go into the trash except under special conditions.  Contact your EH&S Specialist to learn more.BSL3 and ABSL3 laboratories must autoclave out all wastes. Please see the description of steam autoclaving below and the Autoclave Quality Control Procedures at the end of this chapter.


Sterilization  and Disinfection


There is an essential difference between the terms disinfection and sterilization. As the word implies, sterilization is the complete rendering of all viable materials non-viable. Disinfection is less broad or thorough. It is the sufficient reduction in quantity of organisms present to render them harmless. 

At the minimum, all infectious or biological materials, and all contaminated equipment or apparatus should be disinfected before being washed, stored or discarded. There are a number of alternative methods available to achieve sterilization and disinfection. The specific method used will depend on a number of parameters such as the agents, area surfaces, sensitivity of equipment to chemicals or temperature and the facility design. These guidelines are not intended to be a comprehensive listing of all potential methods or chemicals used. Contact the BSO or your EH&S Specialist for specific recommendations.

Steam Autoclaving  The recommended method for sterilization of biohazardous material is steam autoclaving.  Since treatment conditions to achieve sterility will vary in relation to the volume of materials treated, its contamination level, the moisture content, and other factors care should be exercised in using this method of sterilization.  In general, it is recommended that the autoclave be operated at a temperature of 121 °C and run for a minimum of 30 minutes.

The use of steam autoclaves at UCSF for destroying waste is limited to work in BSL2* or BSL3 laboratories, or ABSL3 facilities. These autoclaves must meet stringent requirements for certification under the California Medical Waste Management Act for medical waste disposal. Even after autoclaving, waste from these autoclaves is disposed of as pathological waste, which is collected by EH&S and sent out for incineration. Biohazardous waste from BSL2 labs is also collected by EH&S for offsite autoclaving and disposal. See the Autoclave Quality Control Program at the end of this chapter for more information.

For non-waste autoclaving, the recommendations of the manufacturer of a particular autoclave should be followed in order to provide an adequate pressure/temperature/time cycle to ensure sterilization. It is also recommended that plastic autoclaving bags with a color indicator be used to give a visual indication that the material is indeed sterile. This is especially important when highly potent biological agents are involved.

The use of sterilization tape is required on all contaminated materials undergoing all types of sterilizations listed above. However, since these tapes are likely to be dislodged during the process, it is also required that red medical waste bags are also capable of having lettering that states “autoclaved” or similar, that changes color, or appears after sterilization cycle is complete. This confirms that the surface of the bag met sterilization criteria.

The following is a listing of adequate time and temperature for most common steam sterilizations using autoclaves.

  • Laundry 250 °F (121° C) for 30 minute with 15 minutes prevaccum of 27" Hg.
  • Waste  250° F (121°C) for 1 hour with 15 minute prevaccum of 27" Hg.
  • Glassware 250°F (121°C) for 1 hour with 15 minute of pre-vacuum of 27" Hg for a full rack of glassware. Ensure that glassware is in a secondary container of metal or heat-resistant plastic, so that any broken glass is kept from the chamber bottom. Do not place glassware directly on an autoclave rack.
  • Liquids Liquid biological waste can usually be diluted with sufficient bleach (final dilution of 1:10) and allowed to stand for 30 minutes before being disposed down the drain. In instances where media or other non-waste liquids are sterilized, use 250° F (121 °C) for 1 hour for gallon quantities of liquid.  Liquids should not be treated using pre-vacuum, as this can cause the liquid to boil over.

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Vivarium Autoclaving

  • Carcasses Animal carcasses are almost never autoclaved, they are disposed of as pathological waste for incineration. In rare cases where they are autoclaved, use 250° F (121°C), 30 minute minimum, no prevacuum. Time depends on volume, moisture and density, and is determined by trial.
  • Bedding 250° F (121°C) for 30 minutes or more, with a prevacuum of 27” Hg., Time depends on volume, moisture and density and determined by trial


Gas Sterilization

Gas sterilization is reserved for entire laboratory sterilization after a major contaminating spill, or for large pieces of equipment that cannot be rendered safe by other means. All laboratory gas sterilization is conducted by outside vendors with specialized equipment and training in order to meet strict safety and environmental requirements. LARC staff is specially trained to sterilize animal housing rooms, and these operations are done with oversight and monitoring by EH&S.


 Liquid Disinfection

An alternative method to dry heat sterilization of re-usable (not waste) sharps, glass, etc. is the disinfection of the material using a chemical agent. The recommended method is to soak the sharps, glass, and other materials for a period of time in the liquid disinfectant. The period of time “contact time” is dependent upon the nature of the chemical, the amount of contamination, the type of base material (metal, plastic, glass), and the resistance of the organism(s) to disinfection by the chemical being used.


The most common liquids fall under one of the following categories:


Quaternary Ammonium Compounds

These can be acceptable as general use disinfectants to control vegetative bacterial and non-lipid-containing viruses. However, they are not active against bacterial spores or many viruses at the compounds’ usual use concentration (1:750). The Institutional Biosafety Committee (IBC) must approve use of quaternary ammonium compounds.


Phenolic Compounds

These are recommended for killing of vegetative bacteria, including Mycobacterium tuberculosis, fungi and lipid-containing viruses, spores and non-lipid-containing viruses. However, they are toxic, and their use must be approved by the IBC.


Chlorine Compounds

These are recommended for virtually all disinfecting procedures provided the available chlorine needed is used. Low concentrations of available chlorine (about 500 ppm) can be used for cleaning environmental surfaces if no known contamination by infectious agents is present. Household bleach is the most common type used. A 1:10 dilution of household bleach will provide sufficient strength. Bleach is corrosive, and this must be considered when disinfecting certain materials. It may be necessary to follow a wipe down with bleach with another with clear water to prevent corrosion. Also, as a corrosive, bleach must be stored as a hazardous material.



Although these show poor activity against bacterial spores they can be used for general disinfection (75-150 ppm). They are effective against many vegetative bacteria and viruses. Because of the limited range of effectiveness, their use must be approved by the IBC.

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In concentrations of 60% to 70% ethanol in water, ethanol solutions are very good general use disinfectants, however they exhibit no activity against bacterial spores.  Ethanol disinfection has two significant concerns. Because these solutions evaporate rapidly, sufficient liquid must be used to ensure adequate contact time. This is at least 30 seconds for environmental surfaces, and could be more depending on the nature of the contamination. Also, these solutions are highly flammable. Their use in the presence of or proximity to heat sources is potentially very dangerous. Isopropyl alcohol is slightly less effective than ethanol. If used, the optimal concentration is 60% isopropyl alcohol in water.


Formaldehyde Solutions

At a concentration of 8%, formalin exhibits good activity against vegetative bacteria, spores, and viruses. However, this is toxic, and its use must be approved by the IBC.



Solutions of 8% formalin in 70% alcohol are considered very good for disinfection purposes because of their effectiveness against vegetative bacteria, spores and viruses. However, they are toxic, and their use must be approved by the IBC.

Due to the carcinogenic nature of formaldehyde the facility must have a specially designed ventilation system and is subject to air monitoring requirements. Contact EH&S if you intend to use this method.


Activated Glutaraldehyde

2% solutions exhibit good activity against vegetative bacteria, spores and viruses. Their use, however, must be limited and controlled because of their toxic properties and hazards of damage to the eye. This material’s use must be approved by the IBC.


Ultraviolet Light

Under very limited conditions of UV radiation intensity and exposure time, certain ultraviolet radiation will kill many kind of microorganisms; its greatest effectiveness is against vegetative forms. Room-wide use of UV has been shown to be ineffective in reducing or eliminating airborne contamination. Use in biosafety cabinets is also discouraged because it is an inadequate substitute for surface disinfection. After surface disinfection that is done properly, additional methods such as UV are not necessary, and can lead to accidental injury if someone uses the cabinet without turning off the UV lights.

The eyes and skin should not be exposed to direct or strongly reflecting UV radiation. Adequate eye and skin protection must be worn when working in an UV irradiated area. Ensure that specialty goggles or safety glasses with side shields that provide protection in the far ultraviolet light range are worn when working in a UV irradiated area. Face shields, caps, gloves, gowns, etc. will protect skin.

Overexposure of eyes will result in a painful inflammation of the conjunctiva, cornea and iris. Symptoms will develop 3 to 12 hours following exposure and will disappear in a day or two. Long period of exposure to high intensity UV radiation may damage the eyes permanently.

Exposure to the skin will produce erythema in 1 to 8 hours following exposure.

UCSF Autoclave Quality Control Program

Medical (Red Bag) Waste Policy & Procedures

Contact your EH&S Specialist to learn more.

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Chapter 8

Responding to Emergencies Involving Biohazardous Materials


Biological Emergencies




In any spill scenario, the priority of actions is determined by the "PEP" rule - People, Environment, and Property. The highest priority is to provide aid to injured personnel and prevent spill area access to others.  Next, action should be taken to prevent environmental damage if it can be done without endangering personnel.  An example would be to prevent a radioactive biomaterial or a potent toxin from entering a sanitary drain by placing an absorbent in the flow path. Finally, action to prevent property damage should be taken if it can be done safely


Small spills involving most biological materials used at UCSF may be handled by laboratory personnel.  If a spill is large or if laboratory personnel are uncomfortable handling the spill on their own, call the UCSF emergency number to obtain help from EH&S:

  • From Parnassus, Mt. Zion, Laurel Hts., Mission Bay: Call 9-911
  • From SFGH: Call 415-206-8522

Laboratory personnel must be prepared to clean up small spills of biological or biohazardous material. Keep basic clean up equipment on hand and ensure that all laboratory staff are trained to clean up spills.  Researchers working with Risk Group 2 or 3 (RG2, RG3) materials should prepare fresh 1:10 bleach solutions weekly for routine decontamination.  Clean up spills of non-biohazardous biological materials using steps 3-9 below


Clean up Procedures:

  • If someone is injured and contaminated, provide first aid assistance if possible and ask an uncontaminated co-worker to call 9-911 for medical assistance.  Do not take a contaminated person to the emergency room unless told by emergency room staff to do so.  If a person is contaminated but not injured, remove contaminated clothing and help the person use an emergency shower or eyewash as needed.  Call 9-911 for medical guidance.
  • If a biohazardous spill is in the open laboratory, alert people in the vicinity and evacuate the laboratory immediately. The last person out closes the doors. Do not re-enter for at least 30 minutes so aerosols can be cleared to minimize the risk of inhalation exposure.  Do not spread contamination beyond the laboratory by staying as close to the laboratory as possible, and disinfecting shoes.  Proceed as follows:



1. Post signs, and keep personnel not involved in cleaning up the spill away from the area.

2. For RG2 agents: Wear disposable gloves, eye protection, and a lab coat.  For RG3 agents: Wear a disposable gown, gloves, eye protection, shoe covers, and a respirator. Also contact Biosafety Officer at 415-514-2824 for spills of RG3 agents.

3. Remove contaminated sharps from the spill using forceps or tongs, NOT your hands!

4.Cover the spill with paper towels or other absorbent material.  Avoid making the spilled material splash or spray.

5. Pour a freshly prepared 1:10 dilution of household bleach around the edges of the spill and work inward to the center. Allow 20 minutes for the bleach to kill the organisms.

6. Use additional paper towels to wipe up the spill, working from the edges into the center.

7. After initial cleanup, flood the spill area with bleach and let stand for at least 20 minutes.

8. Use paper towels to absorb spill, then wipe-down with clean paper towels soaked with bleach.

9. Disinfect any equipment, walls, or other areas likely to have been splashed by the spill.

10. Discard paper towels into a red biohazard bag if used to clean up RG2 or RG3 materials.

11. Thoroughly wash your hands and any contaminated skin with soap and water.

12. Notify a Biosafety Officer at 415-514-2824 if the spill is large, involves RG3 materials, recombinant DNA materials, a toxin, or if an injury or inhalation exposure may have occurred.

  • If a spill is found when opening a centrifuge, close the centrifuge as soon as possible, evacuate the laboratory immediately and do not re-enter for 30 minutes, then disinfect using steps 3-9 above.
  • If the spill is found when opening a rotor or bucket, close the rotor and move it and its contents to a biosafety cabinet (BSC) before opening to disinfect using steps 3-9.  Disinfect the centrifuge interior.
  • If the spill is inside a BSC, evacuation is not necessary.  Follow steps 3-9 and keep the BSC running for at least 15 minutes after the cleanup is done.  Clean the spill tray below the work area and the trough below the air intake grill while the BSC is running.


Exposure and Needlesticks

Exposures to any biological material (whether resulting in injury or not) and on-the-job needlesticks must be reported to the 24 hour UCSF Occupational Health Exposure Hotline.  In particular, it is very important that an individual who has been exposed to any substance potentially containing bloodborne pathogens call the Hotline immediately to receive advice on time-sensitive post-exposure prophylaxis.



AT SFGH: 415-353-7842

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Chapter 9

Biological Safety Training



EH&S conducts training classes for the Campus Community on a regular basis. The classes meet the regulatory requirements mandated by OSHA and the California Department of Health Services. These cover general health and safety issues, and do not replace requirements for supervisors to train or make certain employees are trained in the specific hazards of their workplace.


What Safety Training is Needed?

Accessing the UC Learning Center safety trainings:




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Chapter 10

Animal Biosafety


Animal research is highly regulated, and UCSF is committed to full compliance with all regulatory agencies and oversight groups. Everyone involved in the use of animals in research at UCSF must receive the approval of the UCSF Institutional Animal Care and Use Committee (IACUC).

A Biological Use Authorization application (BUA) to work with animals involving the use of rDNA (including generation of, but not the purchase of transgenic animals) and/or infectious or transmissible agents must be submitted as an online BUA application to the IBC for review and approval, in addition to requiring approval from the IACUC. (Orientation and Reference Guide for Online BUA Application in RIO)

For online BUA applications, applicants must fill in the Animal Involvement section available from the link  Applicants must describe the work involving animals and any hazards that UCSF Laboratory Animal Resource Center (LARC) staff may be exposed to, and how applicants will ensure that LARC staff are protected.  Assistance may be available from LARC through the LARC Assistant Manager of Husbandry at 415-502-1242, or email before completing the form.

Animal biosafety levels are assigned by the IBC for each BUA involving animal use. Once approved, LARC must be contacted prior to initiation of the research to ensure that safe operating procedures will be established.  For Animal Biosafety Level Criteria (ABSL1-4), please see the CDC/NIH document Biosafety in Microbiological and Biomedical Laboratories (BMBL) 5th edition, Section V, located here: ( These requirements are also briefly summarized in the table in chapter 1 of this manual.

Higher-risk, complicated, or unusual animal projects are assigned a Biosafety Considerations Meeting by the IBC and/or the Biosafety Officer (BSO). The meeting includes project-related scientists, animal facility staff, a BSO, IACUC, and occupational health professionals. At the Biosafety Considerations Meeting, the PIdescribes the project, its goals, significance, and challenges. The BSO and all in attendance discuss the details of the project and conduct a risk assessment (including discussion of the possible routes of exposure of biohazardous materials to staff). Any special conditions designated by the IBC, applicable occupational health concerns, and medical surveillance are discussed in the meeting.  The meeting continues until consensus is reached regarding research-related procedures, required equipment and PPE, waste disposal, animal care and use issues, and emergency response procedures, among other items.


Disposal of Biohazardous Animal Carcasses and Large Animal Parts

Animal carcasses and body parts that are recognizable or greater than 1 cubic inch (or 2 cm) must be disposed of through the approved vendor under contract with UCSF, currently Stericycle.  Biohazardous animal carcasses must be double bagged in red biohazard bags, transported in leak-proof containers and taken to freezers located in LARC for storage until vendor pick-up.


Animal Procedures:


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Chapter 11

Packaging, Shipping and Transport of Biomedical / Biohazardous Materials

1. Packaging, Shipping , and Transport

Federal (Department of Transportation, 49 CFR §171-175) and international agencies (ICAO (the branch of the United Nations that governs all international civil aviation matters), IATA (International Air Transport Association) have in place numerous regulations for shipping of dangerous goods by surface or air.

Anyone packaging, handling, shipping or transporting hazardous materials must receive training in the general requirements of handling hazardous materials as well as function specific training for the specific task(s) performed. Training is required before performing any tasks associated with shipping hazardous materials and periodically thereafter. UCSF requires retraining every two years for anyone shipping biological agents since air transport is routinely involved. Nonconformance of these regulations can result in a fine and/or imprisonment.


The online UCSF Safe Shipping Training can be found at the UC Learning Center website:  All documentation related to shipping biomaterials must be retained for a minimum of 2 years.

2. Shipment of Category A infectious substances

·        Category A infectious substances includes any “Infectious substance which is transported in a form that, when exposure to it occurs, is capable of causing permanent disability, life-threatening or fatal disease in otherwise healthy humans or animals.”

·        Examples of Category A infectious substances designated by scientists at WHO and the U.S. Department of Health and Human Services (HHS) are listed in table below.

Table 3.6.D: Indicative Examples of Infectious Substances Included in Category A in Any Form Unless Otherwise Indicated (



Click to enlarge


  1. The Shipper’s Declaration of Dangerous Goods documentation is required for shipping Category A infectious substances.
  2. Packing Instruction 620 is used for shipping Category A Infectious Substances

3. Shipment of Category B Infectious Substances

  • Category B Infectious substances (Biological Substance, category B) include any infectious substance that does NOT meet criteria for inclusion in Category A. Category B Infectious substances includes diagnostic or clinical specimens
  • The Shipper’s Declaration of Dangerous Goods documentation is NOT required for shipping Category B infectious substances.
  • Packing Instruction 650 is used for shipping Category B Infectious Substances


printable pdf version



4. Shipping Using Dry Ice.

  • Dry Ice is considered a Dangerous Good. Training and certification are required, and the package must be labeled and shipped accordingly.
  • Dry ice is a Class 9 Dangerous Good
  • Dry ice MUST be declared with marking, labeling and documentation
  • Dry ice must NEVER be placed in a sealed container
  • Use Packing Instruction 954 for shipment with dry ice

5. Transport of Biomaterials within UCSF

Transport of frozen and/or active biomaterials (Risk Group 1 or 2) between UCSF campus locations within San Francisco city limits is permitted. This process may not be used to transfer biomaterials between different UC campuses or to other off-site destinations (including UCSF affiliates located outside of San Francisco) without approval of the Biosafety Officer. Those with Biosafety Level 3 (BSL3) laboratories must call the UCSF Biosafety Officer (BSO) for specialized procedures.

The following rules apply:

(1) Laboratory personnel to move biomaterials by coolers.

Biomaterials (either active or frozen cultures) may be moved in thermally stable transport containers such as Igloo® or Coleman®-style hard-sided picnic coolers with securing latches. Primary containers must be placed within secondary containers that are leak proof and have tightly fitting lids. Materials requiring transport at non-ambient temperature must be packed in coolers that include enough heat or cold source packs to keep materials at required temperature for duration of transfer. Wadded newspaper or bags of Styrofoam peanuts are commonly used to take up unused space to prevent contents shifting and to maintain temperature as long as possible. Do not use loose Styrofoam peanuts. Outer containers must be sealed and secured shut with heavy-duty duct or shipping tape.

(2)  Laboratory personnel to move biomaterials without coolers.

Primary containers used to transport biomaterials at ambient temperatures must be placed in leak proof secondary containers with tightly fitting lids. Wadded newspaper or bags of Styrofoam peanuts are commonly used to take up unused space to prevent contents shifting. Do not use loose Styrofoam peanuts. Outer container must have biohazardous label affixed and visible.


a) All cultures must be transferred to leak proof, screw-cap unbreakable plastic containers (primary container). Do not use slip-cap culture tubes or stoppered containers.

b) All containers with biohazardous materials must display biohazard symbol and have attached to the top outside a leak proof plastic bag that contains the following information:

  • Name and phone number of the PI and that of an alternate contact,
  • Originating building and room number,
  • Destination room number,
  • Inventory and description of biohazards of contents.


a) Biohazardous materials must be transported by two persons with appropriate knowledge of materials involved and emergency procedures in the event of a spill or other accident. Appropriate PPE must be worn (gloves, laboratory coat, safety glasses or goggles, masks or face shields) when actively handling biohazardous materials during packaging and unpacking at new location. During transport, street clothes should be worn, but PPE should remain available in case of spills. Persons involved in transport must take with them 2 1L spray bottles of fresh 0.5% bleach solution, sufficient absorbent material to disinfect and remove spills, and sufficient large plastic bags (not red biohazard bags) to contain used absorbent materials.

b) After packaging, actual transport of biohazardous materials must be completed within 2 – 3 hours from beginning location to final destination.

c) DO NOT move biohazardous materials in incubators.

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Chapter 12

Importation and Exportation Permits for Biological Materials

Importation Permits for Etiologic Agents

Certain materials require import permits prior to entering the United States. Below is a table outlining these permit requirement. Most agencies have indicated that if there is doubt whether a permit is required it is best to submit the permit application and the agency will decide. If you have any questions please call the Biosafety Office at (415) 514-2824 or the appropriate agency.

Table of Required Permits


Material to be Imported


Call (404) 718-2077 or visit the CDC web site at for further information

Etiologic agents - infectious agent known to cause disease in man. This includes, but is not limited to, bacteria, viruses, rickettsia, parasites, yeasts and molds. In some instances, agents which are suspected of causing human disease also require a permit.

Biological materials - Unsterilized specimens of human and animal tissue (including blood), body discharges, fluids, excretions or similar material, when known or suspected of being infected with disease transmissible to man.

Animals - Any animal known or suspected of being infected with any disease transmissible to man. Importation of turtles of less than 4 inches in shell length and all non-human primates require an importation permit issued by the Division of Quarantine. Telephone (404) 639-1437 for further information.

Insects - Any living insect, or other living arthropod, known or suspected of being infected with any disease transmissible to man. Also, if alive, any fleas, flies, lice, mites, mosquitoes, or ticks, even if uninfected. This includes eggs, larvae, pupae, and nymphs as well as adult forms.

Snails - Any snails capable of transmitting schistosomiasis. No mollusks are to be admitted without a permit from either Centers for Disease Control and Prevention or the Department of Agriculture. Any shipment of mollusks with a permit from either agency will be cleared immediately.

Bats - All live bats. Bats may also require a permit from the U.S. Department of Interior, Fish and Wildlife Services.


Call (310) 851-3300 or visit the USDA web site at


for further information

Materials derived from animals or exposed to animal-source materials. Materials which require a permit include animal tissues, blood, cells or cell lines of livestock or poultry origin, RNA/DNA extracts, hormones, enzymes, monoclonal antibodies for IN VIVO use in non-human species, certain polyclonal antibodies, antisera, bulk shipments of test kit reagents, and microorganisms including bacteria, viruses, protozoa, and fungi. Exceptions to this requirement are human and non-human primate tissues, serum, and blood.

Dairy products (except butter and cheese), and meat products (e.g., meat pies, prepared foods) from countries with livestock diseases exotic to the U.S.

Foreign plant pests injurious to plants grown in the United States.

Designated noxious weeds, which are of foreign origin and new to or not widely prevalent in the United States.

Insects, Mites, and Nematodes Introduced for Biological Control of Weeds in the United States.

Biological control organisms imported, shipped, and released in the United States.

Insects and Mites Commonly Included in Shipments as Host Material for Biological Control Agents.

Domestic Plant Pests Regulated by Federal or State Quarantines.

Low-Risk Organisms, including Arthropods and Pathogens.

Non-regulated domestic plant pests shipped into an area in the United States where the pests do not occur.

USDI (Department of


Call (202) 208-3100 for

further information

Certain live animals and all live bats

State Agencies

Some animal species or pathogens used in research may also require a permit from a State agency. The most commonly needed state permit for researchers at UCSF is the “Restricted Species Permit” from the Department of Fish and Game (DFG). These are animals and plants that have the potential to be either ecologically invasive or destructive to native species. Their website, located here:

contains this link:

to the regulation describing the animals that require a state permit, whether or not a federal permit is also needed (CCR 14 §671(c)).

The instructions for obtaining the “Scientific Collecting Permit” are also on the DFG web page.

Additionally, the state Department of Agriculture may have requirements for importing species’ that can potentially threaten agricultural crops or livestock. Their website, located here:


provides additional guidance.

Export of Infectious Materials

The export of infectious material may require a license from the Department of Commerce. EH&S will help each export of infectious material to determine if an export permit is required. If a permit is required EH&S will assist with the process. For export and shipping infectious materials out of the country and related questions, contact Peili Zhu at EH&S,, Tel: 415-514-2824

The United States has imposed restrictions on certain kinds of information and items are shipped out of the country since the 1940s. In general, US Export Control regulations cover four main types of University activities:

  1. Transfers of controlled information, including technical data to persons and entities outside the United States;
  2. Shipment of controlled physical items, such as scientific equipment, biological samples, high tech instruments or computers that require export licenses from the United States to a foreign country;
  3. Verbal, written, electronic, or visual disclosures of controlled scientific and technical information related to export controlled items to foreign nationals (“deemed exports”), even when it occurs within the United States; and
  4. Travel to certain sanctioned or embargoed countries for purposes of teaching or performing research.

These requirements are not new, and are specific for each type of material and or technology as well as to the specific country to which it is being transferred. The activities are governed by complex federal regulations that cross several agencies.

In order to help the faculty navigate through these requirements the UC system has purchased and is licensing a new software tool to assist campuses with export control compliance. The software system performs many tasks. The most useful feature is the will help staff members determine if export permits or export licenses are required.

For assistance please contact as follows:

For shipping items out of the country and related questions, contact Peili Zhu at EH&S


For general questions related to Federal Export Control Regulations, please contact

For shipping items out of the US and related questions, please contact of Environmental Health & Safety.

For questions related to Sponsored Research agreements, please contact in Contracts and Grants or in the Industry Contract Division of the Office of Sponsored Research.


Additional information on Export controls can be found at:

University of California Office of the President (UCOP)

University of California, San Francisco Office of Ethics and Compliance- Export-Control (UCSF)


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Chapter 13

Biological Toxins

Biological toxins are poisons produced by various biological agents which may include (but is not limited to) bacteria, fungi, protozoa, plants, reptiles, amphibians, fish, echinoderma (spiny urchins and starfish), mollusks, and insects.


LD50 (ug/kg)*

Alpha conotoxin


Alpha bungarotoxin


Alpha hemolysin


Botulinum Toxin








Cholera toxin


Clostridium difficile enterotoxin A




Crotalus snake venome


Diphtheria toxin






Pertussis toxin




Tetanus toxin




The UCSF Institutional Biosafety Committee (IBC) regulates and reviews the possession, use, and transfer of biological toxins. Registration of biological toxins is required on an active Biological Use Authorization (BUA) in RIO.

- LD50 values for most commonly used for Biological Toxins

*Please note that the LD50 values are from a number of sources.

Toxins not on the list above may still require registration. For more information, please contact the Biosafety Officer at 415-514-2824.

Select Agents Toxins

For Select Agent toxins, refer to Chapter 14.

Working with and Disposing of Biological Toxins

Because they can be extremely hazardous, even in minute quantities, biological toxins require strict safeguards against their inhalation, absorption through skin or mucous membranes (typically due to a splash), ingestion, or percutaneous injury.

Considerations for Conducting Work with Biological Toxins:


  • Review Safety Data Sheets (SDS) prior to using a given toxin.
  • Perform dilutions of powdered toxin in chemical fume hood.
  • Avoid sharps usage.
  • Follow UCSF Procedures for Using Toxins in Rodents when using biological toxins in animals.


  • Use of appropriate PPE is required (i.e. lab coats or gowns, gloves, eye protection, etc.)


  • Dispose of liquid and solid toxin waste as hazardous chemical waste (through EH&S).


  • Establish appropriate security measures to protect against unauthorized access to toxin(s).
  • Establish and maintain logbook.

Accidental Exposure

If there is an Accidental Exposure to biological toxins:

  • Flush exposed area with copious amounts of water for 15 minutes.
  • Contact Occupational Health Service Exposure Hotline immediately (415-353-7842).If symptomatic, immediately seek medical attention at the Emergency Department.
  • Call the Biosafety Officer (415-514-2824) within 72 hours to report the exposure.

In the event of a large scale spill or emergency, contact the EH&S Response Team at 9-911.

Health Surveillance

All personnel, including future students and employees, who handle tetanus, diphtheria, and/or pertussis toxin must be enrolled in the UCSF Occupational Health / Environmental Health and Safety Medical Surveillance program. Please contact the Public Health Officer (415-514-3531).

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Chapter 14

Select Agents


Select Agents are materials that have been identified by the U.S. Government as agents that have potential use in biological terrorism or warfare. The Department of Health and Human Services (DHHS), within the U.S. Centers for Disease Control and Prevention (CDC) and the Animal Plant Health Inspection Service (APHIS), within the United States Department of Agriculture (USDA) regulate Select Agents in the United States and its territories. Each agency has developed a list of Select Agents, including human, animal and plant pathogens, and high-risk toxins of biological origin. Detailed information regarding the Select Agent program can be accessed at the National Select Agent Registry (NSAR) web site.

1. List of Select Agents

The most current list of select agents can be found here:

2.Toxin Amounts Permissible Per Principal Investigator

Regulated toxins of biological origin (see table below) can be ordered, used, or maintained in the laboratory provided the total quantity per PI, for all areas under the PI’s control, does not exceed the limits posted in the table below, unless both UCSF and the Principal Investigator are registered with the CDC or USDA for Select Agent use.

The most current list of “Maximum Allowable Quantities” can be found here:

Toxin Amounts Permissible per Principal Investigator

HHS Toxins [§73.3(d)(3)]



100 mg

Botulinum neurotoxins

0.5 mg

Short, paralytic alpha conotoxins

100 mg

Diacetoxyscirpenol (DAS)

1000 mg


100 mg


100 mg

Staphylococcal enterotoxins (Subtypes A, B, C, D, and E)

5 mg

T-2 toxin

1000 mg


100 mg

It is important to ensure that the total amount of toxin per PI in a laboratory is maintained below these limits at all times for exemption from registration and restrictive Select Agent requirements. Failure to register a Select Agent is a criminal offense, punishable by up to five years in prison and/or $500,000 in fines.  (Public Health Security & Preparedness Response Act of 2002, s. 231(c)).

3.  Possession, Use, or Transfer of Select Agents

In order to possess, use, send or receive Select Agents in amounts equal to or greater than those listed at the NSAR for a given agent, an institution and each individual who will have access to the Select Agent(s) must first satisfy each of the following requirements:

  • Register with U.S. governing bodies (CDC and/or APHIS) through UCSF EH&S.
  • Official authorization granted for each individual requesting access to Select Agents provided by the U.S. Federal Bureau of Investigation, the applicable U.S. governing body, and UCSF.

Please note that violations of Select Agent rules and regulations can lead to severe criminal or civil penalties.  Imprisonment and fines up to $250,000 may be levied against individuals who are found to be in violation of these laws.

4. Registration of Possession, Use or Transfer of Select Agents.

All activity involving Select Agents must be registered with UCSF EH&S prior to initiation. Please contact the EH&S Biosafety group at 514-2824 to initiate a registration for your proposed Select Agent activity.

The following bullets summarize the Select Agent registration and compliance pathway at UCSF:

  • Notify EH&S of your intent to possess, use or transfer Select Agents.
  • Complete an update of the APHIS/CDC Form, Application for Registration:
  • Complete FBI Form FD961 and file with UCSF EH&S for registration with applicable federal entity.
  • Complete 2 sets of FBI fingerprint cards for initiation of background investigation check.
  • Complete EH&S applicable training programs.
  • Satisfactory completion of EH&S laboratory inspection of proposed work practices, safety equipment, and facilities, to evaluate compliance with CDC/APHIS, and Select Agent regulatory requirements (Safety and Security).
  • Receive final approval and authorization from EH&S, FBI, and the applicable governing body for you and each individual requesting access to Select Agents, for the proposed storage location, and research areas.

Your laboratory will be subject to EH&S and federal inspections or audits prior to initiation of work and at any time during your possession of Select Agents.

5. Discovery of Select Agents, Unknown Samples, or Missing Samples

Please notify EH&S immediately if:

  • You identify any Select Agent pathogen or toxin listed on the current federal list that was not previously registered by your lab.
  • You discover a toxin not previously reported by your laboratory in excess of the federal maximum allowable quantities listed above.
  • You discover any unknown materials in your laboratory for assistance with identification.

These discoveries must be reported to the applicable governmental institution(s).

6. Intrafacility Transfer of Select Agents

Select agent pathogens and toxins may not be transferred outside of, to, or within UCSF unless EH&S and federal approval has been granted.  An intra-facility transfer is defined as the transfer of a Select Agent from one EH&S and federally registered Select Agent lab to a similarly registered laboratory.  Select Agents may not be transferred to a laboratory that is not registered with EH&S and the applicable governmental institution.  Once approved, intra-facility transfers will be overseen by EH&S.

Please contact the EH&S Biosafety group for additional information.

7. Destruction of Select Agents or Unknown Samples

Select Agent pathogens or toxins may not be destroyed until EH&S and the applicable government institution have provided approval for the destruction.  Once approval has been granted for the destruction of Select Agents, EH&S will officially assume possession of the material and record its destruction.  The governing institution will alert UCSF if witnesses are required.

If you have any questions regarding the UCSF or Federal Select Agent process, please contact the EH&S Biosafety group at 415-514-2824.

Additional Information on the Select Agent Program may be found at the following web sites:


National Select Agent Registry (NSAR) (

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Chapter 15

Working with Aerosol Transmissible Diseases (ATD)

Working with Aerosol Transmissible Pathogens in the Laboratory

Each laboratory at UCSF that works with Aerosol Transmissible Pathogens-Laboratory (ATPs-L)  as specified in Appendix D of the California Occupational Safety and Health Standards board Title 8, section 5199 must submit a Biological Use Authorization (BUA) to the UCSF Institutional Biosafety Committee (IBC) that authorizes the possession, storage, transfer, and use of the biohazardous materials. The BUA must be reviewed and approved by the IBC before a laboratory is permitted to work with ATPs-L. The IBC will evaluate the engineering controls and PPE requirements during the BUA review process.

Approved BUA must provide a risk assessment in accordance with the methodology included in Section II of the BMBL for each agent and procedure involving the handling of ATPs-L. The BUA must contain sufficient information and detail to serve as a useful training document for laboratory employees and students.  The BUA must describe the procedures and measures to establish, implement and maintain an effective program to minimize research laboratory employee exposure to ATPs-L.  The BUA must include a Health Surveillance Program that ensures all vaccinations as recommended by applicable public health guidelines are available for specific laboratory operations, and methods for investigation and medical follow up for exposure incidents.

Additional requirements of CCR, Title 8, Sec. 5199 are outlined in the approved BUA.                        


Aerosol Transmissible Disease Exposure Control Plan (ATD) in Dentistry

At the UCSF School of Dentistry, all patients are screened for ATDs and those with suspected or confirmed ATDs are referred to their medical provider if they show any signs or symptoms of ATD.  All staff members who observe patients with any signs or symptoms of ATDs are to give the patient a mask and alert the attending faculty and student dentist of the patient’s symptoms. The attending faculty member and student dentist will isolate the patient, if possible, into a private operatory. The attending faculty and student dentist shall wear all PPE, including mask, gown, gloves and eyewear. The attending faculty and student dentist shall refer the patient to their primary health care provider for a medical screening, and shall require a clearance from the medical provider prior to the patient being treated in the UCSF dental clinics.                      


Policy on Zoonotic Aerosol Transmissible Diseases


Individuals involved in the care and use of animals may be at an increased risk of exposure to diseases that are transmitted from animals to humans by infectious aerosols. Although zoonotic diseases are uncommon in modern animal facilities, UCSF has established the following procedures to minimize the risk of transmission of aerosol transmissible diseases (ATD) to individuals involved in the care and use of research animals. These procedures are designed to comply with the California Occupational Safety and Health Administration (Cal-OSHA) Zoonotic ATD Standard Cal-OSHA CCR Title 8 Sec 5199.1.

Scope and Application:

These procedures apply to all personnel working with, or exposed to, animals or their unfixed tissues including but not limited to veterinary staff, animal care technicians, research personnel, facilities personnel, Environmental Health and Safety Staff, IACUC staff and IACUC Committee members.

Control Methods:

Several control measures are utilized to reduce the risk for introducing or transmitting zoonotic ATDs at UCSF laboratory animal facilities. These include quality veterinary care, adequate quarantine and animal acquisition procedures, sound work practices and personal protective equipment.

Veterinary Care

1) The Laboratory Animal Resource Center’s (LARC) central animal care program conducts full husbandry operations during weekends and holidays, under the coordination of the Animal Resources Managers.

2) All LARC-housed animals are observed at least daily and veterinary care is available at all times.

3) Research and LARC staffs are trained to contact the LARC on-call veterinarian if any unexpected clinical signs develop in a research animal.

  • An emergency on-call veterinarian is available for emergencies or off hours medical needs or consultation at all times.
  • The on call veterinarian number is posted in all appropriate animal activity areas on campus.

4) In the unlikely event a LARC veterinarian suspects or confirms a research animal of harboring a zoonotic ATD, the following procedures may be initiated;

  • The housing room may be placed under quarantine and access restricted to trained LARC and research personnel.
  • Samples for initial or confirmatory testing may be submitted to the appropriate diagnostic laboratories.
  • EH&S and/or the Biosafety Officer are notified of any suspected or confirmed zoonotic ATD.
  • The Biosafety Officer and/or EH&S will specify personal protective equipment, including respiratory protection, needed for entry into the housing room.


1) LARC veterinarians, managers, and veterinary nurses are trained annually in the use of power air purifying respirators (PAPRs).
2) Only trained LARC and research staffs, with appropriate respiratory protection as prescribed by the Biosafety Officer, are permitted access to an animal that is suspected of harboring a zoonotic ATD.
  • Research labs housing animals in the positive room are immediately notified of the suspected or confirmed ATD case by the LARC veterinarian on the case. The Biosafety Officer shall confirm that notification occurred.
  • A meeting with LARC veterinarian(s), Biosafety and Occupational Health staffs is scheduled to review the agent and the approaches available for managing the suspected/ confirmed case.
  • Personnel with possible exposure to an animal harboring a suspected zoonotic ATD will be trained in appropriate symptom monitoring and exposure follow up will be conducted through Occupational Health Services.

Animal Quarantine and Acquisition                                                                                      

1) Dogs, Cats, Pigs and Rabbits

  • Random source animals are not accepted by UCSF. Only purpose bred animals of known health status from class A dealers or AAALAC accredited facilities are accepted.
  • Animals are evaluated for good health upon arrival at the facility. Any animal not appearing healthy will be examined by a veterinarian.
  • Sick animals may be isolated from healthy animals, as prescribed by a LARC veterinarian.

2) Non-Human Primates

  • Non-human primate medical records are reviewed and approved by a LARC veterinarian and appropriate diagnostics and treatments are instituted before importation.
  • California source primates are transferred directly from the shipping crates into the animal room. Animals are visually examined for good health upon arrival. Any animal appearing unhealthy would be further examined by a veterinarian.
  • Quarantine of non-California source monkeys is in compliance with state laws
  • which mandate animals be isolated to pre-approved rooms for a minimum of 30 days. As required by the California Department of Public Health (CDPH), quarantined animals receive a tuberculin skin test and veterinary examination upon entry which are repeated again 30 days later.
  • Sick primates are isolated at the cage level within the animal quarters and receive a prompt cage evaluation by the LARC veterinarian to determine appropriate actions.

3) Sheep

  • UCSF has an extensive Q fever exclusion program.
  • UCSF purchases sheep only from approved vendors based on LARC review of their preventative health programs and the Q-fever serology screening of the incoming sheep.
  • All adult sheep are tested twice by ELISA serology and confirmed to be seronegative prior to transport to UCSF facilities. A PCR on the buffy coat is performed on all incoming lambs. Additionally, a PCR is performed on the amniotic fluid of any pregnant ewe prior to transport to UCSF when possible as part of the research protocol. Only PCR negative and seronegative postpartum ewes are allowed entrance into UCSF facilities. Male sheep require only 2 serologically negative tests.

Work Practices

1) Procedures that may result in the aerosolization of pathogens include, but are not limited to, necropsy, dentistry, and certain clinical, surgical and laboratory procedures.

  • Appropriate PPE and respirator protection must be used when performing such a procedure on an animal suspected or confirmed of harboring a zoonotic ATD.
  • Persons NOT involved in these procedures shall be excluded from the area, unless they use the respiratory protection and PPE required for employees performing these procedures.

2) Staff members should perform all manipulations of potentially infectious materials so as to minimize aerosol production.

3) Hand hygiene is an important means for preventing laboratory acquired infections. Workers should wash their hands after removing gloves and before leaving the laboratory, procedure room, or animal room.

4) Eating, drinking, and smoking are prohibited in all animal housing and procedural spaces.

5) All reusable equipment and procedural spaces must be appropriately decontaminated after use.

6) Contaminated waste materials must be disposed of and packaged in accordance with the UCSF Medical Waste Policy.

Personal Protective Equipment (PPE)

1) Personal protective equipment requirements for individuals with exposure to elevated risk animals and/or their unfixed tissues is determined by the IBC in accordance with recommendations outlined in the Biosafety in Microbiological and Biomedical Laboratories (5th edition).

2) Careful work practices and rigorous use of PPE is recommended to reduce the risk of exposure to zoonotic pathogens.

3) Biological safety cabinets should be used when manipulating infectious materials. Workers may also rely on personal protective devices, such as respirators, to minimize exposure to infectious aerosols.


1) Occupational health and safety information for staff with animal exposure is available in pamphlets and online under “Working Safely with Animals” at

2) The UCSF Medical Health Screening questionnaire must be completed annually by all individuals with exposure to animals or their tissues.

  • This questionnaire provides an individualized risk assessment for all animal users and categorizes each individual’s risk level based on the species worked with.
  • Information on zoonoses is provided to the animal user as part of this risk assessment.

3) All new and current UCSF employees/research personnel who work with animals at UCSF are required to complete Animal Biosafety Level Training which is included in the online “Biosafety” training course.

Researchers who will work at ABSL3 facilities must take the “Animal Biosafety Level 3” training. This training provides information on the following:

  • Animal Biosafety Levels
  • Appropriate personal hygiene practices
  • Safe work practices
  • PPE
  • Decontamination
  • Waste disposal

4) All individuals with exposure to live Old World non-human primates must complete an in person Herpes B training prior to beginning work as well as an online Herpes B training. Both of these trainings are refreshed annually.

5) All individuals who will work with Old World, non-human primate tissues, blood, or other potentially infectious materials must also complete both the in-person and online Herpes B trainings. For these workers, the in-person training is one time only, but the online training is refreshed annually.

6) All individuals with exposure to sheep or their unfixed tissues must complete an online Q fever training once every three years.


1) A Biological Use Authorization application (BUA) to work with animals involving infectious or transmissible agents must be submitted as an online BUA application to the IBC for review and approval.

2) Animal biosafety levels are assigned by the IBC for each BUA involving animal use.

3) Once approved, LARC must be contacted prior to initiation of the research to ensure that safe operating procedures will be established.

4) Higher-risk, complicated, or unusual animal projects are assigned a Biosafety Considerations Meeting by the IBC.

  • The meeting includes project-related scientists, animal facility staff, a biosafety officer (BSO), and occupational health professionals.
  •  The BSO and all in attendance discuss the details of the project and conduct a risk assessment (including discussion of the possible routes of exposure of biohazardous materials and zoonotic agents to staff).
  •  Any special conditions designated by the IBC, applicable occupational health concerns, and medical surveillance are discussed.
  •  The meeting continues until consensus is reached regarding research-related procedures, required equipment, PPE, waste disposal, animal care and use issues, and emergency response procedures.

5) Biohazardous animal carcasses and body parts must be disposed of through a contract vendor approved to haul infectious waste.  Biohazardous animal carcasses must be double bagged in red biohazard bags, transported in leak-proof containers and taken to freezers located in LARC for storage until vendor pick-up.

Medical Surveillance

1) All individuals with exposure to sheep are screened annually for Q fever in accordance with the UCSF Sheep Worker Policy on Surveillance and Training.

2) Individuals with exposure to Old World non human primates must provide one time proof of measles immunity prior to beginning work and participate in annual tuberculosis screening.

Old World Primate Worker Policy on Surveillance and Training.

3) Medical surveillance services are provided by UCSF Occupational Health Services.

Investigation of Occupational Injuries or Illnesses

1) The UCSF Occupational Health and Safety Exposure Hotline operates 24 hours daily for the provision of emergency care of acute biologic exposures. The Exposure Hotline Pager (415-353-7842) is answered by a live operator who connects the affected employee with an Exposure Hotline clinician.

2) All research related exposures including potential zoonotic ATD exposures are reported to the Biosafety Officer 415-514-2824 and Public Health Officer 415-514-3531 and an exposure investigation is conducted.

3) In the event of an exposure to a communicable disease, the campus exposure plan is followed. (

  • This plan assigns actions and responsibilities for confirming a campus exposure, identifies those people likely exposed to a communicable disease and determines the risk of transmission and the appropriate follow-up activities.


UC Santa Barbara Office of Research. [Internet]. 2011. Zoonotic Diseases. [Cited 3 January 2011].

NRC (National Research Council). Guide for the Care and Use of Laboratory Animals. Washington, DC: National Academy Press; 1996.

NRC (National Research Council). Occupational Health and Safety in the Care and Use of Research Animals. Washington, DC: National Academy Press; 1997.

Public Health Service. Biosafety in Microbiological and Biomedical Laboratories, 5th ed. Washington, DC: US Government Printing Office; 2009.

Title 8, California Code of Regulations 5199.1, Aerosol Transmissible Disease Standard – Zoonotic

If you have any questions, contact EH&S Biosafety Officer at 415-514-2824.                                


Appendix 1: Aerosol Transmissible Zoonotic Pathogens and Current Status at UCSF LARC Facilities



Host / Reservoir

Documented @ UCSF; and presumed to be still present No Active Monitoring / Current positives not known Actively monitored and currently not at UCSF Monitoring and Risk Reduction Activities


(Mycobacterium tuberculosis or bovis)

Non-Human Primates     X Non-human primates are screened semi-annually. Employees with primate exposure are screened annually.

Q Fever

(Coxiella burnetii)

Sheep     X Extensive Q fever exclusion program in place for all imported animals. Employees with sheep exposure have titers checked annually.
Herpes B Old World Primates X     Education and training. PAPRs used during dental procedures.
Measles (Rubeola) Non-Human Primates     X All employees must show proof of measles immunity prior to working with non-human primates.
Hantavirus Wild Rodents   X   Used under ABSL2 conditions. Bioconsiderations meeting required for wild rodent users.


(Chlamydia psittaci)

Finches, Sheep     X Employee education and training.

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Chapter 16

Health Surveillance Program

All research protocols involving biological hazards are reviewed by the UCSF Institutional Biosafety Committee (IBC) for approval. The Medical Director of UCSF Occupational Health Services sits on the IBC as an ad hoc member. All required or recommended health surveillance programs are designed to protect the health of the laboratory personnel involved and implemented by the Occupational Health Program in coordination with recommendations from the IBC. The existing health surveillance programs are described in the Biological Use Authorization (BUA) forms.  The following table summarizes these programs and identifies where to find additional information about each.




Animal Exposure

  • Enrollment into program through completion of baseline Medical Health Screening (MHS) questionnaire
  • Annual renewal of MHS


  • Initial MHS questionnaire, annual renewal
  • Initial screening appointment with UCSF Occupational Health Services (OHS), completion of Q fever questionnaire and baseline titer
  • Mandatory annual Q fever titer and screening questionnaire
  • Q fever titer results with interpretation from OHS
  • Online Q fever training required every 3 years.
  • One-time species orientation with a LARC veterinary nurse prior to work with sheep or sheep tissue
  • Q fever exclusion program – all adult sheep tested twice by ELISA and confirmed seronegative prior to transport to UCSF facilities

Herpesvirus simiae

  • Initial MHS questionnaire, annual renewal
  • Initial and annual Tuberculosis Screening (for work with live Old World primates only)
  • One-time proof of measles immunity (for work with live Old or New World primates only)
  • Annual online Herpes B training
  • Annual Herpes B in-person training (for work with live Old World primates)
  • Herpes B medical alert card
  • Herpes B exposure protocol


  • Enrollment into program prior to start of work with poliovirus
  • Polio vaccination or declination
  • Poliovirus exposure protocol

Yellow Fever

  • Enrollment into program prior to start of work with Yellow Fever
  • Yellow Fever vaccination or declination
  • Review of Immunization Practices Advisory Committee recommendations on Yellow Fever vaccination

Tuberculosis (TB)

  • Enrollment into program prior to start of work with TB
  • Semi-annual TB screening
  • TB exposure protocol
  • Respirator protection – medical clearance and fit testing

Toxins – Diphtheria, Pertussis and Tetanus

  • Enrollment into program prior to start of work with toxin(s)
  • Tdap vaccination or declination
  • Pertussis and Diphtheria toxin exposure protocols

Vaccinia Virus

  • Enrollment into program prior to start of work with virus
  • One-time counseling and vaccination through OHS for those working directly with virus culture and/or infected animals
  • Declination, if contraindication identified or no direct contact with vaccinia virus
  • Vaccinia immunization policy
  • Vaccinia exposure protocol

Prion Research

  • Specialized training
  • Prion exposure protocol

Influenza virus

  • Enrollment into program prior to start of work with Influenza virus
  • Influenza vaccination or declination


  • Hepatitis B vaccination or declination
  • Vaccine compliance form retention by OHS
  • Annual online Bloodborne Pathogens training
  • Use of Universal Precautions at all times

Custom Program

  • PI responsibility
  • Designed to meet special circumstances of unique research
  • Described in detail in BUA application


The last program, Custom, is a special program that a Principal Investigator (PI) may choose to develop if the research calls for a unique or tailored surveillance approach. Such a program should be carefully designed and well justified. The Institutional Biosafety Committee, in consultation with the Occupational Health Program, will determine the program’s acceptability.

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Chapter 17

Audits and Inspections

EH&S Inspection     


EH&S conducts both scheduled and unannounced inspections of laboratories on a regular basis. Inspections are not limited to biosafety, but rather encompass additional research-related categories such as chemical, fire and life, radiation, and general safety.

For biological safety, a typical inspection of a BSL1 or BSL2 laboratory will include (but may not be limited to) evaluation of the following items for compliance and/or accuracy:

A.  Administration

  • PI name and contact information, department, location posted
  • BUA approval number(s) posted/available
  • Biohazardous material(s), use locations, and biosafety levels listed on BUA
  • Emergency procedures and phone numbers posted
  • Active personnel listed on BUA

B.  Equipment

  • Biosafety Cabinet annual certification and work practices
  • Autoclave issues (if used for medical waste)
  • Eyewash present and inspected (for BSL2 facilities)
  • Proper use of laboratory equipment (biosafety cabinets, centrifuges, sonicators, cell sorters, etc.) with bioagents

C. Labeling

  • Biohazard labels present at the entrance to the laboratory, on equipment, and waste containers

D.  Personnel Exposure Control

  • Use of appropriate Personal Protective Equipment (PPE)
  • Adherence to applicable medical surveillance program(s)
  • Safety practices followed for aerosol-generating procedures
  • Decontamination of work areas

E. Personnel Training

  • Lab Safety for Researchers/Biosafety trainings
  • Bloodborne Pathogens training (if needed)
  • Animal Biosafety Level  III training (if needed)
  • Q-fever or Herpes-B training (if needed)
  • Safe Shipping of Biohazards/Dry Ice training (if needed)

F. Waste Handling

  • Proper disposal of dry and liquid biohazardous waste
  • Decontamination procedures followed
  • Autoclave certified for medical waste decontamination

G.  Use of sharps

  • Sharps storage
  • Sharps disposal

H.  Select Agents (when applicable)

  • Security maintained
  • Usage logs maintained
  • Facility maintained

EH&S provides laboratories with inspection reports detailing inspection findings. EH&S will work with laboratory personnel to correct deficiencies within a reasonable timeframe.

Regulatory Agency Inspection

Notify EH&S immediately upon receipt of an inspection notice from any regulatory agency. For your protection, EH&S must be involved and participate in all lab inspections.

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