CLASSE Safety Handbook

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Biological Safety

Biological hazards at CLASSE are restricted to CHESS. Specific practices for CHESS appear below; general resources are the CDC publication "Biosafety in Microbiological and Biomedical Laboratories (5th Edition)", available here, and the set of EHS BioSafety Manuals (access restricted to those with a Cornell NetId).

Biohazards are separated into four safety classifications: BSL-1, BSL-2, BSL-3, and BSL-4. BSL-1 is the lowest level and requires minimal precautions. BSL-2 hazards, agents of moderate potential hazard to personnel and the environment, do not have to be contained in the biohazard facility. However, those BSL-2 hazards such as the Cocksackie virus or the more commonly known Hepatitis B virus, are generally used only in the biohazard facility. BSL-3 hazards, agents which may cause serious or potentially lethal disease as a result of exposure by inhalation, include viruses such as Mycobacterium tuberculosis. CHESS prohibits the presence of BSL-3 or the more hazardous BSL-4 materials, the latter of which are dangerous and exotic agents which pose a high individual risk of life-threatening disease.

The CHESS F1 station and the accompanying access room, control room, and biohazard room constitute the CHESS biohazard facility. This facility provides a place for CHESS users to work with biological samples that require up to BSL-2-level precautions. Some BSL-2 work can be approved for the cold room.

When biohazards are transported into the lab, they must be double-sealed and stored in sturdy containers that are clearly marked with a biohazard symbol.

Biohazard Procedures at CHESS

  • Biohazardous agents which may be used at CHESS are restricted to small amounts of viruses of classification BSL-2 or below. Use of these materials must be approved in advance by the CHESS User Safety Subcommittee and CLASSE Safety Committee. The safety binder at the ops desk will have a list of the approved viruses for a user's current visit.
  • All users of biohazards must have received appropriate training, either at the user's home institution (P.I. certifies training) or at CHESS (cognizant Safety Officer certifies training). Users should verify training at the time they sign out radiation badges.
  • The cognizant Safety Officer, or designee, will check in biohazards, inform the CHESS operator about them, and write on the safety whiteboard: station, nature of hazard, Safety Officer's name and phone number.
  • BSL-2 procedures (see below) are to be followed for handling BSL-2 viruses (this document is provided to all users of such materials and is also available in the safety binder at the ops desk and on-line in the "Procedures" section). Note particularly:
    • Viral materials must be checked in and out.
    • BSL-2 materials are restricted to certain areas (usually the F-1 station), which are labeled with biohazard signs. Access to these areas is restricted to those who need to be there.
    • Surfaces, equipment, and personnel must be protected from contact with infectious material. Absorbent paper for covering surfaces is stored in F-1.
    • Bleach or other suitable disinfectant must be on hand in any areas where biohazards will be handled, also a sharps container and biohazard bags.
  • In the case of a small, contained spill, users can clean it up themselves. For a larger spill, or other emergency, or incomplete cleanup of a small spill, users will notify the CHESS operator, who will call in the cognizant Safety officer.
  • Emergency procedures are in the safety binder at the operator's desk.
  • A container for biohazardous waste is located in the F-1 prep area. At the conclusion of the experiment, all biohazardous waste must be placed in biohazard bags or sharps containers, labeled, and placed in this container for later pickup by EHS. A supply of labels are kept with the container; more can be obtained from EHS.
  • Hazardous materials must be checked out by the safety officer on completion of the experiment.

Spills of virus-containing material

  • Small spill on benchtop, table, or floor
    • Wear protective equipment (lab coat, gloves, goggles).
    • Cover spill with paper towels soaked in disinfectant.
    • For BSL-2 viruses, allow 20 minutes for all virus to be inactivated.
    • Use paper towels to wipe up spill, working from edges inward.
    • Clean spill area with fresh towels soaked in disinfectant.
    • Place all used towels in a biohazard bag.
  • Larger spill on benchtop, table, or floor
    • Block access to area of spill.
    • Inform CHESS operator, who will contact cognizant Safety Officer if necessary.
    • Clean up spill, as above. For a large volume of spilled material, pour additional disinfectant on it after covering area with paper towels.
    • When cleanup is complete, remove barrier around area and inform operator.
  • Small spill on equipment in hutch
    • Clean up as much as possible, as for spill on benchtop.
    • Turn off and remove lamp.
  • Larger spill on equipment, or other difficult-to-clean items
    • Block access to area of spill.
    • Have CHESS operator contact Safety Officer and/or EHS for help in cleaning up spill.
  • Exposure of personnel to virus
    • Inform CHESS operator.
    • If medical attention is required, contact Gannett Clinic or Cayuga Medical Center.

Procedures for BSL-2 materials at CHESS

In general, NIH/CDC guidelines for dealing with BSL-2 material should be followed. Relevant practices for areas in which viruses will be handled include:
  • No eating, drinking, smoking, applying contacts or cosmetics; no pipetting by mouth.
  • Wear appropriate personal protective equipment (PPE) - at least gloves and lab coat.
  • Wash hands after removing gloves or handling biohazardous material.
  • Restrict personnel access while work with biohazards is in progress.
  • Decontaminate work surfaces at least once a day.
  • Use a biosafety cabinet when there is danger of creating infectious aerosols.

Specific procedures for working with crystals at CHESS are:
  1. Crystals of the virus will be brought to CHESS in a double-sealed, appropriately labeled container, as required by the DOT for transport of infectious materials. Crystallization trays or sealed capillaries, containing unfrozen crystals, will be surrounded with absorbent material and sealed within a sturdy outer container. Frozen crystals will be contained in vials enclosed in a Dewar or dry shipper; the container will be secured so that it cannot tip over.
  2. Virus crystals will be usually be kept in the F-1 station. However, they may also be stored in another room, such as the cold room or the chemistry lab, if necessary (e.g. if crystals must be mounted in the cold or if they are being used at the A-1 or F-2 stations). The cognizant Safety Officer, or his/her designate, is to verify the nature and amount of viral materials brought by the user.
  3. Biohazard warning signs will be placed on the doors of all rooms in which crystals will be stored or used. Access to areas in which crystals will be handled will be restricted to the investigators, the CHESS and MacCHESS operators, and members of the CHESS User Safety Subcommittee and CLASSE Safety Committee. If other personnel require access to such an area, the crystals shall be first contained in a suitable box, except for a crystal actually mounted on the oscillation camera.
  4. Table and bench tops in the storage and mounting area will be covered with plastic-backed absorbent paper, which is soft enough so that any dropped capillary or crystal will not bounce off, and absorbent enough to soak up any spills. When crystals are actually being manipulated, it is recommended to cover the immediate area with absorbent paper wetted with disinfectant, so that any dropped crystal will be inactivated.
  5. In the hutch, any surfaces on which a capillary or crystal might fall will be covered with plastic-backed absorbent paper. If frozen crystals are being used, any equipment which could be contaminated in case of failure of the cryosystem (e.g. the rotation stage) should be protected by a plastic shield which can be removed and decontaminated. Freezing of crystals directly into the cold stream is permitted, provided coverage of surfaces and equipment is adequate to catch any viral material which could be dropped in the mounting process. A germicidal lamp will be available in the hutch, in case decontamination is needed.
  6. Mounting of crystals into capillaries, or freezing of crystals into liquid nitrogen (or other substance such as propane), will be performed in the room where the crystals are stored, or in the F-1 Biosafety Cabinet. The Biosafety Cabinet is to be used when there is a possibility of creating aerosols during the mounting process. Flammable materials such as propane are not to be used in the Biosafety Cabinet.
  7. Loaded goniometer heads will be carried from the storage and mounting area into the hutch enclosed in sealed, non-breakable containers. If such a container is dropped, any spill of viral material will be contained within it. Crystals frozen in the storage and mounting area will be transported to the hutch in a container of liquid nitrogen which is enclosed in an outer container to catch any spills.
  8. Because of the containment procedures given above, any spill (e.g. a dropped crystal or a broken capillary) should be limited to an absorbent paper-covered surface or the interior of a container. The users will clean up the spill, using bleach or other suitable disinfectant to decontaminate any places (e.g. absorbent paper or the inside of the outer container) where viral material might have landed. Broken capillaries are to be placed in a "sharps" container for later disposal. In the unlikely case of a spill which involves unprotected surfaces or equipment, or in which an aerosol may have been produced, the cognizant Safety Officer will be consulted to determine appropriate decontamination procedures. A reminder of procedures to follow in case of spills will be posted in the crystal mounting and storage area, and in the hutch.
  9. Used capillaries are to be placed in a "sharps" container. Used frozen crystals are to be either disposed of in a biohazard bag (use disinfectant solution to wash a crystal out of a cryoloop into a small container and put the container in the bag, if the loop is to be salvaged) or stored in a Dewar, still frozen, for possible later use.
  10. At the completion of their experiments, the users will roll up the absorbent paper and dispose of it in a biohazard bag. All surfaces which could have been contacted by virus will be washed with a suitable disinfectant, e.g. bleach or alcohol. The materials used for this cleanup, e.g. paper towels, will also be disposed of in the biohazard bag. Biohazard bags and sharps containers of used capillaries will be placed in a biohazard container (provided by CHESS) for later pickup by Cornell EHS. The cognizant Safety Officer, or designate, is to verify that no biohazardous materials have been left at CHESS, except in the biohazard container.
End of Biological Safety
Topic revision: r15 - 27 Aug 2021, RigelLochner
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