PREVENT AND MANAGE AMPLICON CONTAMINATION IN YOUR LAB

WHAT IS AMPLICON USE ENGINEERING CONTROLS CONTAMINATION?

Engineering controls can help contain potential When polymerase chain reaction (PCR) is used to amplicons at the source. Perform aerosol-generating amplify gene targets, large numbers of amplified activities such as unsealing plates, opening caps/lids nucleic acid molecules, or amplicons, are generated. after centrifuging and pipetting inside a biosafety Nucleic acid amplicons are not infectious or cabinet, fume hood or other type of negatively- hazardous to human health. However, if not pressured ventilated enclosure. Do not use a laminar contained, amplicons can potentially contaminate flow hood or PCR clean hood that blows air toward surrounding surfaces and equipment, personnel and the user. Consult with EH&S if unsure about research experiments. Contamination is also possible appropriate enclosures. when working with DNA and DNA products such as plasmid preparations. Implement these engineering controls as applicable:  For pipetting: use filter tips and slow speeds. If SARS-CoV-2 nucleic acid contamination reaches  For centrifuging: use aerosol containment safety one’s nasal passages via inhalation or touching of cups or sealed rotors, and unload inside a one’s face with contaminated hands, COVID-19 nasal biosafety cabinet or fume hood. Place small swab test results may be affected and return as centrifuges inside a biosafety cabinet or fume positive or inconclusive, despite the individual not hood. At a minimum, wait 10 minutes to allow having an active SARS-CoV-2 infection at the time of aerosols to settle before opening plates or tubes. testing. Such personnel may be asymptomatic with no  For house vacuum lines: use liquid disinfectant known exposure to a COVID-19 positive individual. traps with in-line HEPA filters.

Preventing and managing amplicon contamination is  For shaking incubators: use flasks with vented essential to focus public health guidance to those caps to contain aerosols. affected by active SARS-CoV-2 infections and to prevent unnecessary isolation or quarantine of those PPE AND LAB PRACTICES working with SARS-CoV-2 nucleic acids or their close contacts. Appropriate PPE and lab practices can reduce the

potential for contamination on surfaces, clothing, skin WORK FLOW MANAGEMENT and mucous membranes. Do not wear PPE outside the lab, and do not take PPE home for laundering.

Ideally, work with amplified PCR product should be  Wear disposable procedure masks for tasks isolated from other work areas, such as in dedicated involving amplicons. Dispose of masks when rooms. If separate rooms are not possible, physically leaving the lab or moving to a different work area. isolate work areas or experiments as best possible  A face shield can help reduce the touching of and keep dedicated reagents and materials in each one’s face or mask with contaminated hands. area. Have clean personal protective equipment (PPE)  N95s can be worn as an extra layer of protection. available at each work area. People, reagents,  Consult EH&S resources on voluntary respirator equipment and notebooks should not move from a use for more information. dirty area back to a clean area.

Page 1 | May 5, 2021 www.ehs.washington.edu | 206.543.7262 | [email protected]  Consider disposable lab coats with elastic wrist function for 10,000 hours or about one year. Thus, if cuffs and/or the use of disposable sleeves. UV lamps are not tested for efficacy, they can provide Remove and dispose of coats and sleeves before a false sense of security. The safest applications for leaving the work area. UV decontamination are using lamps that are  Wear gloves for all tasks. Change gloves installed inside an enclosure, such as a biosafety frequently, between tasks and if contaminated. cabinet or PCR clean hood. Consult with EH&S Wash hands and put on clean gloves before regarding the safety of any UV decontamination moving to a new work area. equipment prior to purchase or installation.  Follow standard donning and doffing procedures for PPE, and wash hands before leaving the lab. REDUCE CLUTTER AND  Do not bring lab PPE, notebooks or pens home. PERSONAL ITEMS

 Limit clutter in the lab, and be aware that porous items such as notebooks and cardboard can be difficult to decontaminate.  Do not handle personal items such as phones and headphones in the lab or near amplicon work areas.  Consider that personal items such as watches or jewelry on wrists can become contaminated.

Remove personal items or wear lab coats with MONITOR, CLEAN AND wrist cuffs with gloves pulled up over the cuff. DECONTAMINATE COVID-19 TESTING

Work with EH&S to conduct environmental sampling MODIFICATIONS to detect the presence and spread of amplicon contamination. Clean and decontaminate throughout Lab personnel should get tested for COVID-19 if: the day to continually remove amplicons from the lab.  They have had a known close contact with a For chemical decontamination, dilutions of 10% COVID-19 positive person and are not fully bleach should be made fresh daily with a contact time vaccinated; or of at least 10 minutes. Water or 70% ethanol can be  They are experiencing any COVID-19 symptoms used to remove bleach residue. (even if fully vaccinated).  Decontaminate potentially contaminated and When testing for COVID-19, schedule the test in the high touch lab surfaces with 10% bleach daily and morning before working in the lab or after washing between work sessions. hands, showering, and changing clothes after working  Consider DNAZap or DNA Away for degradation in the lab. of nucleic acids in amplicon rich lab areas.  If you test positive or inconclusive for COVID-19,  Decontaminate pipettes, lab pens and other items report this to UW EH&S ([email protected]) and daily and between users. identify yourself to the UW EH&S contact tracer as  Ethanol and isopropanol are not sufficient to a researcher that works with SARS-CoV-2 nucleic remove nucleic acid residue. acid products. Ultraviolet (UV) light can also be used to render DNA  You may be advised by the EH&S contact tracer to non-amplifiable, but the drawbacks to UV disinfection get retested and isolate at home while EH&S are that it cannot reach all surfaces due to shadowing, confirms whether your results are related to an can degrade plastics, and does not work as well as the active infection or a nucleic acid contamination lamps age or get dirty. Most UV lamps are expected to event.

Please contact EH&S Biological Safety at [email protected] or 206-2221-7770 for more information.

Page 2 | May 5, 2021 www.ehs.washington.edu | 206.543.7262 | [email protected]