Safety for Biobanks: Strategies for Safe COVID-19 Specimens Handling

A schematic representation of safety strategies for COVID-19 biobanks
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The COVID-19 pandemic has spread to almost every country around the world. In less than 4 months, this new disease has affected more than 1,800,000 people and caused almost 120,000 deaths. There are no effective treatments or vaccines for COVID-19. Therefore, while scientists search for therapeutic options, many governments have turned to patient testing and contract tracing to control the outbreak.

This has put biobanks at the forefront of COVID-19 pandemic control. High quality COVID-19 specimens are essential to both diagnostic testing and research, and biobanks are a vital repository for these specimens.

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The Risks of Working with COVID-19 Specimens

COVID-19 is caused by the newly identified virus, SARS-CoV-2. COVID-19 biobank workers are understandably concerned about their safety and how to best protect themselves against this new virus. It is not yet clear exactly how SARS-CoV-2 is transmitted. However, studies have found SARS-CoV-2 viral RNA in feces, blood and saliva (1). Moreover, other coronaviruses, such as MERS-CoV, responsible for the Middle East Respiratory Syndrome outbreak in 2012, are spread by droplets, fomites and aerosolized virus (2). This means that human biospecimens, particularly those from the respiratory tract of COVID-19 patients, pose a significant risk for biobank staff (3).

To mitigate these risks, many governments have issued safety guidelines for COVID-19 biobanks. The good news for biobank personnel is that these guidelines generally follow Good Laboratory Practices and standard biological safety precautions for work with infectious materials. Many COVID-19 biobanks already work within these safety standards and so should be set up to maintain safety.

Staff Training

Staff training is a key part of maintaining COVID-19 lab safety, according to guidelines from the U.S. Centers for Disease Control and Prevention (CDC) and the U.K government (3,5). Lab managers are responsible for ensuring that all staff are competent and up-to-date with COVID-19 guidelines, risk assessments, Standard Operating Procedures (SOPs), emergency procedures and general safety precautions (1, 9). A Laboratory Information Management System (LIMS) can help keep biobank documents in one, easy-to-find place and record all staff training.

CloudLIMS, a COVID-19 LIMS, helps manage training and competency records of personnel working with COVID-19 specimens

Risk Assessments

Both the CDC and the UK government recommend that labs undertake site-specific and activity-specific risk assessments for any work involving COVID-19 specimens (3,5). This includes assessing whether assays and testing procedures can cause the spread of aerosolized virus or droplets. COVID-19 biobanks can use a LIMS to keep all risk assessments up-to-date and in one central place. A LIMS can also keep track of which staff members have read a risk assessment .

Staff Communication and Biospecimen Labeling

Guidelines recommend that all biospecimens from COVID-19 patients are clearly labeled and that staff collecting specimens notify biobank workers of any potentially infected samples (5). A LIMS platform can ensure accurate biospecimen labeling and tracking.

Biospecimen Handling

The quality of biospecimens can significantly impact diagnostic testing, preclinical and clinical research. Poor quality specimens lead to inaccurate test results and experimental errors. Therefore it is very important, both to maintain sample quality and to ensure COVID-19 lab safety, that all staff use validated SOPs and standard biological safety procedures when handling any COVID-19 specimens (3,5).

Labs can perform routine COVID-19 diagnostic testing in BSL-2 labs in the U.S. or CL2 labs in the U.K (3,5).  Routine testing includes using automated instruments, processing specimens, and staining or microscopy of fixed smears or formalin-fixed tissue. However, any work culturing or propagating SARS-CoV-2 must be done in a BSL-3 or CL3 lab (1,3,5).

All work with COVID-19 specimens should be done in a certified Class II Biological Safety Cabinet with a HEPA filter (1). Likewise, staff should use HEPA-filtered incubators to culture any COVID-19 specimens (1). Wherever possible staff should decontaminate the outside of specimen containers before removing them from the safety cabinet (3).

Personal protective equipment (PPE), including disposable gloves, laboratory coat or gown, and eye protection, is essential for COVID-19 biobank safety. Biobanks should have a dedicated area where staff can don and remove PPE. It is just as important for staff to wash hands before leaving the lab (3,5).

Storage

Controlled and monitored storage conditions are another key part of maintaining sample quality. COVID-19 biospecimens are potentially infectious and so should be stored in a BSL-2/CL2 lab or higher (1). Staff can use a LIMS to track the location and storage conditions of all biospecimens and thus maintain sample integrity and COVID-19 biobank safety (8).

Packaging and Shipping

The World Health Organization recommends COVID-19 biospecimens be shipped at 2-8°C for a short time period or frozen at -70°C in a viral transport medium and shipped on dry ice (6). COVID-19 biospecimens must be packaged and shipped according to national and international (if applicable) regulations for biological substances and dangerous goods (5). Each country has specific labeling, documentation and transport requirements. Biobank and lab staff can use a COVID-19 LIMS to make sure they have the correct documentation that complies with local guidelines. A LIMS can also track shipping conditions such as temperature to help maintain biospecimen quality.

A free COVID-19 LIMS for biobanks to seamlessly locate stored COVID-19 specimens and to track incoming and outgoing shipments

Cleaning and Waste Handling

All work surfaces and equipment should be decontaminated with a disinfectant effective against enveloped RNA viruses (3,5,7). Biobanks can dispose of any COVID-19 specimens as biohazardous waste with no additional precautions (5).

Industry Support for COVID-19 Testing

The Federal Emergency Management Agency (FEMA) and the U.S. Department of Health and Human Services (HHS) are helping public health laboratories to access supplies and reagents for COVID-19 diagnostic testing free of charge (10). Some companies are also offering their products free of charge to help the world fight the global pandemic. CloudLIMS, an ISO 9001:2015 certified informatics company, is offering its pre-configured, COVID-19 LIMS free of charge to COVID-19 diagnostic testing, research laboratories & biobanks, enabling them to set up in days, seamlessly manage data, automate workflows, and follow international standards and best practices, such as CLIA, ISO 15189, HIPAA, ISO 20387, GLP, etc.

Conclusion

Biobanks play an essential part in controlling the COVID-19 pandemic. A LIMS can help maintain biospecimen quality and biobank safety by allowing complete tracking of all biospecimens and comprehensive documentation of safety procedures, risk assessments, staff training, specimen shipping and storage conditions.

References

  1. COVID-19 Biospecimen Guidelines. University of California San Francisco Office of Research (Online). Accessed Apr 9, 2020 at: https://research.ucsf.edu/covid-19-biospecimen-guidelines
  2. Middle East Respiratory Syndrome (MERS) Transmission. Centers for Disease Control and Prevention (Online). Accessed Apr 10, 2020 at: https://www.cdc.gov/coronavirus/mers/about/transmission.html
  3. Guidance COVID-19: safe handling and processing for samples in laboratories. GOV.UK (Online). Accessed Apr 10, 2020 at: https://www.gov.uk/government/publications/wuhan-novel-coronavirus-guidance-for-clinical-diagnostic-laboratories/wuhan-novel-coronavirus-handling-and-processing-of-laboratory-specimens
  4. SARS (Severe Acute Respiratory Syndrome). World Health Organization (Online). Accessed online at: https://www.who.int/ith/diseases/sars/en/
  5. Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19). Centers for Disease Control and Prevention (Online). Accessed Apr 10, 2020 at: https://www.cdc.gov/coronavirus/2019-ncov/lab/lab-biosafety-guidelines.html
  6. Laboratory testing for coronavirus disease (COVID-19) in suspected human cases. World Health Organization. March 19, 2020. https://apps.who.int/iris/handle/10665/331501
  7. Pesticide Registration. List N: Disinfectants for Use Against SARS-CoV-2. United States Environmental Protection Agency (Online). Accessed Apr 10, 2020 at: https://www.epa.gov/pesticide-registration/list-n-disinfectants-use-against-sars-cov-2
  8. Biobanking Best Practices for COVID-19 Specimens https://cloudlims.com/blog/biobanking-best-practices-for-covid-19-specimens.html
  9. COVID-19 Clinical Data Management using LIMS https://cloudlims.com/blog/covid-19-clinical-data-management-using-lims.html
  10. Laboratory Capacity. Get and Keep America Open: Supporting states, tribes, localities, and territories. Accessed Apr 21, 2020 at: https://www.cdc.gov/coronavirus/2019-ncov/php/open-america/laboratory.html
Shonali is the Chief Operating Officer at CloudLIMS.com. In a career spanning over twenty years, Shonali Paul has built a long and impressive track record of success in high technology bioinformatics workflow solutions, strategic collaborations, developing operational strategy and directing new business initiatives from conception through execution. She has helped build the research and development center and is the key driver of the product and scientific teams. She has been extensively published in journals such as Biopreservation and Biobanking and Lab Manager and has given numerous talks at ISBER, ESBB, and Labroots. She has been a member of the marketing committee and the IT working group and is now the chair of the Member Relations Committee at ISBER, the International Society for Biological and Environmental Repositories.