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Working with SARS-CoV-2 samples

Sample processing, storage and disposal

What rules and occupational safety measures apply for which types of SARS-CoV-2 samples? Find useful information here.

Latest recommendations

The Committee on Biological Agents (ABAS) has classified the SARS-CoV-2 pathogen as risk group 3 and protection level 2 (resolution 1/2020 dated 19 February 2020, last updated on 1 Ovtober). There are currently no specific official recommendations for activities at biobanks. Hence the German Biobank Node (GBN) and German Biobank Alliance (GBA) are following the ABAS recommendation on safety measures during sampling and diagnostics of SARS-CoV-2 (resolution 6/2020 dated 1 October 2020). GBN has also interviewed a number of biosafety officers at various sites in Germany on the subject.

According to the ABAS, non-targeted activities for laboratory diagnostics of SARS-CoV-2 – based on biological specimens (e.g. sample preparation and processing, and virus inactivation for molecular biology techniques, PCR) – can be performed under protection level 2 conditions.

BioStoffV identifies a total of four protection levels to which activities involving biological agents from the various risk groups are assigned. The regulations are referred to as levels, as the regulations for the lower protection levels also apply to the higher ones – so in this case, the regulations of levels 1 and 2 are relevant. These relate to constructional, technical and organisational measures as well as to employees’ personal protective equipment. The Technical Rules for Biological Agents TRBA 100 (5) and TRBA 250 (4) inform on the requirements for these protection levels.

In the following presentations, Bettina Meinung (QM Core Team, GBN) and Dr. Jörg Schibel (Biosafety Officer, University Hospital Tübingen) outline the recommendations and regulations, and discuss their implementation by biobanks. Meinung and Schibel gave these presentations during a GBN webinar on handling infectious samples held on 29 April 2020. See here for the full webinar documentation.

 

Handling different types of samples

According to the current state of knowledge, the SARS-CoV-2 virus can be transmitted by inhaling aerosols and through contact with mucous membranes (nose, mouth, eyes). According to the ABAS resolution dated 1 October 2020, vessels containing respiratory samples should therefore only be opened in a Class II biosafety cabinet with laminar air flow. During the exchange with GBN, the biosafety experts recommended that all SARS-CoV-2 sample types in which the virus is detectable should be handled in a Class II biosafety cabinet. They also stated that the separate storage of SARS-CoV-2 samples is not necessary as long as the samples are labelled accordingly.

Information on the different types of samples, their handling in case of non-targeted activities and storage is detailed below.

Sample type

Handling (non-targeted activities)

Storage

Swabs
Upper respiratory tract: nasopharyngeal and oropharyngeal swabs
Lower respiratory tract: bronchoalveolar lavage (BAL), sputum, tracheal aspirate

Protection level 2
Class II biosafety cabinet 1
Respiratory mask (min. FFP-2) recommended 1

Protection level 2,
separate storage not necessary

Plasma, serum, whole blood, PBMCs

Protection level 21
Class II biosafety cabinet 2
No/hardly any virus detectable 3, 4, 6, 8

Protection level 2,
separate storage not necessary

Stool

To be handled like blood: Class II biosafety cabinet 2
Virus detectable 3, 4, 5, 7, infectivity not clarified

Protection level 2,
separate storage not necessary

Urine

No virus detectable 3,4,5

Protection level 2,
separate storage not necessary

Last updated: 12.05.2020

Virus inactivation

To minimise the risk of infection, virus inactivation is recommended when processing SARS-CoV-2 samples. Inactivation should above all be considered for highly infectious samples from the respiratory tract. It should be noted, however, that this may render the samples unusable for certain subsequent analytical procedures.

In general, work with samples containing viruses should be carried out in a Class II biosafety cabinet until the final step of inactivation. In preparation for a polymerase chain reaction (PCR) test to detect the virus, it is possible to render the virus inactive through proteinase K digestion by heating briefly at 70°C (approx. five minutes). Another possibility for chemical inactivation is to use 6 M guanidinium isothiocyanate, which destroys the virus envelope after a few seconds and exposes the RNA.

Disposal

In its recommendation on occupational health and safety measures for sampling and diagnosis of SARS-CoV-2, the ABAS (resolution of 01.10.2020) recommends the disposal of non-liquid waste according to waste code 18 01 04. According to the classification of the Robert Koch Institute, such waste includes disposable items such as syringe bodies. According to the ABAS decision, the usual occupational safety measures must be observed and personal protective equipment must be worn when disposing of these items. Those responsible would have to pack the waste into closed and tear-proof plastic bags - used pointed or sharp objects such as cannulas and scalpels into unbreakable and puncture-proof containers.

Liquid waste such as smear media or vessels filled with blood or secretion would first have to be inactivated or disposed of in tear-proof, moisture-resistant and sealed containers in accordance with waste code number ASN 18 01 03*.

 

Further literature

  1. Resolution of the Committee on Biological Agents (ABAS) dated 1 October 2020
  2. Recommendation from biosafety experts from various sites in Germany (conference with GBN on 16 April 2020)
  3. Detection of SARS-CoV-2 in Different Types of Clinical Specimens. Wenling Wang, Yanli Xu, Ruqin Gao et al. JAMA. Published online on 11 March 2020. doi: 10.1001/jama.2020.3786
  4. Clinical presentation and virological assessment of hospitalized cases of coronavirus disease 2019 in a travel-associated transmission cluster. Roman Woelfel, Victor Max Corman, Wolfgang Guggemos, Michael Seilmaier, Sabine Zange, Marcel A Mueller, Daniela Niemeyer, Patrick Vollmar, Camilla Rothe, Michael Hoelscher, Tobias Bleicker, Sebastian Bruenink, Julia Schneider, Rosina Ehmann, Katrin Zwirglmaier, Christian Drosten, Clemens Wendtner. 2020. doi: https://doi.org/10.1101/2020.03.05.20030502
  5. Evidence for gastrointestinal infection of SARS-CoV-2. Fei Xiao, Meiwen Tang, Xiaobin Zheng, Ye Liu, Xiaofeng Li, Hong Shan. Gastroenterology. 2020. doi: https://doi.org/10.1053/j.gastro.2020.02.055
  6. SARS-CoV-2 asymptomatic and symptomatic patients and risk for transfusion transmission. Victor M. Corman, Holger F. Rabenau, Ortwin Adams, Doris Oberle, Markus B. Funk, Brigitte Keller-Stanislawski, Jörg Timm, Christian Drosten, Sandra Ciesek. 2020. medRxiv preprint doi: https://doi.org/10.1101/2020.03.29.20039529
  7. Asymptomatic cases in a family cluster with SARS-CoV-2 infection. Pan X, Chen D, Xia Y, Wu X, Li T, Ou X, Zhou L, Liu J. 2020. Lancet Infect Dis 20(4):410–1.
  8. Transcriptomic characteristics of bronchoalveolar lavage fluid and peripheral blood mononuclear cells in Covid-19 patients. Yong Xiong et al. 2020. Emerging Microbes & Infections, 9:1, 761-770, DOI: https://doi.org/10.1080/22221751.2020.1747363

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