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 Table of Contents  
Year : 2021  |  Volume : 11  |  Issue : 5  |  Page : 230-236

The medical diagnostic laboratory: Bio-safety precautions for handling and processing of specimens during COVID-19 pandemic

Department of Biochemistry, Sir Ganga Ram Hospital, New Delhi, India

Date of Submission12-Apr-2021
Date of Decision17-Aug-2021
Date of Acceptance10-Sep-2021
Date of Web Publication30-Oct-2021

Correspondence Address:
Dr. Seema Bhargava
Department of Biochemistry, Sir Ganga Ram Hospital, New Delhi
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/cmrp.cmrp_35_21

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The coronaviruses are single-stranded RNA viruses, one of which is responsible for the current outbreak of coronavirus disease-19. COVID-19 has affected health-care workers including laboratory personnel worldwide in an alarming and unprecedented manner. In India too, the huge number of infected health-care staff has further weighed down our already over-burdened health-care system. While their protection is of paramount importance, it is also essential that these personnel adhere to the specific bio-safety practices to minimize their exposure to this disease. In this article, our objective is to provide guidelines for laboratories while working with COVID-19 samples to reduce the human and economic burden in the current pandemic. A risk assessment of all policies must be done and standard operating procedures on all 'Safe Laboratory Practices and Procedures' must be readily available for the staff. Dividing the laboratory functions into three broad phases, namely pre-examination, examination and post-examination, the precautions outlined for each stage must be followed stringently with the frequency defined as per the workload of the laboratory. The safety measures must cover all the laboratory processes including sample disposal. Decontamination too plays a major role and must be performed as per the standard national and international guidelines. Hence, following special precautions in the laboratory while working through the COVID-19 pandemic will not only minimize the risk of infection to the laboratory staff and but also help reduce the mortality and morbidity associated with this disease.

Keywords: COVID-19, health-care workers, laboratory, precautions

How to cite this article:
Bhargava S, Manocha A, Kankra M, Singla P, Sharma A, Sharma M. The medical diagnostic laboratory: Bio-safety precautions for handling and processing of specimens during COVID-19 pandemic. Curr Med Res Pract 2021;11:230-6

How to cite this URL:
Bhargava S, Manocha A, Kankra M, Singla P, Sharma A, Sharma M. The medical diagnostic laboratory: Bio-safety precautions for handling and processing of specimens during COVID-19 pandemic. Curr Med Res Pract [serial online] 2021 [cited 2021 Dec 3];11:230-6. Available from: http://www.cmrpjournal.org/text.asp?2021/11/5/230/329701

  The Medical Diagnostic Laboratory: Special Precautions in COVID-19 Pandemic Top

The coronavirus was first detected in 1965 as B814 by Tyrrel and Bynoe in the human embryonic tracheal organ cultures obtained from the respiratory tract of an adult suffering from the common cold. Around the same time, Hamre and Procknow grew a virus from the samples obtained from medical students suffering from a cold. Both the B814 and Hamre's virus (which she named 229E) had the same properties unrelated to any known myxo or paramyxo viruses. However, again, around the same time, McIntosh et al. identified several strains of ether-sensitive infecting agents from cultures taken from human respiratory tracts. Since they were grown in organ cultures, these viruses were named 'OC'. In the late 1960s, virologists found that some human and animal viruses-infectious bronchitis virus, mouse hepatitis virus, transmissible gastroenteritis virus of swine – all demonstrated the same morphological features on electron microscopy, including the crown-like appearance of the surface projections. This group of viruses was, therefore, named coronavirus.[1]

The coronaviruses are positive sense single-stranded RNA viruses. In the past five decades, seven strains of this virus have been identified that infect humans causing respiratory symptoms of varying severity and mortality. These are (1) HCoV-229E causing mild respiratory disease (mostly common cold), (2) HCoV-OC43 causing mild respiratory disease (mostly common cold), (3) HCoV-NL63 causing mild respiratory disease, (4) HCoV-HKU1 causing mild respiratory disease, (5) SARS-CoV causing severe acute respiratory syndrome (2003) 9% mortality, (6) MERS-CoV causing Middle East respiratory syndrome (MERS) (2012) 30% mortality and (7) SARS-CoV2 causing severe acute respiratory syndrome (2019) 2.17% mortality as of 04/04/2021. Of these, the HCoV-229E (1) and HCoV-NL63 (3) belong to the alpha genus.

The COVID-19 pandemic has affected the world since the fall of 2019 and has taken a huge toll on global mortality and morbidity. The health-care community was worst affected, with 3.8% health-care workers (HCW) affected in China and an alarming 10.7% in Italy. In India too, the huge number of COVID infections further weighed down our overburdened health-care system with 10.9 million cases of COVID-19, the second maximum number of cases only after the USA, and an official death figure of 165,101 (1.31%) as on 4th April, 2021.[2] With 0.76 doctors and only 0.7 beds for admission per 1000 people, Indian HCWs had a daunting task of dealing with the pandemic.[3] Right through this unparalleled medical calamity, laboratories played an exceedingly important role in isolating the virus as well as in diagnosing the disease. Hence, the protection of its health staff by following the recommended bio-safety procedures is of paramount importance to minimise their risk of infection.

Due to the high transmissibility of the causative virus, SARS CoV 2, extra precautions are required to be taken by health-care workers including laboratory personnel while dealing with patients or potentially infective body fluids and tissues. The International Federation of Clinical Chemistry and Laboratory Medicine (IFCC), in March, 2020, released their recommendations on the role of the laboratory and appropriate safety measures during the current pandemic.[4] In August, 2020, IFCC also published an information guide on COVID-19 and this has been updated from time-to-time describing the role of the laboratory at different stages of patient care, through epidemiological surveillance, diagnosis, prognosis, therapeutic monitoring and post-infection surveillance.[5]

In this article, our objective is to provide the guidelines for safe working practices specifically during COVID-19, including hand hygiene and proper use of personal protective equipment (PPE) for laboratories functioning at bio-safety levels (BSLs) 1-3 to protect our key medical staff and reduce the human and economic burden in the current pandemic. Since the diagnostic accuracy of laboratory results depend on various factors in the pre-examination, examination and post-examination phases, it would also be pertinent to stress on the importance of staff training and the risk analysis that needs to be implemented for each process so as to minimize all possible risks due to the virus.

  Bio-Safety Levels Top

BSLs are ranked from 1 to 4 with each level having specific controls for containment of biological agents and microbes [Table 1]. The primary risks that determine the levels of containment are the nature of the work conducted, transmissibility, infectivity and severity of disease. All “standard precautions” should be followed in BSL facilities with strict hand hygiene and decontamination of surfaces should be done routinely.[6]
Table 1: Bio-safety recommendations for clinical laboratories in the Covid-19 pandemic

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BSL 1, the lowest level, applies to clinical laboratory work posing minimal potential threat to the personnel and environment and do not consistently cause disease, such as exposure to  Escherichia More Details coli. These laboratories should be separated by doors from the rest of the facility and work here can be done on open benches using basic PPE of level D.

BSL 2 includes laboratories where work is associated with pathogenic or infectious organisms causing moderate hazard of disease, such as Hepatitis A virus, Staphylococcus aureus. BSL 2 laboratories have the next higher level of barriers, i.e. speciality safety equipment and facilities, sink and a readily available eyewash station and self-closing doors installed at all access points. Personnel wear level C PPE and most operations are performed within class I biological safety cabinets (BSCs). Access regulations of these laboratories are stricter than for BSL 1 facilities with restricted or no entry for immunocompromised and immunesuppressed personnel. Negative-pressure containment is generally maintained and exhausted air may require filtration.

BSL 3 practices are required for all agents (viruses and bacteria) that may cause serious or lethal disease via aerosol transmission, like inhalation of particles or droplets, for example, Mycobacterium tuberculosis, SARS COV 2. These laboratories require higher level of protective primary barriers, including solid-front wrap-around gowns, scrub suits or coveralls and respirators (Level B PPE). Self-closing double-door access separating the laboratory from general corridors is mandatory at all times including use of class II BSC. Ventilation must be maintained through ducted, directional airflow by drawing air into the laboratory from clean areas and no recirculation allowed. In case of accidental exposure, samples must be collected from all at-risk personnel for appropriate testing.

BSL 4 facilities provide maximum protection and containment while working on extremely dangerous agents posing high risk of life-threatening disease, like the Ebola virus or agents with unknown risks of pathogenicity and transmission. BSL 4 laboratories are made in separate buildings or isolated zones, with dedicated air supply and exhaust ventilation, the air stream being filtered through high-efficiency particulate air filters. Level A PPE is used and all work performed in class III BSC. Along with BSL 3 practices, additional requirements for BSL 4 laboratories are change of clothing before entry, a shower on exit and decontamination of all materials before leaving the facility. Globally, just a few BSL 4 laboratories exist, including the National Institute of Virology, Pune, India.

  Hand Hygiene Top

Hand washing, a simple, public health measure was one of World Health Organisation's (WHO) initial recommendations when the COVID-19 pandemic had just started and little was known about the novel coronavirus. Alongside the use of masks, today hand hygiene persists as one of the most important ways to prevent COVID-19 transmission. Just 20 seconds of scrubbing with a 70% alcohol-based hand sanitiser or with soap and water can wash away the coronavirus in addition to other common infectious diseases such as typhoid and cholera.[7]

  Personal Protective Equipment Top

Since PPE serves as a barrier between the body (a viable host) and the infectious material, three important things must be considered while selecting its suitability for handling COVID-19 specimens. These include the types of anticipated exposure, durability and appropriateness of the PPE for the task and finally the fit. The components of PPE include goggles, face shield, mask, gloves, respirators, coverall/gowns, head cover and shoe covers. They provide protection to the respiratory system, eyes, skin, hands, feet, face, head, body and based on the degree of protection offered, PPE is divided into four categories D (lowest) to A (highest). Levels of PPE worn by laboratory staff are dictated both by the nature of the pathogens being tested and the type of work being performed [Table 1]. However, a thorough risk assessment for the level of PPE to be used should always be done as per the different laboratory procedures. All laboratory staff must be trained in donning and doffing as well as disposal of used PPE. Appropriate signage, an alcohol-based hand rub, checklist and chairs should be available in designated donning and doffing area.[8]

  Staff Training Top

The ISO 15189:2012 in clause 5.1.5 specifies the broad areas in which training of the staff must be carried out, including health and safety. With the emergence of COVID-19, training of staff in safe handling of specimens containing the SARS CoV-2 virus has become a top priority. Since this virus is highly contagious, continuous training and retraining in the safety measures is the key to a safe working environment in the laboratory and hence must be incorporated in the training curriculum.[9]

It is essential that standard operating procedures (SOPs) on 'Safe Laboratory Practices and Procedures' with special emphasis on precautions to be taken during the pandemic, be readily available for the laboratory personnel in the language easily understood by them. These practices must also be an important part of the induction training of the new employees. Procedures such as training and re-training, pre- and post-training competency assessments and SOP's with 'Read and Understood' documentation should be adopted so that the entire laboratory staff is trained in the safe handling of samples. Specialized training on inhalation and ingestion risks, handling, decontamination and disposal of hazardous samples and post-exposure prophylaxis should be incorporated in the daily safety practices. The conventional face to face concept of teaching should be avoided and replaced by online trainings/classes on any of the digital video conference platforms. To promote social distancing, spacing out of laboratory work stations and staggered meal timings are recommended.

While training the laboratory personnel, individual learning differences must be taken into account so that the gaps in knowledge can be overcome by revision of training and regular evaluations. Post-training as well as at regular interval competence assessments is a good way to assess the effectiveness of training.

  Risk Analysis Top

To assess the risk of COVID-19, it is important to understand the work processes that cause transmission of the virus, the laboratory personnel who are at greater risk of acquiring infection and whether this risk is controllable or uncontrollable. A risk assessment plan should be developed in the laboratory which includes risk identification, assessment and mitigation [Figure 1]. Probability and severity ratings should be calculated to identify the final hazard score. The WHO has also developed a risk assessment tool to determine the risk of SARS CoV-2 infection in the HCWs as per their job responsibilities.[10],[11]
Figure 1: Risk assessment plan for laboratories during COVID-19

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  Pre-Examination Phase Top

Sample collection

Improper or inadequate collection of the samples can lead to erroneous results and consequently misdiagnosis of the patients' condition. Hence, sample collection forms the critical first step in the entire process of testing. A separate dedicated area with adequate privacy must be provided for collection. Patients should maintain social distancing of minimum 6 feet while waiting for phlebotomy and face masks should be made mandatory. Phlebotomy chairs must be sanitised after every use and phlebotomy room decontaminated. Based on the WHO guidelines, all specimens (swabs, body fluids, blood and faeces etc.) must be treated as potentially infectious [Table 2].[12] Phlebotomists, wearing appropriate PPE, should be specifically trained for the sample collection of suspected or confirmed COVID patients. Since face shields provide good facial protection, they may be used if splattering or splashing of infected body fluids or liquids is anticipated. Re-use of tourniquets can facilitate spread of virus, so the use of disposable tourniquets should be preferred.[13]
Table 2: Viral content in various specimen types

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A comprehensive and detailed SOP for sample collection must be available to all the phlebotomists with special emphasis on the collection techniques of the specific samples required for diagnosing COVID-19. During phlebotomy, care should be taken to see that the primary containers are neither under nor overfilled. The specimens should be appropriately labelled and the surface of the tubes decontaminated before being transported to the laboratory. After swabbing the tonsils and posterior pharynx, the oro-pharyngeal swab should be placed in the labelled tube containing viral transport medium (VTM). The nasal swab, after obtaining the specimen from both the nostrils, is also placed in the VTM tube containing the throat swab. It is recommended that ready-to-use VTMs be free from turbidity or any growth and should be used within their expiry date. However, in case any turbidity is detected, the whole batch of VTMs must be discarded.[14] The biowaste generated during the process of sample collection must be disposed as per the latest guidelines.

A novel method for the collection of throat or nasal swabs has been used in the current pandemic in the form of a chamber called COVSACK (COVID Sample Collection Kiosk).The advantage of this chamber is that it can be sprayed with fine droplets of disinfectant and can be sanitized within 3 min. This chamber reduces the number of PPEs used during phlebotomy, while at the same time, providing adequate protection to the phlebotomist.[15]

Sample packaging and transport

Maintaining the quality of samples is top priority for diagnostic accuracy; therefore, it is important that a robust transportation protocol for the samples be designed and the concerned laboratory staff be well trained. Viral samples must be transported as category A, UN2814 (Infectious Substance affecting humans) and safe packaging and transport of samples be done as per UN3373 (Biological Substance Category B).[16]

Samples should be transported immediately to the laboratory, at the recommended temperatures, within the specified time frame [Table 3] and with the requisite patient information. The sample vacutainers must be transported in triple packaging with universal precautions. This involves placing primary tubes in one leak proof covering, followed by the second leak proof layer and then placing them in a transportation box labelled with a bio-hazard symbol.[17] The VTM containing part of the tube should be in direct contact with the frozen gel packs during transportation. Repeated freezing and thawing of specimens should be avoided. Earlier, the Centre for Disease Control and Prevention (CDC) had recommended that no COVID confirmed or suspected samples should be transported through the pneumatic shute system for fear of possible aerosol formation and virus dissemination. However, this directive has recently been modified; samples can now be transported via pneumatic tube systems, with the exception of respiratory specimens, which should be transported manually in an upright position.[18],[19]
Table 3: Collection and recommended temperatures for transportation and storage of COVID-19 specimens

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Sample receipt and processing

Since COVID-19 can spread to the laboratory staff during sample collection, transportation or processing, the vacutainers/other sample containers must be disinfected at each stage. Once received in the laboratory, the sample containers must be removed from their packaging and wiped with a disinfectant at each stage in the reverse order.

The maximum chance of aerosol formation occurs during centrifugation; hence, it is imperative to centrifuge with aerosol tight lids on swing bucket rotors. The centrifuge should be allowed to come to a complete halt before opening the lid. After use, the rotor or safety bucket of the centrifuge should be decontaminated by spraying with disinfectants and allowing to air dry.[5] In the event of a spill during centrifugation, the spill response procedures outlined in the section of decontamination must be adhered to. BSCs should be used to minimize exposure and to avoid the risk of aerosol generation. It is best to avoid de-capping of tubes; however, if unavoidable, the caps of all evacuated tubes should be removed with help of gauze soaked in 1% hypochlorite solution and in a direction away from face. This procedure should be performed in Class I BSC. Activities such as tissue processing which cannot be conducted within BSC should be separately evaluated and performed.[20]

  Examination Phase Top

General considerations to be followed for prompt, accurate and precise testing in this phase include proper work desk instructions especially for the specialised tests used for diagnosing COVID-19, maintenance and calibration schedules of equipment and verification of new assays, especially the molecular assays, as per standard guidelines. Laboratory staff should also be trained in the internal and external quality assurance policies and procedures of the laboratory so as to provide confidence in the reliability of the test results. Furthermore, adequate supply of reagents and consumables must be maintained and storage at the manufacturers' recommended temperatures must be ensured.[21]

The current approaches for the diagnosis and management of COVID-19 infection include molecular and serological testing, viral culture methods, inflammatory markers, biochemical and haematological analysis. The use of BSCs should be promoted and technical SOPs followed to prevent any errors such as misinterpretation of expression profiles, lack of harmonisation of primers and probes, non-specific polymerase chain reaction annealing, etc.[22]

To prevent aerosol generation, fully automated analysers should be preferred over semi-auto-analysers. Liquid waste generated from these analysers should be collected in closed containers, autoclaved and then disposed.[23] The use of plastic tissue grinders in histopathology should be preferred and frozen sections avoided. Cryostats should be shielded and wearing of face shields by the operator when using them is mandatory. After use, the cryostats should be decontaminated by bringing the temperature to 20° centigrade. The use of forceps is advisable while handling films and smears for microscopy and all slides should be autoclaved before disposal.[24]

  Post-Examination Phase Top

This phase includes the important steps of review and reporting of results by authorised personnel, as well as decontamination and disposal of biomedical waste, with the latter two becoming even more critical in this pandemic.

  Decontamination Top

The WHO recommends the use of disinfectants that are effective against enveloped viruses similar to novel coronavirus such as MERS due to the comparable genetic characteristics. Some commonly used disinfectants used in the laboratory are mentioned in [Table 4] while less effective biocidal agents may also be used as per manufacturer's instructions for the disinfection of general surface and equipment. The minimal contact time recommended for surface disinfection is 1 minute or as per the manufacturer instructions. In case of large spills of blood or body fluids, the WHO has recommended 1% sodium hypochlorite for a contact period of 30 min. Particular attention should be paid not only to the selection of the disinfectant but also to the contact time, dilution (i.e. concentration of the active ingredient) and the period of stability of the prepared working solution. It is important that the disinfectants be freshly prepared and consumed within 24 hours for maximum efficiency.[5],[24],[25],[26]
Table 4: Common disinfectants for laboratory use

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As per the IFCC task force recommendations on laboratory safety in COVID-19 pandemic, all working surfaces/work benches, instruments and frequently touched surfaces in the laboratory (e.g. door handles, refrigerators, freezers, etc.,) should be disinfected more frequently, perhaps every 3 hours. Equipment should be disinfected at the start and end of sample analysis. At the end of the day, the final surface decontamination should include a wipe-down of the work stations. A second wiping with sterile water is needed when a corrosive disinfectant such as bleach is used.[7]

As complete inactivation of slow viruses called 'prions' is difficult to achieve, it is important to stress upon the use of disposable instruments and a disposable protective covering for the work surfaces of the BSCs whenever possible.[8]

  Disposal of Biomedical Waste Top

Laboratory biomedical waste includes all blood/tissue specimens, all disposables used in sample collection/processing and used PPE. Adequately labelled biohazard containers for the collection of waste should be placed near the working areas. All contaminated sharps, also treated as infectious waste, should be disposed in puncture proof containers fitted with lids. This infectious waste is to be collected in coloured bags as per the national and international guidelines for the disposal of biomedical waste recommendations and autoclaved at 121°C and 15 psi for 60 min using chemical and/or biological indicators. These are then labelled as 'COVID-19 waste' and handed over to a certified biomedical waste treatment facility in double layered bags for disposal. Since all specimens collected for COVID testing are considered potentially infectious, laboratory personnel must adhere to the guidelines. During the process of waste disposal also, it is imperative to use appropriate PPE and maintain proper hand hygiene practices.[24],[25]

  Occupational Health Top

The risk to the laboratory staff during the pandemic should be assessed and appropriate bio-safety guidelines, as recommended by the international agencies such as CDC and WHO followed. Daily temperature monitoring and hand hygiene of the laboratory personnel should be promoted. Any exposure of the staff to a suspected or confirmed case of COVID-19 should be reported to the COVID-19 clinic of their institution or the nearest hospital and medical advice sought. In case of any staff member testing positive, contact tracing and quarantine measures should be immediately put in place. Post-exposure, the working area or equipment should be appropriately decontaminated. Trainings and retraining on occupational health should be conducted at regular intervals. WHO also developed a technical guidance document regarding COVID-19 for HCWs which elaborates their rights, roles and responsibilities. Risk assessment tool to determine the risk of SARS CoV-2 infection in the HCWs as per their job responsibilities.[11],[27]

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Conflicts of interest

There are no conflicts of interest.

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  [Figure 1]

  [Table 1], [Table 2], [Table 3], [Table 4]


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