Journal of Cytology
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Year : 2020  |  Volume : 37  |  Issue : 2  |  Page : 67-71
Indian academy of cytologists national guidelines for cytopathology laboratories for handling suspected and positive COVID-19 (SARS-COV-2) patient samples

Indian Academy of Cytologists, India

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Date of Submission08-Apr-2020
Date of Acceptance08-Apr-2020
Date of Web Publication23-Apr-2020


COVID-19, caused by the SARS-CoV-2 virus, has been declared a pandemic by the World Health Organization. This scenario has impacted the way we practice cytopathology. Cytology laboratories receive fresh and potentially infectious biological samples including those from the respiratory tract, from COVID-19 positive or suspected patients. Hence, the Indian Academy of Cytologists thought it necessary and fit to bring forth appropriate guidelines starting from transportation, receipt, processing, and reporting of samples in the COVID-19 era. The guidelines are prepared with the aim of safeguarding and protecting the health care personnel including laboratory staff, trainees and cytopathologists by minimizing exposure to COVID-19 so that they remain safe, in order to able to provide a continuous service. We hope that these national guidelines will be implemented across all cytopathology laboratories effectively.

Keywords: COVID-19, cytology, cytopathology, guidelines, SARS-CoV-2

How to cite this article:
Srinivasan R, Gupta P, Rekhi B, Deb P, Nijhawan VS, Prasoon D, Iyer V, Mathur S, Gupta N, Kamal M, Goel MM, Chakrabarti I, Jena M, Rao RN, Rajwanshi A, Raju S, Verma S, Pinto R. Indian academy of cytologists national guidelines for cytopathology laboratories for handling suspected and positive COVID-19 (SARS-COV-2) patient samples. J Cytol 2020;37:67-71

How to cite this URL:
Srinivasan R, Gupta P, Rekhi B, Deb P, Nijhawan VS, Prasoon D, Iyer V, Mathur S, Gupta N, Kamal M, Goel MM, Chakrabarti I, Jena M, Rao RN, Rajwanshi A, Raju S, Verma S, Pinto R. Indian academy of cytologists national guidelines for cytopathology laboratories for handling suspected and positive COVID-19 (SARS-COV-2) patient samples. J Cytol [serial online] 2020 [cited 2023 Mar 23];37:67-71. Available from:

Coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) on 11th March 2020. It is the first pandemic caused by a coronavirus, specifically, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2 virus), a member of the betacoronavirus family.[1] The disease emerged in December 2019 with the initial cases reported from Wuhan, the capital city of Hubei province in the People's Republic of China, and soon spread widely to involve more than 190 countries across the globe. As it is caused by a novel coronavirus, the exact pathophysiology of the disease, its course, and therapeutics are not fully understood, as of now. As a result, this pandemic has led to considerable anxiety and panic not only in the general public but also among the health care workers (HCWs). Hence, the executive committee of the Indian Academy of Cytologists along with few co-opted members have prepared guidelines for pre-analytical, analytical, and post-analytical steps in cytopathology laboratory, and which are in the best interests and safety of the laboratory personnel, to provide guidance to the laboratories across India.

The first case of COVID-19 in India was reported on 30 January 2020 in the Kerala state. At the time of this writing, there are around 11,000 COVID-19 positive cases in India, with more than 300 deaths.[2] With each passing day, these numbers continue to swell. Although some experts argue that the disease curve for India is not as steep as for other developed nations of the world, nevertheless, the increasing numbers might soon prove to be overwhelming for the existing health care facilities in India.

As a part of the preventive strategies, many public health care measures, especially social distancing, have been recommended to the masses. Health care facilities have recommended minimizing the nonessential hospital visits and prioritizing the elective inpatient and outpatient procedures. The basic aim of these recommendations is to limit the spread of the disease among the general public as well as among the HCWs. If consistently followed, these measures can lead to less chance of exposure to potentially infectious samples, reduced workload on the lab facilities of a hospital, thereby allowing for convenient reallocation of the laboratory personnel in teams, so that if one team is exposed the others are still available to manage the laboratory.

Cytology is a special branch of pathology where there is a unique opportunity for the cytopathologist to interact with patients at the time of performing procedures, such as fine-needle aspiration cytology (FNAC). At the same time the cytopathologists, cytotechnologists, technicians, and other laboratory personnel are also susceptible to contracting infections, such as COVID19, as they have repeated exposure at close quarters to potentially infectious patients as well as specimens, including oral scrapes, lavage, and sputum. Therefore, it is imperative to have certain guidelines in place, in the best interest of the laboratory staff as well as for patients, whom they cater to.

The World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC) have recommended basic interim guidelines to be adopted for the working of laboratories during the current pandemic.[3],[4] When applied to cytology laboratories, these guidelines can be broadly stratified into the following categories:

  1. Fine needle aspiration in COVID-19 suspected or confirmed cases
  2. Sample processing in the laboratory
  3. Sample discarding
  4. Management of spills in the laboratory
  5. Surface disinfection and equipment decontamination
  6. Care of the laboratory staff
  7. Reporting of the cytology samples
  8. Training of the cytopathology residents.

   Sample/fna Requisition forms Top

In hospitals with hospital information system (HIS) available, online request forms are supported and can be accessed by the laboratory. However, when HIS is not available, the laboratory can e-mail the request form which can be filled and returned by e-mail/WhatsApp to the departments to have a digital workflow (e-requisition forms). If these are not possible in one's setup, it must be ensured that a clean requisition form, filled in by the clinician with all the patient details, should accompany the sample. If the sample is from COVID-19 suspect/positive case, the same must be explicitly mentioned on the request form separately or it may be color tagged.

FNA in COVID-19 confirmed or suspected cases

  • Cytopathologists/cytopathology residents may be expected to perform FNAs from any palpable swellings in suspected or confirmed COVID-19 patients
  • Any such procedure would qualify as close contact and, hence, mandates the use of a complete set of personal protective equipment (PPE) including laboratory gown, gloves, goggles, face shield, and N95 (or powdered air-purifying) respirator.[5] As the pandemic evolves, it is likely to remain in the community and these good clinical-laboratory practices should continue to be observed by the personnel performing FNA including residents/postgraduate trainees/cytopathologists/cytotechnologist/interventional radiologist. At the minimum, the personnel is advised to don a surgical gown, cap, N95 mask, goggles, and adequate face shield
  • Donning and doffing of PPE should be done only in a specially designated area for the same (not in the laboratory itself). Proper guidelines for donning and doffing of such equipment need to be followed[6]
  • Patients who come for FNA should be advised to wear a mask during their entire interaction with the medical team. In case the mask interferes with the procedure, it should be removed by the patient only for that period when its removal is desired. During such a period, when the patient is without a mask, his/her head should be positioned in such a way that they preferably breathe away from the HCW. They should also be counseled not to cough during the entire procedure. In case the patient is uncooperative, the procedure may be abandoned and the referring clinician is informed for further course of action
  • Following the FNA procedure, expelling the material from the needle hub and syringe invariably leads to the generation of droplets and aerosol and, hence, the cytopathologists should be well prepared to minimize the exposure to these. The material should preferably NOT be expelled at all from the needle. However, if inevitable, the same should be expelled very gently from the needle. The personnel should hold their face as far as possible during this procedure. Again, while making a smear it is recommended that slides are held as far as possible from oneself. It is inevitable that spraying of some aspirated material occurs on the table which should be sanitized as per procedure detailed below
  • All PPE must be changed as per doffing guidelines and hand washing must be performed thoroughly for >20 s after the procedure
  • Drying of the smears by shaking them or blowing air should not be done as this can lead to the generation of aerosol. Air-drying of the smears should be ideally performed in class II biosafety cabinets (BSCs)[7]
  • The used needles should be discarded in sharp-resistant waste containers. Burning of needles also can lead to the generation of aerosol and, hence, adequate care is to be used by laboratory staff. The syringe hub should be cut and the entire syringe should be disinfected using solutions with proven action against enveloped viruses including 0.1–1% hypochlorite solution, ethanol in concentrations ranging from 62 to 71%, and 0.5% hydrogen peroxide. Once disinfected, the syringes should be discarded in biohazard waste bags specifically labeled as COVID-19[8],[9]
  • The patient access area/suite is usually located adjacent to the FNA clinic/laboratory. The number of attendants per patient should be restricted to one. In this area, there should be display/standees, preferably in local language/dialect, for patients and their accompanying attendant for educating them to preferably wear a protective face mask, regular hand washing and maintain social distancing. If they are not wearing face masks, they should be counseled that sneezing/coughing should be directed to their sleeve
  • There should be access to soap and water and an alcohol-based sanitizer at the crucial locations within the laboratory.

Sample processing in the cytopathology laboratory

  • Access to the laboratory should be restricted to authorized personnel only
  • Types of samples that can be received in the cytology laboratories, during this pandemic, may include sputum, bronchoalveolar lavage (BAL), endotracheal tube aspirates, and other respiratory secretions[8],[9]
  • The samples should be collected in appropriately labeled, tightly-capped, sterile tubes/containers and sent to the cytopathology laboratory either in a biohazard zip-lock bags kept inside a leak-proof cryobox with a biohazard label or a triple packaging system can be used wherein the primary receptacle containing the sample is kept inside a second protective watertight and leak-proof receptacle which, in turn, is covered by a third receptacle to prevent any kind of physical damage to the secondary receptacle during transport[8]
  • A trained hospital attendant should transport the sample to the laboratory, as soon as possible. Under no circumstance should the material be handed over to the relative of the patient who would be likely in close contact with the patient for transport to the laboratory
  • Cytotechnician should wear protective gear in the form of gown, gloves, cap, N95 mask/triple layer surgical mask, and preferably goggles Fresh, unfixed specimens should be transported by hand, and NOT shipped with pneumatic-tube systems.[3]
  • All fresh cytology samples received in the laboratory should be considered potentially infectious (may contain the SARS-CoV-2 virus even in samples from undiagnosed, asymptomatic patients) and hence, universal precautions need to be followed while handling such samples[3]
  • A number of steps involved in routine sample processing including the opening of the sample containers, removing tightly fitted caps of the tubes, diluting, shaking, vortexing, and centrifugation may lead to aerosol generation. Care should be taken to minimize the exposure to the aerosol generated during the sample processing by using adequate PPE and performing these steps in class II BSCs[7],[8]
  • In case of non-availability of class II BSCs, and if centrifugation is absolutely necessary, the same should be undertaken using capped tubes. Following centrifugation, the lid of the centrifuge should be opened gently and the samples should be rested for full 5 min followed by gentle removal of the caps
  • Fixation of the cytology samples in alcohol-based fixatives (with alcohol concentration more than 70%) or formalin can lead to the inactivation of the novel coronavirus. However, in the case of fixation is done using weaker alcohol-based fixatives, additional precautionary measures as indicated above need to be used[9]
  • The laboratories routinely practicing rapid onsite evaluation (ROSE) should use this as a judgment call and should restrict this to significant cases. The personnel involved in ROSE technique should use PPE.

Sample discarding

  • All the residual samples should be discarded in appropriate disinfectants with confirmed virucidal activity against enveloped viruses. These include 0.1% sodium hypochlorite solution, 0.5% hydrogen peroxide, 62–71% ethanol, quaternary ammonium compounds, or phenolic solutions[8],[10]
  • The sample tubes and containers should also be disinfected by adding in 0.1-1% hypochlorite solution (to be prepared fresh each day) or other disinfectant solutions as previously recommended, followed by discarding in separate biohazard waste bags labeled as COVID-19.[8] Please note that single-use tubes are recommended, their cleaning and subsequent re-use are discouraged.

Management of sample spills in the laboratory

  • The decontamination of laboratory surfaces in the event of sample spillage should be done immediately using appropriate disinfectants with proven virucidal action against enveloped viruses. The most commonly used is a 1% sodium hypochlorite solution.[8]

Surface disinfection and equipment decontamination

  • The SARS-CoV-2 virus has been shown to remain viable on inanimate surfaces for up to 3 days. Hence, it is recommended to decontaminate all laboratory surfaces multiple times a day, using appropriate disinfectant solutions (as described for sample discarding). All the working surfaces along with the laboratory furniture, doorknobs, computer peripherals, and equipment need to be decontaminated[9],[11]
  • Care needs to be taken to follow the manufacturers' instructions regarding the concentration of these disinfectant solutions and their contact time with the surface to be disinfected (ranges from 5 to15 min).[9],[11]

Biomedical waste management

  • Following processing of sample and following FNA performed on a COVID-19 positive/suspected patient, the full PPE is to be discarded into appropriately designated bins labeled as COVID and as per hospital policy
  • All laboratory-generated biomedical waste from COVID-19 positive/suspected samples must be processed as per local/institutional regulations and as mandated by pollution control policy and guidelines made by the Central Pollution Control Board, India.[12]

Care of the laboratory Staff

  • It is recommended that the entire lab staff is not exposed at the same time. The staff can be divided into a minimum of 2–3 teams (depending upon the staff count), which can be posted for fixed periods, without allowing any direct contact between the members of various working teams. This system can help in ensuring the availability of the staff to manage the laboratory, in the unfortunate event of any of the teams being exposed to the disease
  • Reallocation of the duties of the laboratory staff and cytopathologists may be undertaken by the laboratory chief based on the sample loads being encountered by the individual cytology laboratories
  • The laboratory personnel needs to be continuously trained and educated regarding the precautions to be taken while processing the potentially infectious samples
  • They need to be trained regarding proper donning and doffing of PPE
  • All the laboratory personnel should be advocated to frequently and thoroughly wash their hands with soap and water (for at least 20 s) and should be trained for good microbiological practices and procedures (GMPP)[3]
  • Alcohol-based hand sanitizers containing at least 70% alcohol can be used for the disinfection of the hands
  • Access to the laboratory should be strictly limited.

The laboratory personnel should be directed to immediately report any clinical symptoms suggestive of COVID-19 (lower respiratory symptoms and/or fever) and should be referred to the dedicated COVID specialist team based on the clearly defined protocol for further management.[13]

Reporting of the cytopathology samples

  • Cytopathologists may wear non-sterile gloves while reporting to avoid direct contact with the slides. However, this needs to be rationalized depending upon the ease of availability of gloves[9]
  • Microscopes to be sanitized by 70% alcohol/hand sanitizer solution before initiating the reporting
  • Reporting cytopathologists may report independently rather than with the entire team of cytotechnologists/residents/trainees/fellows
  • If reporting as a team, no more than three members at a multi-header station keeping at least 1-meter distance is recommended
  • Digital reporting may be undertaken wherever the facility is available
  • All pathologists must wash their hands at the end of reporting for >20 s and/or hand sanitizer application.

Storage and cataloging of slides and blocks

  • Once reporting of samples is done, the cataloging of slides and blocks and their storage is undertaken as per regulations and adequate care should be taken by the personnel in the form of wearing non-sterile gloves and face mask while doing so.

Training of the cytopathology residents/fellows

  • This would be a significant issue for academic institutes, focusing on service as well as education of the medical graduate and postgraduates. Teaching rooms should be well ventilated with adequate fresh airflow. Teaching activities, involving the gathering of more than 10 people in a limited closed space, may be suspended temporarily
  • Alternatively, online teaching resources, such as Zoom (Zoom Video Communications, Inc. San Jose, CA), can be explored for conducting resident and fellow teaching sessions.[9] In institutes where digital slide scanners are available, slide scanning can be actively utilized and online teaching sessions can be conducted using the saved image files. The training of residents should not be compromised in any way and innovative methods of teaching, including online continuing medical education CMEs and webinars, avoiding contact, and maintain social distancing may be encouraged and adopted
  • The residents can be encouraged to maintain their duty rosters digitally, on their cell phones and Laptops. At all times, it is important that the transfer of laboratory information, especially patient-related, is carefully regulated by the respective institution or the organization.

NOTE: These guidelines prepared are based on our existing knowledge of COVID-19 and existing practices in the management of other infectious diseases like HIV, etc., and are in line with the current recommendations of Indian Council of Medical Research, and Ministry of Health and Family Welfare, Govt. of India.[2] These guidelines will be updated if the need arises. The updated guidelines will be available on the website of the Indian Academy of Cytologists,

To summarize, social distancing, practicing personal hygiene, maintaining the preventive measures while performing cytology procedures as well as at the time of sample handling and storage will be helpful in minimizing the risk of acquiring COVID-19 and being able to serve the health care organizations in the best possible manner during these uncertain and difficult times. It is time to incorporate and encourage the usage of digital technology at the workplace in all possibilities, during this time of social distancing, in a secure and regulated manner. The safety of laboratory personnel is of utmost importance and it is hoped that these guidelines will be adhered to by all cytopathology laboratories. Stay Safe is our motto in the current scenario.

Financial support and sponsorship


Conflicts of interest

There are no conflicts of interest.

   References Top

Ministry of Health and Family Welfare. Government of India. COVID-19 India, as on 14th April 2020. Available from:  Back to cited text no. 2
World Health Organization. Laboratory biosafety guidance related to the novel coronavirus (2019-nCoV). Interim guidance. Available from:  Back to cited text no. 3
Centers for Disease Control and Prevention (CDC). Interim laboratory biosafety guidelines for handling and processing specimens associated with coronavirus disease 2019 (COVID-19). Available from:  Back to cited text no. 4
World Health Organization. Rational use of personal protective equipment (PPE) for coronavirus disease (COVID-19). Interim guidance. Available from:  Back to cited text no. 5
European Centre for Disease Prevention and Control. Guidance for wearing and removing personal protective equipment in healthcare settings for the care of patients with suspected or confirmed COVID-19. Available from:  Back to cited text no. 6
Centers for Disease Control and Prevention. Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with SARS-CoV. Available from:  Back to cited text no. 7
Tan SS, Yan B, Saw S, Lee CK, Chong AT, Jureen R, et al. Practical laboratory considerations amidst the COVID-19 outbreak: early experience from Singapore. J Clin Pathol 2020. doi: 10.1136/jclinpath-2020-206563.  Back to cited text no. 8
Pambuccian SE. The COVID-19 pandemic: Implications for the cytology laboratory. J Am Soc Cytopathol 2020.  Back to cited text no. 9
United States Environmental Protection Agency. List N: Disinfectants for use against SARS- CoV-2. Available from: against-sars-cov-2.  Back to cited text no. 10
van Doremalen N, Bushmaker T, Morris DH, Holbrook MG, Gamble A, Williamson BA, et al. Aerosol and surface stability of SARS- CoV-2 as compared with SARS-CoV-1. N Engl J Med 2020. doi: 10.1056/NEJMc2004973.  Back to cited text no. 11
Central Pollution Control Board guidelines. Available from:  Back to cited text no. 12
Centers for Disease Control and Prevention. Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with SARS-CoV. Available from:  Back to cited text no. 13

Correspondence Address:
Dr. Radhika Srinivasan
Secretary, Indian Academy of Cytologists
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/JOC.JOC_44_20

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