Coronavirus Disease 2019 (COVID-19) Autopsy Guidance FAQ

Postmortem swab specimens for COVID-19 testing should include an upper respiratory tract swab, nasopharyngeal (NP) swab, lower respiratory tract swab, and lung swab from each lung. If NP swab specimens cannot be obtained, acceptable alternatives for upper respiratory swab specimens include an oropharyngeal specimen, or a nasal mid-turbinate swab, or an anterior nares (nasal swab) specimen, or nasopharyngeal wash/aspirate or nasal aspirate specimen.

Separate swab specimens should be obtained for testing of other respiratory pathogens and other postmortem testing.

Formalin-fixed autopsy tissues should be obtained from lung, upper airway, and other major organs.

If only a postmortem NP swab is being collected, individuals in the room during specimen collection should be limited to healthcare personnel obtaining the specimen.

Since collection of NP swab specimens from deceased persons will not induce coughing or sneezing, a negative-pressure room is NOT required if ONLY an NP swab is being collected from the decedent.

In addition to postmortem specimens, any remaining specimens (eg, NP swab, sputum, serum, stool) that may have been collected prior to death should be retained.

Please refer to Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19) for more information.

Obtain a postmortem nasopharyngeal (NP) swab specimen for COVID-19 testing. If NP swab specimens cannot be obtained, acceptable alternatives for upper respiratory swab specimens include an oropharyngeal specimen, or a nasal mid-turbinate swab, or an anterior nares (nasal swab) specimen, or nasopharyngeal wash/aspirate or nasal aspirate specimen.

Separate NP swabs should be obtained for testing of other respiratory pathogens.

If only a postmortem NP swab is being collected, individuals in the room during specimen collection should be limited to healthcare personnel obtaining the specimen.

Since collection of NP swab specimens from deceased persons will not induce coughing or sneezing, a negative-pressure room is NOT required if ONLY an NP swab is being collected from the decedent.

In addition to postmortem specimens, any remaining specimens (eg, NP swab, sputum, serum, stool) that may have been collected prior to death should be retained.

Please refer to Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19) for more information.

Obtain postmortem swab specimens for testing of other respiratory pathogens.

Other postmortem microbiologic and infectious disease testing should be performed, as indicated.

Formalin-fixed autopsy tissues should be obtained from lung, upper airway, and other major organs.

If only a postmortem nasopharyngeal (NP) swab is being collected, individuals in the room during specimen collection should be limited to healthcare personnel obtaining the specimen. If NP swab specimens cannot be obtained, acceptable alternatives for upper respiratory swab specimens include an oropharyngeal specimen, or a nasal mid-turbinate swab, or an anterior nares (nasal swab) specimen, or nasopharyngeal wash/aspirate or nasal aspirate specimen.

Since collection of NP swab specimens from deceased persons will not induce coughing or sneezing, a negative-pressure room is NOT required if ONLY an NP swab is being collected from the decedent.

In addition to postmortem specimens, any remaining specimens (eg, NP swab, sputum, serum, stool) that may have been collected prior to death should be retained.

Please refer to Interim Guidelines for Collecting, Handling, and Testing Clinical Specimens from Persons for Coronavirus Disease 2019 (COVID-19) for more information.

For nasopharyngeal (NP) swab collection

If NP swab specimens cannot be obtained, acceptable alternatives for upper respiratory swab specimens include an oropharyngeal specimen, or a nasal mid-turbinate swab, or an anterior nares (nasal swab) specimen, or nasopharyngeal wash/aspirate or nasal aspirate specimen.

Wear nonsterile, nitrile gloves when handling potentially infectious materials.

If there is a risk of cuts, puncture wounds, or other injuries that break the skin, wear heavy-duty gloves over the nitrile gloves.

Wear a clean, long-sleeved, fluid-resistant or impermeable gown to protect skin and clothing.

Use a plastic face shield or a face mask and goggles to protect the face, eyes, nose, and mouth from splashes of potentially infectious bodily fluids.

Personal protective equipment (PPE) recommendations for autopsies

Use double surgical gloves interposed with a layer of cut-proof synthetic mesh gloves.

Use a fluid-resistant or impermeable gown.

Use a waterproof apron.

Wear goggles or a face shield.

Use a National Institute for Occupational Safety and Health (NIOSH)–certified disposable N95 respirator or higher. Powered, air-purifying respirators (PAPRs) with HEPA filters may provide increased worker comfort during extended autopsy procedures. When respirators are necessary to protect workers, employers must implement a comprehensive respiratory protection program in accordance with the OSHA Respiratory Protection standard (see Respiratory Protection) that includes medical examinations, fit-testing, and training.

Surgical scrubs, shoe covers, and a surgical cap should be used per routine protocols (see CDC pamphlet). Doff (take off) PPE carefully to avoid contaminating yourself and do so before leaving the autopsy suite or adjacent anteroom.

After removing PPE, discard the PPE in the appropriate laundry or waste receptacle. Reusable PPE (eg, goggles, face shields, and PAPRs) must be cleaned and disinfected according to the manufacturer’s recommendations before reuse.

Immediately after doffing PPE, wash hands with soap and water for 20 seconds. If hands are not visibly dirty and soap and water are not available, an alcohol-based hand sanitizer that contains 60-95% alcohol may be used.

However, if hands are visibly dirty, always wash hands with soap and water before using alcohol-based hand sanitizer. Avoid touching the face with gloved or unwashed hands. Ensure that hand hygiene facilities are readily available at the point of use (eg, at or adjacent to the PPE doffing area).

Standard precautions, contact precautions, and airborne precautions with eye protection (goggles or a face shield) should be followed during the autopsy. Many of the following procedures are consistent with existing guidelines for safe work practices in the autopsy setting. Please refer to Interim Infection Prevention and Control Recommendations for Patients with Suspected or Confirmed Coronavirus Disease 2019 (COVID-19) in Healthcare Settings and Guidelines for Safe Work Practices in Human and Animal Medical Diagnostic Laboratories for more information.

General precautions

Aerosol-generating procedures such as use of an oscillating bone saw should be avoided for known or suspected COVID-19 cases. Consider using hand shears as an alternative cutting tool. If an oscillating saw is used, attach a vacuum shroud to contain aerosols.

Allow only one person to cut at a given time.

Limit the number of personnel working in the autopsy suite at any given time to the minimum number of people necessary to safely conduct the autopsy.

Limit the number of personnel working on the human body at any given time.

Use a biosafety cabinet for the handling and examination of smaller specimens and other containment equipment whenever possible.

Use caution when handling needles or other sharps, and dispose of contaminated sharps in puncture-proof, labeled, closable sharps containers.

A logbook including names, dates, and activities of all workers participating in the postmortem and cleaning of the autopsy suite should be kept to assist in future follow up, if necessary. Include custodian staff entering after hours or during the day.

Engineering precautions

Autopsies on known or suspected COVID-19 cases should be conducted in airborne infection isolation rooms (AIIRs). These rooms are at negative pressure to surrounding areas, have a minimum of 6 air changes per hour (ACH) for existing structures and 12 ACH for renovated or new structures, and have air exhausted directly outside or through a HEPA filter.

Doors to the room should be kept closed except during entry and egress.

If an AIIR is not available, ensure the room is negative pressure with no air recirculation to adjacent spaces.

A portable HEPA recirculation unit could be placed in the room to provide further reduction in aerosols.

Local airflow control (ie, laminar flow systems) can be used to direct aerosols away from personnel.

If use of an AIIR or HEPA unit is not possible, the procedure should be performed in the most protective environment possible.

Air should never be returned to the building interior, but should be exhausted outdoors, away from areas of human traffic or gathering spaces and away from other air intake systems.

Implementing proper biosafety and infection control practices is critical when collecting specimens. Please refer to Interim Laboratory Biosafety Guidelines for Handling and Processing Specimens Associated with Coronavirus Disease 2019 (COVID-19) for additional information.

Collection of postmortem swab specimens for COVID-19 testing

For suspected COVID-19 cases, collect and test postmortem nasopharyngeal (NP) swabs and, if an autopsy is performed, lower respiratory tract specimens (lung swabs). If NP swab specimens cannot be obtained, acceptable alternatives for upper respiratory swab specimens include an oropharyngeal specimen, or a nasal mid-turbinate swab, or an anterior nares (nasal swab) specimen, or nasopharyngeal wash/aspirate or nasal aspirate specimen.

If the diagnosis of COVID-19 was established before death, collection of these specimens for COVID-19 testing may not be necessary. Medical examiners, coroners, and pathologists should work with their local or state health department to determine the capacity for testing postmortem swab specimens.

Per the US Food and Drug Administration, antibody tests have not been validated for diagnosing COVID-19; they have limited value by themselves for an immediate diagnosis of suspected COVID-19.

Use only synthetic fiber swabs with plastic shafts. Do not use calcium alginate swabs or swabs with wooden shafts, as they may contain substances that inactivate some viruses and inhibit polymerase chain reaction (PCR) testing.

Place swabs immediately into sterile tubes containing 2-3 mL of viral transport media.

NP and lung swab specimens should be kept in separate vials.

Refrigerate specimens at 2-8°C and ship overnight to the CDC on ice pack.

Upper respiratory tract specimen collection: NP swab

Insert a swab into the nostril parallel to the palate.

Leave the swab in place for a few seconds to absorb secretions.

Swab both NP areas with the same swab.

Lower respiratory tract specimen collection: lung swabs

Collect one swab from each lung (left and right).

Options for lung swab collection include the following and may depend on the institution’s standard practices or type of autopsy procedure (eg, full or in situ autopsy):

• During the internal examination, after the heart-lung block is removed, insert one swab as far down into the tracheobronchial tree as possible on either side (left and right).
• First wipe the surface of each lung with an iodine-containing disinfectant and clean and dry the surface; then, use a sterile scalpel to cut a slit of the lung and insert the swab to collect a sample on either side.

Storage of postmortem swab specimens

Store specimens at 2-8°C for up to 72 hours after collection.

If a delay in testing or shipping is expected, store specimens at -70°C or below.

Collection of postmortem specimens for other routine testing

Separate postmortem specimens (eg, NP or lung swabs) should be collected for routine testing of respiratory pathogens at either clinical or public health laboratories. Note that clinical laboratories should NOT attempt viral isolation from specimens collected from known or suspected COVID-19 cases.

Other postmortem specimen collection and evaluations should be directed by the decedent’s clinical and exposure history, scene investigation, and gross autopsy findings, and it may include routine bacterial cultures, toxicology, and other studies.

Collection of fixed autopsy tissue specimens

The preferred specimens would be a minimum of 8 blocks and fixed tissue specimens representing samples from the respiratory sites listed below in addition to specimens from major organs (including liver, spleen, kidney, heart, and GI tract) and any other tissues showing significant gross pathology. The recommended respiratory sites include the following:

• Trachea (proximal and distal)
• Central (hilar) lung with segmental bronchi, right and left primary bronchi
• Representative pulmonary parenchyma from right and left lung

Collection of tissue samples roughly 4-5 mm in thickness (ie, sample would fit in a tissue cassette) is recommended for optimal fixation.

The volume of formalin used to fix tissues should be 10 times the volume of tissue.

Place tissue in 10% buffered formalin for 3 days (72 hours) for optimal fixation.

Follow standard precautions should transfer of a body of a suspected COVID-19 decedent be necessary.

If splashing of fluids is expected, ensure proper personal protective equipment is available.

Follow standard bagging procedures.

Postmortem care workers should beware of the risk of puncture, tearing, or failure of body bags. Risk factors may include the following:

• Sharp objects (eg, jewelry, piercings, medical instruments) on the decedent
• Weight of the decedent
• Quality of the body bag, considering factors such as degradation over time, storage, or shipment (eg, bag is brittle or broken)

Follow routine transportation protocols after the body has been bagged.

Disinfect the bag with a disinfectant approved by the US Environmental Protection Agency. Wear disposable nitrile gloves while handling the bag. Ensure the disinfectant meets the criteria for use against SARS-CoV-2 and is applied in accordance with the manufacturer’s recommendations.