Laboratory Testing for MERS

Testing for MERS-CoV

CDC recommends that clinicians and public health departments consider a full differential diagnosis, and order pathogen-specific testing based on the most likely etiology for the patient's clinical presentation. In most scenarios in the United States, this likely indicates testing for other more common pathogens before testing for MERS-CoV; the pre-test probability is likely higher for most other respiratory viruses and/or common bacterial pathogens.

If there is strong suspicion that a person under investigation (PUI) is infected with MERS-CoV, simultaneous testing for MERS-CoV along with other possible pathogens can be considered following discussion with state and local health departments.

Healthcare providers should consider testing for:

• Common viral respiratory pathogens, including SARS-CoV-2, influenza A, influenza B, respiratory syncytial virus (RSV), human metapneumovirus, human parainfluenza viruses, seasonal human coronaviruses, adenovirus, enterovirus/rhinovirus, and other respiratory viruses;
• Streptococcus pneumoniae, Chlamydia pneumophila,Legionella pneumophila, Mycoplasma pneumoniae, and other bacterial pathogens that cause severe lower respiratory infections.

How to request laboratory testing

Multiple public health laboratories offer diagnostic MERS-CoV PCR testing. Contact your local/state health department to notify them of the PUI and to request MERS-CoV testing. If your state health department is unable to test but feels testing is warranted, they should call CDC's Emergency Operations Center at 770-488-7100 for CDC consultation and to request CDC testing.

Types of tests

Molecular Tests

Molecular tests diagnose active infection (presence of MERS-CoV). Real-time reverse-transcription polymerase chain reaction (rRT-PCR) assays are molecular tests that detect viral genetic material in clinical specimens.

CDC developed an rRT-PCR assay that is the primary test for MERS diagnostic purposes in the United States. FDA granted Emergency Use Authorization for this test.

Specimen Types for Molecular Tests

For this rRT-PCR assay, CDC recommends collecting multiple specimens, including lower (bronchoalveolar lavage, sputum and tracheal aspirates) and upper (nasopharyngeal and oropharyngeal swabs) respiratory specimens. For patients with possible MERS-CoV pneumonia, lower respiratory specimens are the preferred specimen type, because they have higher test sensitivity.

Laboratory guidelines

Biosafety Guidelines for Handling and Processing Specimens Associated with MERS-CoV

Biosafety precautions should be taken in collecting and handling specimens that may contain MERS-CoV. Timely communication between clinical and laboratory staff is essential to minimize the risk incurred in handling specimens from patients with possible MERS-CoV infection. Such specimens should be labeled accordingly and alert the receiving laboratory to ensure proper specimen handling. General and specific biosafety guidelines for handling MERS-CoV specimens are provided below.

For additional detailed instructions, please refer to the following:

• Biosafety in Microbiological and Biomedical Laboratories (BMBL) – 6^th Edition
• Laboratory Biosafety Manual – Third Edition
• Prevention and Control for Hospitalized MERS Patients

Any procedure with the potential to generate fine-particulate aerosols (e.g., vortexing or sonication of specimens in an open tube) should be performed in a Class II Biological Safety Cabinet (BSC). Appropriate physical containment devices (e.g., centrifuge safety buckets; sealed rotors) should be used for centrifugation. Ideally, rotors and buckets should be loaded and unloaded in a BSC. Perform any procedures outside a BSC in a manner that minimizes the risk of exposure to a pathogen as a result of an inadvertent specimen release.

After specimens are processed, decontaminate work surfaces and equipment with appropriate disinfectants. Use any EPA-registered hospital disinfectant. Follow manufacturer's recommendations for use, including dilution (i.e., concentration), contact time, and care in handling.

Autoclave all disposable waste.

Specific Guidelines for Handling MERS-CoV in Laboratory Settings

Clinical and microbiology laboratories should follow standard laboratory practices, including Standard Precautions, when handling potential MERS-CoV specimens. For additional information, see Biosafety in Microbiological and Biomedical Laboratories (BMBL) 6^th Edition.

The following activities must be performed in a BSL-3 facility using BSL-3 work practices:

• Propagating MERS-CoV in cell culture
• Characterizing viral agents recovered in cultures of MERS-CoV specimens

The following activities must be performed in Animal BSL-3 facilities using Animal BSL-3 work practices:

• Inoculating animals for potential recovery of virus from MERS-CoV specimens
• Inoculating animals for characterization of MERS-CoV

Specimen collection overview

Before collecting and handling specimens for MERS-CoV testing, determine whether the person meets the current definition for a PUI for MERS-CoV infection.

Specimen Type and Priority

CDC recommends collecting one or multiple specimens from each site after symptom onset, if possible. Specimen types include:

1. Lower respiratory (bronchoalveolar lavage, sputum and tracheal aspirates)
2. Upper respiratory (nasopharyngeal and oropharyngeal swabs)

Collection of two specimen types is strongly recommended when using the CDC MERS rRT-PCR assay. Lower respiratory tract specimens are preferred, but collecting nasopharyngeal and oropharyngeal (NP/OP) specimens, in addition to a lower respiratory tract specimen, is strongly recommended depending upon the length of time between symptom onset and specimen collection. Respiratory specimens should be collected as soon as possible after symptoms begin. Ideally, the specimens should be collected within 7 days of symptom onset. However, if more than a week has passed since symptom onset and the patient is still symptomatic, respiratory specimens should still be collected, especially lower respiratory tract specimens.

Specimens can be stored at 2-8°C for up to 72 hours after collection. If extraction cannot be completed within 72 hours, specimens should be stored at -70°C or lower as soon as possible after collection. Label specimen containers with two primary patient identifiers, in accordance with Clinical Laboratory Improvement Amendments (CLIA) regulations for diagnostic testing: specimen type and the date the specimen was collected. Ship all specimens on dry ice. If submitting specimens to CDC for MERS-CoV testing, detailed instructions are provided in the CDC-10488 test order.

Respiratory Specimens

1. Lower respiratory tract

Bronchoalveolar lavage, tracheal aspirate – Collect 2-3 mL into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.

Sputum – Have the patient rinse the mouth with water and then expectorate deep cough sputum directly into a sterile, leak-proof, screw-cap sputum collection cup or sterile dry container.

2. Upper respiratory tract

Nasopharyngeal (NP) AND oropharyngeal (OP) swabs

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 PCR testing. Place swabs immediately into sterile tubes containing 2-3 mL of viral transport media. Viral transport media must be used; universal or other transport media cannot be tested at CDC. Please ensure the swabs are only in viral transport media.

After collection, NP and OP specimens can be combined, placing both swabs in the same vial.

Nasopharyngeal swab – Insert a swab into the nostril parallel to the palate and advance to enter the nasopharyngeal space. Leave the swab in place for a few seconds to absorb secretions. Remove the swab and place immediately into sterile tube containing 2-3 mL of viral transport media.

Oropharyngeal swab (e.g., throat swab) – Swab the posterior pharynx, avoiding the tongue. Place swab immediately into sterile tubes containing 2-3 mL of viral transport media.

Sending specimens

Package, ship, and transport specimens from suspected MERS PUIs according to the current edition of the International Air Transport Association (IATA) Dangerous Goods Regulations. Shipments from outside of the United States may require an importation permit that can be obtained from CDC.

Specimens should be shipped on dry ice. When shipping frozen specimen from long distances or from international locations, use sufficient dry ice to ensure specimens remain frozen during the entire transport process.

All specimens must be prepared in a manner that prevents the risk of breakage and spillage during transport. Seal specimen containers with Parafilm^® (primary container) and place in zippered plastic bags (secondary container). Ensure sufficient absorbent material is placed in the secondary container to absorb the entire contents if a leakage event occurs. Whenever possible, separate the primary containers (containing specimen) to reduce any potential risk of breakage. When shipping large numbers of specimens, organize them in a sequential manner in boxes with separate compartments for each specimen.

Additional recommendations:

• Do not place any dry ice in the primary container or secondary container, foam envelopes, zippered plastic bags, cryovial boxes, or hermetically sealed containers.
• Do not place primary containers sideways or upside down in zippered plastic bags.
• Do not place any paperwork in the secondary containers or zippered plastic bags, so as not to damage the paperwork.
• Do not use biohazard/autoclave bags to prepack your materials due to the inadequate seal of these bags.

For additional information, consultation, or the CDC shipping address, contact the CDC Emergency Operations Center at 770-488-7100. Ship specimens for overnight delivery. If weekend delivery is planned, special arrangements must be made with the shipping company.

Interpreting results

A MERS diagnosis requires a positive test result from a molecular test, which indicates that MERS-CoV genetic material was detected in a patient's clinical specimen. Confirmatory testing for any positive MERS test performed at a public health laboratory needs to be done by CDC. Refer to the specific test's instructions for use for details on how to interpret test results.

Interpretation of a negative rRT-PCR test result depends on multiple factors, including specimen type and time since illness onset. Collecting and testing multiple specimens may increase confidence that the person under investigation does not have an active infection.