Microbiology COVID-19 Testing Information
Updated March 11, 2022
The Microbiology Laboratory is offering COVID-19 (SARS-CoV-2 virus) testing. Please read the information below carefully and in its entirety.
For questions regarding patient testing criteria, visit HEIC intranet or for a specific question not addressed in the algorithms, please contact HEIC or the Command Center at your respective institution.
1. Standard testing protocol for most patients:
- Order Epic test LAB49627 COVID-19 (Coronavirus) NAT (nucleic acid amplification test), nasopharyngeal (NP).
- A single NP swab is collected and placed in universal viral transport media.
- If collection of a NP swab is not possible, see the Specimen Collection section for alternates to NP swabs.
- Flu A/B+RSV + COVID-19 test (LAB49650) is no longer recommended because influenza incidence has declined and supplies are allocated to COVID-19 testing. Please order the standalone COVID-19 test (LAB49627) test as above.
- If Influenza testing is still required, order Epic test LAB49650 for the Influenza A+B/RSV nucleic acid amplification test (NAT) + COVID-19 NAT test for nasopharyngeal (NP) swabs.
- A single NP swab is collected and placed in universal viral transport media for both tests.* The COVID-19 NAT will be setup on all samples regardless of the Influenza A&B & RSV NAT results.
2. Hematologic/oncology patients with respiratory symptoms or patients admitted to the pediatric ICU:
- Order Epic test LAB49627 COVID-19 (Coronavirus), NP test as above.
- If clinically indicated, order the respiratory pathogen panel, NP swab ("RVP") (LAB45380) separately.
- Due to the current supply shortage, ordering of the RVP (LAB45380) test should be minimized to patients in whom the result will impact management.
3. Inpatient testing of sputum specimens:
- Order Epic test LAB49628 COVID-19 (Coronavirus) NAT, Sputum
- Sputum specimens are processed as routine specimens with a turn-around of up to 24 hours. They cannot be run on the Stat or Urgent testing platforms.
- The CDC website recommends against induced sputum.
4. Inpatient testing of endotracheal aspirates:
- Order Epic test LAB50361 COVID-19 (Coronavirus) NAT, Endo/Trach Suction
- Endotracheal/nasotracheal aspirate specimens are processed as routine specimens with a turn-around of up to 24 hours. They cannot be run on the Stat or Urgent testing platforms.
5. Intubated patients/patients undergoing bronchoscopy:
- Order LAB49625 COVID-19 (Coronavirus) NAT, BAL (bronchoalveolar lavage).
- BAL specimens are processed as routine specimens with a turn-around of up to 24 hours. They cannot be run on the Stat or Urgent testing platforms. - If clinically indicated, order the respiratory pathogen panel, BAL ("RVP") (LAB45382).
Specimen Collection: Nasopharyngeal (NP) and bilateral nasal mid-turbinate (NMT) swabs should be collected and placed in universal viral transport media.
- If collection of a nasopharyngeal swab is not possible, the following alternates are acceptable and can be ordered under LAB49627 COVID-19 (Coronavirus) NAT, NP:
- An oropharyngeal swab (OP) can be collected and placed in universal viral transport media.
- For symptomatic patients, bilateral nasal mid-turbinate (NMT) swab OR bilateral nasal swab (anterior nares) can be collected and placed in universal viral transport media. - Note: For these scenarios, please enter an Epic order comment stating the source and hand-write OP or NMT on the specimen label.
Lower respiratory tract specimen collection:
- Sputum and endotracheal aspirate specimens should be collected in a leak-proof sterile container.
- If a bronchoscopy is performed, the BAL sample should be submitted in a leak-proof sterile container.
Specimen Transport: Please see the chart below to differentiate which samples can and cannot be sent through the pneumatic tube system.
USE TUBE SYSTEM | DO NOT USE TUBE SYSTEM |
---|---|
Stool (except from COVID-19 Person Under Investigation (PUI) or known COVID-19 positive) | (Double bag and hand carry to the Microbiology Laboratory) The following respiratory specimens, regardless of order type/test:
|
Other specimens not included in "do not use tube system" list (except from COVID-19 PUI or known COVID-19 positive) | Stool from patients who are PUI or known COVID-19 positive |
If transport to the laboratory is delayed (>2 hours) or for courier transport from affiliate hospitals, please refrigerate or transport the samples on cold packs.
This section expires 6/30/2022. Please contact the Microbiology Laboratory for updated copy.
Please do not send any respiratory samples for COVID-19 testing through the pneumatic tube system. These samples should be double bagged and hand carried to the Microbiology laboratory.
Upper Respiratory Tract Specimen Collection | ||
Symptomatic Testing: A single nasopharyngeal (NP) swab is collected and placed in viral/universal transport media. | ||
SAP # | Name of Swab | Comments |
Due to product variability, please consult JHM Supply Chain for latest SAP # | Mini tip flocked (< 2 mm) swab & viral transport media (VTM or UTM) *Note- product may differ from image due to substitute products ![]() |
|
Upper Respiratory Tract Specimen Collection | ||
Asymptomatic Testing (or if an NP swab cannot be obtained): A single, bilateral nasal mid-turbinate (NMT) swab is collected and placed in viral/universal transport media. | ||
SAP # | Name of Swab | Comments |
Due to product variability, please consult JHM Supply Chain for latest SAP # |
Larger tip (< 5 mm) swabs placed in viral transport media *Note- product may differ from image due to substitute products ![]() |
|
Lower Respiratory Tract Specimen Collection: Sputum, Endo/Nasotracheal Aspirate, or Bronchoalveolar Lavage (BAL) | ||
SAP # | Name of Transport Container | Comments |
133070 | Sterile cup![]() |
|
1545 | Suction Trap![]() |
|
Task order lists are made available to the Command Centers and HEIC throughout the day to notify which patients are on the molecular run(s) and when results are expected to be available.
Effective, Tuesday April 21st the Medical Microbiology Laboratory will no longer call positive COVID-19 results to ordering ED and Inpatient providers. Positive results will still be communicated by HEIC, which receives Epic mobile push notifications. Providers should also follow-up on COVID-19 results in Epic. Providers can select the "bell" icon when placing the order, or from the Lab Tracking Summary report, to have a push notification sent to Haiku or Canto on their mobile devices. The current turn-around time for COVID-19 NAT results is less than 24 hours.

Please do not call the laboratory for the results, they will be available in Epic.
Test Method | Manufacturer/Technology | Specimen | SARS-Cov-2 Gene Target(s) | Package Insert |
---|---|---|---|---|
ePlex® RP2 | GenMark (rt- PCR, e-sensor array detection) | NP | N | download |
Xpert® Xpress SARS-CoV-2/Flu/RSV | Cepheid (fully automated, rt-PCR) | NP | N2, E | download |
Accula | Mesa Biotech Inc (PCR and lateral flow) | Combined nasal/OP swab | N gene | download |
NeuMoDxTM SARS-CoV-2 Assay | Qiagen (fully automated, rt-PCR) | NP NMT Validated in house for asymptomatic screening | N, NSP2 | download |
Cobas® SARS-CoV-2 | Roche (fully automated, rt-PCR) | NP NMT Validated in house for asymptomatic screening | ORF1ab, E | download |
Aptima® SARS-CoV-2 (Panther® System | Hologic (TMA) | NP NMT Nasal | ORF1ab | download |
BD SARS-CoV-2 reagents, BD MAXTM system | BD Diagnostics, Inc (rt-PCR) | NP NMT | N1, N2 | download |
Alinity m | Abbott (fully automated, rt-PCR) | NP NMT BAL | RdRp, N | download |
RealStar® SARS CoV-2 RT-PCR kit LDT | Altona (rt-PCR) | NP OP BAL Sputum/ENT | E, S | download |
PerkinElmer® LDT | Perkin Elmer (rt-PCR) | NP NMT | ORF1ab, NP | download |
CDC 2019-nCoV | IDT (rt-PCR) | NP | N1, N2 | download |
OP: oropharyngeal swab
NMT: nasal mid-turbinate swab (deep nasal swab)
NS: nasal swab (anterior nares)
BAL: bronchoalveolar lavage
rt-PCR: reverse transcriptase polymerase chain reaction
» FAQ for Rapid Antigen COVID-19 testing (POC)
Below are the provider and patient fact sheets for each SARS-CoV-2 testing platform available at the Johns Hopkins Medical Microbiology Laboratory that have received EUA status. The performance characteristics have been verified internally.
SARS-CoV-2 testing platform | Fact Sheets: Patients | Fact Sheets: Healthcare Providers |
---|---|---|
NeuMoDx Molecular, Inc SARS-CoV-2 Assay | View PDF | View PDF |
Cepheid Xpert Xpress SARS-CoV-2 Test | View PDF | View PDF |
Genmark Diagnostics ePlex SARS-CoV-2 Test | View PDF | View PDF |
BD MAX BioGx SARS-CoV-2 Test | View PDF | View PDF |
Mesa Accula SARS-CoV-2 Test | View PDF | View PDF |
CDC 2019-nCoV Real-Time RT-PCR Diagnostic Panel | View PDF | View PDF |
Altona Reagents RealStar SARS CoV-2 Laboratory-Developed Test | Pending FDA EUA |
As the situation is rapidly evolving and as we experience increased test volumes, turnaround times for all routine microbiology tests may be impacted.
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