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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.

Testing capacity +
Current testing capacity is 2500 samples per day. Testing runs are performed 24 hours a day, 7 days a week.
Test ordering +
Follow testing recommendations (algorithms available through HEIC intranet):

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 and transport +

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:

  • Bronchoalveolar lavage (BAL)
  • Nasopharyngeal (NP) swab in viral transport
  • Bilateral nasal mid-turbinate (NMT) swab in viral transport
  • Sputum (expectorated, or induced)
  • Bronchial wash
  • Endotracheal secretions
  • Nasopharyngeal aspirates
  • Pleural fluid
  • ANY respiratory specimen for the AFB laboratory
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.



Preferred Sample Collection Containers and Transport Media +

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.

» Download this section

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
Mini tip flocked swab and viral transport media
  • Viral transport media are equivalent; however, swab type may vary depending on supply availability. Mini-tip flocked swabs (<2 mm) preferred for NP collection. Larger swab heads (5 mm) should only be used for oropharyngeal (OP), bilateral nasal mid-turbinate (NMT) or bilateral nasal (anterior nares) swab collection.
  • If clinically indicated, these collection swabs and viral transport media can be used for additional viral respiratory testing.
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
  • Viral transport media are equivalent; however, swab type may vary depending on supply availability. Mini-tip flocked swabs (< 2 mm) are preferred for NP collection. Larger swab heads (5 mm) should only be used for OP, bilateral NMT or bilateral nasal swab collection.
  • An OP swab can be collected and placed in universal viral transport media.
  • For symptomatic patients, bilateral NMT swab OR bilateral nasal swab (anterior nares) can be collected and placed in universal viral transport media.
Lower Respiratory Tract Specimen Collection: Sputum, Endo/Nasotracheal Aspirate, or Bronchoalveolar Lavage (BAL)
SAP # Name of Transport Container Comments
133070 Sterile cup
sterile cup
  • Sputum: Order Epic test LAB49628 COVID-19 (Coronavirus), 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.
  • Endo/nasotracheal aspirate: Order Epic test LAB50361 COVID-19 (Coronavirus), Endo/Trach Suction

    - Endo/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
1545 Suction Trap
suction trap
  • BAL: 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).

» Download this section



Test results +
The turnaround time for The Johns Hopkins COVID-19 test is less than 24 hours and will vary based on test volumes and the tiered testing assignment (Stat, Urgent or Routine).

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.

covid test result

Please do not call the laboratory for the results, they will be available in Epic.

Testing Platforms +
Eleven assays are validated in the Medical Microbiology Laboratory to perform SARS-CoV-2 molecular testing. The performance characteristics for each platform have been verified internally. For details about each assay including the analytical performance per EUA, follow the link to each assay's FDA EUA package insert.

Test Method Manufacturer/Technology Specimen SARS-Cov-2 Gene Target(s) Package Insert
ePlex® RP2GenMark
(rt- PCR, e-sensor array detection)
NPNdownload
Xpert® Xpress
SARS-CoV-2/Flu/RSV
Cepheid
(fully automated, rt-PCR)
NPN2, Edownload
AcculaMesa Biotech Inc
(PCR and lateral flow)
Combined nasal/OP swabN genedownload
NeuMoDxTM SARS-CoV-2 AssayQiagen
(fully automated, rt-PCR)
NP
NMT
Validated in house for asymptomatic screening
N, NSP2download
Cobas® SARS-CoV-2Roche
(fully automated, rt-PCR)
NP
NMT
Validated in house for asymptomatic screening
ORF1ab, Edownload
Aptima® SARS-CoV-2
(Panther® System
Hologic (TMA)NP
NMT
Nasal
ORF1abdownload
BD SARS-CoV-2 reagents, BD MAXTM systemBD Diagnostics, Inc
(rt-PCR)
NP
NMT
N1, N2download
Alinity mAbbott
(fully automated, rt-PCR)
NP
NMT
BAL
RdRp, Ndownload
RealStar® SARS CoV-2 RT-PCR kit LDTAltona (rt-PCR)NP
OP
BAL
Sputum/ENT
E, Sdownload
PerkinElmer® LDTPerkin Elmer (rt-PCR)NP
NMT
ORF1ab, NPdownload
CDC 2019-nCoVIDT (rt-PCR)NPN1, N2download
NP: nasopharyngeal swab
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)


Provider and Patient Fact Sheets for EUA Testing Platforms +
The Emergency Use Authorization (EUA) process allows U.S. Food and Drug Administration (FDA) to facilitate the availability of diagnostic tests to be used in the case of public health emergencies. The coronavirus disease 2019 (COVID-19) pandemic, caused by SARS-CoV-2 virus, has been declared a public health emergency. As part of the EUA process, the FDA requires fact sheets to be shared with providers and patients.

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
Surge testing +
When the numbers of submitted samples exceed our daily testing capacity, we will forward samples to Quest Diagnostics. If samples are sent to Quest extended turnaround times are to be expected (5-7 days). In addition to these testing options, clinicians may choose to send samples to the Maryland State Health Laboratory following their approval process.
COVID-19 Testing Statistics +
Test Volume and Positivity Rate
click graph to enlarge


As the situation is rapidly evolving and as we experience increased test volumes, turnaround times for all routine microbiology tests may be impacted.