Explify Respiratory Pathogens by Next Generation Sequencing (INACTIVE as of 11/18/19: Refer to 3002026 in the November Hotline)
Ordering Recommendation

Detect respiratory pathogens in patients with pneumonia.

Massively Parallel Sequencing
3-6 days
New York DOH Approval Status
Specimens from New York clients will be sent out to a New York DOH approved laboratory, if possible.
Submit With Order
ARUP Consult®
Disease Topics
Specimen Required
Patient Preparation
Bronchoalveolar lavage (BAL) 
Specimen Preparation
Transfer 2 mL to a sterile container. (Min: 1.2 mL) 
Storage/Transport Temperature
Unacceptable Conditions
Specimen source required. 
Ambient: Unacceptable; Refrigerated: 4 days; Frozen: 30 days 
Reference Interval
By report
Interpretive Data
This test detects potential respiratory pathogens by unbiased next-generation cDNA and DNA sequencing of viral, bacterial, and fungal transcriptome and genome sequences. Sequencing data are interpreted by the Explify software.

Negative results do not rule out viral, bacterial, or fungal infections. Targeted, PCR-based tests are generally more sensitive and are preferred when specific pathogens are suspected, especially for DNA viruses (Adenovirus, CMV, HHV6, HSV, and VZV), mycobacteria, and fungi.

The analytical sensitivity of this test depends on the cellularity of the sample and the concentration of all microbes present. Analytical sensitivity is assessed using Internal Controls that are added to each sample. Sequencing data for Internal Controls is quantified. Samples with Internal Control values below the validated minimum may have reduced analytical sensitivity or contain inhibitors and are reported as 'Reduced Analytical Sensitivity'. Additional respiratory pathogens to those reported cannot be excluded in samples with 'Reduced Analytical Sensitivity'.

Due to the complexity of next generation sequencing methodologies, there may be a risk of false-positive results. Contamination with organisms from the upper respiratory tract during specimen collection can also occur. The detection of viral, bacterial, and fungal nucleic acid does not imply organisms causing invasive infection. Results from this test need to be interpreted in conjunction with the clinical history, results of other laboratory tests, epidemiologic information, and other available data. Confirmation of positive results by an alternate method may be indicated in select cases.

Test developed and characteristics determined by ARUP Laboratories.

Compliance Statement B: For laboratory developed tests not using a RUO kit, and for FDA approved, cleared or 510(k) exempt assays with alterations. This test was developed and its performance characteristics determined by ARUP Laboratories. The U. S. Food and Drug Administration has not approved or cleared this test; however, FDA clearance or approval is not currently required for clinical use. The results are not intended to be used as the sole means for clinical diagnosis or patient management decisions.

Hotline History
View Hotline History
Component Test Code*Component Chart NameLOINC
2013695Respiratory Pathogens by NGS48767-8
2013696EER Respiratory Pathogens by NGS11526-1
2013697Respiratory Pathogens by NGS, Source31208-2
* Component test codes cannot be used to order tests. The information provided here is not sufficient for interface builds; for a complete test mix, please click the sidebar link to access the Interface Map.