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Discontinuation of certain specialty tests
The Department of Pathology & Laboratory Medicine, Microbiology Division, will discontinue certain specialty tests that are currently offered in-house: viral culture, Chlamydia culture, and direct immunofluorescence assay for Varicella-zoster virus and Pneumocystis jirovecii, Adenovirus, Human Metapneumovirus, Influenza Virus, Type A & B, Parainfluenza Virus, Types 1, 2, 3 and Respiratory Syncytial Virus. With the increased availability of molecular testing for microorganism identification, most of the methodologies above are no longer the preferred methods. These methodologies require specific laboratory expertise, specialized equipment, are time consuming, and are less sensitive than molecular methods. The Microbiology Division is working to validate and provide additional infectious disease molecular testing in-house in the near future to replace many of these methodologies.

Important consideration: Patients can be colonized with organisms that are detected by molecular assays due to the increased sensitivity; therefore, positive results should be interpreted in the context of the clinical presentation.

Effective date: Oct. 14, 2021

Molecular Microbiology assays offered at UCI:

UCI Test (codes)
Acceptable specimen
BK Virus DNA by PCR, Quant (SBKQTB)
BK Virus DNA by PCR, Quant (SBKQTU)
Chlamydia trachomatis and Neisseria gonorrhoeae by PCR (CTNG)
Urine, cervical, vaginal and male urethral
Coronavirus Disease 2019 (COVID-19), Priority (SCOVD)
Nasopharyngeal swab
Coronavirus Disease 2019 (COVID-19), Routine (SCOV)
Nasopharyngeal swab
Coronavirus Disease 2019 (COVID-19), STAT (SCOVS)
Nasopharyngeal swab
Cytomegalovirus DNA by PCR, Quant (SCMVQT)
Plasma and bronchoalveolar lavage (BAL)
DiaSorin Influenza A, B and RSV (SFABR)
Nasopharyngeal swab
Hepatitis B DNA by PCR, Quant (SHEBQT)
Hepatitis C RNA by PCR, Qual (SHCVVL)
Herpes Simplex Virus Type 1 and 2 by PCR, CSF (SHSVCS)
Herpes Simplex Virus Type 1 and 2 by PCR, Lesions (SHSVMC)
Mucocutaneous lesion
HIV 1 RNA by PCR, Quant (SHIVQT)
Human Papilloma Virus (HPV), High Risk with 16 and 18 Genotype by PCR (SHPVHR)
Cervical sample in Thin-Prep
Influenza A, B, RSV and SARS-CoV2 (SCFR) Inpatients Only
Nasopharyngeal swab
Respiratory Pathogen Panel by PCR (SRP2)
This test is limited to in-patients, requires approval

Nasopharyngeal swab

Molecular assays not performed in-house will be sent to a reference laboratory. See the table below for a list defined tests available in Epic. For tests not defined in Epic, they should be ordered under miscellaneous.

UCI Discontinued Test (code)
Recommended test
Acceptable specimen
Chlamydia culture (CULCHL)
Chlamydia trachomatis Culture
Test code: XCTC
Laboratory: ARUP

Not recommended for routine detection of Chlamydia trachomatis (CT). Use to detect CT in medico legal settings and to assess suspected treatment failure. May be considered for anatomic locations for which amplified testing has not been validated.
- Cervical
- Eye
- Peritoneal fluid
- Rectal
- Urethral swab
Also acceptable for newborns:
- Nasopharyngeal aspirate
- Swab
- Washing
Pneumocystis jiroveci, Immunofluorescence (PARPNE)
Pneumocystis jiroveci Quantitative Real-time PCR
Test code: VRPNEU
Laboratory: Viracor
- Bronchial/tracheal wash
- Bronchoalveolar lavage (BAL
- Tracheal aspirate
- Whole blood
Respiratory Virus Panel, Immunofluorescence:
- Adenovirus (CULADD)
- Human Metapneumovirus (CULMPV)
- Influenza Virus, Type A & B (CULIND,)
- Parainfluenza Virus Types 1, 2, 3 (CULPID)
- Respiratory Syncytial Virus (CULRSD)
Respiratory Viral Panel TEM-PCR
Test code: VRRVP
Laboratory: Viracor
- Respiratory source
Varicella-Zoster Virus, Immunofluorescence (CULVZD)
Varicella-zoster virus by PCR
Test code: XVZPCR
Laboratory: ARUP
- Plasma
- Ocular fluid
- Serum
- Tissue
- Vesicle fluid

A summary of all tests offered by our laboratory services can be found here:


Cassiana Bittencourt, MD
Division of Clinical Microbiology

Edwin S. Monuki, MD, PhD
Department of Pathology & Laboratory Medicine

  1. Uyeki et al. Clinical Practice Guidelines by the Infectious Diseases Society of America: 2018 Update on Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management of Seasonal Influenza. Clinical Infectious Diseases, Volume 68, Issue 6, 15 March 2019, Pages e1–e47.
  2. Miller et al. A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology. Clinical Infectious Diseases, Volume 67, Issue 6, 31 August 2018, Pages e1–e94.
  3. Manual of Clinical Microbiology. 12th ed. Chapter 83. Algorithms for detection and identification of virus. ASM Press, 2019.
  4. Chotiprasitsakul et al. Performance of real-time PCR and immunofluorescence assay for diagnosis of Pneumocystis pneumonia in real-world clinical practice. PLoS One. 2020 Dec 21;15(12):e0244023.

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