New Tests and Test Updates
New Virology Tests
On Nov. 1, 2011, the Microbiology Laboratory will initiate significant changes in the way clients order virology testing. With a growing number of molecular virology tests (and more in the pipeline), as well as additional test options, we need to change to implement test specific ordering.
This change will apply to all of the virology testing (molecular as well as the remaining viral cultures) performed in the GML microbiology laboratory.
Nine (9) test specific order codes will be utilized at this time:
Respiratory Virus PCR Testing
1. Influenza A&B and RSV PCR (PCRABR)
- Includes testing for Influenza A&B and RSV.
- PCRABR includes a rapid antigen test for RSV for patients ≤ 5 y.o.
- If the RSV rapid antigen test is positive, the PCR ABR will not routinely
be performed.
- PCRABR is only performed Nov. 1-April 30 (Influenza and RSV season).
- PCRABR is the recommended test for all outpatients.
2. Respiratory Viral Panel PCR (RVPCR)
- Includes testing for Influenza A (H1, H3 and non-typeable), Influenza B, RSV A and B, Adenovirus, Parainfluenza Virus types 1-3, Rhinovirus, and Human Metapneumovirus.
- From Nov.1-April 30, RVPCR includes a rapid antigen test for RSV for patients ≤ 5 y.o. The RVPCR assay will be performed regardless of the rapid RSV result.
- RVPCR is the recommended test for all inpatients.
Importantly, you cannot order PCRABR and RVPCR on the same specimen.
Herpes Virus Family PCR Testing
3. Herpes Simplex 1&2 and Varicella Zoster Virus PCR (PCRHVZ)
- When ordering this test, do not order the individual tests for HSV (PCRHSV) or VZV (PCRVZV).
- Recommended test for dermatological (skin) specimens.
4. Herpes Simplex 1&2 PCR (PCRHSV)
- Order for CSF specimens and specimens collected with a swab/UTM (e.g. oral, genital, rectal, skin, and eye specimens).
- Varicella Zoster PCR (PCRVZV)
- Order for specimens collected with a swab/UTM (e.g., eye, skin specimens).
Viral Culture Testing
6. Varicella Zoster Viral Culture (VZVVC)
- Order for specimens not normally collected with a swab.
7. Herpes Simplex 1&2 Viral Culture (HSVVC)
- Order for non-CSF and for specimens not normally collected with a swab.
8. Cytomegalovirus Viral Culture (CMVVC)
- Order for all specimen types.
- Enterovirus Viral Culture (EVVC)
- Order for all specimen types.
Discontinued Tests
Viral Culture (VCULT)
- This test will no longer be offered as of Nov. 1.
Rapid Influenza A/B Assay (RPDFLU)
- This test will not be offered at all this year due to the poor performance characteristics (sensitivity/specificity) of the current commercial assays.
- As an alternative, we recommend Influenza A&B and RSV PCR (PCRABR) assay.
Rapid Respiratory Syncytial Virus Assay (RPDRSV)
- This test will not be offered at all this year. As an alternative, we recommend Influenza A&B and RSV PCR (PCRABR) assay.
Future Direction
We plan in the future to migrate some of the remaining viral culture tests listed above to PCR assays. It requires considerable effort and time to validate the molecular assays as most are not FDA cleared; hence the need to progressively migrate the assays/specimen types over time.
Recent changes in reference ranges or alert limits:
The following changes took effect October 17:
Urine albumin:
Normal: 0-29 mg/24 hours
High: 30-300 mg/24 hours
Very High and Nephrotic: >(greater than) 300 mg/24 hours
Microalbumin Creatinine Ratio (MICALB):
Albumin - random urine: 0-2 mg/dL.
Creatinine - urine: Undefined.
Microalbumin ratio:
Normal: 0-29 mg/g creatinine
High: 30-300 mg/g creatinine
Very High and Nephrotic: >(greater than) 300 mg/g creatinine
Fasting Plasma Glucose (GLUFP):
Based on guidelines from American Diabetes Association:
Fasting glucose < 100 mg/dL ~ normal
100 mg/dL <= fasting glucose < 126 mg/dL ~ pre-diabetes
fasting glucose >= 126 mg/dL ~ diabetes, confirmed by repeat testing on a different day.
Alert limits: Below 40 mg/dL, above 200 mg/dL.
PCR Testing on CSF
PCR testing of CSF specimens is now considered standard of care for the diagnosis of meningitis and meningoencephalitis caused by Herpes Simplex Virus (HSV 1 and HSV 2). On Tuesday, October 4, 2011, the microbiology laboratory at Geisinger Medical Center will begin performing PCR testing for HSV 1 and HSV 2 from CSF specimens in-house at GMC. Previously, PCR testing for these viruses from CSF specimens was sent to a reference lab for testing.
For Proven Diagnostics clients, the test code for Herpes Simplex Virus PCR is PCRHSV. This includes testing for both HSV 1 and HSV 2.
Testing will be performed once each day, 7 days a week, for specimens received in the microbiology laboratory on or before 9:00 A.M. No stat testing will be offered for these tests. The minimum specimen volume for this testing is 1-2 ml of CSF in a sterile collection tube (do not add Universal Transport Media-UTM). Transport to the laboratory at 2-8°C.
If you have any questions about these tests, please contact microbiology laboratory director Dr. Paul Bourbeau (pbourbeau@geisinger.edu) or microbiology technical specialist Lisa Scicchitano (lscicchitano@geisinger.edu) at 1-866-869-1334.
New Test for Two Polymorphisms in the Interleukin 28B Gene
Recent genome-wide association studies (GWAS) have identified IL28B genetic polymorphisms as strong determinants of response to pegylated interferon (PEG-IFN) plus ribavirin (alpha RBV) treatment in HCV genotype 1-infected individuals. Single nucleotide polymorphisms (SNPs) rs12979860 C/T and rs8099917 T/G, located upstream of the interleukin 28B gene encoding interferon lambda 3, are strongly associated with treatment-induced viral clearance. For SNP rs12979860, the favorable C allele has been associated with a 2-3 fold greater rate of sustained virological response following PEG-IFN alpha/RBV therapy and increased spontaneous viral clearance in patients infected with HCV genotype 1, while the T allele is a risk factor for non-response. The variation in rs12979860 C allele prevalence explains much of the observed racial differences in treatment response rates. In a recent US study, the more favorable CC genotype was observed in 37% of Caucasians, 29% of Hispanics, and 14% of African Americans tested. For SNPrs8099917, the favorable T allele is associated with a higher rate of sustained virologic response after therapy and increased spontaneous viral clearance in individuals infected with HCV genotype 1, while the G allele is a risk factor for non-response.
The IL28B genotype is only one of many factors that can influence response rates to PEG-IFN alpha/RBV treatment. The AASLD guidelines state “Treatment decisions should be individualized based on severity of liver disease, the potential for serious side effects, the likelihood of treatment response, the presence of comorbid conditions, and the patient’s readiness for treatment”. For genotypes other than type 1, the usefulness of these SNPs for predicting response to therapy is unknown.
Real-time polymerase chain reaction (PCR) with allele specific TaqMan probes is used to detect both single nucleotide polymorphisms. No other polymorphisms are detected by this assay. Mutations in other genes and non-genetic factors that may affect response to hepatitis C therapy are not detected. Rare diagnostic errors may occur due to primer site mutations.
Any questions should be directed to the Molecular Diagnostics Laboratory or Dr. Barbara Paynton at 1-800-695-6491.
Changes in Normal Ranges (Age Stratification)
The following changes took effect August 30:
Ammonia (AMON) (umol/L)
0 to 14 days: 56-107
15 days to < 2 years: 40-80
2 years to < 18 years: 11-35
GGTP (U/L)
0 to 182 days: <=132
183 days to <1 year: <=39
1 year to <13 years: <=22
13 years to < 18 years - female: <=24
13 years to <18 years male: <=42
> 18 years: Male: 11-51. Female 7-33.
AST (U/L)
0-10 days: 47-150
11 days - < 4 yr: <77
4 yr - < 7 yr: <53
7 yr - < 13 yr: <48
13 yr to <18 yr: <44
> 18 yr: Male 10-50. Female 10-35.
ALT (U/L)
0 - <1 yr: <49
> 1 yr: Male: 10-50. Female: 10-35.
Alkaline Phosphatase (ALKP)
(U/L)
0-30d: <=406
31d - <4 yr: <=387
4 yr - <7 yr Female: <=321
7 yr - < 13yr Female: <=397
13 yr - < 16 yr Female: <=217
16 year and above Female: <=153
4 yr - < 10 yr Male: <=344
10 yr - <16 yr Male: <=424
16 yr - <18 yr Male: <=238
18 year and above Male: <=153
Lactate Dehydrogenase (LD) (U/L)
0- < 1 yr: <438
1 yr - <4 yr: <338
4 yr - <7 yr: <314
7 yr - < 13 yr: <307
13 yr - < 18 yr Male: <304
13 yr - < 18 yr Female: < 271
> 18 yr: 90-250
