Trends in molecular diagnostics
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1 Trends in molecular diagnostics Detection of target genes of interest Quantification Infectious diseases HIV Hepatitis C & B TB / MAC Cytomegalovirus Herpes simplex Varicella zoster CT/GC HPV Profiling mutations associated with disease outcome Hepatitis C genotype HIV drug resistance genotype Host genetic factors Thrombophilia CyP450 drug metabolism HLA type
2 Key developments Technology Uptake in diagnostic arena Alternative methods to PCR SDA, TMA, LCR, NASBA, bdna Availability of Analyte Specific Reagents (ASR) Trend to real time or kinetic formats Automation Contamination and inhibitor control
3 ? What is driving commercial NAT platform development Reduce sources of error Reduce tedious processes Improve time to result Improved analytical range Improve limit of detection Improve specificity
4 Volumetric errors amplified Tedious manual, repetitive Specimen integrity Pre amplification - extraction
5
6 Post amplification & detection Endpoint detection Volumetric error Fragment size vs. probe hybridisation Time to result Automation calibration issues Result calculations
7 Signal amplification - bdna Comparison of Amplification Methods Virus, bacterium or cell Target RNA or DNA TMA PCR bdna Add primers Add primers & enzymes & enzymes Copies (RNA) 1 detection probe per copy Copies (DNA) 1 detection probe per amplified copy Add probes and branched DNA Multiple detection probes per target HIV, HBV, HCV, CMV Standard curve Amplify signal of label no amplicon issues Overnight High throughput Limited extraction
8 Kinetic / real time product detection
9 Monitoring in Real time Agarose Gel Blotting FRET
10 Real time PCR
11 Real Time PCR with 5 5 Nuclease Assay Product detection during amplification Primer hγ R Q Probe Fluorescence Emission Quenched R Q Q hγ R Fluorescence Emission Detected
12 HIV viral load tests Manufacturer Principle Results Availability Analytical range Roche RT-PCR (gag) copies/ml Widely <50 100,000 (COBAS HIV MONITOR v1.5) (6 hours to result) < ,000 Bayer HIV Branched DNA 3.0 (bdna) (pol) copies./ml (results 2x less than Roche) (36 hours to result) NSW, Vic <50 800,000 Biomerieux HIV-1 QT NASBA (gag) Copies/mL (6 hours to result) NSW <400 1,000,000 <80 500,000 Roche Real time (Taqman) Copies/mL Widely <40 10,000,000 (gag) (4-6 hours to result) Biomerieux EasyQ HIV-1 real time TMA (gag) Copies/mL & IU/mL (4-5 hours to results) 1 lab <40 10,000,000 Abbott Celera Realtime PCR m2000 (pol integrase) copies/ml Widely <40 10,000,000 Artus Realtime PCR Rotorgene Copies/mL Unregistered <40 10,000,000
13 Selected Applications Primary HIV diagnosis & enhanced surveillance Infant HIV diagnosis HIV treatment & progression monitoring
14
15 HIV Testing Direct Detection of Virus p24 antigen detection serology p24 only assays qualitative and quantitative p24 in combination with antibody Serum Virus isolation - culture Nucleic acid detection - (NAT) HIV DNA or RNA? DNA qualitative proviral (cellular) resolution of inconclusive serology diagnosis in infants - maternal antibodies acute infection (pre-seroconversion) RNA quantitative monitoring / serial viral load drug resistance monitoring subtyping treatment and surveillance
16 gp160 gp120 p68 p55 p53 gp41-45 p40 p34 p24 p18 p12 acute established late DNA PCR RNA PCR p24 Ag EIA 3 rd /4 th gen ELISA 1st gen ELISA Incidence EIA 1wk 2wk 3wk 2mo 6mo 1yr 2yr 3yr +8yr
17 Minipool NAT testing in blood donors mini pools of 6 samples each 4 mini pools combined and tested (total = 24 samples in single test)
18 HIV drug resistance testing
19 Breakthrough of resistance
20 DNA sequencing
21
22
23 Neonatal HIV diagnosis
24 Serologic assays Neonatal HIV diagnosis Maternal antibodies persist up to 18 months postpartum Antibody tests not helpful in newborn diagnosis Sero-reversion (pos neg) in serial samples HIV-1 p24 antigen limited value complexed by Ab Virologic assays Virus culture from PBMC Maternal HIV-1 RNA in obstetric setting is useful in predicting risk of perinatal transmission HIV DNA and RNA useful in infant Detection in infant is diagnostic for perinatal HIV infection Useful in timing of transmission (in utero, intrapartum, post partum) Monitoring response to therapy in infected infant
25 48h 14d 1-2mo HIV infection reasonably excluded in non-breast fed infant if negative in 2 or more 1month and 4months 3-6mo 6-12mo >2 negative HIV Ab tests (<1month apart) Loss Ab/ neg DNA = un-infected Infant still Ab+ at 12mo retest 15-18mo >15-18mo Positive 48h (likely intrauterine Infection - early) Positive 14d (likely intrapartum Infection - late) Months post partum HIV RNA/CD HIV Ab+ >18mo = HIV infection? consider cease ZDV px aggressive ARV
26 CASE STUDY
27 BA,RI HIV serology HIV-1/2 Ab/Ag 4 th gen EIA reactive HIV-1/2 3 rd generation EIA - reactive HIV-1/2 rapid test (X2) reactive HIV-1 western blot POSITIVE N P gp160 gp120 p68 p55/51 gp41 p40 HIV direct detection HIV-1 p24 antigen not detected HIV proviral DNA PCR not detected HIV RNA (gag) PCR not detected p34 p24 p18 α-huigg
28 BA,RI 30 y/o African male Ghana Immigration detention centre NSW Heterosexual Exposure FSW 1 year ago Currently 1 1 syphilis Recurrent episodes malaria treated as outpatient several times over last few years
29 What next? Follow up sample and detailed history! HIV serology testing strategies Supplementary EIAs CD4 lymphocyte count 480 (normal) HIV-2 2 serology Negative to specific gp 36 antigens HIV RNA (pol) Not detected by bdna RNA test HIV culture - virus isolation CD8 depleted, IL2 enriched, PHA stimulated PBMC co-culture gp140 gp105 p68 p56 gp36 p34 p26 p16
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