. 2011 Nov;13(6):583–604. doi: 10.1016/j.jmoldx.2011.05.011

Table 1.

STD Assays

Organism	Specimen/sample type	Assay/platform (FDA no.)	Method	Target	Linear range (%)^⁎
Organism	Specimen/sample type	Assay/platform (FDA no.)	Method	Target	Sensitivity	Specificity
HPV	Cervical cytology specimen in ThinPrep PreservCyt and cervical cytology specimen in Specimen Transport Medium	Digene HC2 HPV DNA Test (P890064/S006)^†	Hybridization protection assay with signal amplification using microplate chemiluminescence hybrid capture of RNA-DNA hybrid	RNA probe cocktail for 13 hr types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68) and 5 low-risk types (6, 11, 42, 43, and 44)	93.0^‡	61.1
	Cervical cytology specimen in ThinPrep PreservCyt and cervical cytology specimen in Specimen Transport Medium	Digene HC2 High-Risk HPV DNA typing kit (P890064/S009)^†	Hybridization protection assay with signal amplification using microplate chemiluminescence hybrid capture of RNA-DNA hybrid	RNA probe cocktail to detect 13 hr-HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, and 68)^§	93.0^‡	61.1
	Cervical cytology specimen in ThinPrep PreservCyt	Cervista HPV HR (P080014)^¶	Invader technology	E6/E7/L1; cocktail of 14 hr-HPV DNA probes (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68)^∥; human histone 2 gene (internal control)	92.8	67.2 (aged ≥30 years)
	Cervical cytology specimen in ThinPrep PreservCyt	Cervista HPV 16/18 (P080015)^¶	Invader technology	Cocktail of two types of sequence-specific DNA probes^⁎⁎; human histone 2 gene (internal control)	PPA, 85.7 (65.4–95.0)	NPA, 95.9 (94.9–96.7)
HSV	Vaginal lesion swab only (not for prenatal screening or in females <18 years); collected in Copan Universal Transport Medium or identical Copan- manufactured media formulation; an extractable sample processing control target is added to the specimen before lysis	MultiCode RTx HSV 1&2 Kit (K100336)^††	Real-time PCR using isoC:isoG synthetic DNA bp technology	Glycoprotein gene segment of HSV-1 and HSV-2	HSV-1, 92.4	HSV-1, 98.3
HSV		MagNA Pure LC Total NA Kit and Magna Pure Instrument LightCycler 1.2^‡‡	Real-time PCR using isoC:isoG synthetic DNA bp technology	Glycoprotein gene segment of HSV-1 and HSV-2	HSV-2, 95.2	HSV-2, 93.6
CT	Endocervical (female) and urethral (male) swabs; urine specimens (male and female); gynecological specimens collected in BD SurePath preservative fluid	BD ProbeTec CT Q^x Amplified DNA Assay (K090824, K091724, K081824)^§§	Strand displacement amplification	Alternate region of the cryptic plasmid	94.5	98.9
	Endocervical and vaginal (female) and urethral (male) swabs; urine specimens (male and female); patient-collected vaginal swab specimen is also accepted	APTIMA Assay for Chlamydia trachomatis (K043072, K053446, K061413, K063451)^¶¶	Transcription-mediated amplification	23S rRNA	95.6	98.8
	Specimen that has been processed and tested positive by PACE 2 system for CT	PACE 2 CT (K920302)^¶¶	Probe competition assay; CT confirmation test	23S rRNA	91.7	98.5
	Digene Cervical Sampler or Dacron swab placed in Digene Specimen Transport Medium	Digene HC2 CT-ID DNA Test (K990023, K010892)^†	Hybrid capture	RNA probe cocktail complementary to CT genomic DNA; cryptic plasmid	92.3–97.7^∥∥	98.2–98.6^∥∥
	Endocervical (female) and urethral (male) swabs; urine specimens (male and female)	COBAS AMPLICOR (CT/NG) Test (K973707, K973718, K070174, K053287)^‡‡	PCR	Cryptic plasmid	92.9–94.1	94.7–98.4
NG	Cervical and vaginal (female) and urethral (male) swabs; urine (male and female); PreservCyt specimens; Surepath specimens	BD ProbeTec GC Q^X Amplified DNA Assay (K081825, K090971)^§§	Strand displacement amplification	Pilin gene	99.3	99.4
NG	Vaginal and cervical swabs; urethral swabs (male); urine (male and female); PreservCyt specimen	APTIMA Assay for NG (K043144, K061509, K062440, K063664)^¶¶	Transcription-mediated amplification	16S rRNA	92.3	99.8
	Specimen that has been processed and tested positive by PACE 2 system for NG	PACE 2 NG (K920301)^¶¶	Probe competition assay; GC confirmation test	rRNA	95.1	98.7
	Cervical specimens collected using Digene Cervical Sampler and Digene Swab Specimen Collection kit	Digene HC2 GC-ID DNA Test (K981485, K010893)^†	Hybrid capture	RNA probe cocktail complementary 0.5% of the NG genome, cryptic plasmid	92.6–95.2^∥∥	98.5–98.9^∥∥
	Cervical (female) and urethral (male) swabs; urine (male)	AMPLICOR CT-NG for NG (K974503, K974342, K070172, K053289)^‡‡	PCR	M.NgoPII putative methyl transferase gene of NG	95.9–96.5	98.7–97.3
CT-NG combined	Vaginal (female) and urethral (male) swabs; urine (male and female); patient-collected vaginal swab specimen	RealTime CT-NG assay (K092704, K080739)^⁎⁎⁎	Real-time PCR	CT, cryptic plasmid	CT, 92.5–97.8	CT, 98.3–99.8
		RealTime CT-NG assay (K092704, K080739)^⁎⁎⁎	Real-time PCR	NG, Opa gene	NG, 87.0–100	NG, 99.3–100
	Endocervical (female) and urethral (male) swabs; urine specimens (male and female)	BD ProbeTec ET CT-GC (K012351)^§§	Strand displacement amplification	CT, cryptic plasmid	CT, 92.0	CT, 94.9
		BD ProbeTec ET CT-GC (K012351)^§§	Strand displacement amplification	GC, Pilin gene	GC, 96.1	GC, 98.2
CT-NG combined	Endocervical (female) and urethral (male) swabs; urine specimens (male and female)	APTIMA COMBO 2 (K003395, K022874, K032554, K043224, K060652)^¶¶	Transcription-mediated amplification	CT, 23S rRNA	CT, 95.2–96.5	CT, 97.6–98.7
			Transcription-mediated amplification	NG, 16S rRNA	NG, 96.5–99.1	NG, 98.4–99.4
	Endocervical (female) and urethral (male) swab specimens collected with the PACE Specimen Collection kits	PACE 2C CT-NG (K940979)^¶¶	Probe competition assay	rRNA	CT-NG, 96.8	CT-NG, 93.6
	Cervical specimens collected using Digene HC2 DNA Collection Device or Digene Female Swab Specimen Collection Kit	Digene HC2 CT/GC Dual DNA Test (K981567, K010891)^†,^†††	Hybrid capture	CT-GC RNA probe cocktail	CT, 96.1	CT, 98.7
		Digene HC2 CT/GC Dual DNA Test (K981567, K010891)^†,^†††	Hybrid capture	CT-GC RNA probe cocktail	GC, 93.0	GC, 99.1
HIV-1	Human plasma specimens (ACD-A and EDTA)	RealTime HIV-1 assay (BP060002)^⁎⁎⁎ and m2000 (m2000sp + 2000rt)	Real-time RT-PCR	Integrase region in pol gene	40–10,000,000 copies/mL (HIV-1 groups M, N, and O)
	Plasma extracted from blood collected using EDTA or ACD^‡‡‡	AMPLICOR HIV-1 MONITOR test, version 1.5 (BP950005/4)^‡‡ and COBAS AMPLICOR HIV-1 MONITOR test, version 1.5 (BP950005)^‡‡	End point RT-PCR	142 bp in highly conserved region of Gag gene	Standard, 400–750,0000 copies/mL; ultrasensitive, 50–100,000 copies/mL (HIV-1 group M)
	Plasma separated from blood collected using EDTA	COBAS AmpliPrep/COBAS TaqMan HIV-1 test (BP050069/0)^‡‡ and COBAS AmpliPrep/COBAS TaqMan^‡‡	Real-time RT-PCR	Gag gene	48–10,000,000 copies/mL (HIV-1 group M)
HIV-1	Plasma extracted from blood collected using EDTA or ACD^‡‡‡	VERSANT HIV-1 RNA 3.0 Assay (bDNA) (BP000028/0)^§§§ and VERSANT Molecular System^§§§	bDNA technology	Pol gene	75–500,000 copies/mL (HIV-1 groups M and O)
	Plasma or serum	APTIMA HIV RNA Qualitative Assay (BL103966/5040)^¶¶	Transcription-mediated amplification	Highly conserved regions of HIV-1 RNA	100	99.83
	Plasma or serum	Procleix ULTRIO Assay^¶¶	Transcription-mediated amplification	Highly conserved regions of HIV-1 RNA, HCV RNA, and HBV DNA	100 (ULTRIO)	99.5 (ULTRIO)
	Plasma or serum	Procleix HIV-1, HCV, and/or HBV Discriminatory Assays (BL 125113/33)^¶¶	Transcription-mediated amplification	Highly conserved regions of HIV-1 RNA, HCV RNA, and HBV DNA	100 (HIV-1 discriminatory)	99.7–100 (HIV-1 discriminatory)
	Plasma or serum	COBAS AmpliScreen HIV-1 Test (BL 125059/37)^‡‡	RT-PCR	Gag gene	96.5–98	98.9–99.7
HIV-1 drug resistance^¶¶¶	Plasma samples from blood collected in EDTA	ViroSeq HIV-1 Genotyping System (BK030033)^∥∥∥ and ABI 3100/3130 capillary electrophoresis platform^⁎⁎⁎⁎	RT-PCR, population sequence analysis	HIV-1 subtype B protease gene and partial sequence of the reverse transcriptase regions of the pol gene	Validated for detection of drug-resistance mutations in 40 of 60 mutant/wild-type mixture samples with a viral load range of 2000–750,000 copies/mL
HIV-1 drug resistance^¶¶¶	Plasma samples from blood collected using ACD or EDTA anticoagulants	TRUGENE HIV-1 Genotyping Kit (BK090077)^§§§ and OpenGene DNA Sequencing System^§§§	RT-PCR, population sequence analysis	protease gene and part of the reverse transcriptase regions	Requires samples with viral loads ≥1000 copies/mL

ACD-A, anticoagulant citrate dextrose solution A; bDNA, branched DNA; NPA, negative predictive accuracy; PPA, positive predictive accuracy.

^⁎

Sensitivity, specificity, linear range, and percentage positive or negative agreement with culture data are sourced from FDA submission material or product inserts.

^†

Obtained from Qiagen, Gaithersburg, MD.

^‡

Atypical squamous cells of undetermined significance referral Papanicolaou stain population, Kaiser Study, PreservCyt solution specimens.

^§

Cross-reacts with HPV types 40, 53, and 66.

^¶

Obtained from Hologic, Madison, WI.

^∥

Cross-reacts with HPV types 67 and 70.

^⁎⁎

Cross-reacts with high levels of HPV type 31.

^††

Obtained from EraGen Biosciences, Madison, WI.

^‡‡

Obtained from Roche Molecular Diagnostics, Pleasanton, CA.

^§§

Obtained from BD Diagnostics, Sparks, MD.

^¶¶

Obtained from Gen-Probe, Inc., San Diego, CA.

^∥∥

Depending on brush or swab specimens.

^⁎⁎⁎

Obtained from Abbott Molecular, Inc., Des Plaines, IL.

^†††

This assay is indicated for use as an initial test and requires confirmation with the individual MID assays.

^‡‡‡

ACD specimens will yield approximately 15% lower test results because of the dilution effect of 1.5 mL ACD in the collection tube.

^§§§

Obtained from Siemens Healthcare Diagnostics, Deerfield, IL.

^¶¶¶

Provides information on resistance to nucleoside and nonnucleoside reverse transcriptase and protease inhibitors.

^∥∥∥

Obtained from Celera Diagnostics, Alameda, CA.

^⁎⁎⁎⁎

Obtained from Applied Biosystems, Foster City, CA.