Table 3.

Respiratory Tract and CNS Infection Assays

Organism	Specimen/sample type	Platform/assay (FDA no.)	Method	Target	Sensitivity (%)⁎	Specificity (%)⁎
Respiratory virus panel: influenza A/H1 and A/H3; influenza B; adenovirus; RSV; metapneumovirus (hMPV); parainfluenza (hPIV) 1, 2, and 3; and rhinovirus	Nasopharyngeal swab	xTAG Respiratory Viral Panel (K063765)†	RT-PCR, allele-specific primer extension, tag sorting	Matrix gene of influenza A, Hemagglutinin gene of influenza A/H1 and A/H3	Influenza A, 96.4	Influenza A, 95.9
				Influenza B, adenovirus, RSV A/B metapneumovirus	Influenza A/H1, 100	Influenza A/H1, 100
				Parainfluenza 1, 2, and 3; and rhinovirus	Influenza A/H3, 91.7	Influenza A/H3, 98.7
					Influenza B, 91.5	Influenza B, 96.7
					RSV A, 100	RSV A, 98.4
					RSV B, 100	RSV B, 97.4
					Adenovirus, 78.3	Adenovirus, 100
					hMPV, 96	hMPV, 98.8
					hPIV 1, 100	hPIV 1, 99.8
					hPIV 2, 100	hPIV 2, 99.8
					hPIV 3, 84.2	hPIV 3, 99.6
					Rhinovirus, 100	Rhinovirus, 91.3
Respiratory virus panel: influenza A and B and RSV	Nasopharyngeal swab, cultured clinical specimens	Verigene Respiratory Virus Nucleic Acid Test (K083088)‡ and Verigene Respiratory Virus Nucleic Acid Test on the Verigene SP system (K092566)‡	Multiplex RT-PCR multiplex gold nanoparticle hybridization technology Verigene System‡	Influenza A matrix gene	Influenza A, 99.2	Influenza A, 90.1
				Influenza B NS and matrix genes	Influenza B, 96.8	Influenza B, 98.5
				L and F genes of RSV	RSV, 89.8	RSV, 91.5
	Nasopharyngeal swab	ProFlu+ (K073029, K081030, K092500)§ and SmartCycler¶	Multiplex real-time RT-PCR TaqMan chemistry	Influenza A matrix gene	Influenza A, 100	Influenza A, 92.6
				Influenza B non-structural NS1 and NS2 genes	Influenza B, 97.8	Influenza B, 98.6
				RSV polymerase gene	RSV, 89.5	RSV, 94.9
Respiratory virus panel: influenza A and B and RSV	Nasopharyngeal swab	Simplexa Flu A/B and RSV (K102170)∥; MagNA Pure LC Instrument and the MagNA Pure Total Nucleic Acid Isolation Kit⁎⁎ or a Qiagen QIAamp Viral RNA Mini Kit†† and 3M Integrated Cycler‡‡	Real-time RT-PCR	Target RNA of highly conserved region of matrix protein genes of influenza A and B and RSV	Influenza A, 100	Influenza A, 99.3
					Influenza B, 100	Influenza B, 99.8
					RSV, 98	RSV, 96.9
Respiratory virus: influenza A/H1N1-2009	Nasopharyngeal swabs, nasal swabs, NPAs	Simplexa Influenza A H1N1 (2009) (K100148)∥; MagNA Pure LC Instrument and the MagNA Pure Total Nucleic Acid Isolation Kit⁎⁎ or a Qiagen QIAamp Viral RNA Mini Kit†† and 3M Integrated Cycler‡‡	Real-time PCR	Influenza A matrix gene and unique region in Hemagglutinin gene of 2009 H1N1 influenza virus	% positive agreement for swabs, 100; NPA, 100	% negative agreement for swabs, 92.5; NPA, 96.1
Respiratory virus: influenza A/H1N1-2009	Nasopharyngeal swabs and nasal swabs	CDC Human Influenza Virus Real-Time RT-PCR Detection and Characterization Panel (K101564)§§ and Applied Biosystems 7500 Fast Dx Real-Time PCR Instrument¶¶	Real-time PCR	Influenza A matrix gene and Nucleoprotein gene specific for 2009 H1N1 and Hemagglutinin gene specific for 2009 H1N1	96	96
Respiratory virus panel: seasonal influenza A/H1, A/H3, and A/H1N1-2009	Nasopharyngeal swab	ProFAST+ (K101855)§ and SmartCycler¶	Real-time RT-PCR	Target RNA of conserved region of Hemagglutinin gene	% positive agreement for A/H1, 100; A/H3, 100; A/H1N1-2009, 95.4	% negative agreement for A/H1, 99.0; A/H3, 99.0; A/H1N1-2009, 100
Respiratory virus: influenza A/H5 (Asian lineage)	Nasopharyngeal and throat swabs	JBAIDS Influenza A subtype A/H5 (Asian lineage) (K100287) ∥∥ and JBAIDS Instrument	Real-time RT-PCR	Two target RNA sequences 5′ and 3′ of the Hemagglutinin precursor cleavage site within the conserved regions of the Hemagglutinin gene of influenza A/H5 (Asian lineage) virus	96.9–100	95.3–97.1
Respiratory virus: hPIV	Nasopharyngeal swab	ProParaFlu+ (K091053)§ and SmartCycler¶	Multiplex real-time RT-PCR TaqMan chemistry	Conserved regions of Hemagglutinin-Neuraminidase gene of hPIV 1, 2, and 3	hPIV-1, 88.9	hPIV-1, 99.9
					hPIV-2, 96.3	hPIV-2, 99.8
					hPIV-3, 97.3	hPIV-3, 99.2
Respiratory virus: hMPV	Nasopharyngeal swab	Pro hMPV+ (K082688)§ and SmartCycler¶	Real-time RT-PCR TaqMan chemistry	hMPV: Nucleocapsid gene	% positive agreement, 94.1	% negative agreement, 99.3
Respiratory virus: adenovirus	Nasopharyngeal swab	ProAdeno+ (K102952)§ and SmartCycler¶	Multiplex real-time PCR TaqMan chemistry	Adenovirus serotypes 1–51, Hexon gene	97.5	95.6
Enterovirus	CSF	Xpert EV (K061062) and GeneXpert System¶	Real-time PCR	Consensus region of enterovirus, 5′ UTR between nucleotides 452 and 596	96.3–100	97.0–97.2
	CSF	NucliSENS EasyQ Enterovirus (K063261)⁎⁎⁎ and NucliSENS EasyQ System	NASBA	Enterovirus RNA	70.9–100	99.3–100
MTB	Sputum and bronchial specimens	AMPLIFIED MTD (Mycobacterium Tuberculosis Direct) Test (P940034/S008)†††	Transcription- mediated amplification, hybridization protection assay	Mycobacterial 16S rRNA	96.9	100

hMPV, human metapneumovirus; hPIV, human parainfluenza virus; NASBA, nucleic acid sequence-based amplification; NPA, nasopharyngeal aspirate.

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

^†Obtained from Luminex Corporation, Austin, TX.

^‡Obtained from Nanosphere, Inc., Northbrook, IL.

^§Obtained from Gen-Probe Prodesse, Inc., Waukesha, WI.

^¶Obtained from Cepheid, Sunnyvale, CA.

^∥Obtained from Focus Diagnostics, Inc., Cypress, CA.

^⁎⁎Obtained from Roche Molecular Diagnostics, Pleasanton, CA.

^††Obtained from Qiagen, Gaithersburg, MD.

^‡‡3M, St Paul, MN.

^§§Obtained from the CDC, Atlanta, GA.

^¶¶Obtained from Life Technologies Inc., Carlsbad, CA.

^⁎⁎⁎Obtained from bioMérieux Inc., Durham, NC.

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

^∥∥Obtained from the Department of Defense.