Table 6.

Studies assessing agreement between NAAT platforms.

Authors	Country	Study Type	No. Patients		Demographics†		Specimen	Platform #1			Platform #2			Study Findings (95% CI)
			Total	Cases*	Age (y)‡	% M		Type	Primers	Platform	Type	Primers	Platform	rPPA	rNPA	rOA	rPPV	rNPV	Cohen's κ
Harrington et al. 48	USA	Cohort¶	524	188	nr	nr	Paired NPS in VTM (RealTime) & foam nasal swab (ID NOW) (524 pairs)	Automated Multiplex RT-PCR	RdRp, N	Abbott RealTime	Automated Isothermal NAAT	RdRp	Abbott ID NOW	75% (67.7–80.6)	99% (97.6–99.8)
Moore et al34,a	USA	Cohort||,¶,⁎⁎	200	125	50 ± 17	46%	NPS in VTM (200)	Automated Multiplex RT-PCR	RdRp,  N	Abbott RealTime	Automated Isothermal NAAT	RdRp	Abbott ID NOW	75.2% (66.7–82.5)	100% (95.4–100)
Basu et al. 49	USA	Cohort¶	101	32	(28 - 90)	nr	NPS dry (101)	Automated Multiplex RT-PCR	N2, E	Cepheid Xpert Xpress	Automated Isothermal NAAT	RdRp	Abbott ID NOW	54.8% (37.8–70.8)	98.6% (92.3–99.7)	85.1% (76.9–90.8)	94.4% (74.3–99)	83.1% (73–89.7)
		Cases only¶	15	15	nr	nr	NPS in VTM (15)							66.7%
Hogan et al. JCV, 5–1 50	USA	Case Control††	100‡‡	53‡‡	nr	nr	NPSc (100)	Automated Multiplex RT-PCR	ORF1ab (2)	Hologic Panther	Automated Isothermal NAAT	RdRp	Abbott ID NOW	80.4% (66.9–90.2)	95.9% (86.0–99.5)
Zhen, Smith et al51,b	USA	Cohort††	108	58	nr	nr	NPS in VTM (108)	Automated Multiplex RT-PCR	ORF1ab (2)	Hologic Panther	Automated Isothermal NAAT	RdRp	Abbott ID NOW	87.7% (76–95)	100% (93–100)				0.87 (0.78–0.96)
Smithgall et al. 52	USA	Case Control||¶	113	90	65 (0–101)	60.2%	NPS in VTM or UTM (113)	Automated Multiplex RT-PCR	ORF1, E	Roche cobas 6800	Automated Isothermal NAAT	RdRp	Abbott ID NOW	73.9% (63.2–82.3)	100% (83.4–100)
								Automated Multiplex RT-PCR	ORF1, E	Roche cobas 6800	Automated Multiplex RT-PCR	N2, E	Cepheid Xpert Xpress	98.9% (92.9–100)	92% (72.4–98.6)
Moran et al. 53	USA	Cohort||,⁎⁎	103‡‡	42‡‡	nr	nr	NPS (95), nasal swab (8)	Automated Multiplex RT-PCR	ORF1, E	Roche cobas 6800	Automated Multiplex RT-PCR	N2, E	Cepheid Xpert Xpress			99%
Craney et al. 54	USA	Cohort††	389	147	nr	nr	NPS (389)	Automated Multiplex RT-PCR	ORF1ab (2)	Hologic Panther	Automated Multiplex RT-PCR	ORF1, E	Roche cobas 6800			96.4%			0.922
Zhen, Smith et al51,b	USA	Cohort††	108	58	nr	nr	NPS in VTM (108)	Automated Multiplex RT-PCR	ORF1ab (2)	Hologic Panther	Automated Multiplex RT-PCR	N2, E	Cepheid Xpert Xpress	98.3% (91–100)	100% (93–100)				0.98 (0.95–1.0)
								Automated Multiplex RT-PCR	ORF1ab (2)	Hologic Panther	Automated RT-PCR w/sensor	N	GenMark ePlex	91.4% (81–97)	100% (93–100)				0.91 (0.83–0.99)
Loeffelholz et al39,a	USA, UK, FR, IT	Cohort†† (enriched for positive cases)	18‡‡	8‡‡	nr	nr	NPS, OPS, NPS+OPS, Trach Asp (nr)	Automated Multiplex RT-PCR	RdRp, N	Abbott RealTime	Automated Multiplex RT-PCR	N2, E	Cepheid Xpert Xpress	100% (67.6–100)	100% (77.2–100)
Norz et al. 55	Germany	Case Control††	165‡‡	36‡‡	nr	nr	NPS, OPS (nr)	Automated Multiplex RT-PCR	ORF1, E	Roche cobas 6800	Automated RT-PCR	E	NeuMoDx 96	100%	99.2%

^⁎Case estimated as a positive result of any evaluated platform.

^†Of cohort or cases.

^‡Format: median (range), median(IQR), or mean±SD. Patient Population.

^||Hospitalized patients.

^¶Emergency Room/Immediate Care Center patients.

^⁎⁎Outpatient.

^††not reported.

^‡‡Number of samples (when number of patients not reported).

^aLoeffelholz et al. and Moore et al. also appear in Table 5.

^bZhen, Smith et al. appears twice in Table 6 for ease of comparison of studies of the same platform.

^cDry or VTM status not reported. Rhoads et al. appears twice in Table 5 for ease of comparison of studies of the same platform Abbreviations- CI: confidence interval, E: envelope, IQR: Interquartile range, κ: kappa statistic, M: male, N: nucleocapsid, NAAT: nucleic acid amplification test, No.: number, NPS: nasopharyngeal swab, nr: not reported, OPS: oropharyngeal swab, ORF1ab: open reading frame 1ab, RdRp: RNA-dependent RNA polymerase, rNPA: reported negative percent agreement, rNPV: reported negative predictive value, rOA: reported overall agreement, rPPA: reported positive percent agreement, rPPV: reported positive predictive value, rRT-PCR: real-time Reverse Transcription Polymerase Chain Reaction, S: spike, Trach Asp: Tracheal Aspirate, UTM: universal transport medium, VTM: viral transport medium, y: years.