Table 1.

Categorical and C _t value agreement between extracted/unextracted specimens

	Primer/probe	Positive percent agreement	ΔC t	Negative percent agreement
(A) Extracted versus unextracted/unconcentrated	N1	95.0% (38/40) 95% CI: 83.5%‐98.6%	5.2 ± 4.0	95.1% (39/41) 95% CI: 83.4%‐98.7%
	N2	32.5% (13/40) 95% CI: 20.0%‐48.0%	>15 C t—37/40 specimensa	100% (41/41) 95% CI: 91.4%‐100%
	N3	95.0% (38/40) 95% CI: 83.5%‐98.6%	5.2 ± 3.5	97.6% (40/41) 95% CI: 87.4%‐99.6%
	RP	100% (81/81) 95% CI: 95.5%‐100%	6.9 ± 3.3	NA*
(B) Extracted versus unextracted/concentrated	N1	95.1% (39/41) 95% CI: 83.4%‐98.7%	2.6 ± 2.5	97.5% (39/40) 95% CI: 87.1%‐99.6%
	N2	85.4% (35/41) 95% CI: 85.4%‐93.1%	8.7 ± 2.5	100% (40/40) 95% CI: 91.2%‐100%
	N3	100% (41/41) 95% CI: 91.4%‐100%	2.4 ± 1.9	95.0% (38/40) 95% CI: 83.5%‐98.6%
	RP	100% (81/81) 95% CI: 95.5%‐100%	4.2 ± 2.7	NA*

Note: Summarized here are the observed categorical positive and negative agreement (detected/nondetected) for each CDC primer/probe‐set, between extracted and unextracted specimens (percentage agreement with 95% CI). Data are summarized for comparisons between (a) extracted VTM versus unextracted/unconcentrated VTM and (b) extracted VTM versus unextracted/concentrated VTM. For each evaluation of positive agreement, the table also includes the pairwise C _t‐value difference between extracted and unextracted specimens (ΔC _t = C _{t‐unextracted} − C _{t‐extracted}, mean ± standard deviation).

Abbreviations: CDC, Centers for Disease Control; CI, confidence interval; C _t, cycle‐threshold value; SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2; VTM, viral transport media.

^aA standard deviation could not be meaningfully calculated for N2‐unextracted/unconcentrated, given the preponderance of specimens generated an undetected (>45) C _t value.

^*Negative percent agreement for the RP primer/probe‐set was not applicable (NA), as these SARS‐CoV‐2‐negative specimens still appropriately demonstrate positivity for the RP internal control.