Table 3:

All discordant results with cycle threshold (Ct) values among the multiplex assays in this study

SARS-CoV-2
Reference test		cobas 6800		GeneXpert	LDT	Liat
E	Viral Load (log10 RNA copies/mL)	Orf1a	E	E & N2	E	Orf1 ab & N
32.94	1.693	34.76	33.98	35.2	NEG *	-
34.67	1.167	36.66	36.31	-	NEG	-
35.79	0.827	36.94	35.18	39.2	NEG	POS
36.27	0.681	37.44	35.48	NEG † , ‡	NEG ‡	POS
36.85	0.505	35.5	34.86	38.2	NEG	POS
NEG	NEG	40.79 §	NEG	NEG	NEG	-
NEG	NEG	NEG	NEG	-	36.89 ¶	-
NEG	NEG	NEG	NEG	NEG	-	POS
19.81	5.682	20.49	20.14	-	21.80 (plus Flu A detected with Ct 40.46)**	-

Influenza A
Reference Test		cobas 6800	GeneXpert		LDT	Liat
Flu A1	Flu A2	Flu A	Flu A1	Flu A2	Flu A	Flu A
33.1	33.3	31.62	29.9	31.2	NEG	POS

^* Visual inspection revealed amplification at Ct >35, but not detected by instrument

^† SARS-CoV-2 endpoint reported by GeneXpert was 1

^‡ Sample collected from patient 1 day earlier was positive for SARS-CoV-2 by reference method (Ct 32.44); likely false negative by GeneXpert and LDT

^§ Sample collected December 2018, prior to COVID-19 pandemic and was positive for parainfluenza 2 (Ct 25.3); likely false positive SARS-CoV-2 by cobas

^¶ Sample collected February 2020 and was positive for human metapneumovirus (Ct 29.21); likely false positive SARS-CoV-2 by LDT

^** Sample was highly positive for SARS-CoV-2 and no Influenza A was detected by reference method nor cobas; likely false positive Influenza A by LDT

LDT = Laboratory-developed test