Table 5.

Compilation of the types of controls and corresponding examples used in the context of NAATs targeted for SARS-CoV-2 detection.

	Classification			Stage screened	Common examples	Source
Controls	External	Positive	Whole process	Entire workflow	Inactivated whole virus, armored SARS-CoV-2 RNA, VLPs	(Wang et al., 2021; Yan et al., 2021)
			Stage	RNA extraction	Inactivated whole virus, armored SARS-CoV-2 RNA, VLPs	(Wang et al., 2021)
				Reverse transcription	SARS-CoV-2 genomic RNA, In vitro transcribed mRNA	(SoRelle et al., 2020)
				cDNA amplification	Plasmid DNA, SARS-CoV-2 genomic RNA, In vitro transcribed mRNA	(Petrillo et al., 2020; SoRelle et al., 2020)
		Negative	Whole process	Contamination in the entire workflow	Non-infected, cultured human cell lines	(Petrillo et al., 2020)
				Specificity in the entire workflow	Human specimens infected or spiked with human infecting RNA virus (e.g. Influenza A and B, RSV)	(Lee et al., 2020)
			Stage	Contamination during RNA extraction	Nuclease-free water	(Petrillo et al., 2020)
				Contamination associated with reverse transcription	Nuclease-free water	(Petrillo et al., 2020)
				Contamination associated with cDNA amplification	Nuclease-free water	(Petrillo et al., 2020)
	Internal	Positive	Endogenous	RNA extraction	Human cells mRNA (e.g. β actin, RNase P), 18S RNA	(Yan et al., 2020)
				Collection of human samples	Human cells mRNA (e.g. β actin, RNase P), 18S RNA	(Yan et al., 2020)
				Reagent/Equipment malfunction	Human cells mRNA (e.g. β actin, RNase P), 18S RNA	(Yan et al., 2020)
			Exogenous	RNA extraction	Non-pathogenic virus (e.g. AoGV, MS2 phage), armored non-SARS-CoV-2 RNA, VLPs	(Calvez et al., 2020; Hasan et al., 2020; Yan et al., 2020)
				Reverse transcription	Non-SARS-CoV-2 RNA (e.g. PVY)	(Calvez et al., 2020)
				cDNA amplification	Plasmid DNA, non-SARS-CoV-2 RNA (e.g. PVY)	(Calvez et al., 2020)
				Inhibition of cDNA amplification	Non-pathogenic virus, armored non-SARS-CoV-2 RNA, VLPs, non-SARS-CoV-2 RNA, Plasmid DNA	(Calvez et al., 2020; Hasan et al., 2020)
				Reagent/Equipment malfunction	Non-pathogenic virus, armored non-SARS-CoV-2 RNA, VLPs, non-SARS-CoV-2 RNA, Plasmid DNA	(Calvez et al., 2020; Hasan et al., 2020)