Table A1.

Assay details.

Laboratory ID	RNA Extraction Method (Specimen Volume)	RT-PCR Amplification Strategy	Negative Control	% of Extracted RNA Used	Coverage (PR, RT aa)	Minimum Read Depth a	Minimum Variant Count b	Analysis Pipeline
1	QIAamp Viral RNA Mini kit (0.14 mL)	RT with primerID, then nested PCR	Water	50%	PR 1–99, RT 34–122 and 152–236	Varies	NA c	TCS pipeline in house
2	ViroSeq RNA extraction kit (0.5 mL)	RT then nested PCR	Water	10%	PR 1–99, RT 1–440	1000	1000	CLC Genomics Workbench and In-house
3	QIAamp Viral RNA Mini kit (1 mL)	One-step RT-PCR then nested PCR	Water	10%	PR 6–99, RT 1–251	1000	50	HyDRA [35]
4	MagnaPure LC (0.5 mL)	One-step RT-PCR, then nested PCR	Water	30%	PR 1–99, RT 1–250	330	NA c	Geneious
5	QIAamp Viral RNA Mini kit (0.14 mL)	One-step RT-PCR then nested PCR	Water	10%	PR 1–99 RT 1–300	100	5	Trim Galore!, HydDRA [35]
6	NucliSENS easyMAG (0.4 mL)	One-step RT-PCR, then nested PCR	Water	~9%	PR 1–99, RT 1–250	100	5	HyDRA [35]
7	QIAamp UltraSens Virus kit (0.5 mL)	Primary RT-PCR, then nested PCR	Fetal bovine serum	16.7%	PR 5–99, RT 1–320	1000	NA c	In-house [36]
8	QIAamp Viral RNA Mini kit (0.14 mL)	One-step RT-PCR then nested PCR	Water	25 %	PR 1–99, RT 1–440	1000	10	PASeq.org [35]
9	EZ1 Advance XL (variable) d	RT then nested PCR	Water	16.7%	PR 1–99, RT 1–240	1000	10 e	Hivmmer [9]
10	NucliSENS easyMAG (0.5 mL)	RT then nested PCR	Water	6.7%	PR 1–99, RT 1–400 or 1–240	100	NA c	MiCall [35]

^a minimum number of reads required for data quality assurance. ^b minimum number of individual variants required for reporting. ^c in some analysis pipelines, the minimum variant count is not specified, although in practice is defined by the minimum coverage and variant proportion. ^d volume adjusted based on viral load to contain at least 5000 copies. ^e and ≥1% of total coverage at site.