Table 1.

Collection of laboratory methods used for SARS-CoV-2 wastewater-based genomic surveillance (WWGS)

Method	Available options
Sampling Sources and Scales	WRF: Raw Sewage [11, 20, 21, 51–64]
	WRF and Hospital: Raw Sewage [65]
	Manholes: Raw Sewage [23]
	WRF and Manholes: Raw Sewage [66]
	WRF: Sludge [67]
	WRF: Raw Sewage and Treated Effluent [68]
	Building and WRF: Raw Sewage [19, 39, 67]
Samling Type and Frequency	Grab [54, 56, 67, 69]
	Grab: 1x, 2 × a week [57]
	3-h composite [66]
	24-h composite [11, 23, 51, 53, 55, 63–66, 69–71]
	24-h composite: 1x [20, 60, 62], 2x [21, 59], 3x [19, 66], 5x [19] a week
	Grab and 24-h composite [39, 52, 68]
Concentration Technique	Ultrafiltration [11, 21, 23, 52, 58–60, 65]
	Ultracentrifugation [56, 66]
	PEG precipitation [53, 55, 57, 61, 62, 66]
	Electronegative Membrane Filtration [20, 39, 63, 71, 72]
	Centrifugal Ultrafiltration [51, 64, 68, 69]
	AI(OH)3 precipitation [68]
	Affinity Capture Magnetic Hydrogel [68]
Extraction Method	QIAamp Viral RNA mini kit [52, 57, 61, 64, 66, 69]
	RNeasy mini kit [11, 23, 65]
	NucliSens Kit [56, 58, 60]
	RNeasy PowerMicrobiome Kit [59]
	MagMAX-96 Viral RNA isolation kit [21]
	Viral RNA/DNA Concentration and Extraction Kit from Wastewater (Promega) [53]
	Wizard® Enviro Total Nucleic Acid Kit (Promega) [73]
	Direct-zol 96 MagBead RNA kit [53, 62]
	Chemagic Prime Viral DNA/RNA 300 Kit H96 [20]
	Qiagen AllPrep DNA/RNA minikit [71]
	NucliSENS easyMAG [63]
	EZ1 Virus Mini Kit [51]
	NucliSENS MiniMag Nucleic Acid Purification System [68]
	Maxwell RSC Pure Food GMO and authentication kit [54]
	Zymo QuickRNA-Viral Kit [39]
	Magnetic-bead based with MagMAX Viral/Pathogen II Nucleic Acid Isolation Kit [39]
	Zymo Quick-RNA Fecal/Soil Microbe Microprep Kit [67]
Quantification Method	RT-qPCR [11, 19, 21, 23, 39, 51, 53–66, 68, 71]
	ddPCR [53, 59, 60, 67]
	dPCR [23]
	V2GqPCR [72, 74]
Sequencing Panel	ARTIC v1, v3 [11, 20, 21, 39, 51–54, 57, 63, 67, 68], v4 [23, 66] and v4.1 [23] panel
	Swift Nomalase Amplicon SARS CoV-2 Panel (SNAP) [19, 55, 62, 65]
	Tiled amplicon approach [58, 59]
	EasySeq™ RC-PCR SARS CoV-2 WGS kit v3.0 [56]
	VarSkip 1a panel [53]
	NEBNext Fast DNA Library Prep Set for Ion Torrent and Ion Xpress Barcode Adapters [61]
	NEBNext VarSkip Short SARS-CoV-2 Primer [20]
	Illumina Respiratory Virus Oligo Panel [71]
	CleanPlex SARS-CoV-2 FLEX Pane [69]
Sequencing platform	Illumina [19–21, 23, 39, 51–58, 62–65, 67–69, 71]
	Oxford Nanopore [11, 58, 59]
	Ion Torrent [71, 75]
	Sanger [11]