REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
Respiratory (21 targets) control panel	Microbiologics	Cat. No 8217
Biological samples
RNA samples	Ministry of Health (MOH) hospitals in the western region in Saudi Arabia	N/A
Wastewater samples	The wastewater equalization tank in KAUST, Thuwal, Saudi Arabia	N/A
Chemicals, peptides, and recombinant proteins
TRIzol	Invitrogen	Cat. No 15596018
Critical commercial assays
Direct-Zol RNA Miniprep kit	Zymo Research	Cat. No R2070
NEB ProtoScript II reverse transcriptase	New England Biolabs	Cat. No M0368
Invitrogen SuperScript IV reverse transcriptase	Thermo Fisher Scientific	Cat. No 18090010
RNase H	New England Biolabs	Cat. No M0523S
Respiratory Virus PCR Panel kit	Diagenode diagnostics	DDGR-90-L048
AMPure XP beads	Beckman Coulter	Cat. No A63882
TwistAmp® Basic kit	TwistDx	Cat. No MSPPTABAS03KIT
QIAquick PCR purification kit	QIAGEN	Cat. No 28106
Ligation sequencing kit	Oxford Nanopore Technologies	Cat. No SQK-LSK109
Native Barcoding Expansion 96	Oxford Nanopore Technologies	Cat. No EXP-NBD196
Flow cell (R9.4.1)	Oxford Nanopore Technologies	Cat. No FLO-MIN106D
Deposited data
Raw and analyzed data	This paper	SRA database (accession ID PRJNA638039)
Additional supplemental files	This paper	Mendeley Data (https://dx.doi.org/10.17632/35g7t55h4c.1)
Oligonucleotides
rRT-PCR assay for SARS-CoV-2	Integrated DNA Technologies	Cat. No 10006770
rRT-PCR assay for FluA	Integrated DNA Technologies	Cat. No 1079729
PMMoV-F: TCAAATGAGAGTGGTTTGACC TTAACGTTTGA	Integrated DNA Technologies	N/A
PMMoV-R: AACTCATCGGACACTGTGTTGCC TGTTAGAC	Integrated DNA Technologies	N/A
pair4-F: GCTGGTTCTAAATCACCCATTCAGT	Integrated DNA Technologies	N/A
pair4-R: TCTGGTTACTGCCAGTTGAATCTG	Integrated DNA Technologies	N/A
pair5-F: TTGGGATCAGACATACCACCCA	Integrated DNA Technologies	N/A
pair5-R: CAACACCTAGCTCTCTGAAGTGG	Integrated DNA Technologies	N/A
pair9-F: CCAGCAACTGTTTGTGGACCT	Integrated DNA Technologies	N/A
pair9-R: AGCAACAGGGACTTCTGTGC	Integrated DNA Technologies	N/A
pair10-F: GACCCCAAAATCAGCGAAAT	Integrated DNA Technologies	N/A
pair10-R: TGTAGCACGATTGCAGCATTG	Integrated DNA Technologies	N/A
pair13-F: CCAGAGTACTCAATGGTCTTTGTTC	Integrated DNA Technologies	N/A
pair13-R: ACCCAACTAGCAGGCATATAGAC	Integrated DNA Technologies	N/A
ACTB-F: CCCAGCCATGTACGTTGCTATCCAGGC	Integrated DNA Technologies	N/A
ACTB-R: ACAGCTTCTCCTTAATGTCACGCACGAT	Integrated DNA Technologies	N/A
influA-F: ATGAGYCTTYTAACCGAGGTCGAAACG	Integrated DNA Technologies	N/A
influA-R: TGGACAAANCGTCTACGCTGCAG	Integrated DNA Technologies	N/A
HAdVs-F: GCCGAGAAGGGCGTGCGCAGGTA	Integrated DNA Technologies	N/A
HAdVs-R: TACGCCAACTCCGCC CACGCGCT	Integrated DNA Technologies	N/A
HCoV-F: ATGGTCAAGGAGTTCCCAT TGCTTTCGGAGTA	Integrated DNA Technologies	N/A
HCoV-R: GGGCCGGTACCGAGATAGT AGAAATACCATCTCG	Integrated DNA Technologies	N/A
Software and algorithms
RTNano	This paper	https://github.com/milesjor/RTNano