REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
SARS-CoV-2	National Culture Collection for Pathogens, Korea National Institute of Health, Korea	NCCP 43326
Chemicals, Peptides, and Recombinant Proteins
Penicillin-streptomycin	GIBCO	Cat#15140163
TRIzol	Invitrogen	Cat#15596018
Actinomycin D	Sigma-Aldrich	Cat#A9415; CAS: 50-76-0
Critical Commercial Assays
DMEM	GIBCO	Cat#11995065
FBS	GIBCO	Cat#10082147
Recombinant DNase I (RNase-free)	Takara	Cat#2270A
RNeasy MinElute Cleanup Kit	QIAGEN	Cat#74204
SuperScript IV Reverse Transcriptase	Invitrogen	Cat#18090200
Q5® High-Fidelity 2X Master Mix	NEB	Cat#M0492L
Gel Extraction Kit	Labopass	Cat#CMG0112
MEGAscript T7 Transcription Kit	Invitrogen	Cat#AMB13345
Oligo Clean & Concentrator	Zymo Research	Cat#D4061
1 Kb Plus DNA Ladder	Invitrogen	Cat#10787026
Direct RNA sequencing kit	Oxford Nanopore Technologies	Cat#SQK-RNA002
SUPERase•In RNase Inhibitor	Invitrogen	Cat#AM2696
Flow Cell (R9.4.1)	Oxford Nanopore Technologies	Cat#FLO-MIN106D
MinION device	Oxford Nanopore Technologies	Cat#MinION; RRID: SCR_017985
Dynabeads® mRNA Purification Kit	Invitrogen	Cat#61006
MGIEasy RNA Directional Library Prep Set	MGI	Cat#1000006385
MGISEQ-200RS High-throughput Sequencing Kit (PE100)	MGI	Cat#1000005233
MGISEQ-200RS Sequencing Flow Cell	MGI	Cat#1000003794
DNBSEQ-G50RS sequencer	MGI	Cat#DNBSEQ-G50RS
Deposited Data
RNA-seq using MGISEQ-200	This study	https://doi.org/10.17605/OSF.IO/8F6N9
Nanopore direct RNA sequencing	This study	https://doi.org/10.17605/OSF.IO/8F6N9
Figure S3 original files	This study	https://doi.org/10.17632/bkhbpvtg7h.1
Experimental Models: Cell Lines
Vero	ATCC	Cat#CCL-81
Oligonucleotides
The oligonucleotides used in this study were listed in Table S1	This study	N/A
Software and Algorithms
guppy 3.4.5	Oxford Nanopore Technologies	https://community.nanoporetech.com/sso/login?next_url=%2Fdownloads
minimap2 2.17	Li, 2018	https://github.com/lh3/minimap2
poreplex 0.5.0	Hyeshik Chang, Seoul National University, Korea	https://github.com/hyeshik/poreplex
SciPy 1.4.1	Virtanen et al., 2020	https://www.scipy.org/; RRID: SCR_008058
STAR 2.7.3a	Dobin et al., 2013	https://github.com/alexdobin/STAR; RRID: SCR_015899
tombo 1.5	Oxford Nanopore Technologies, Stoiber et al., 2017	https://github.com/nanoporetech/tombo
Other
Chlorosebus sabaeus genome and annotation	ENSEMBL release 99	ChlSab1.1 (GCA_000409795.2)
yeast ENO2 cDNA	SGD	SGD: YHR174W
human ribosomal DNA complete repeat unit	GenBank	GenBank: U13369.1
SARS-CoV-2 isolate Wuhan-Hu-1, complete genome	GenBank	GenBank: NC_045512.2
SARS-CoV-2 isolate BetaCoV/Korea/KCDC03/2020, partial genome	GISAID	GISAID: EPI_ISL_407193