Genomic diversity of SARS-CoV-2 can be accelerated by mutations in the nsp14 gene

. 2023 Feb 16;26(3):106210. doi: 10.1016/j.isci.2023.106210

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains

Recombinant SARS-CoV-2	This study	N/A
Recombinant SARS-CoV-2 (nsp14-P203L)	This study	N/A
Escherichia coli DH5-a	New England Biolabs	Cat#C2987

Chemicals, peptides, and recombinant proteins

TransIT-LT1 Transfection Reagent	Takara	Cat# MIR2300
Fetal bovine serum	Gibco	Cat# 42Q7361K
Penicillin-streptomycin	Nacalai	Cat# 09367-34
DMEM (high glucose)	Nacalai Tesque	Cat# 08459-64
DMEM high glucose powder	Sigma	Cat# D5648
HEPES(1M)	Gibco	Cat# 15630080
Amphotericin B solution (250 ug/mL)	Sigma	Cat# A2942
Gentamicin Sulfate Solution (50mg/ml)	nacalai	Cat# 11980-14
7.5% NaHCO3	Sigma	Cat# S8761-100ML
SeaPlaque Agarose	Lonza	Cat# 50100
SeaKem Agarose	Lonza	Cat# 50074
G418	Nacalai Tesque	Cat# 09380-44

Critical commercial assays

QIAamp viral RNA mini kit	Qiagen	Cat# 52906
PrimeSTAR GXL DNA polymerase	Takara	Cat# R050A
ProtoScript II Reverse Transcriptase	New England Biolabs	Cat# M0368S
NEBNext® Ultra™ II Non-Directional RNA Second Strand Synthesis Module	New England Biolabs	Cat# E6111S/L
SureSelectXT HS and XT Low input enzymatic fragmentation kit	Agilent	Cat# 5191-4080
NovaSeq 6000 S4 Reagent Kit v1.5 (200 cycles)	Illumina	Cat# 20028313
PrimeScript 1st strand cDNA Synthesis Kit	Takara	Cat# 6110A
Custom probe	Agilent	https://www.agilent.com/cs/library/applications/application-sars-cov-2-sequencing-5994-4538en-agilent.pdf

Deposited data

Viral genome sequencing data by RNA-seq	DDBJ Sequence Read Archive	Accession number: DRR411740 - DRR411753

Experimental models: Cell lines

Human: HEK293-hACE2/hTMPRSS2 cells	This study	N/A
African green monkey (Chlorocebus sabaeus): VeroE6/TMPRSS2 cells	JCRB Cell Bank	JCRB1819

Oligonucleotides

Linker/F1-F: CTATATAAGCAGAGCTCGTTT AGTGAACCGTattaaaggtttataccttcccaggtaac	Torii et al.²⁶	N/A
F1/F2-R: cagattcaacttgcatgg cattgttagtagccttatttaaggctcctgc	Torii et al.²⁶	N/A
F1/F2-F: gcaggagccttaaataaggctacta acaatgccatgcaagttgaatctg	Torii et al.²⁶	N/A
F2/F3-R: ggtaggattttccactacttcttcaga gactggttttagatcttcgcaggc	Torii et al.²⁶	N/A
F2/F3-F: gcctgcgaagatctaaaaccagtctct gaagaagtagtggaaaatcctacc	Torii et al.²⁶	N/A
F3/F4-R: ggtgcacagcgca gcttcttcaaaagtactaaagg	Torii et al.²⁶	N/A
F3/F4-F: caccactaattcaacctattggtgctttg gacatatcagcatctatagtagctggtgg	Torii et al.²⁶	N/A
F4/F5-R: gtttaaaaacgattgtgcatcagctgactg	Torii et al.²⁶	N/A
F4/F5-F: cacagtctgtaccgtctgcggtatgtgga aaggttatggctgtagttgtgatc	Torii et al.²⁶	N/A
F5/F6-R: gcggtgtgtacatagcctcataaaactca ggttcccaataccttgaagtg	Torii et al.²⁶	N/A
F5/F6-F: cacttcaaggtattgggaacctgagttttatg aggctatgtacacaccgc	Torii et al.²⁶	N/A
F6/F7-R: catacaaactgccaccatcacaaccagg caagttaaggttagatagcactctag	Torii et al.²⁶	N/A
F6/F7-F: ctagagtgctatctaaccttaacttgcctggt tgtgatggtggcagtttgtatg	Torii et al.²⁶	N/A
F7/F8-R: ctagagactagtggcaataaaacaagaaaa acaaacattgttcgtttagttgttaac	Torii et al.²⁶	N/A
F7/F8-F: gttaacaactaaacgaacaatgtttgtttttcttg ttttattgccactagtctctag	Torii et al.²⁶	N/A
F8/F9-R: gcagcaggatccacaagaacaacagccctt gagacaactacagcaactgg	Torii et al.²⁶	N/A
F8/F9-F: ccagttgctgtagttgtctcaagggctgttgtt cttgtggatcctgctgc	Torii et al.²⁶	N/A
F9/Linker-R: GGAGATGCCATGCCGACCC tttttttttttttttttttttttttgtcattctcctaag	Torii et al.²⁶	N/A
F9/Linker-F: cttaggagaatgacaaaaaaaaaaaaaaa aaaaaaaaaaGGGTCGGCATGGCATCTCC	Torii et al.²⁶	N/A
Linker/F1-R: gttacctgggaaggtataaacctttaatAC GGTTCACTAAACGAGCTCTGCTTATATAG	Torii et al.²⁶	N/A

Recombinant DNA

Plasmid: pCSII-sars-cov-2 F1	Torii et al.²⁶	N/A
Plasmid: pCSII-sars-cov-2 F2	Torii et al.²⁶	N/A
Plasmid: pCSII-sars-cov-2 F3	Torii et al.²⁶	N/A
Plasmid: pCSII-sars-cov-2 F4	Torii et al.²⁶	N/A
Plasmid: pcDNA3.1.-sars-cov-2 F5	Torii et al.²⁶	N/A
Plasmid: pcDNA3.1.-sars-cov-2 F6	Torii et al.²⁶	N/A
Plasmid: pcDNA3.1.-sars-cov-2 F6 (nsp14-P203L)	This study	N/A
Plasmid: pCSII-sars-cov-2 F7	Torii et al.²⁶	N/A
Plasmid: pCSII-sars-cov-2 F8	Torii et al.²⁶	N/A
Plasmid: pCSII-sars-cov-2 F9	Torii et al.²⁶	N/A
Plasmid: pMW118 CoV2-CMVlinker	Torii et al.²⁶	N/A

Software and algorithms

MAFFT version v7.453	Katoh and Standley²⁷	https://mafft.cbrc.jp/alignment/software
WebLogo 3	Crooks et al.¹⁴	https://weblogo.threeplusone.com
ProtTest3 version 3.4.2	Darriba et al.²⁸	https://github.com/ddarriba/prottest3
RAxML-NG version 1.0.0	Kozlov et al.²⁹	https://github.com/amkozlov/raxml-ng
CD-HIT-EST version 4.8.1	Li et al.³⁰	https://sites.google.com/view/cd-hit
ModelTest-NG	Darriba et al.³¹	https://github.com/ddarriba/modeltest
MEGA X	Kumar et al.³²	https://www.megasoftware.net
TranslatorX	Abascal et al.³³	http://translatorx.co.uk
Datamonkey software	Weaver et al.³⁴	https://www.datamonkey.org
cutadapt version 3.2	Martin³⁵	https://cutadapt.readthedocs.io/en/v3.2/
BWA version 0.7,17-r1188	Li and Durbin³⁶	http://bio-bwa.sourceforge.net
MuTect2 in GATK suite version 4.2	McKenna et al.³⁷	https://github.com/broadinstitute/gatk/releases
PyMOL molecular graphics system v2.4.0	The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC	https://pymol.org/
BeAtMuSiC program version 1.0	Dehouck et al.³⁸	http://babylone.3bio.ulb.ac.be/beatmusic/
GraphPad Prism software version 9.4.0	GraphPad Software	https://www.graphpad.com/scientific-software/prism/
FigTree v1.4.4	http://tree.bio.ed.ac.uk/software/figtree/	http://tree.bio.ed.ac.uk/software/figtree/
R v4.2.1	The R Foundation	https://www.r-project.org/
Python v3.7	Python Software Foundation	https://www.python.org

Other

GISAID EpiCoV database	Shu et al.¹²	https://epicov.org/epi3/epi_set/230110sz