Fetal bovine serum (fbs)

The human non-small cell lung carcinoma cell line NCI-H1299 were cultivated in RPMI medium 1640 (Gibco, Life Technologies, Carlsbad, CA, USA) containing 4.5 g/L D-Glucose, 2.383 g/L HEPES Buffer, L-Glutamine, 1.5 g/L Sodium Bicarbonate, and 110 mg/L Sodium Pyruvate, supplemented with 50 units/mL Penicillin, 50 mg/mL Streptomycin (Gibco), and 10% (vol/vol) FBS (Labtech, Heathfield, UK). The human embryonic kidney cell line HEK-293 were cultivated in Dulbecco’s Modified Eagle Medium (Gibco) containing 4.5 g/L D-Glucose, L-Glutamine, and Pyruvate, supplemented with 50 units/ mL Penicillin, 50 mg/mL Streptomycin (Gibco), and 10% (v/v) FBS (Labtech). All cell cultures were maintained 37 °C with 5% CO2 in a humidified incubator.

HEK293T/17 cells (abbreviated herein as 293T cells) were obtained from American Type Culture Collection (ATCC, CRL-11268). Caco2 cells were a gift from Dalan Bailey (Pirbright Institute) and originally obtained from ATCC. Calu-3 cells were purchased from AddexBio (C0016001). Vero.E6 cells were obtained from the National Institute for Biological Standards and Control. HeLa-TZM-bl cells (expressing luciferase and beta-galactosidase under the control of HIV-1 LTR) were obtained from the Centre for AIDS Reagents (CFAR). All cell lines were grown in Dulbecco’s modified Eagle’s medium (DMEM, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Labtech) and 1% Pen Strep (penicillin-streptomycin, Thermo Fisher Scientific), and maintained in humidified 5% CO2 incubators at 37 °C. Cells were passaged every 2 to 4 d when they reached 80 to 90% confluency. Caco2 cells were transduced with IFITM1/2/3 lentivectors as described previously (50 (link)) and selected with 10 μg/mL puromycin (Merck) to produce stable cell lines expressing individual HA-tagged IFITM proteins. IFITM expression was confirmed by flow cytometry. Primary normal (healthy) bronchial epithelial (NHBE-A) cells were cultured for 5 to 7 passages and differentiated at an air-liquid interface as previously described (11 (link)). After 21 to 24 d of differentiation, cells were used in infection experiments.

WT p53 and p53^−/− HCT116 E2F1 CRISPR cells were generated from cell lines (ATCC) according to the protocol described by Ran et al.^{40 (link)}. E2F1 CRISPR single guide RNA sequence: 5′-GCATTCTTCTTCTGGCTGGG-3′. HCT116, MCF7, U2OS and T47D (ATCC) cells were cultured in Dulbecco’s modified Eagle medium (DMEM) (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (Labtech, Heathfield, UK) and 1% penicillin/streptomycin (Gibco, Life Technologies, Carlsbad, CA, USA). All cell lines were tested for mycoplasma contamination before use. Selective PRMT5 inhibitor (T1–44) and the less active analogue (T1–68) (synthesized by Argonaut Therapeutics Ltd, Oxford, UK) (Supplementary Table S1) were used for 48 h at 1 μM final concentration, unless otherwise stated. T1–44 is a close derivative of EPZ015666^{41 (link)} and exhibits high specificity for PRMT5 (EC50 of T1–44 against asymmetric PRMT1 enzyme was 1.88 mM).

mESCs used in this study (tet::GATA4-mCherry and tet::GATA6) have an inducible GATA4 or GATA6 transgene based on the KH2 mESC line (16 (link)).
Cells were cultured on 0.1%-gelatin-coated cell culture flasks in Glasgow Minimum Essential Medium (Gibco, Waltham, MA) supplemented with 10% fetal bovine serum (Labtech, Marietta, GA), 2 mM glutamax (Gibco), 1 mM sodium pyruvate (Sigma-Aldrich, St. Louis, MO), 0.1 mM nonessential amino acids (Sigma-Aldrich), 0.1 mM 2-mercatoethanol (Gibco), and 5 × 10⁵ U/mL leukemia inhibitory factor (Merck Millipore, Burlington, MA).
Medium was changed daily, and cells were passaged when a confluency of 70–80% was reached. Cells were detached with 1 mL 0.05% trypsin-EDTA (Gibco) and resuspended in 5 mL culture medium. Cell suspension was gently homogenized by pipetting and centrifuged at 1000 rotations per minute for 3 min. Subsequently, cells were washed with 5 mL culture medium. Cells were maintained in their respective medium at 37°C and 5% CO₂.

Favipiravir, kindly provided by Toyama Chemical Company under a material transfer agreement, was reconstituted in dimethyl sulfoxide (DMSO) and frozen into aliquots. MDCK and 293T cells were grown in Dulbecco modified Eagle medium (Gibco) with the addition of 10% fetal bovine serum (Labtech), 1% nonessential amino acids (Gibco), and 1% penicillin-streptomycin (Sigma-Aldrich). A/England/195/2009 (Eng195) is an early isolate from the 2009 A(H1N1) pandemic provided by Public Health England (PHE).

The wt-SiHa cells and IFITM1/IFITM3 null cells, which were described previously [43 (link)], were grown in RPMI 1640 medium (Invitrogen, Waltham, MA, USA), supplemented with 10% (v/v) fetal bovine serum (Labtech, East Sussex, UK) and 1% penicillin/streptomycin (Invitrogen, Waltham, MA, USA), and incubated at 37 °C with 5% CO₂.