Generation of quality-controlled SARS-CoV-2 variant stocks

Maren de Vries, Grace O. Ciabattoni, Bruno A. Rodriguez-Rodriguez, Keaton M. Crosse, Dominick Papandrea, Marie I. Samanovic, Dacia Dimartino, Christian Marier, Mark J. Mulligan, Adriana Heguy, Ludovic Desvignes, Ralf Duerr, Meike Dittmann

Published: 2023-10-12 DOI: 10.1038/s41596-023-00897-6

SARS-CoV-2 variants

quality control

viral stocks

clonal isolation

protocol development

AI 解读

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Genetic circuit design automation with Cello 2.0

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

A practical guide to scanning light-field microscopy with digital adaptive optics

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

MOF-derived nanoporous carbons with diverse tunable nanoarchitectures

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

查看全部

Sections

Figures

References

World Health Organization. WHO Coronavirus (COVID-19) Dashboard. Available at http://covid19.who.int/ (2023).
de Vries, M. et al. A comparative analysis of SARS-CoV-2 antivirals characterizes 3CLpro inhibitor PF-00835231 as a potential new treatment for COVID-19. J. Virol. 95, e01819-20 (2021).
FDA. Emergency Use Authorization (Eua) of Paxlovid for Coronavirus Disease 2019 (Covid-19). Available at http://www.fda.gov/media/155051/download (2023).
Samanovic, M. I. et al. Robust immune responses are observed after one dose of BNT162b2 mRNA vaccine dose in SARS-CoV-2-experienced individuals. Sci. Transl. Med. 14, eabi8961 (2022).
Samanovic, M. I. et al. Vaccine-acquired SARS-CoV-2 immunity versus infection-acquired immunity: a comparison of three COVID-19 vaccines. Vaccines (Basel) 10, 2152 (2022).
Kister, I. et al. Hybrid and vaccine-induced immunity against SAR-CoV-2 in MS patients on different disease-modifying therapies. Ann. Clin. Transl. Neurol. 9, 1643–1659 (2022).
Kister, I. et al. Cellular and humoral immunity to SARS-CoV-2 infection in multiple sclerosis patients on ocrelizumab and other disease-modifying therapies: a multi-ethnic observational study. Ann. Neurol. 91, 782–795 (2022).
Izmirly, P. M. et al. Evaluation of immune response and disease status in systemic lupus erythematosus patients following SARS–CoV-2 vaccination. Arthritis Rheumatol. 74, 284–294 (2022).
Ching, K. L. et al. ACE2-containing defensosomes serve as decoys to inhibit SARS-CoV-2 infection. PLoS Biol. 20, 1–25 (2022).
Rona, G. et al. The NSP14/NSP10 RNA repair complex as a Pan-coronavirus therapeutic target. Cell Death Differ. 29, 285–292 (2022).
Rodriguez-Rodriguez, B. A. et al. A neonatal mouse model characterizes transmissibility of SARS-CoV-2 variants and reveals a role for ORF8. Nat. Commun. 14, 3026 (2023).
Lokugamage, K. G. et al. Type I interferon susceptibility distinguishes SARS-CoV-2 from SARS-CoV. J. Virol. 94, e01410-20 (2020).
Yount, B. et al. Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus. Proc. Natl. Acad. Sci. USA 100, 12995–13000 (2003).
Drosten, C. et al. Identification of a novel coronavirus in patients with severe acute respiratory syndrome. N. Engl. J. Med. 348, 1967–1976 (2003).
Scobey, T. et al. Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus. Proc. Natl. Acad. Sci. USA 110, 16157–16162 (2013).
Coleman, C. M. & Frieman, M. B. Growth and quantification of MERS-CoV infection. Curr. Protoc. Microbiol. 2015, 15E.2.1–15E.2.9 (2015).
Sun, F. et al. SARS-CoV-2 quasispecies provides an advantage mutation pool for the epidemic variants. Microbiol. Spectr. 9, e0026121 (2021).
Bal, A. et al. Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation in France. Nat. Commun. 13, 6316 (2022).
Russell, C. D. et al. Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study. Lancet Microbe 2, e354–e365 (2021).
Singh, V., Upadhyay, P., Reddy, J. & Granger, J. SARS-CoV-2 respiratory co-infections: incidence of viral and bacterial co-pathogens. Int. J. Infect. Dis. 105, 617–620 (2021).
Swets, M. C. et al. SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses. Lancet 399, 1463–1464 (2022).
Örd, M., Faustova, I. & Loog, M. The sequence at SpikeS1/S2 site enables cleavage by furin and phospho-regulation in SARS-CoV2 butnot in SARS-CoV1 or MERS-CoV. Sci. Rep. 10, (2020).
Jackson, C.B., Farzan, M., Chen, B. & Choe, H. Mechanisms of SARS-CoV-2 entry intocells. Nat. Rev. Mol. Cell Biol. 23, (2022).
Meng, B. et al. Altered TMPRSS2 usage by SARS-CoV-2Omicron impacts infectivity and fusogenicity. Nature 603, 706–714 (2022).
Koch, J. et al. TMPRSS2 expression dictates the entry route used by SARS‐CoV‐2 to infect host cells. EMBO J. 40, e107821 (2021).
Takeda, M. Proteolytic activation of SARS-CoV-2 spike protein. Microbiol. Immunol. 66, 15–23 (2022).
Klimstra, W. B. et al. SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected hospitalized COVID-19 patients. J. Gen. Virol. 101, 1156–1169 (2020).
Vu, M. N. et al. QTQTN motif upstream of the furin-cleavage site plays a key role in SARS-CoV-2 infection and pathogenesis. Proc. Natl. Acad. Sci. USA 119, 1–7 (2022).
Funnell, S. G. P. et al. A cautionary perspective regarding the isolation and serial propagation of SARS-CoV-2 in Vero cells. NPJ Vaccines 6, 83 (2021).
Johnson, B. A. et al. Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis. Nature 591, 293–299 (2021).
Chen, Y. et al. Genetic mutation of SARS-CoV-2 during consecutive passages in permissive cells. Virol. Sin. 36, 1073–1076 (2021).
Chung, H., Noh, J. Y., Koo, B. S., Hong, J. J. & Kim, H. K. SARS-CoV-2 mutations acquired during serial passage in human cell lines are consistent with several of those found in recent natural SARS-CoV-2 variants. Comput. Struct. Biotechnol. J. 20, 1925–1934 (2022).
Duerr, R. et al. Delta-Omicron recombinant escapes therapeutic antibody neutralization. iScience 26, 106075 (2023).
Sonnleitner, S. T. et al. The mutational dynamics of the SARS-CoV-2 virus in serial passages in vitro. Virol. Sin. 37, 198–207 (2022).
Matsuyama, S. et al. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells. Proc. Natl. Acad. Sci. USA 117, 7001–7003 (2020).
Sasaki, M. et al. SARS-CoV-2 variants with mutations at the S1/S2 cleavage site are generated in vitro during propagation in TMPRSS2-deficient cells. PLoS Pathog. 17, e1009233 (2021).
Kalamvoki, M. & Norris, V. A defective viral particle approach to COVID-19. Cells 11, 302 (2022).
Girgis, S. et al. Evolution of naturally arising SARS-CoV-2 defective interfering particles. Commun. Biol. 5, 1–12 (2022).
Mautner, L. et al. Replication kinetics and infectivity of SARS-CoV-2 variants of concern in common cell culture models. Virol. J. 19, 1–11 (2022).
Mlcochova, P. et al. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 599, 114–119 (2021).
Willett, B. J. et al. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nat. Microbiol. 7, 1161–1179 (2022).
McGrath, M. E. et al. SARS-CoV-2 variant spike and accessory gene mutations alter pathogenesis. Proc. Natl. Acad. Sci. USA 119, e2204717119 (2022).
Iwata-Yoshikawa, N. et al. Essential role of TMPRSS2 in SARS-CoV-2 infection in murine airways. Nat. Commun. 13, 6100 (2022).
Plavec, Z. et al. SARS-CoV-2 production, purification methods and UV inactivation for proteomics and structural studies. Viruses 14, 4–15 (2022).
Bernard-Raichon, L. et al. Gut microbiome dysbiosis in antibiotic-treated COVID-19 patients is associated with microbial trans and bacteremia. Nat. Commun. 13, 5926 (2022).
Samanovic, M. I. et al. Robust immune responses areobserved after one dose of BNT162b2 mRNA vaccine dose in SARS-CoV-2 experiencedindividuals. 14, 1–31 (2022).
Case, J. B., Bailey, A. L., Kim, A. S., Chen, R. E. & Diamond, M. S. Growth, detection, quantification, and inactivation of SARS-CoV-2. Virology 548, 39–48 (2020).
Xie, X. et al. Engineering SARS-CoV-2 using a reverse genetic system. Nat. Protoc. 16, 1761–1784 (2021).
Chaudhry, M. Z. et al. Rapid SARS-CoV-2 adaptation to available cellular proteases. J. Virol. 96, e0218621 (2022).
Baczenas, J. J. et al. Propagation of SARS-CoV-2 in Calu-3 cells to eliminate mutations in the furin cleavage site of spike. Viruses 13, 2434 (2021).
Yamada, S. et al. Assessment of SARS-CoV-2 infectivity of upper respiratory specimens from COVID-19 patients by virus isolation using VeroE6/TMPRSS2 cells. BMJ Open Respir. Res. 8, e000830 (2021).
Duerr, R. et al. Dominance of Alpha and Iota variants in SARS-CoV-2 vaccine breakthrough infections in New York City. J. Clin. Invest. 131, e152702 (2021).
McAuley, J. et al. Optimal preparation of SARS-CoV-2 viral transport medium for culture. Virol. J. 18, 53 (2021).
Rosenthal, S. H. et al. Development and validation of a high throughput SARS-CoV-2 whole-genome sequencing workflow in a clinical laboratory. Sci. Rep. 12, 2054 (2022).
Laporte, M. et al. The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways. PLoS Pathog. 17, e1009500 (2021).
Peacock, T. P. et al. The altered entry pathway and antigenic distance of the SARS-CoV-2 Omicron variant map to separate domains of spike protein. Preprint at http://www.biorxiv.org/content/10.1101/2021.12.31.474653v2 (2022).
Rottem, S., Kosower, N. S. & Kornspan, J. D. Contamination of tissue cultures by mycoplasmas. In Biomedical Tissue Culture (eds. Ceccherini-Nelli, L. & Matteoli, B.) (IntechOpen, 2012).
Watanabe, I. & Okada, S. Effects of temperature on growth rate of cultured mammalian cells (L5178Y). J. Cell Biol. 32, 309–323 (1967).
Clements, G. B. Selection of biochemically variant, in some cases mutant, mammalian cells in culture. Adv. Cancer Res. 21, 273–390 (1975).
Stacey, G. N. & Masters, J. R. Cryopreservation and banking of mammalian cell lines. Nat. Protoc. 3, 1981–1989 (2008).
La Scola, B. et al. Viral RNA load as determined by cell culture as a management tool for discharge of SARS-CoV-2 patients from infectious disease wards. Eur. J. Clin. Microbiol. Infect. Dis. 39, 1059–1061 (2020).
Francis, R. et al. High-speed large-scale automated isolation of SARS-CoV-2 from clinical samples using miniaturized co-culture coupled to high-content screening. Clin. Microbiol. Infect. 27, 128.e1–128.e7 (2021).
Sonnleitner, S. T. et al. An in vitro model for assessment of SARS-CoV-2 infectivity by defining the correlation between virus isolation and quantitative PCR value: isolation success of SARS-CoV-2 from oropharyngeal swabs correlates negatively with Cq value. Virol. J. 18, 71 (2021).
Sung, A. et al. Isolation of SARS-CoV-2 in viral cell culture in immunocompromised patients with persistently positive RT-PCR results. Front. Cell. Infect. Microbiol. 12, 804175 (2022).
Rhoads, D. et al. College of American Pathologists (CAP) Microbiology Committee perspective: caution must be used in interpreting the cycle threshold (Ct) value. Clin. Infect. Dis. 72, e685–e686 (2021).
Potter, R. F. et al. Evaluation of PCR cycle threshold values by patient population with the quidel lyra SARS-CoV-2 assay. Diagn. Microbiol. Infect. Dis. 101, 115387 (2021).
Arora, D. J. S., Tremblay, P., Bourgault, R. & Boileau, S. Concentration and purification of influenza virus from allantoic fluid. Anal. Biochem. 144, 189–192 (1985).
Mbiguino, A. & Menezes, J. Purification of human respiratory syncytial virus: superiority of sucrose gradient over percoll, renografin, and metrizamide gradients. J. Virol. Methods 31, 161–170 (1991).
Putnak, R. et al. Development of a purified, inactivated, dengue-2 virus vaccine prototype in Vero cells: immunogenicity and protection in mice and rhesus monkeys. J. Infect. Dis. 174, 1176–1184 (1996).
Ali, A. & Roossinck, M. J. Rapid and efficient purification of Cowpea chlorotic mottle virus by sucrose cushion ultracentrifugation. J. Virol. Methods 141, 84–86 (2007).
Hankaniemi, M. M. et al. Optimized production and purification of Coxsackievirus B1 vaccine and its preclinical evaluation in a mouse model. Vaccine 35, 3718–3725 (2017).
Leibowitz, J., Kaufman, G. & Liu, P. Coronaviruses: propagation, quantification, storage, and construction of recombinant mouse hepatitis virus. Curr. Protoc. Microbiol. Chapter 15, Unit 15E.1 (2011).
Su, S. et al. Epidemiology, genetic recombination, and pathogenesis of coronaviruses. Trends Microbiol. 24, 490–502 (2016).
Heguy, A. et al. Amplification artifact in SARS-CoV-2 Omicron sequences carrying P681R mutation, New York, USA. Emerg. Infect. Dis. 28, 881–883 (2022).
Gribble, J. et al. The coronavirus proofreading exoribonuclease mediates extensive viral recombination. PLoS Pathog. 17, 1–28 (2021).
Katoh, K., Rozewicki, J. & Yamada, K. D. MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. Brief. Bioinform. 20, 1160–1166 (2018).
Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739 (2011).
Los Alamos National Laboratory. HIV Sequence Database. Highlighter. Available at http://www.hiv.lanl.gov/content/sequence/HIGHLIGHT/highlighter_top.html (2022).
V’kovski, P., Kratzel, A., Steiner, S., Stalder, H. & Thiel, V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat. Rev. Microbiol. 19, 155–170 (2021).

Generation of quality-controlled SARS-CoV-2 variant stocks

Supplementary information

Reporting Summary

推荐阅读