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SARS-CoV-2 rapidly evolves lineage-specific phenotypic differences when passaged repeatedly in immune-naïve mice

Willett et al., Communications Biology, doi:10.1038/s42003-024-05878-3
Feb 2024  
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Mouse study demonstrating that SARS-CoV-2 can rapidly acquire mutations altering infectivity, disease severity, and drug resistance even without selective pressure. Antigenic drift can undermine variant-specific treatments like monoclonal antibodies and highly specific antivirals like paxlovid, suggesting that less variant specific treatments and polypharmacy targeting multiple viral and host proteins may be more effective as SARS-CoV-2 evolves.
Willett et al., 16 Feb 2024, Canada, peer-reviewed, 17 authors. Contact: ioannis.ragoussis@mcgill.ca.
This PaperMiscellaneousAll
SARS-CoV-2 rapidly evolves lineage-specific phenotypic differences when passaged repeatedly in immune-naïve mice
Julian Daniel Sunday Willett, Annie Gravel, Isabelle Dubuc, Leslie Gudimard, Ana Claudia Dos Santos Pereira Andrade, Émile Lacasse, Paul Fortin, Ju-Ling Liu, Jose Avila Cervantes, Jose Hector Galvez, Haig Hugo Vrej Djambazian, Melissa Zwaig, Anne-Marie Roy, Sally Lee, Shu-Huang Chen, Jiannis Ragoussis, Louis Flamand
Communications Biology, doi:10.1038/s42003-024-05878-3
The persistence of SARS-CoV-2 despite the development of vaccines and a degree of herd immunity is partly due to viral evolution reducing vaccine and treatment efficacy. Serial infections of wild-type (WT) SARS-CoV-2 in Balb/c mice yield mouse-adapted strains with greater infectivity and mortality. We investigate if passaging unmodified B.1.351 (Beta) and B.1.617.2 (Delta) 20 times in K18-ACE2 mice, expressing the human ACE2 receptor, in a BSL-3 laboratory without selective pressures, drives human health-relevant evolution and if evolution is lineage-dependent. Late-passage virus causes more severe disease, at organism and lung tissue scales, with late-passage Delta demonstrating antibody resistance and interferon suppression. This resistance co-occurs with a de novo spike S371F mutation, linked with both traits. S371F, an Omicron-characteristic mutation, is co-inherited at times with spike E1182G per Nanopore sequencing, existing in different within-sample viral variants at others. Both S371F and E1182G are linked to mammalian GOLGA7 and ZDHHC5 interactions, which mediate viral-cell entry and antiviral response. This study demonstrates SARS-CoV-2's tendency to evolve with phenotypic consequences, its evolution varying by lineage, and suggests non-dominant quasi-species contribution. Part of the difficulty in responding to the COVID-19 pandemic has been predicting viral evolution and its impact on clinically relevant traits, such as disease severity, infectivity, and treatment resistance 1 . The basic biology of the severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is well understood 2 . However, knowledge of SARS-CoV-2 evolution is limited. Many RNA viruses, like SARS-CoV-2, exist as quasispecies, meaning viral populations contain a multitude of mutants subjected to continuous selection, competition, and genetic variation [3] [4] [5] [6] [7] [8] [9] . These alleles give plasticity to the viral population allowing for rapid adaptation/selection to a variety of circumstances 10 . Viral evolution is also complex and affected by several factors, including host genetic background 11 , host immune status 12 , the organs targeted by the virus 13 , and a population's collective immunity 14 . As a result, it has been difficult to predict the emergence of new variants with altered virulence. Several SARS-CoV-2 variants of concern (VOC) have emerged, each with mutations providing dissemination advantages 1 . The SARS-CoV-2 Alpha variant (B.1.1.7) gained a growth advantage and rapidly spread globally due to the spike protein N501Y mutation that enhanced affinity for
Reporting summary Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article. Data availability The numerical source data behind the graphs in the Figs. 2-8 can be found in Supplementary Data 1. VCF files used to complete computational analyses are available at https://zenodo.org/records/10460318. Raw data file for Illumina and Nanopore sequencing can be found on the NCBI BioProject using accessing codes PRJNA1068670 and PRJNA1069731, respectively. All numerical source data for graphs/charts are provided in the supplementary material section. Author contributions J.D.S.W. conceived of the computational analyses needed for this study, completed all computational analysis of viral sequencing data, and wrote the majority of the manuscript. L.F. and J.R. conceived of the study. L.F. contributed to manuscript revisions, wrote sections relevant to animal models and antibody neutralization studies and performed analysis of results. J.R. supervised sequencing data generation and analysis. Competing interests All authors declare no competing interests.
References
Ahmed, Coping with stress: the mitokine GDF-15 as a biomarker of COVID-19 severity, Front. Immunol
Belsky, COVID-19 in immunocompromised patients: a systematic review of cancer, hematopoietic cell and solid organ transplant patients, J. Infect
Benjamini, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J. R. Stat. Soc. Ser. B (Methodol.)
Berri, Early plasma interferon-beta levels as a predictive marker of COVID-19 severe clinical events in adult patients, J. Med Virol
Cao, 2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection, Nature
Capobianchi, Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy, Clin. Microbiol. Infect
Captur, Plasma proteomic signature predicts who will get persistent symptoms following SARS-CoV-2 infection, EBioMedicine
Carapito, Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort, Sci. Transl. Med
Chen, Reiling, Quick, Ragoussis, Artic nCoV-2019 McGill modified lunascript reverse transcriptase sequencing protocol, doi:10.17504/protocols.io.bjgekjte
Cherian, SARS-CoV-2 spike mutations, L452R, T478K, E484Q and P681R, in the second wave of COVID-19 in Maharashtra, India, Microorganisms
Chung, Noh, Koo, Hong, Kim, 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
Clausen, SARS-CoV-2 infection depends on cellular heparan sulfate and ACE2, Cell
Combadiere, LOX-1-expressing immature neutrophils identify critically-Ill COVID-19 patients at risk of thrombotic complications, Front Immunol
Diez, Mateu, Domingo, Selection of antigenic variants of foot-and-mouth disease virus in the absence of antibodies, as revealed by an in situ assay, J. Gen. Virol
Domingo, New observations on antigenic diversification of RNA viruses, antigenic variation is not dependent on immune selection, J. Gen. Virol
Dubuc, Cytokines and lipid mediators of inflammation in lungs of SARS-CoV-2 infected mice, Front. Immunol
Dupont, Neutralizing antibody activity in convalescent sera from infection in humans with SARS-CoV-2 and variants of concern, Nat. Microbiol
Fernandes, The UCSC SARS-CoV-2 genome browser, Nat. Genet
Freed, Silander, SARS-CoV2 Genome Sequencing Protocol (1200bp Amplicon "Midnight
Freed, Vlkova, Faisal, Silander, Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding, Biol. Methods Protoc
Gadotti, IFN-gamma is an independent risk factor associated with mortality in patients with moderate and severe COVID-19 infection, Virus Res
Garrison, Haplotype-based variant detection from shortread sequencing
Gerstung, Reliable detection of subclonal single-nucleotide variants in tumour cell populations, Nat. Commun
Gu, Adaptation of SARS-CoV-2 in BALB/c mice for testing vaccine efficacy, Science
Huang, Q493K and Q498H substitutions in spike promote adaptation of SARS-CoV-2 in mice, EBioMedicine
Jacobs, Haidar, Mellors, COVID-19: Challenges of viral variants, Annu Rev. Med
Jary, Evolution of viral quasispecies during SARS-CoV-2 infection, Clin. Microbiol. Infect
Johnson, Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis, Nature
Karamitros, SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies, J. Clin. Virol
Kent, The human genome browser at UCSC, Genome Res
Khalil, Elemam, Maghazachi, Chemokines and chemokine receptors during COVID-19 infection, Comput Struct. Biotechnol. J
Khatib, Within-Host Diversity of SARS-CoV-2 in COVID-19 patients with variable disease severities, Front. Cell Infect. Microbiol
Kim, The roles of APOBEC-mediated RNA editing in SARS-CoV-2 mutations, replication and fitness, Sci. Rep
Kärber, Beitrag zur kollektiven behandlung pharmakologischer reihenversuche, Arch. f. Exp. Pathol. u. Pharmakol
Lacasse, SARS-CoV-2 Nsp2 contributes to inflammation by activating NF-kappaB, Viruses
Lee, SARS-CoV-2 delta variant induces enhanced pathology and inflammatory responses in K18-hACE2 mice, PLoS One
Li, Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM, doi:10.48550/arXiv.1303.3997
Lin, ORF8 contributes to cytokine storm during SARS-CoV-2 infection by activating IL-17 pathway, iScience
Lipman, Safo, Chekouo, Multi-omic analysis reveals enriched pathways associated with COVID-19 and COVID-19 severity, PLoS One
Liu, Delta spike P681R mutation enhances SARS-CoV-2 fitness over alpha variant, Cell Rep
Liu, The N501Y spike substitution enhances SARS-CoV-2 infection and transmission, Nature
Martinez-Gonzalez, SARS-CoV-2 mutant spectra at different depth levels reveal an overwhelming abundance of low frequency mutations, Pathogens
Martinez-Gonzalez, SARS-CoV-2 point mutation and deletion spectra and their association with different disease outcomes, Microbiol. Spectr
Mclaren, The ensembl variant effect predictor, Genome Biol
Motozono, SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity, Cell Host Microbe
Mukund, Mathee, Subramaniam, Plasmin cascade mediates thrombotic events in SARS-CoV-2 infection via complement and platelet-activating systems, IEEE Open J. Eng. Med. Biol
Oladunni, Lethality of SARS-CoV-2 infection in K18 human angiotensin-converting enzyme 2 transgenic mice, Nat. Commun
Pietzner, Genetic architecture of host proteins involved in SARS-CoV-2 infection, Nat. Commun
Planas, Reduced sensitivity of SARS-CoV-2 variant delta to antibody neutralization, Nature
Popovic, Biothermodynamics of viruses from absolute zero (1950) to virothermodynamics, Vaccines (Basel)
Popovic, Martin, Head, COVID infection in 4 steps: thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease, Heliyon
Popovic, Pantovic Pavlovic, Pavlovic, Ghosts of the past: elemental composition, biosynthesis reactions and thermodynamic properties of Zeta P.2, Theta P.3, Kappa B.1
Popovic, Popovic, Strain wars: competitive interactions between SARS-CoV-2 strains are explained by gibbs energy of antigen-receptor binding, Microb. Risk Anal
Popovic, SARS-CoV-2 strain wars continues: chemical and thermodynamic characterization of live matter and biosynthesis of Omicron BN.1, CH.1.1 and XBC variants, Microb. Risk Anal
Rahimi, Talebi Bezmin Abadi, Implications of the emergence of a new variant of SARS-CoV-2, VUI-202012/01, Arch. Med Res
Ramachandran, Comparison of variant callers for wastewaterbased epidemiology, medRxiv, doi:10.1099/mgen.0.000933
Rao, Evolutionary dynamics of lndels in SARS-CoV-2 spike glycoprotein, Evol. Bioinform. Online
Reiling, Roy, Chen, Ragoussis, McGill nanopore LibPrep protocol, 10 ng NB, doi:10.17504/protocols.io.bjkvkkw6
Rueca, Compartmentalized replication of SARS-Cov-2 in upper vs. lower respiratory tract assessed by whole genome quasispecies analysis, Microorganisms
Song, The main protease of SARS-CoV-2 cleaves histone deacetylases and DCP1A, attenuating the immune defense of the interferon-stimulated genes, J. Biol. Chem
Sonnleitner, The mutational dynamics of the SARS-CoV-2 virus in serial passages in vitro, Virol. Sin
Staab-Weijnitz, FK506-binding protein 10, a potential novel drug target for idiopathic pulmonary fibrosis, Am. J. Respir. Crit. Care Med
Stelzer, The GeneCards ssuite: from gene data mining to disease genome sequence analyses, Curr. Protoc. Bioinforma
Sui, Li, Venzon, Berzofsky, SARS-CoV-2 spike protein suppresses ACE2 and type I interferon expression in primary cells from macaque lung bronchoalveolar lavage, Front Immunol
Sun, Characterization and structural basis of a lethal mouseadapted SARS-CoV-2, Nat. Commun
Sun, SARS-CoV-2 Quasispecies provides an advantage mutation pool for the epidemic variants, Microbiol. Spectr
Tada, Convalescent-phase sera and vaccine-elicited antibodies largely maintain neutralizing titer against global SARS-CoV-2 variant spikes, mBio
Tarres-Freixas, Heterogeneous infectivity and pathogenesis of SARS-CoV-2 variants Beta, Delta and Omicron in transgenic K18-hACE2 and wildtype mice, Front Microbiol
Tonkin-Hill, Patterns of within-host genetic diversity in SARS-CoV-2, Elife
Turakhia, Pandemic-scale phylogenomics reveals the SARS-CoV-2 recombination landscape, Nature
V'kovski, Kratzel, Steiner, Stalder, Thiel, Coronavirus biology and replication: implications for SARS-CoV-2, Nat. Rev. Microbiol
Van Cleemput, Organ-specific genome diversity of replicationcompetent SARS-CoV-2, Nat. Commun
Velavan, Host genetic factors determining COVID-19 susceptibility and severity, EBioMedicine
Wang, Chen, Wei, Mechanisms of SARS-CoV-2 evolution revealing vaccine-resistant mutations in Europe and America, J. Phys. Chem. Lett
Wang, Network pharmacology and bioinformatics analyses identify intersection genes of vitamin D3 and COVID-19 as potential therapeutic targets, Front Pharm
Wasik, Influenza viruses in mice: deep sequencing analysis of serial passage and effects of sialic acid structural variation, J. Virol
Willett, Data for: SARS-CoV-2 rapidly evolves lineage-specific phenotypic differences when passaged repeatedly in immune-naïve mice, doi:10.5281/zenodo.10460450
Wu, Palmitoylation of SARS-CoV-2 S protein is essential for viral infectivity, Signal Transduct. Target Ther
Wu, Zhu, Liu, Sun, Wu, An integrative multiomics analysis identifies putative causal genes for COVID-19 severity, Genet. Med
Xu, SARS-CoV-2 impairs interferon production via NSP2induced repression of mRNA translation, Proc. Natl Acad. Sci. USA
Yang, Targeting intracellular Neu1 for coronavirus infection treatment, iScience
Zeng, Neutralization of SARS-CoV-2 variants of concern harboring Q677, H. mBio
Zeng, Yu, Cheng, The interactions of ZDHHC5/ GOLGA7 with SARS-CoV-2 spike (S) protein and their effects on S protein's subcellular localization, palmitoylation and pseudovirus entry, Virol. J
Zhang, Qin, Sun, Chu, Zhou, Function of protein S-palmitoylation in immunity and immune-related diseases, Front. Immunol
Zhao, Omicron SARS-CoV-2 mutations stabilize spike up-RBD conformation and lead to a non-RBM-binding monoclonal antibody escape, Nat. Commun
Zheng, COVID-19 treatments and pathogenesis including anosmia in K18-hACE2 mice, Nature
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' 'Virus Res. 289, 198171 (2020).', 'journal-title': 'Virus Res.'}, { 'key': '5878_CR31', 'doi-asserted-by': 'publisher', 'first-page': 'e28361', 'DOI': '10.1002/jmv.28361', 'volume': '95', 'author': 'F Berri', 'year': '2023', 'unstructured': 'Berri, F. et al. Early plasma interferon-beta levels as a predictive ' 'marker of COVID-19 severe clinical events in adult patients. J. Med ' 'Virol. 95, e28361 (2023).', 'journal-title': 'J. Med Virol.'}, { 'key': '5878_CR32', 'doi-asserted-by': 'publisher', 'first-page': '976', 'DOI': '10.1016/j.csbj.2021.01.034', 'volume': '19', 'author': 'BA Khalil', 'year': '2021', 'unstructured': 'Khalil, B. A., Elemam, N. M. & Maghazachi, A. A. Chemokines and ' 'chemokine receptors during COVID-19 infection. Comput Struct. ' 'Biotechnol. J. 19, 976–988 (2021).', 'journal-title': 'Comput Struct. Biotechnol. J.'}, { 'key': '5878_CR33', 'doi-asserted-by': 'publisher', 'first-page': 'e0069621', 'DOI': '10.1128/mBio.00696-21', 'volume': '12', 'author': 'T Tada', 'year': '2021', 'unstructured': 'Tada, T. et al. Convalescent-phase sera and vaccine-elicited antibodies ' 'largely maintain neutralizing titer against global SARS-CoV-2 variant ' 'spikes. mBio 12, e0069621 (2021).', 'journal-title': 'mBio'}, { 'key': '5878_CR34', 'doi-asserted-by': 'publisher', 'first-page': '1433', 'DOI': '10.1038/s41564-021-00974-0', 'volume': '6', 'author': 'L Dupont', 'year': '2021', 'unstructured': 'Dupont, L. et al. Neutralizing antibody activity in convalescent sera ' 'from infection in humans with SARS-CoV-2 and variants of concern. Nat. ' 'Microbiol 6, 1433–1442 (2021).', 'journal-title': 'Nat. Microbiol'}, { 'key': '5878_CR35', 'doi-asserted-by': 'publisher', 'first-page': '991', 'DOI': '10.1038/s41588-020-0700-8', 'volume': '52', 'author': 'JD Fernandes', 'year': '2020', 'unstructured': 'Fernandes, J. 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The interactions of ZDHHC5/GOLGA7 ' 'with SARS-CoV-2 spike (S) protein and their effects on S protein’s ' 'subcellular localization, palmitoylation and pseudovirus entry. Virol. ' 'J. 18, 257 (2021).', 'journal-title': 'Virol. J.'}, { 'key': '5878_CR39', 'doi-asserted-by': 'publisher', 'first-page': '231', 'DOI': '10.1038/s41392-021-00651-y', 'volume': '6', 'author': 'Z Wu', 'year': '2021', 'unstructured': 'Wu, Z. et al. Palmitoylation of SARS-CoV-2 S protein is essential for ' 'viral infectivity. Signal Transduct. Target Ther. 6, 231 (2021).', 'journal-title': 'Signal Transduct. Target Ther.'}, { 'key': '5878_CR40', 'doi-asserted-by': 'publisher', 'first-page': '661202', 'DOI': '10.3389/fimmu.2021.661202', 'volume': '12', 'author': 'Y Zhang', 'year': '2021', 'unstructured': 'Zhang, Y., Qin, Z., Sun, W., Chu, F. & Zhou, F. Function of protein ' 'S-palmitoylation in immunity and immune-related diseases. Front. ' 'Immunol. 12, 661202 (2021).', 'journal-title': 'Front. Immunol.'}, { 'key': '5878_CR41', 'doi-asserted-by': 'publisher', 'first-page': '593', 'DOI': '10.1038/s41586-022-04980-y', 'volume': '608', 'author': 'Y Cao', 'year': '2022', 'unstructured': 'Cao, Y. et al. BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by ' 'Omicron infection. Nature 608, 593–602 (2022).', 'journal-title': 'Nature'}, { 'key': '5878_CR42', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/s41467-020-19996-z', 'volume': '11', 'author': 'M Pietzner', 'year': '2020', 'unstructured': 'Pietzner, M. et al. Genetic architecture of host proteins involved in ' 'SARS-CoV-2 infection. Nat. Commun. 11, 6397 (2020).', 'journal-title': 'Nat. Commun.'}, { 'key': '5878_CR43', 'doi-asserted-by': 'publisher', 'first-page': 'e2204539119', 'DOI': '10.1073/pnas.2204539119', 'volume': '119', 'author': 'Z Xu', 'year': '2022', 'unstructured': 'Xu, Z. et al. SARS-CoV-2 impairs interferon production via NSP2-induced ' 'repression of mRNA translation. Proc. Natl Acad. Sci. 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Bioinforma.'}, { 'key': '5878_CR46', 'doi-asserted-by': 'publisher', 'first-page': '752612', 'DOI': '10.3389/fimmu.2021.752612', 'volume': '12', 'author': 'B Combadiere', 'year': '2021', 'unstructured': 'Combadiere, B. et al. LOX-1-expressing immature neutrophils identify ' 'critically-Ill COVID-19 patients at risk of thrombotic complications. ' 'Front Immunol. 12, 752612 (2021).', 'journal-title': 'Front Immunol.'}, { 'key': '5878_CR47', 'doi-asserted-by': 'publisher', 'first-page': '874637', 'DOI': '10.3389/fphar.2022.874637', 'volume': '13', 'author': 'S Wang', 'year': '2022', 'unstructured': 'Wang, S. et al. Network pharmacology and bioinformatics analyses ' 'identify intersection genes of vitamin D3 and COVID-19 as potential ' 'therapeutic targets. 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Risk Anal. 21, 100202 (2022).', 'journal-title': 'Risk Anal.'}, { 'key': '5878_CR56', 'doi-asserted-by': 'crossref', 'first-page': '334', 'DOI': '10.3390/vaccines10020334', 'volume': '10,', 'author': 'M Popovic', 'year': '2022', 'unstructured': 'Popovic, M. Biothermodynamics of viruses from absolute zero (1950) to ' 'virothermodynamics (2022). Vaccines (Basel) 10, 334 (2022).', 'journal-title': 'Vaccines (Basel)'}, { 'key': '5878_CR57', 'doi-asserted-by': 'publisher', 'first-page': '569', 'DOI': '10.1016/j.arcmed.2021.01.001', 'volume': '52', 'author': 'F Rahimi', 'year': '2021', 'unstructured': 'Rahimi, F. & Talebi Bezmin Abadi, A. Implications of the emergence of a ' 'new variant of SARS-CoV-2, VUI-202012/01. Arch. Med Res. 52, 569–571 ' '(2021).', 'journal-title': 'Arch. Med Res.'}, { 'key': '5878_CR58', 'doi-asserted-by': 'publisher', 'first-page': '840757', 'DOI': '10.3389/fmicb.2022.840757', 'volume': '13', 'author': 'F Tarres-Freixas', 'year': '2022', 'unstructured': 'Tarres-Freixas, F. et al. Heterogeneous infectivity and pathogenesis of ' 'SARS-CoV-2 variants Beta, Delta and Omicron in transgenic K18-hACE2 and ' 'wildtype mice. Front Microbiol. 13, 840757 (2022).', 'journal-title': 'Front Microbiol.'}, { 'key': '5878_CR59', 'doi-asserted-by': 'publisher', 'DOI': '10.1128/mBio.02510-21', 'volume': '12', 'author': 'C Zeng', 'year': '2021', 'unstructured': 'Zeng, C. et al. Neutralization of SARS-CoV-2 variants of concern ' 'harboring Q677H. mBio 12, e0251021 (2021).', 'journal-title': 'mBio'}, { 'key': '5878_CR60', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/s41467-022-32665-7', 'volume': '13', 'author': 'Z Zhao', 'year': '2022', 'unstructured': 'Zhao, Z. et al. Omicron SARS-CoV-2 mutations stabilize spike up-RBD ' 'conformation and lead to a non-RBM-binding monoclonal antibody escape. ' 'Nat. Commun. 13, 4958 (2022).', 'journal-title': 'Nat. Commun.'}, { 'key': '5878_CR61', 'doi-asserted-by': 'publisher', 'first-page': '658428', 'DOI': '10.3389/fimmu.2021.658428', 'volume': '12', 'author': 'Y Sui', 'year': '2021', 'unstructured': 'Sui, Y., Li, J., Venzon, D. J. & Berzofsky, J. A. SARS-CoV-2 spike ' 'protein suppresses ACE2 and type I interferon expression in primary ' 'cells from macaque lung bronchoalveolar lavage. Front Immunol. 12, ' '658428 (2021).', 'journal-title': 'Front Immunol.'}, { 'key': '5878_CR62', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/s41598-022-19067-x', 'volume': '12', 'author': 'K Kim', 'year': '2022', 'unstructured': 'Kim, K. et al. The roles of APOBEC-mediated RNA editing in SARS-CoV-2 ' 'mutations, replication and fitness. Sci. Rep. 12, 14972 (2022).', 'journal-title': 'Sci. 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' 'https://www.protocols.io/view/34-midnight-34-sars-cov2-genome-sequencing-protoc-14egn2q2yg5d/v1 ' '(2021).', 'DOI': '10.17504/protocols.io.btsrnnd6'}, { 'key': '5878_CR68', 'doi-asserted-by': 'publisher', 'unstructured': 'J Reiling, S., Roy, A.-M., Chen, S.-H. & Ragoussis, I. nCoV-2019 McGill ' 'nanopore LibPrep protocol, 10 ng NB. Protocols.io ' 'https://doi.org/10.17504/protocols.io.bjkvkkw6 (2020).', 'DOI': '10.17504/protocols.io.bjkvkkw6'}, { 'key': '5878_CR69', 'unstructured': 'Garrison, E.P.M.G. Haplotype-based variant detection from short-read ' 'sequencing. arXiv https://arxiv.org/pdf/1207.3907.pdf (2012).'}, { 'key': '5878_CR70', 'doi-asserted-by': 'publisher', 'unstructured': 'Detection of prevalent SARS-CoV-2 variant lineages in wastewater and ' 'clinical sequences from cities in Québec, Canada. medRxiv ' 'https://doi.org/10.1101/2022.02.01.22270170 (2022).', 'DOI': '10.1101/2022.02.01.22270170'}, { 'key': '5878_CR71', 'doi-asserted-by': 'publisher', 'DOI': '10.1038/ncomms1814', 'volume': '3', 'author': 'M Gerstung', 'year': '2012', 'unstructured': 'Gerstung, M. et al. Reliable detection of subclonal single-nucleotide ' 'variants in tumour cell populations. Nat. Commun. 3, 811 (2012).', 'journal-title': 'Nat. Commun.'}, { 'key': '5878_CR72', 'doi-asserted-by': 'publisher', 'first-page': '117693432110646', 'DOI': '10.1177/11769343211064616', 'volume': '17', 'author': 'RSP Rao', 'year': '2021', 'unstructured': 'Rao, R. S. P. et al. Evolutionary dynamics of lndels in SARS-CoV-2 spike ' 'glycoprotein. Evol. Bioinform. Online 17, 11769343211064616 (2021).', 'journal-title': 'Evol. Bioinform. Online'}, { 'key': '5878_CR73', 'doi-asserted-by': 'publisher', 'unstructured': 'Ramachandran, V. K. et al. Comparison of variant callers for ' 'wastewater-based epidemiology. medRxiv. ' 'https://doi.org/10.1099/mgen.0.000933 (2022).', 'DOI': '10.1099/mgen.0.000933'}, { 'key': '5878_CR74', 'doi-asserted-by': 'publisher', 'unstructured': 'Li, H. Aligning sequence reads, clone sequences and assembly contigs ' 'with BWA-MEM. arXiv https://doi.org/10.48550/arXiv.1303.3997 (2013).', 'DOI': '10.48550/arXiv.1303.3997'}, { 'key': '5878_CR75', 'doi-asserted-by': 'publisher', 'DOI': '10.1186/s13059-016-0974-4', 'volume': '17', 'author': 'W McLaren', 'year': '2016', 'unstructured': 'McLaren, W. et al. The ensembl variant effect predictor. Genome Biol. ' '17, 122 (2016).', 'journal-title': 'Genome Biol.'}, { 'key': '5878_CR76', 'doi-asserted-by': 'publisher', 'first-page': '996', 'DOI': '10.1101/gr.229102', 'volume': '12', 'author': 'WJ Kent', 'year': '2002', 'unstructured': 'Kent, W. J. et al. The human genome browser at UCSC. Genome Res. 12, ' '996–1006 (2002).', 'journal-title': 'Genome Res.'}, { 'key': '5878_CR77', 'first-page': '289', 'volume': '57', 'author': 'Y Benjamini', 'year': '1995', 'unstructured': 'Benjamini, Y. & H, Y. Controlling the false discovery rate: a practical ' 'and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B ' '(Methodol.) 57, 289–300 (1995).', 'journal-title': 'J. R. Stat. Soc. Ser. B (Methodol.)'}, { 'key': '5878_CR78', 'doi-asserted-by': 'publisher', 'unstructured': 'Willett, J. et al. Data for: SARS-CoV-2 rapidly evolves lineage-specific ' 'phenotypic differences when passaged repeatedly in immune-naïve mice. ' 'Zenodo https://doi.org/10.5281/zenodo.10460450 (2024).', 'DOI': '10.5281/zenodo.10460450'}, { 'key': '5878_CR79', 'doi-asserted-by': 'publisher', 'first-page': 'e0267047', 'DOI': '10.1371/journal.pone.0267047', 'volume': '17', 'author': 'D Lipman', 'year': '2022', 'unstructured': 'Lipman, D., Safo, S. E. & Chekouo, T. Multi-omic analysis reveals ' 'enriched pathways associated with COVID-19 and COVID-19 severity. PLoS ' 'One. 17, e0267047 (2022).', 'journal-title': 'PLoS One.'}, { 'key': '5878_CR80', 'doi-asserted-by': 'publisher', 'first-page': '220', 'DOI': '10.1109/OJEMB.2020.3014798', 'volume': '1', 'author': 'K Mukund', 'year': '2020', 'unstructured': 'Mukund, K., Mathee, K. & Subramaniam, S. Plasmin cascade mediates ' 'thrombotic events in SARS-CoV-2 infection via complement and ' 'platelet-activating systems. IEEE Open J. Eng. Med. Biol. 1, 220–227 ' '(2020).', 'journal-title': 'IEEE Open J. Eng. Med. Biol.'}, { 'key': '5878_CR81', 'doi-asserted-by': 'publisher', 'first-page': '2076', 'DOI': '10.1038/s41436-021-01243-5', 'volume': '23', 'author': 'L Wu', 'year': '2021', 'unstructured': 'Wu, L., Zhu, J., Liu, D., Sun, Y. & Wu, C. An integrative multiomics ' 'analysis identifies putative causal genes for COVID-19 severity. Genet. ' 'Med. 23, 2076–2086 (2021).', 'journal-title': 'Genet. Med.'}, { 'key': '5878_CR82', 'doi-asserted-by': 'publisher', 'first-page': '102293', 'DOI': '10.1016/j.isci.2021.102293', 'volume': '24', 'author': 'X Lin', 'year': '2021', 'unstructured': 'Lin, X. et al. ORF8 contributes to cytokine storm during SARS-CoV-2 ' 'infection by activating IL-17 pathway. iScience 24, 102293 (2021).', 'journal-title': 'iScience'}, { 'key': '5878_CR83', 'doi-asserted-by': 'publisher', 'first-page': '1043', 'DOI': '10.1016/j.cell.2020.09.033', 'volume': '183', 'author': 'TM Clausen', 'year': '2020', 'unstructured': 'Clausen, T. M. et al. SARS-CoV-2 infection depends on cellular heparan ' 'sulfate and ACE2. Cell 183, 1043–1057.e15 (2020).', 'journal-title': 'Cell'}, { 'key': '5878_CR84', 'doi-asserted-by': 'publisher', 'first-page': '106037', 'DOI': '10.1016/j.isci.2023.106037', 'volume': '26', 'author': 'D Yang', 'year': '2023', 'unstructured': 'Yang, D. et al. Targeting intracellular Neu1 for coronavirus infection ' 'treatment. iScience 26, 106037 (2023).', 'journal-title': 'iScience'}, { 'key': '5878_CR85', 'doi-asserted-by': 'publisher', 'first-page': '820350', 'DOI': '10.3389/fimmu.2022.820350', 'volume': '13', 'author': 'DS Ahmed', 'year': '2022', 'unstructured': 'Ahmed, D. S. et al. Coping with stress: the mitokine GDF-15 as a ' 'biomarker of COVID-19 severity. Front. Immunol. 13, 820350 (2022).', 'journal-title': 'Front. Immunol.'}, { 'key': '5878_CR86', 'doi-asserted-by': 'publisher', 'first-page': 'eabj7521', 'DOI': '10.1126/scitranslmed.abj7521', 'volume': '14', 'author': 'R Carapito', 'year': '2022', 'unstructured': 'Carapito, R. et al. Identification of driver genes for critical forms of ' 'COVID-19 in a deeply phenotyped young patient cohort. Sci. Transl. Med. ' '14, eabj7521 (2022).', 'journal-title': 'Sci. Transl. Med.'}, { 'key': '5878_CR87', 'doi-asserted-by': 'publisher', 'first-page': '104293', 'DOI': '10.1016/j.ebiom.2022.104293', 'volume': '85', 'author': 'G Captur', 'year': '2022', 'unstructured': 'Captur, G. et al. Plasma proteomic signature predicts who will get ' 'persistent symptoms following SARS-CoV-2 infection. EBioMedicine 85, ' '104293 (2022).', 'journal-title': 'EBioMedicine'}], 'container-title': 'Communications Biology', 'original-title': [], 'language': 'en', 'link': [ { 'URL': 'https://www.nature.com/articles/s42003-024-05878-3.pdf', 'content-type': 'application/pdf', 'content-version': 'vor', 'intended-application': 'text-mining'}, { 'URL': 'https://www.nature.com/articles/s42003-024-05878-3', 'content-type': 'text/html', 'content-version': 'vor', 'intended-application': 'text-mining'}, { 'URL': 'https://www.nature.com/articles/s42003-024-05878-3.pdf', 'content-type': 'application/pdf', 'content-version': 'vor', 'intended-application': 'similarity-checking'}], 'deposited': { 'date-parts': [[2024, 2, 19]], 'date-time': '2024-02-19T15:05:45Z', 'timestamp': 1708355145000}, 'score': 1, 'resource': {'primary': {'URL': 'https://www.nature.com/articles/s42003-024-05878-3'}}, 'subtitle': [], 'short-title': [], 'issued': {'date-parts': [[2024, 2, 16]]}, 'references-count': 87, 'journal-issue': {'issue': '1', 'published-online': {'date-parts': [[2024, 12]]}}, 'alternative-id': ['5878'], 'URL': 'http://dx.doi.org/10.1038/s42003-024-05878-3', 'relation': {}, 'ISSN': ['2399-3642'], 'subject': [ 'General Agricultural and Biological Sciences', 'General Biochemistry, Genetics and Molecular Biology', 'Medicine (miscellaneous)'], 'container-title-short': 'Commun Biol', 'published': {'date-parts': [[2024, 2, 16]]}, 'assertion': [ { 'value': '21 May 2023', 'order': 1, 'name': 'received', 'label': 'Received', 'group': {'name': 'ArticleHistory', 'label': 'Article History'}}, { 'value': '1 February 2024', 'order': 2, 'name': 'accepted', 'label': 'Accepted', 'group': {'name': 'ArticleHistory', 'label': 'Article History'}}, { 'value': '16 February 2024', 'order': 3, 'name': 'first_online', 'label': 'First Online', 'group': {'name': 'ArticleHistory', 'label': 'Article History'}}, { 'value': 'All authors declare no competing interests.', 'order': 1, 'name': 'Ethics', 'group': {'name': 'EthicsHeading', 'label': 'Competing interests'}}], 'article-number': '191'}
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