Evolution of enhanced innate immune evasion by SARS-CoV-2

[1]  G. Kroemer,et al.  Induction of transposable element expression is central to innate sensing , 2021 .

[2]  V. Olieric,et al.  Crystal structure of SARS-CoV-2 Orf9b in complex with human TOM70 suggests unusual virus-host interactions , 2021, Nature Communications.

[3]  Graham W. Taylor,et al.  Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England , 2021, Nature.

[4]  M. Santiago,et al.  Interferon Resistance of Emerging SARS-CoV-2 Variants , 2021, bioRxiv.

[5]  Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution , 2021, Virology.

[6]  N. G. Davies,et al.  Increased mortality in community-tested cases of SARS-CoV-2 lineage B.1.1.7 , 2021, Nature.

[7]  P. Calistri,et al.  Infection sustained by lineage B.1.1.7 of SARS-CoV-2 is characterised by longer persistence and higher viral RNA loads in nasopharyngeal swabs , 2021, International Journal of Infectious Diseases.

[8]  S. Mallal,et al.  Altered Subgenomic RNA Expression in SARS-CoV-2 B.1.1.7 Infections , 2021, bioRxiv.

[9]  Jie Zhou,et al.  Increased transmission of SARS-CoV-2 lineage B.1.1.7 (VOC 2020212/01) is not accounted for by a replicative advantage in primary airway cells or antibody escape , 2021, bioRxiv.

[10]  S. Kissler,et al.  Densely sampled viral trajectories suggest longer duration of acute infection with B.1.1.7 variant relative to non-B.1.1.7 SARS-CoV-2 , 2021, medRxiv.

[11]  S. Kishigami,et al.  SARS-CoV-2 D614G spike mutation increases entry efficiency with enhanced ACE2-binding affinity , 2021, Nature Communications.

[12]  M. Biggerstaff,et al.  Emergence of SARS-CoV-2 B.1.1.7 Lineage — United States, December 29, 2020–January 12, 2021 , 2021, MMWR. Morbidity and mortality weekly report.

[13]  R. Siliciano,et al.  Heightened resistance to host type 1 interferons characterizes HIV-1 at transmission and after antiretroviral therapy interruption , 2021, Science Translational Medicine.

[14]  Carl A. B. Pearson,et al.  Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England , 2021, Science.

[15]  D. A. Jackson,et al.  Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity , 2020, Cell.

[16]  E. Meshorer,et al.  Transposable elements as sensors of SARS-CoV-2 infection , 2021 .

[17]  M. Noursadeghi,et al.  SARS-CoV-2 sensing by RIG-I and MDA5 links epithelial infection to macrophage inflammation , 2020, bioRxiv.

[18]  Haiyong Peng,et al.  SARS-CoV-2 spike-protein D614G mutation increases virion spike density and infectivity , 2020, Nature Communications.

[19]  Lisa E. Gralinski,et al.  SARS-CoV-2 D614G variant exhibits efficient replication ex vivo and transmission in vivo , 2020, Science.

[20]  Vineet D. Menachery,et al.  Spike mutation D614G alters SARS-CoV-2 fitness , 2020, Nature.

[21]  S. Chanda,et al.  SARS-CoV-2 Orf6 hijacks Nup98 to block STAT nuclear import and antagonize interferon signaling , 2020, Proceedings of the National Academy of Sciences.

[22]  Miguel Correa Marrero,et al.  Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms , 2020, Science.

[23]  Barbara B. Shih,et al.  Genetic mechanisms of critical illness in COVID-19 , 2020, Nature.

[24]  Steven M. Holland,et al.  Autoantibodies against type I IFNs in patients with life-threatening COVID-19 , 2020, Science.

[25]  Jacques Fellay,et al.  Inborn errors of type I IFN immunity in patients with life-threatening COVID-19 , 2020, Science.

[26]  Andrew D Smith,et al.  Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore , 2020, bioRxiv.

[27]  L. Ren,et al.  Activation and evasion of type I interferon responses by SARS-CoV-2 , 2020, Nature Communications.

[28]  V. Aguiar-Pulido,et al.  Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis , 2020, Communications Biology.

[29]  Ze-Guang Han,et al.  SARS-CoV-2 Orf9b suppresses type I interferon responses by targeting TOM70 , 2020, Cellular & Molecular Immunology.

[30]  William L. Hamilton,et al.  Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study , 2020, The Lancet Infectious Diseases.

[31]  Andrew R. Leach,et al.  The Global Phosphorylation Landscape of SARS-CoV-2 Infection , 2020, Cell.

[32]  D. Burton,et al.  Isolation of potent SARS-CoV-2 neutralizing antibodies and protection from disease in a small animal model , 2020, Science.

[33]  Rachel S. G. Sealfon,et al.  SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes , 2020, bioRxiv.

[34]  Benjamin J. Polacco,et al.  A SARS-CoV-2 Protein Interaction Map Reveals Targets for Drug-Repurposing , 2020, Nature.

[35]  S. Baker,et al.  Coronavirus endoribonuclease targets viral polyuridine sequences to evade activating host sensors , 2020, Proceedings of the National Academy of Sciences.

[36]  M. Müller,et al.  Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform , 2020, Nature.

[37]  Victor M Corman,et al.  Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR , 2020, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[38]  Benjamin M. Gyori,et al.  Assembling a corpus of phosphoproteomic annotations using ProtMapper to normalize site information from databases and text mining , 2019, bioRxiv.

[39]  Nora Schmidt Novel Functions of Host TRIM28 in Restricting Influenza Virus Infections , 2019 .

[40]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[41]  Geo Pertea,et al.  Transcriptome assembly from long-read RNA-seq alignments with StringTie2 , 2019, Genome Biology.

[42]  Joshua M. Korn,et al.  Tumor-derived IFN triggers chronic pathway agonism and sensitivity to ADAR loss , 2018, Nature Medicine.

[43]  D. Sabatini,et al.  RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway , 2018, Science Advances.

[44]  J. Sáez-Rodríguez,et al.  Benchmark and integration of resources for the estimation of human transcription factor activities , 2018, bioRxiv.

[45]  G. Towers,et al.  Are Evolution and the Intracellular Innate Immune System Key Determinants in HIV Transmission? , 2017, Front. Immunol..

[46]  Pedro Beltrão,et al.  Benchmarking substrate-based kinase activity inference using phosphoproteomic data , 2016, bioRxiv.

[47]  P. Borrow,et al.  Resistance of Transmitted Founder HIV-1 to IFITM-Mediated Restriction , 2016, Cell host & microbe.

[48]  Joel Selkrig,et al.  An atlas of human kinase regulation , 2016, Molecular Systems Biology.

[49]  Mariano J. Alvarez,et al.  Network-based inference of protein activity helps functionalize the genetic landscape of cancer , 2016, Nature Genetics.

[50]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[51]  S. Joel,et al.  Kinase-Substrate Enrichment Analysis Provides Insights into the Heterogeneity of Signaling Pathway Activation in Leukemia Cells , 2013, Science Signaling.

[52]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[53]  Yufei Shan,et al.  Tom70 mediates activation of interferon regulatory factor 3 on mitochondria , 2010, Cell Research.

[54]  P. Cohen,et al.  Use of the Pharmacological Inhibitor BX795 to Study the Regulation and Physiological Roles of TBK1 and IκB Kinase ϵ , 2009, Journal of Biological Chemistry.

[55]  B. Lindenbach Measuring HCV infectivity produced in cell culture and in vivo. , 2009, Methods in molecular biology.

[56]  Anne E Carpenter,et al.  CellProfiler: image analysis software for identifying and quantifying cell phenotypes , 2006, Genome Biology.

[57]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[58]  H Green,et al.  Serial cultivation of strains of human epidermal keratinocytes: the formation of keratinizing colonies from single cells. , 1975, Cell.