Spike and nsp6 are key determinants of SARS-CoV-2 Omicron BA.1 attenuation

[1]  Guanqun Liu,et al.  An optimized circular polymerase extension reaction-based method for functional analysis of SARS-CoV-2 , 2023, Virology Journal.

[2]  R. Webby,et al.  Characterization of SARS-CoV-2 Omicron BA.4 and BA.5 isolates in rodents , 2022, Nature.

[3]  N. Dixit,et al.  Modelling how the altered usage of cell entry pathways by the SARS-CoV-2 Omicron variant may affect the efficacy and synergy of TMPRSS2 and Cathepsin B/L inhibitors , 2022, bioRxiv.

[4]  William T. Harvey,et al.  SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway , 2022, Nature Microbiology.

[5]  M. Lipsitch,et al.  Clinical outcomes associated with SARS-CoV-2 Omicron (B.1.1.529) variant and BA.1/BA.1.1 or BA.2 subvariant infection in Southern California , 2022, Nature Medicine.

[6]  Arvind H. Patel,et al.  The altered entry pathway and antigenic distance of the SARS-CoV-2 Omicron variant map to separate domains of spike protein , 2022, bioRxiv.

[7]  L. Giaquinto,et al.  The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle , 2022, Nature.

[8]  G. Ye,et al.  Cryo-EM structure of a SARS-CoV-2 omicron spike protein ectodomain , 2022, Nature Communications.

[9]  K. Francis,et al.  Fatal Neurodissemination and SARS-CoV-2 Tropism in K18-hACE2 Mice Is Only Partially Dependent on hACE2 Expression , 2022, Viruses.

[10]  M. Diamond,et al.  Characterization and antiviral susceptibility of SARS-CoV-2 Omicron/BA.2 , 2022, Research square.

[11]  N. Daneman,et al.  Estimates of SARS-CoV-2 Omicron Variant Severity in Ontario, Canada. , 2022, JAMA.

[12]  B. Luan,et al.  Spike protein-independent attenuation of SARS-CoV-2 Omicron variant in laboratory mice , 2022, bioRxiv.

[13]  L. Poon,et al.  SARS-CoV-2 Omicron variant replication in human bronchus and lung ex vivo , 2022, Nature.

[14]  A. Kaneda,et al.  Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant , 2022, Nature.

[15]  Karl A. Soetebier,et al.  Trends in Disease Severity and Health Care Utilization During the Early Omicron Variant Period Compared with Previous SARS-CoV-2 High Transmission Periods — United States, December 2020–January 2022 , 2022, MMWR. Morbidity and mortality weekly report.

[16]  H. Woo,et al.  Omicron: A Heavily Mutated SARS-CoV-2 Variant Exhibits Stronger Binding to ACE2 and Potently Escapes Approved COVID-19 Therapeutic Antibodies , 2022, Frontiers in Immunology.

[17]  T. Treangen,et al.  Notes from the Field: Early Evidence of the SARS-CoV-2 B.1.1.529 (Omicron) Variant in Community Wastewater — United States, November–December 2021 , 2022, MMWR. Morbidity and mortality weekly report.

[18]  Larissa B. Thackray,et al.  SARS-CoV-2 Omicron virus causes attenuated disease in mice and hamsters , 2022, Nature.

[19]  A. Sigal.  Milder disease with Omicron: is it the virus or the pre-existing immunity? , 2022, Nature Reviews Immunology.

[20]  Luke Taylor.  Covid-19: Omicron drives weekly record high in global infections , 2022, BMJ.

[21]  Jun Yu,et al.  SARS-CoV-2 non-structural protein 6 triggers NLRP3-dependent pyroptosis by targeting ATP6AP1 , 2022, Cell Death & Differentiation.

[22]  S. Madhi,et al.  SARS-CoV-2 Omicron-B.1.1.529 leads to widespread escape from neutralizing antibody responses , 2022, Cell.

[23]  Jordan J. Clark,et al.  Activity of convalescent and vaccine serum against SARS-CoV-2 Omicron , 2021, Nature.

[24]  M. Nussenzweig,et al.  Plasma Neutralization of the SARS-CoV-2 Omicron Variant , 2021, The New England journal of medicine.

[25]  K. To,et al.  Attenuated replication and pathogenicity of SARS-CoV-2 B.1.1.529 Omicron , 2021, Nature.

[26]  K. To,et al.  SARS-CoV-2 Omicron variant shows less efficient replication and fusion activity when compared with Delta variant in TMPRSS2-expressed cells , 2021, Emerging microbes & infections.

[27]  T. Ndung’u,et al.  Omicron extensively but incompletely escapes Pfizer BNT162b2 neutralization , 2021, Nature.

[28]  P. Maes,et al.  Considerable escape of SARS-CoV-2 Omicron to antibody neutralization , 2021, Nature.

[29]  J. Bhiman,et al.  Early assessment of the clinical severity of the SARS-CoV-2 Omicron variant in South Africa , 2021, medRxiv.

[30]  O. Dyer.  Covid-19: Omicron is causing more infections but fewer hospital admissions than delta, South African data show , 2021, BMJ.

[31]  Liyuan Liu,et al.  Striking antibody evasion manifested by the Omicron variant of SARS-CoV-2 , 2021, Nature.

[32]  L. Poon,et al.  Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021 , 2021, Emerging infectious diseases.

[33]  Philip L. Tzou,et al.  Coronavirus Resistance Database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons , 2021, bioRxiv.

[34]  J. Blanco,et al.  Evaluation of SARS-CoV-2 entry, inflammation and new therapeutics in human lung tissue cells , 2021, bioRxiv.

[35]  K. Überla,et al.  Cloning of a Passage-Free SARS-CoV-2 Genome and Mutagenesis Using Red Recombination , 2021, International journal of molecular sciences.

[36]  J. Dennehy,et al.  Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater , 2021, Nature Communications.

[37]  Jourdan K. Ewoldt,et al.  SARS-CoV-2 Disrupts Proximal Elements in the JAK-STAT Pathway , 2021, Journal of virology.

[38]  Ilya J. Finkelstein,et al.  Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes , 2021, Science.

[39]  F. Grieder,et al.  Nonhuman primate models for SARS-CoV-2 research: Consider alternatives to macaques , 2021, Lab Animal.

[40]  D. Fremont,et al.  Identification of SARS-CoV-2 spike mutations that attenuate monoclonal and serum antibody neutralization , 2021, Cell Host & Microbe.

[41]  H. Rothan,et al.  Neuroinvasion and Encephalitis Following Intranasal Inoculation of SARS-CoV-2 in K18-hACE2 Mice , 2020, bioRxiv.

[42]  W. Kamitani,et al.  Establishment of a reverse genetics system for SARS-CoV-2 using circular polymerase extension reaction , 2020, bioRxiv.

[43]  M. Beltramello,et al.  Mapping Neutralizing and Immunodominant Sites on the SARS-CoV-2 Spike Receptor-Binding Domain by Structure-Guided High-Resolution Serology , 2020, Cell.

[44]  Shuwen Liu,et al.  Structural and functional properties of SARS-CoV-2 spike protein: potential antivirus drug development for COVID-19 , 2020, Acta Pharmacologica Sinica.

[45]  Edward C. Holmes,et al.  A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology , 2020, Nature Microbiology.

[46]  Jessie Huang,et al.  SARS-CoV-2 Infection of Pluripotent Stem Cell-derived Human Lung Alveolar Type 2 Cells Elicits a Rapid Epithelial-Intrinsic Inflammatory Response , 2020, bioRxiv.

[47]  C. Yao,et al.  SARS-CoV-2 infection of primary human lung epithelium for COVID-19 modeling and drug discovery , 2020, bioRxiv.

[48]  Qiang Zhou,et al.  A neutralizing human antibody binds to the N-terminal domain of the Spike protein of SARS-CoV-2 , 2020, Science.

[49]  A. Sette,et al.  The receptor binding domain of the viral spike protein is an immunodominant and highly specific target of antibodies in SARS-CoV-2 patients , 2020, Science Immunology.

[50]  Linqi Zhang,et al.  Human neutralizing antibodies elicited by SARS-CoV-2 infection , 2020, Nature.

[51]  T. Uyeki,et al.  Pathology and Pathogenesis of SARS-CoV-2 Associated with Fatal Coronavirus Disease, United States , 2020, Emerging infectious diseases.

[52]  Stefano Pascarella,et al.  Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy , 2020, Journal of Infection.

[53]  Linqi Zhang,et al.  Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor , 2020, Nature.

[54]  D. Kotton,et al.  Derivation of self-renewing lung alveolar epithelial type II cells from human pluripotent stem cells , 2019, Nature Protocols.

[55]  T. Wileman,et al.  Coronavirus NSP6 restricts autophagosome expansion , 2014, Autophagy.

[56]  K. Bienz,et al.  RNA Replication of Mouse Hepatitis Virus Takes Place at Double-Membrane Vesicles , 2002, Journal of Virology.

[57]  M. Krečmerová,et al.  Lipases as Tools in the Synthesis of Prodrugs from Racemic 9-(2,3-Dihydroxypropyl)adenine , 2012, Molecules.

[58]  Eleanor,et al.  Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity , 2022 .

[59]  R. Neher,et al.  Nextclade: clade assignment, mutation calling and quality control for viral genomes , 2021, J. Open Source Softw..