Corpus overview


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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1576)

ProteinN (446)

NSP5 (376)

ComplexRdRp (213)

ProteinE (120)


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SARS-CoV-2 Proteins
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    Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples

    Authors: Jennifer R. Hamilton; Elizabeth C. Stahl; Connor A. Tsuchida; Enrique Lin-Shiao; C. Kimberly Tsui; Kathleen Pestal; Holly K. Gildea; Lea B. Witkowsky; Erica A. Moehle; Shana L. McDevitt; Matthew McElroy; Amanda Keller; Iman Sylvain; Ariana Hirsh; Alison Ciling; Alexander J. Ehrenberg; - IGI SARS-CoV-2 consortium; Bradley R. Ringeisen; Garth Huberty; Fyodor D. Urnov; Petros Giannikopoulos; Jennifer A. Doudna; Tiannan Guo

    doi:10.1101/2021.01.10.21249151 Date: 2021-01-11 Source: medRxiv

    Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 MESHD in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI-FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection MESHD prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against the gold standard, nasopharyngeal swab specimens. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.

    Characteristics of changes in circulating markers of alveolar epithelial and endothelial injury in acute respiratory distress syndrome with COVID-19 MESHD

    Authors: Kentaro Tojo; Natsuhiro Yamamoto; Takahiro Mihara; Miyou Abe; Takahisa Goto; Kathleen Pestal; Holly K. Gildea; Lea B. Witkowsky; Erica A. Moehle; Shana L. McDevitt; Matthew McElroy; Amanda Keller; Iman Sylvain; Ariana Hirsh; Alison Ciling; Alexander J. Ehrenberg; - IGI SARS-CoV-2 consortium; Bradley R. Ringeisen; Garth Huberty; Fyodor D. Urnov; Petros Giannikopoulos; Jennifer A. Doudna; Tiannan Guo

    doi:10.1101/2021.01.10.21249528 Date: 2021-01-11 Source: medRxiv

    The time course and specific contributions of alveolar epithelial MESHD and endothelial injury to the pathogenesis of acute respiratory distress syndrome MESHD ( ARDS MESHD) with coronavirus disease MESHD ( COVID-19 MESHD) remain unclear. Here, we evaluated the characteristics of circulating markers of alveolar epithelial MESHD and endothelial injury MESHD in 107 serum samples from nine ARDS MESHD patients and eight non-ARDS patients, all with COVID-19 MESHD. Although both the alveolar epithelial MESHD and endothelial injury markers were markedly elevated in the COVID-19 MESHD ARDS MESHD patients, our data indicate that the endothelial injury, which continues for a longer period than the epithelial injury, seems to be the main contributor to alveolar MESHD barrier disruption.

    The landscape of human brain immune response in patients with severe COVID-19 MESHD

    Authors: John F Fullard; Hao-chih Lee; Georgios Voloudakis; Shengbao Suo; Zhiping Shao; Cyril Peter; Behnam Javidfar; Wen Zhang; Shan Jiang; Andre Corvelo; Emma Woodoff-Leith; Dushyant P Purohit; Gabriel E Hoffman; Schahram Akbarian; Mary Fowkes; John Crary; Guo-Cheng Yuan; Panos Roussos; Garth Huberty; Fyodor D. Urnov; Petros Giannikopoulos; Jennifer A. Doudna; Tiannan Guo

    doi:10.1101/2021.01.08.425999 Date: 2021-01-11 Source: bioRxiv

    In coronavirus disease 2019 MESHD ( COVID-19 MESHD), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection MESHD, the relationship between brain tropism, neuroinflammation and host immune response has not been well characterized. We analyzed 68,557 single-nucleus transcriptomes from three brain regions (dorsolateral prefrontal cortex, medulla oblongata and choroid plexus MESHD) and identified an increased proportion of stromal cells and monocytes in the choroid plexus of COVID-19 MESHD patients. Differential gene expression, pseudo-temporal trajectory and gene regulatory network analyses revealed microglial transcriptome perturbations, mediating a range of biological processes, including cellular activation, mobility and phagocytosis. Quantification of viral spike S1 protein PROTEIN and SARS-CoV-2 transcripts did not support the notion of brain tropism MESHD. Overall, our findings suggest extensive neuroinflammation in patients with acute COVID-19 MESHD.

    Immunological and cardio-vascular pathologies associated with SARS-CoV-2 infection MESHD in golden syrian hamster

    Authors: John F Fullard; Hao-chih Lee; Georgios Voloudakis; Shengbao Suo; Zhiping Shao; Cyril Peter; Behnam Javidfar; Wen Zhang; Shan Jiang; Andre Corvelo; Emma Woodoff-Leith; Dushyant P Purohit; Gabriel E Hoffman; Schahram Akbarian; Mary Fowkes; John Crary; Guo-Cheng Yuan; Panos Roussos; Garth Huberty; Fyodor D. Urnov; Petros Giannikopoulos; Jennifer A. Doudna; Tiannan Guo

    doi:10.1101/2021.01.11.426080 Date: 2021-01-11 Source: bioRxiv

    Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 infection MESHD in golden Syrian hamster (GSH) causes lungs pathology and resembles to human corona virus disease MESHD ( Covid-19 MESHD). Extra-pulmonary pathologies and immunological parameters of SARS-CoV-2 infection MESHD remained undefined in GSH. Using in silico modelling, we identified the similarities between human and hamster angiotensin-converting enzyme-2 (ACE-2), neuropilin-1 (NRP-1) that bind to receptor-binding domain (RBD) and S1 fragment of spike protein PROTEIN of SARS-CoV-2. SARS-CoV-2 infection MESHD led to lung pathologies, and cardiovascular complications MESHD ( CVC MESHD) marked by interstitial coronary fibrosis MESHD and acute inflammatory response. Serum lipidomic and metabolomic profile of SARS-CoV-2-infected MESHD GSH revealed changes in serum triglycerides (TG) and low-density lipoprotein (LDL), and alterations in metabolites that correlated with Covid19 MESHD. Together, we propose GSH as an animal model to study SARS-CoV-2 infection MESHD and its therapy associated with pulmonary and extra-pulmonary pathologies.

    Hypoxia reduces cell attachment of SARS-CoV-2 spike PROTEIN protein by modulating the expression of ACE2 HGNC and heparan sulfate

    Authors: Endika Prieto-Fernandez; Leire Egia-Mendikute; Laura Vila-Vecilla; So Young Lee; Alexandre Bosch; Adrian Barreira-Manrique; Ana Garcia del Rio; Asier Antonana-Vildosola; Borja Jimenez-Lasheras; Asis Palazon; Emma Woodoff-Leith; Dushyant P Purohit; Gabriel E Hoffman; Schahram Akbarian; Mary Fowkes; John Crary; Guo-Cheng Yuan; Panos Roussos; Garth Huberty; Fyodor D. Urnov; Petros Giannikopoulos; Jennifer A. Doudna; Tiannan Guo

    doi:10.1101/2021.01.09.426021 Date: 2021-01-11 Source: bioRxiv

    A main clinical parameter of Covid-19 MESHD pathophysiology is hypoxia MESHD. Here we show that hypoxia decreases MESHD the attachment of the receptor binding domain (RBD) and the S1 subunit (S1) of the spike PROTEIN protein to epithelial cells. In Vero E6 cells, hypoxia MESHD reduces the protein levels of ACE2, which might in part explain the observed reduction of the infection MESHD rate. However, hypoxia MESHD also inhibits the binding of the spike to human lung epithelial cells lacking ACE2 HGNC expression, indicating that hypoxia MESHD modulates the expression of additional binding partners of SARS-CoV-2. We show that hypoxia MESHD also decreases the total cell surface levels of heparan sulfate, a known attachment receptor of SARS-CoV-2, by reducing the expression of syndecan-1 HGNC and syndecan3 HGNC, the main proteoglycans containing heparan sulfate. Our study indicates that hypoxia MESHD acts to prevent SARS-CoV-2 infection MESHD, suggesting that the hypoxia MESHD signaling pathway might offer therapeutic opportunities for the treatment of Covid-19 MESHD.

    Potent SARS-CoV-2 Neutralizing Antibodies Directed Against Spike N-Terminal Domain Target a Single Supersite

    Authors: Gabriele Cerutti; Yicheng Guo; Tongqing Zhou; Jason Gorman; Myungjin Lee; Micah Rapp; Eswar R Reddem; Jian Yu; Fabiana Bahna; Jude Bimela; Yaoxing Huang; Phinikoula S Katsamba; Liu Lihong; Manoj S Nair; Reda Rawi; Adam S Olia; Pengfei Wang; Gwo-Yu Chuang; David D Ho; Zizhang Sheng; Peter D Kwong; Lawrence Shapiro; Tiannan Guo

    doi:10.1101/2021.01.10.426120 Date: 2021-01-11 Source: bioRxiv

    Numerous antibodies that neutralize SARS-CoV-2 have been identified, and these generally target either the receptor-binding domain (RBD) or the N-terminal domain ( NTD HGNC) of the viral spike. While RBD-directed antibodies have been extensively studied, far less is known about NTD HGNC-directed antibodies. Here we report cryo-EM and crystal structures for seven potent NTD HGNC-directed neutralizing antibodies in complex with spike or isolated NTD HGNC. These structures defined several antibody classes, with at least one observed in multiple convalescent donors. The structures revealed all seven antibodies to target a common surface, bordered by glycans N17, N74, N122, and N149. This site - formed primarily by a mobile {beta}-hairpin and several flexible loops - was highly electropositive, located at the periphery of the spike, and the largest glycan-free surface of NTD HGNC facing away from the viral membrane. Thus, in contrast to neutralizing RBD-directed antibodies that recognize multiple non-overlapping epitopes, potent NTD HGNC-directed neutralizing antibodies target a single supersite.

    Molecular Dynamics Analysis of a Flexible Loop at the Binding Interface of the SARS-CoV-2 Spike PROTEIN Protein Receptor-Binding Domain

    Authors: Jonathan K Williams; Baifan Wang; Andrew Sam; Cody L Hoop; David A Case; Jean Baum; Eswar R Reddem; Jian Yu; Fabiana Bahna; Jude Bimela; Yaoxing Huang; Phinikoula S Katsamba; Liu Lihong; Manoj S Nair; Reda Rawi; Adam S Olia; Pengfei Wang; Gwo-Yu Chuang; David D Ho; Zizhang Sheng; Peter D Kwong; Lawrence Shapiro; Tiannan Guo

    doi:10.1101/2021.01.08.425965 Date: 2021-01-11 Source: bioRxiv

    Since the identification of the SARS-CoV-2 virus as the causative agent of the current COVID-19 pandemic MESHD, considerable effort has been spent characterizing the interaction between the Spike protein PROTEIN receptor-binding domain (RBD) and the human angiotensin converting enzyme 2 HGNC ( ACE2 HGNC) receptor. This has provided a detailed picture of the end point structure of the RBD- ACE2 HGNC binding event, but what remains to be elucidated is the conformation and dynamics of the RBD prior to its interaction with ACE2 HGNC. In this work we utilize molecular dynamics simulations to probe the flexibility and conformational ensemble of the unbound state of the receptor-binding domain from SARS-CoV-2 and SARS-CoV MESHD. We have found that the unbound RBD has a localized region of dynamic flexibility in Loop 3 and that mutations identified during the COVID-19 pandemic MESHD in Loop 3 do not affect this flexibility. We use a loop-modeling protocol to generate and simulate novel conformations of the CoV2-RBD Loop 3 region that sample conformational space beyond the ACE2 HGNC bound crystal structure. This has allowed for the identification of interesting substates of the unbound RBD that are lower energy than the ACE2 HGNC-bound conformation, and that block key residues along the ACE2 HGNC binding interface. These novel unbound substates may represent new targets for therapeutic design.

    Immunogenicity and Protective Efficacy of an Intranasal Live-attenuated Vaccine Against SARS-CoV-2 in Preclinical Animal Models

    Authors: Jun-Guy Park; Fatai S. Oladunni; Mohammed A. Rohaim; Jayde Whittingham-Dowd; James Tollitt; Bakri M Assas; Wafaa Alhazmi; Abdullah Almilaibary; Munir Iqbal; Pengxiang Chang; Renee Escalona; Vinay Shivanna; Jordi B. Torrelles; John J Worthington; Lucy H. Jackson-Jones; Luis Martinez-Sobrido; Muhammad Munir; Gwo-Yu Chuang; David D Ho; Zizhang Sheng; Peter D Kwong; Lawrence Shapiro; Tiannan Guo

    doi:10.1101/2021.01.08.425974 Date: 2021-01-11 Source: bioRxiv

    The global deployment of an effective and safe vaccine is currently a public health priority to curtail the coronavirus disease 2019 MESHD ( COVID-19 MESHD) pandemic caused by severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2). Here, we evaluated a Newcastle disease virus (NDV)-based intranasal vectored-vaccine in mice and hamsters for its immunogenicity, safety and protective efficacy in challenge studies with SARS-CoV-2. The recombinant (r)NDV-S vaccine expressing spike (S) protein PROTEIN of SARS-CoV-2 administrated via intranasal route in mice induced high levels of SARS-CoV-2-specific neutralizing immunoglobulin A (IgA) and IgG2a antibodies and T cell-mediated immunity. Hamsters vaccinated with two doses of vaccine showed complete protection from clinical disease including lung infection MESHD, inflammation MESHD, and pathological lesions after SARS-CoV-2 challenge. Importantly, a single or double dose of intranasal rNDV-S vaccine completely blocked SARS-CoV-2 shedding in nasal turbinate and lungs within 4 days of vaccine administration in hamsters. Taken together, intranasal administration of rNDV-S has the potential to control infection at the site of inoculation, which should prevent both the clinical disease and transmission to halt the spread of the COVID-19 pandemic MESHD.

    Modular basis for potent SARS-CoV-2 neutralization by a prevalent VH1-2-derived antibody class

    Authors: Micah Rapp; Yicheng Guo; Eswar Reddy Reddem; Lihong Liu; Pengfei Wang; Jian Yu; Gabriele Cerutti; Jude Bimela; Fabiana Bahna; Seetha Mannepalli; Baoshan Zhang; Peter D. Kwong; David D. Ho; Lawrence Shapiro; Zizhang Sheng; Luis Martinez-Sobrido; Muhammad Munir; Gwo-Yu Chuang; David D Ho; Zizhang Sheng; Peter D Kwong; Lawrence Shapiro; Tiannan Guo

    doi:10.1101/2021.01.11.426218 Date: 2021-01-11 Source: bioRxiv

    Antibodies with heavy chains that derive from the VH1-2 gene constitute some of the most potent SARS-CoV-2-neutralizing antibodies yet identified. To provide insight into whether these genetic similarities inform common modes of recognition, we determined structures of the SARS-CoV-2 spike PROTEIN in complex with three VH1-2-derived antibodies: 2-15, 2-43, and H4. All three utilized VH1-2-encoded motifs to recognize the receptor-binding domain (RBD), with heavy chain N53I enhancing binding and light chain tyrosines recognizing F486RBD. Despite these similarities, class members bound both RBD up and down conformations of the spike, with a subset of antibodies utilizing elongated CDRH3s to recognize glycan N343 on a neighboring RBD - a quaternary interaction accommodated by an increase in RBD separation of up to 12 angstrom. The VH1-2-antibody class thus utilizes modular recognition encoded by modular genetic elements to effect potent neutralization, with VH-gene component MESHD specifying recognition of RBD MESHD and CDRH3 component specifying quaternary interactions.

    Immunogenicity and efficacy of the COVID-19 MESHD candidate vector vaccine MVA SARS 2 S in preclinical vaccination

    Authors: Alina Tscherne; Jan Hendrik Schwarz; Cornelius Rohde; Alexandra Kupke; Georgia Kalodimou; Leonard Limpinsel; Nisreen M.A. Okba; Berislav Bosnjak; Inga Sandrock; Sandro Halwe; Lucie Sauerhering; Katrin Printz; Liangliang Nan; Elke Duell; Sylvia Jany; Astrid Freudenstein; Joerg Schmidt; Anke Werner; Michelle Gellhorn; Michael Kluever; Wolfgang Guggemos; Michael Seilmaier; Clemens Wendtner; Reinhold Foerster; Bart Haagmans; Stephan Becker; Gerd Sutter; Asisa Volz

    doi:10.1101/2021.01.09.426032 Date: 2021-01-11 Source: bioRxiv

    The severe acute respiratory syndrome MESHD (SARS) coronavirus 2 (SARS-CoV-2) has emerged as the infectious agent causing the pandemic coronavirus disease MESHD coronavirus disease 2019 MESHD ( COVID-19 MESHD) with dramatic consequences for global human health and economics. Previously, we reached clinical evaluation with our vector vaccine based on vaccinia virus MVA against the Middle East respiratory syndrome coronavirus (MERS-CoV) MESHD, which causes an infection in humans similar to SARS and COVID-19 MESHD. Here, we describe the construction and preclinical characterization of a recombinant MVA expressing full-length SARS-CoV-2 spike PROTEIN ( S) protein PROTEIN (MVA-SARS-2-S). Genetic stability and growth characteristics of MVA-SARS-2-S, plus its robust synthesis of S antigen, make it a suitable candidate vaccine for industrial scale production. Vaccinated mice produced S antigen-specific CD8+ T cells and serum antibodies binding to S glycoprotein PROTEIN that neutralized SARS-CoV 2. Prime-boost vaccination with MVA-SARS-2-S MESHD protected mice sensitized with a human ACE2 HGNC-expressing adenovirus from SARS-CoV-2 infection MESHD. MVA-SARS-2-S is currently being investigated in a phase I clinical trial as aspirant for developing a safe and efficacious vaccine against COVID-19 MESHD.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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