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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (1865)

ProteinN (508)

NSP5 (401)

ComplexRdRp (235)

ProteinE (135)


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SARS-CoV-2 Proteins
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    Scalable, Micro-Neutralization Assay for Qualitative Assessment of SARS-CoV-2 (COVID 19) Virus-Neutralizing Antibodies in Human Clinical Samples

    Authors: Michael R Holbrook; Richard S Bennett; Elena N Postnikova; Janie Liang; Robin Gross; Dawn Gerhardt; Shalamar Georgia-Clark; Yingyun Cai; Shuiqinq Yu; Lindsay Marron; Greg Kocher; Steven Mazur; Saurabh Dixit; Vladimir V Lukin

    doi:10.1101/2021.03.05.434152 Date: 2021-03-05 Source: bioRxiv

    As the severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) pandemic was expanding, it was clear that effective testing for the presence of neutralizing antibodies in the blood of convalescent patients would be critical for development of plasma-based therapeutic approaches. To address the need for a high-quality neutralization assay against SARS CoV 2, a previously established fluorescence reduction neutralization assay (FRNA) against Middle East respiratory syndrome MESHD coronavirus (MERS-CoV) was modified and optimized. The SARS-CoV-2 FRNA provides a quantitative assessment of a large number of infected cells through use of a high content imaging system. Because of this approach, and the fact that it does not involve subjective interpretation, this assay is more efficient and more accurate than other neutralization assays. In addition, the ability to set robust acceptance criteria for individual plates and specific test wells provided further rigor to this assay. Such agile adaptability avails use with multiple virus variants. By February 2021, the SARS-CoV-2 FRNA had been used to screen over 5,000 samples, including acute and convalescent plasma or serum samples and therapeutic antibody treatments, for SARS-CoV-2 neutralizing titers.

    SARS-CoV-2-host chimeric RNA-sequencing reads do not necessarily signify virus integration into the host DNA

    Authors: Anastasiya Kazachenka; George Kassiotis

    doi:10.1101/2021.03.05.434119 Date: 2021-03-05 Source: bioRxiv

    The human genome bears evidence of extensive invasion by retroviruses and other retroelements, as well as by diverse RNA and DNA viruses. High frequency of somatic integration of the RNA virus severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) into the DNA of infected cells was recently suggested, partly based on the detection of chimeric RNA-sequencing (RNA-seq) reads between SARS-CoV-2 RNA and RNA transcribed from human host DNA. Here, we examined the possible origin of human-SARS-CoV-2 chimeric reads in RNA-seq libraries and provide alternative explanations for their origin. Chimeric reads were frequently detected also between SARS-CoV-2 RNA and RNA transcribed from mitochondrial DNA or episomal adenoviral DNA present in transfected cell lines, which was unlikely the result of SARS-CoV-2 integration. Furthermore, chimeric reads between SARS-CoV-2 RNA and RNA transcribed from nuclear DNA was highly enriched for host exonic, than intronic or intergenic sequences and often involved the same, highly expressed host genes. These findings suggest that human-SARS-CoV-2 chimeric reads found in RNA-seq data may arise during library preparation and do not necessarily signify SARS-CoV-2 reverse transcription, integration in to host DNA and further transcription.

    Mental Health, Greenness and Nature Related Behaviours in the Adult Population of Stockholm County during Covid-19 MESHD-related Restrictions

    Authors: Mare Lõhmus; Cecilia U. D. Stenfors; Tomas Lind; André Lauber; Antonios Georgelis

    id:10.20944/preprints202103.0201.v1 Date: 2021-03-05 Source: Preprints.org

    International data suggests that exposure for nature is beneficial for mental health and well-being. The restrictions related to Covid-19 pandemic MESHD have created a setting that allows us to investigate the importance of greenness exposure on mental health during a period of increased isolation and worry. Based on 2060 responses from an online survey in the Stockholm County, Sweden, we investigated: 1) weather the Covid-19 pandemic MESHD changed peoples’ life-style and nature-related habits, and 2) if peoples’ mental health differed depending on their exposure to greenness. Neighbourhood greenness levels were quantified by using the average Normalized Difference Vegetation Index (NDVI) within 50m, 100m, 300m, and 500m buffers surrounding the participant’s place of residence. We found that the number of individuals that reported that they visited natural areas “often” was significantly higher during the pandemic than before the pandemic. Higher levels of greenness surrounding one’s location of residence were in general associated with higher mental health/wellbeing and vitality scores, and less symptoms of depression MESHD, anxiety MESHD, and perceived and cognitive stress MESHD, after adjustments for demographic variables and walkability. In conclusion, the results from the present study provided support to the suggestion that contact with nature may be important for mental health in extreme circumstances.

    Radial Extracorporeal Shock Wave Therapy to Support Breathing in Case of Coronavirus Disease 2019 MESHD ( COVID-19 MESHD): A Case Report

    Authors: Peter Stiller; Christoph Schmitz

    id:10.20944/preprints202103.0192.v1 Date: 2021-03-05 Source: Preprints.org

    Many patients with Coronavirus disease 2019 MESHD ( COVID-19 MESHD) suffer from shortness of breath MESHD and severe chest pain MESHD. Here we report successful therapy of a patient with diagnosis of COVID-19 MESHD, severe chest pain MESHD and significant shortness of breath MESHD, using radial extracorporeal shock wave therapy (rESWT). The latter started seven days after beginning of symptoms and drug therapy without success, and involved daily application of 15.000 to 20.000 radial extracorporeal shock waves over the intercostal muscles as well as the paravertebral muscles of the thoracic and lumbar spine, diaphragm and flanks. Immediately after the first rESWT session the patient experienced significant pain MESHD relief and improvement of breathing. Four days later the pain MESHD had completely subsided and breathing was largely normalized. This type of noninvasive, non-pharmacologic treatment could help many COVID-19 MESHD patients or patients who still suffer from breathing problems weeks after having been infected with SARS-CoV-2, giving them back quality of life.

    Ribosome-profiling reveals restricted post transcriptional ex-pression of antiviral cytokines and transcription factors during SARS-CoV-2 infection MESHD

    Authors: Marina R Alexander; Aaron M Brice; Petrus Jansen Van Vuren; Christina Rootes; Leon Tribolet; Christopher Cowled; Andrew G.D. Bean; Cameron R Stewart

    doi:10.1101/2021.03.03.433675 Date: 2021-03-04 Source: bioRxiv

    The global COVID-19 pandemic MESHD caused by SARS-CoV-2 has resulted in over 2.2 million deaths. Disease outcomes range from asymptomatic to severe with, so far, minimal genotypic change to the virus so understanding the host response is paramount. Transcriptomics has become incredibly important in understanding host-pathogen interactions; however, post-transcriptional regulation plays an important role in infection and immunity through translation and mRNA stability, al-lowing tight control over potent host responses by both the host and the invading virus. Here we apply ribosome profiling to assess post-transcriptional regulation of host genes during SARS-CoV-2 infection MESHD of a human lung epithelial cell line (Calu-3). We have identified numerous transcription factors ( JUN HGNC, ZBTB20 HGNC, ATF3 HGNC, HIVEP2 HGNC and EGR1 HGNC) as well as select antiviral cytokine genes, namely IFNB1 HGNC, IFNL1,2 and 3, IL-6 HGNC and CCL5 HGNC, that are restricted at the post-transcriptional level by SARS-CoV-2 infection MESHD and discuss the impact this would have on the host response to infection. This early phase restriction of antiviral transcripts in the lungs may allow high viral load and consequent immune dysregulation typically seen in SARS-CoV-2 infection MESHD.

    Engineered SARS-CoV-2 receptor binding domain improves immunogenicity in mice and elicits protective immunity in hamsters

    Authors: Neil C Dalvie; Sergio A Rodriguez-Aponte; Brittany L Hartwell; Lisa H Tostanoski; Andrew M Biedermann; Laura E Crowell; Kawaljit Kaur; Ozan Kumru; Lauren Carter; Jingyou Yu; Aiquan Chang; Katherine McMahan; Thomas Courant; Celia Lebas; Ashley A Lemnios; Kristen A Rodrigues; Murillo Silva; Ryan S Johnston; Christopher A Naranjo; Mary Kate Tracey; Joseph R Brady; Charles A Whittaker; Dongsoo Yun; Swagata Kar; Maciel Porto; Megan Lok; Hanne Andersen; Mark G Lewis; Kerry R Love; Danielle L Camp; Judith Maxwell Silverman; Harry Kleanthous; Sangeeta B Joshi; David B Volkin; Patrice M Dubois; Nicolas Collin; Neil P King; Dan H Barouch; Darrell J Irvine; J Christopher Love

    doi:10.1101/2021.03.03.433558 Date: 2021-03-04 Source: bioRxiv

    Global containment of COVID-19 MESHD still requires accessible and affordable vaccines for low- and middle-income countries (LMICs). Recently approved vaccines provide needed interventions, albeit at prices that may limit their global access. Subunit vaccines based on recombinant proteins are suited for large-volume microbial manufacturing to yield billions of doses annually, minimizing their manufacturing costs. These types of vaccines are well-established, proven interventions with multiple safe and efficacious commercial examples. Many vaccine candidates of this type for SARS-CoV-2 rely on sequences containing the receptor-binding domain (RBD), which mediates viral entry to cells via ACE2. Here we report an engineered sequence variant of RBD that exhibits high-yield manufacturability, high-affinity binding to ACE2, and enhanced immunogenicity after a single dose in mice compared to the Wuhan-Hu-1 variant used in current vaccines. Antibodies raised against the engineered protein exhibited heterotypic binding to the RBD from two recently reported SARS-CoV-2 variants of concern (501Y.V1/V2). Presentation of the engineered RBD on a designed virus-like particle (VLP) also reduced weight loss MESHD in hamsters upon viral challenge.

    Saliva testing is accurate for early-stage and presymptomatic COVID-19 MESHD

    Authors: Abigail J Johnson; Shannon Zhou; Susan L Hoops; Benjamin Hillmann; Matthew Schomaker; Robyn Kincaid; Jerry Daniel; Kenneth Beckman; Sophia Yohe; Andrew C Nelson

    doi:10.1101/2021.03.03.21252830 Date: 2021-03-04 Source: medRxiv

    Although nasopharyngeal (NP) samples have been considered the gold standard for COVID-19 MESHD testing, variability in viral load across different anatomical sites could theoretically cause NP samples to be less sensitive than saliva or nasal samples in certain cases. Self-collected samples also have logistical advantages over NP samples, making them amenable to population-scale screening. To evaluate sampling alternatives for population screening, we collected NP, saliva, and nasal samples from two cohorts with varied levels and types of symptoms. In a mixed cohort of 60 symptomatic and asymptomatic participants, we found that saliva had 88% concordance with NP when tested in the same testing lab (n = 41), and 68% concordance when tested in different testing labs (n = 19). In a second cohort of 20 participants hospitalized for COVID-19 MESHD, saliva had 74% concordance with NP tested in the same testing lab, but detected virus in two participants that tested negative with NP on the same day. Medical record review showed that the saliva-based testing sensitivity was related to the timing of symptom onset and disease stage. We find that no sample site will be perfectly sensitive for COVID-19 MESHD testing in all situations, and the significance of negative results will always need to be determined in the context of clinical signs and symptoms. Saliva retained high clinical sensitivity while allowing easier collection, minimizing the exposure of healthcare workers and need for personal protective equipment, and making it a viable option for population-scale testing.

    Comparing SARS-CoV-2 case rates between pupils, teachers and the general population: results from Ger-many

    Authors: Clemens Koestner; Stephan Letzel; Viktoria Eggert; Till Beutel; Pavel Dietz

    doi:10.1101/2021.03.04.21252877 Date: 2021-03-04 Source: medRxiv

    Given the inconsistent state of research regarding the role of pupils and teachers during the SARS-CoV-2 pandemic in Germany, statewide and nationwide data of infection case rates were analyzed to contribute to the discourse. Infection data from official sources ranging from mid to late 2020 were collected, prepared and analyzed to answer the question if pupils, teachers and general population differ in infection case rates or not. Statewide and nationwide data showed that pupils and teachers infection MESHD case rates exceeded those of the general population. However, present data do not necessarily indicate that SARS-CoV-2 cases of pupils and teachers infections MESHD took place at schools. Actually, data demonstrate an increase of infection cases after vacation, indicating that infections of pupils and teachers might occur during leisure time and not in the school setting. In conclusion, it seems appropriate to reconsider school-related measures to mitigate the SARS-CoV-2 pandemic.

    Optimization of an LNP-mRNA vaccine candidate targeting SARS-CoV-2 receptor-binding domain

    Authors: Kouji Kobiyama; Masaki Imai; Nao Jounai; Misako Nakayama; Kou Hioki; Kiyoko Iwatsuki-Horimoto; Seiya Yamayoshi; Jun Tsuchida; Takako Niwa; Takashi Suzuki; Mutsumi Ito; Shinya Yamada; Tokiko Watanabe; Maki Kiso; Hideo Negishi; Burcu Temizoz; Hirohito Ishigaki; Yoshinori Kitagawa; Cong Thanh Nguyen; Yasushi Itoh; Fumihiko Takeshita; Yoshihiro Kawaoka; Ken J Ishii

    doi:10.1101/2021.03.04.433852 Date: 2021-03-04 Source: bioRxiv

    In 2020, two mRNA-based vaccines, encoding the full length of severe acute respiratory syndrome coronavirus 2 MESHD ( SARS-CoV-2) spike PROTEIN protein, have been introduced for control of the coronavirus disease MESHD ( COVID-19 MESHD) pandemic1,2. However, reactogenicity, such as fever MESHD, caused by innate immune responses to the vaccine formulation remains to be improved. Here, we optimized a lipid nanoparticle (LNP)-based mRNA vaccine candidate, encoding the SARS-CoV-2 spike PROTEIN protein receptor-binding domain (LNP-mRNA-RBD), which showed improved immunogenicity by removing reactogenic materials from the vaccine formulation and protective potential against SARS-CoV-2 infection MESHD in cynomolgus macaques. LNP-mRNA-RBD induced robust antigen-specific B cells and follicular helper T cells in the BALB/c strain but not in the C57BL/6 strain; the two strains have contrasting abilities to induce type I interferon production by dendritic cells. Removal of reactogenic materials from original synthesized mRNA by HPLC reduced type I interferon (IFN) HGNC production by dendritic cells, which improved immunogenicity. Immunization of cynomolgus macaques with an LNP encapsulating HPLC-purified mRNA induced robust anti-RBD IgG in the plasma and in various mucosal areas, including airways, thereby conferring protection against SARS-CoV-2 infection MESHD. Therefore, fine-tuning the balance between the immunogenic and reactogenic activity of mRNA-based vaccine formulations may offer safer and more efficacious outcomes.

    SARS-CoV-2 variant with higher affinity to ACE2 HGNC shows reduced sera neutralization susceptibility

    Authors: Monique Vogel; Xinyue Chang; Gilles Sousa Augusto; Mona O Mohsen; Daniel E. Speiser; Martin F Bachmann

    doi:10.1101/2021.03.04.433887 Date: 2021-03-04 Source: bioRxiv

    Background: Several new variants of SARS-CoV-2 have emerged since fall 2020 which have multiple mutations in the receptor binding domain (RBD) of the spike protein PROTEIN. Objective: We aimed to assess how mutations in the SARS-CoV-2 RBD affect receptor affinity to angiotensin-converting enzyme 2 ( ACE2 HGNC) and neutralization by anti-RBD serum antibodies. Methods: We produced a SARS-CoV-2 RBD mutant (RBDmut) with key mutations (E484K, K417N, N501Y) from the newly emerged Brazilian variant. Using Biolayer Interferometry, we analyzed the binding of this mutant to ACE2, and the susceptibility to neutralization by sera from vaccinated mice and COVID-19 MESHD convalescent patients. Results: Kinetic profiles showed increased RBDmut - ACE2 HGNC affinity compared to RBDwt, and binding of vaccine-elicited or convalescent sera was significantly reduced. Likewise, both sera types showed significantly reduced ability to block RBDmut - ACE2 HGNC binding indicating that antibodies induced by RBDwt have reduced capability to neutralize mutant virus. Conclusion: Our physiochemical data show enhanced infectivity and reduced neutralization by polyclonal antibodies of the Brazilian variant of SARS-CoV-2.

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MeSH Disease
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SARS-CoV-2 Proteins


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