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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (654)

ProteinN (149)

NSP5 (75)

ComplexRdRp (46)

ProteinE (43)


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SARS-CoV-2 Proteins
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    Reliable assessment of in vitro SARS-CoV-2 infectivity MESHD by a Rapid Antigen Detection Test

    Authors: Michael Korenkov; Nareshkumar Poopalasingam; Matthias Madler; Kanika Vanshylla; Ralf Eggeling; Maike Wirtz; Irina Fish; Felix Dewald; Lutz Gieselmann; Clara Lehmann; Gerd Faetkenheuer; Henning Gruell; Nico Pfeifer; Eva Heger; Florian Klein

    doi:10.1101/2021.03.30.21254624 Date: 2021-04-06 Source: medRxiv

    The identification and isolation of highly infectious SARS-CoV-2-infected MESHD individuals is an important public health strategy. Rapid antigen detection tests (RADT) are promising candidates for large-scale screenings due to timely results and feasibility for on-site testing. Nonetheless, the diagnostic performance of RADT in detecting infectious individuals is yet to be fully determined. Two combined oro- and nasopharyngeal swabs were collected from individuals at a routine SARS-CoV-2 diagnostic center. Side-by-side evaluations of RT-qPCR and RADT as well as live virus cultures of positive samples were performed to determine the sensitivity of the Standard Q COVID-19 MESHD Ag Test (SD Biosensor/Roche) in detecting SARS-CoV-2-infected MESHD individuals with cultivable virus. A total of 2,028 samples were tested and 118 virus cultures inoculated. SARS-CoV-2 infection MESHD was detected in 210 samples by RT-qPCR, representing a positive rate of 10.36%. The Standard Q COVID-19 MESHD Ag Test yielded a positive result in 92 (4.54%) samples resulting in an overall sensitivity and specificity of 42.86% and 99.89%. For adjusted Ct values <20, <25, and <30 the RADT reached sensitivities of 100%, 98.15%, and 88.64%, respectively. All 29 culture positive samples were detected by RADT. While overall sensitivity was low, Standard Q COVID-19 MESHD RADT reliably detected patients with high RNA loads. Additionally, negative RADT results fully corresponded with the lack of viral cultivability in Vero E6 cells. These results indicate that RADT can be a valuable tool for the detection of individuals that are likely to transmit SARS-CoV-2. RADT testing could therefore guide public health testing strategies to combat the COVID-19 pandemic MESHD.

    Statins Are Associated with Improved 28-day Mortality in Patients Hospitalized with SARS-CoV-2 Infection MESHD

    Authors: Zoe N Memel; Jenny J Lee; Andrea S Foulkes; Raymond T Chung; Tanayott Thaweethai; Patricia P Bloom

    doi:10.1101/2021.03.27.21254373 Date: 2021-04-06 Source: medRxiv

    Background: Statins may be protective in viral infection and have been proposed as treatment in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection MESHD. Objective: We evaluated the effect of statins on mortality in four groups hospitalized with ( SARS-CoV-2) infection MESHD (continued statin, newly initiated statin, discontinued statin, never on statin). Design: In a single center cohort study of 1179 patients hospitalized with SARS-CoV-2 infection MESHD, the outcome of death MESHD, Intensive Care Unit (ICU) admission or hospital discharge was evaluated. Patients statin use, laboratory data, and co-morbidities were determined via chart review and electronic health records. Using marginal structural models to account for timing of statin initiation and competing risks, we compared the likelihood of severe outcomes in the four statin exposure groups. Setting: Academic medical center in the United States Participants: Patients hospitalized with SARS-CoV-2 infection MESHD Measurements: 28-day mortality, ICU admission, or discharge Results: Among 1179 patients, 360 were never on a statin, 311 were newly initiated on a statin, 466 were continued on a statin, and 42 had a statin discontinued. In this cohort, 154 (13.1%) patients died by 28-days. With marginal structural model analysis, statin use reduced the hazard of 28-day mortality (HR 0.566 [CI 0.372, 0.862], p = 0.008). Both new initiation of statins (HR 0.493 [CI 0.253, 0.963], p=0.038) and continuing statin therapy reduced the hazard of 28-day mortality (HR 0.270 [CI 0.114, 0.637], p=0.003). Sensitivity analysis found that statin use was associated with improved mortality for patients > 65 years, but not for patients 65 years or younger. Limitation: Observational design Conclusion: Statin therapy during hospitalization for SARS-CoV-2 infection MESHD, including new initiation and continuation of therapy, was associated with reduced short-term mortality.

    Detection of SARS-CoV-2 antibodies formed in response to the BNT162b2 and mRNA-1237 mRNA vaccine by commercial antibody tests

    Authors: Jamil N Kanji; Ashley Bailey; Jayne Fenton; Sean H. Ling; Rafael Rivera; Sabrina Plitt; Wendy I Sligl; Sean C Taylor; LeeANn Turnbull; Graham Tipples; Carmen L Charlton

    doi:10.1101/2021.03.30.21254604 Date: 2021-04-06 Source: medRxiv

    PURPOSE With rapid approval of SARS-CoV-2 vaccines, the ability of clinical laboratories to detect vaccine-induced antibodies with available high-throughput commercial assays is unknown. We aimed to determine if commercial serology assays can detect vaccine-induced antibodies (VIAs) and understand the vaccination response. METHODS This cohort study recruited healthcare workers and residents of long-term care facilities (receiving the BNT162b2 and mRNA-1273 products, respectively) who underwent serum collection pre-vaccination (BNT162b2 group), 2-weeks post vaccination (both groups), and pre-2nd dose (both groups). Sera were tested for the presence of SARS-CoV-2 IgG using four commercial assays ( Abbott Architect SARS-CoV-2 IgG, Abbott Architect SARS-CoV-2 MESHD IgG II Quant, DiaSorin Liaison Trimeric S IgG MESHD, and GenScript cPASS) to detect VIAs. Secondary outcomes included description of post-vaccination antibody response and correlation with neutralising titers. RESULTS 225 participants (177 receiving BNT162b2 and 48 receiving mRNA-1273) were included (median age 41 years,; 66-78% female). Nucleocapsid IgG was found in 4.1% and 21.9% of the BNT162b2 (baseline) and mRNA-1273 (2-weeks post first dose). All anti-spike assays detected antibodies post-vaccination, with an average increase of 87.2% (range 73.8-94.3%; BNT162b2), and 25.2% (range 23.8-26.7%; mRNA-1273) between the first and last sampling time points (all p<0.05). Neutralising antibodies were detected at all post-vaccine timepoints for both vaccine arms, with increasing titers over time (all p<0.05). CONCLUSION Anti-spike vaccine-induced SARS-CoV-2 IgG are detectable by commercially available high-throughput assays and increases over time. Prior to second dose of vaccination, neutralising antibodies are detectable in 73-89% of individuals, suggesting the majority of individuals would have some degree of protection from subsequent infection.

    Efficient Maternal to Neonatal transfer of SARS-CoV-2 and BNT162b2 antibodies

    Authors: Ofer Beharier; Romina Plitman Mayo; Tal Raz; Kira Nahum Sacks; Letizia Schreiber; Yael Suissa-Cohen; Rony Chen; Rachel Gomez-Tolub; Eran Hadar; Rinat Gabbay-Benziv; Yuval Jaffe Moshkovich; Tal Biron-Shental; Gil Shechter-Maor; Sivan Farladansky-Gershnabel; Hen Yitzhak Sela; Hedi Benyamini-Raischer; Nitzan D Sela; Debra Goldman-Wohl; Ziv Shulman; Ariel Many; Haim Barr; Simcha Yagel; Michal Neeman; Michal Kovo

    doi:10.1101/2021.03.31.21254674 Date: 2021-04-06 Source: medRxiv

    Background: The significant risks posed to mothers and fetuses by COVID-19 MESHD in pregnancy have sparked a worldwide debate surrounding the pros and cons of antenatal SARS-CoV-2 inoculation, as we lack sufficient evidence regarding vaccine effectiveness in pregnant women and their offspring. We aimed to provide substantial evidence for the effect of BNT162b2 mRNA vaccine versus native infection on maternal humoral, as well as transplacentally acquired fetal immune response, potentially providing newborn protection. Methods: A multicenter study where parturients presenting for delivery were recruited at 8 medical centers across Israel and assigned to three study groups: vaccinated (n=86); PCR confirmed SARS-CoV-2 infected MESHD during pregnancy (n=65), and unvaccinated non-infected controls (n=62). Maternal and fetal blood samples were collected from parturients prior to delivery and from the umbilical cord following delivery, respectively. Sera IgG and IgM titers were measured using Milliplex MAP SARS-CoV-2 Antigen Panel (for S1, S2, RBD and N). Results: BNT162b2 mRNA vaccine elicits strong maternal humoral IgG response (Anti-S and RBD) that crosses the placenta barrier and approaches maternal titers in the fetus within 15 days following the first dose. Maternal to neonatal anti- COVID-19 MESHD antibodies ratio did not differ when comparing sensitization (vaccine vs. infection). IgG transfer rate was significantly lower for third-trimester as compared to second trimester infection. Lastly, fetal IgM response was detected in 5 neonates, all in the infected group. Conclusions: Antenatal BNT162b2 mRNA vaccination induces a robust maternal humoral response that effectively transfers to the fetus, supporting the role of vaccination during pregnancy.

    First-in-Human Trial of a Recombinant Stabilized Prefusion SARS-CoV-2 Spike MESHD SARS-CoV-2 Spike PROTEIN Protein Vaccine with Adjuvant of Aluminum Hydroxide and CpG 1018

    Authors: Szu-Min Hsieh; Wang-Da Liu; Yu-Shan Huang; Yi-Jiun Lin; Erh-Fang Hsieh; Wei-Cheng Lian; Charles Chen; I-Chen Tai; Shan-Chwen Chang

    doi:10.1101/2021.03.31.21254668 Date: 2021-04-06 Source: medRxiv

    Design This is a phase 1, dose-escalation open-label trial to evaluate the safety and immunogenicity of MVC-COV1901, a recombinant stabilized prefusion SARS-CoV-2 spike PROTEIN ( S-2P HGNC) protein vaccine with adjuvant of aluminum hydroxide and CpG 1018. Methods We enrolled 45 healthy adults from 20 to 49 years of age to be administered with two vaccinations of MVC-COV1901 in a low dose (LD), middle dose (MD), and high dose ( HD MESHD) of spike protein PROTEIN at 28 days apart. There were 15 participants in each dose group, and all of them were followed up for 28 days after the second vaccination at the time of interim analysis. Adverse events (AEs) and laboratory data were recorded for safety evaluation. Blood samples were collected for wild-type SARS-CoV-2 and pseudovirus neutralization assays as well as SARS-CoV-2 spike PROTEIN-specific immunoglobulin G (IgG) at various times. Overall, the study duration will be 7 months. Results Solicited events were mostly mild and similar in the participants of all three dose groups. No subject experienced fever MESHD. There were no serious nor adverse events of special interest at the time point of this interim report. After the second vaccination, the SARS-CoV-2 spike PROTEIN specific IgG titers increased with peak geometric mean titers at 7178.245 (LD), 7746.086 (MD), and 11220.58 ( HD MESHD), respectively. Serum neutralizing activity was detected by two methods in all participants of MD MESHD and HD MESHD groups, with geometric mean values generally comparable to those of a panel of control convalescent serum specimens. All of the participants in the MD MESHD and HD MESHD groups were seroconverted after the second vaccination. Conclusions The MVC-COV1901 vaccine is safe and elicits remarkable immune responses especially in the MD MESHD and HD MESHD groups.

    The association of ABO blood group HGNC with the asymptomatic COVID-19 MESHD cases in India

    Authors: Prajjval Pratap Singh; Abhishek K Srivastava; Sudhir K Upadhyay; Ashish Singh; Pranav Gupta; Sanjeev Maurya; Shashank Upadhyay; Rudra K Pandey; Anshika Shrivastava; Priya Dev; Vanya Singh; Rahul Mishra; Manoj K Shukla; Govind Chaubey; Pradeep Kumar; Vandana Rai; Yamini B Tripathy; Abhishek Pathak; Vijaya N Mishra; Chandana Basu Mallick; Panjak Shrivastava; Gyaneshwer Chaubey

    doi:10.1101/2021.04.01.21254681 Date: 2021-04-06 Source: medRxiv

    The COVID-19 pandemic MESHD has resulted several waves of infection in many countries worldwide. The large variations in case fatality ratio among different geographical regions suggests that the human susceptibility against this virus varies substantially. Several studies from different parts of the world showed a significant association of ABO blood group HGNC and COVID-19 MESHD susceptibility. It was shown that individuals with blood group O are at the lower risk of coronavirus infection MESHD. To establish the association of ABO blood group HGNC in SARS-CoV-2 susceptibility, we for the first time analysed SARS-CoV-2 neutralising antibodies as well as blood groups among 509 random individuals from three major districts of Eastern Uttar Pradesh region of India. . Interestingly, we found neutralising antibodies in significantly higher percentage of people with blood group AB (0.36) followed by B (0.31), A (0.22) and lowest in people with blood group O (0.11). This indicates that people with blood group AB are at comparatively higher risk of infection than other blood groups. Further, in line to previous reports we too observed that people with blood group O have significantly decreased risk of SARS-CoV-2 infection MESHD. Thus, among the asymptomatic SARS-CoV-2 infected MESHD individuals with blood group AB has highest, whilst blood group O has lowest risk of infection.

    Wide application of minimally processed saliva on multiple RT-PCR kits for SARS-CoV-2 detection in Indonesia

    Authors: Caroline Mahendra; Maria M. M. Kaisar; Suraj R. Vasandani; Sem Samuel Surja; Enty Tjoa; Febie Chriestya; Kathleen Irena Junusmin; Tria A. Widowati; Astrid Irwanto; Soegianto Ali

    doi:10.1101/2021.04.01.21254743 Date: 2021-04-06 Source: medRxiv

    Saliva as a sample matrix has been an attractive alternative for the detection of SARS-CoV-2. However, due to potential variability in collection and processing steps, it is recommended to evaluate a proposed workflow amongst the local population. Here, we aim to validate collection and treatment of human saliva as a direct specimen for RT-qPCR based detection of SARS-CoV-2 in Indonesia MESHD. We demonstrated that SARS-CoV-2 target genes were detected in saliva specimen and remained stable for five days refrigerated or room temperature storage. The method of processing saliva specimen described in this report is free from RNA-extraction step, thereby reduces cost, time, and manpower required for processing samples. The developed method was validated for use on three COVID-19 MESHD RT-PCR kits commercially available. Our developed method achieved 85% agreement rate when compared to paired nasopharyngeal and oropharyngeal swab specimens (NPOP). With the assistance of a specimen sampling device, QuickSpit(TM), collection was found to be more convenient for individuals and improved agreement rate to 90%.

    ADNKA overcomes SARS-CoV2-mediated NK cell inhibition through non-spike antibodies

    Authors: Ceri A Fielding; Pragati Sabberwal; James C Williamson; Edward JD Greenwood; Edward Crozier; Wioleta Zelek; Jeffrey Seow; Carl Graham; Isabella Huettner; Jonathan Edgeworth; Brian Paul Morgan; Kristin Ladell; Matthias Eberl; Ian R Humphreys; Blair Merrick; Sam J Wilson; Paul J Lehner; Edward Wang; Richard J Stanton

    doi:10.1101/2021.04.06.438630 Date: 2021-04-06 Source: bioRxiv

    SARS-CoV-2 antagonises the cellular interferon response, but whether the virus manipulates cellular immunity is unclear. An unbiased proteomic approach to determine how cell surface protein expression is altered on SARS-CoV-2-infected MESHD lung epithelial cells showed downregulation of activating NK cell ligands: B7-H6 HGNC, MICA HGNC, ULBP2 HGNC, and Nectin1 HGNC, but no effect on surface MHC-I expression. NK ligand downregulation correlated with a reduction in NK cell activation by infected cells, and was overcome by antibody-dependent NK cell activation (ADNKA). Depletion of spike-specific antibodies confirmed their dominant role in virus neutralisation, but these antibodies played only a minor role in ADNKA compared to antibodies to other viral proteins, including ORF3a PROTEIN, Membrane, and Nucleocapsid. In contrast, ADNKA induced following vaccination was focussed solely on spike, was weaker than ADNKA following natural infection, and was not boosted by the second dose. These insights have important implications for understanding disease progression, vaccine efficacy, and vaccine design.

    Altered O-glycosylation Level of SARS-CoV-2 Spike MESHD SARS-CoV-2 Spike PROTEIN Protein by Host O-glycosyltransferase Strengthens Its Trimeric Structure

    Authors: Zhijue Xu; Xin Ku; Jiaqi Tian; Han Zhang; Jingli Hou; Can Zhang; Jingjing Shi; Yang Li; Hiroyuki Kaji; Sheng-ce Tao; Atsushi Kuno; Wei Yan; Lin-Tai Da; Yan Zhang

    doi:10.1101/2021.04.06.438614 Date: 2021-04-06 Source: bioRxiv

    The trimeric spike protein (S PROTEIN) mediates host-cell entry and membrane fusion of SARS-CoV-2. S protein PROTEIN is highly glycosylated, whereas its O-glycosylation is still poorly understood. Herein, we site-specifically examine the O-glycosylation of S protein PROTEIN through a mass spectrometric approach with HCD MESHD-triggered-ETD model. We identify 15 high-confidence O-glycosites and at least 10 distinct O-glycan structures on S protein PROTEIN. Peptide microarray assays prove that human ppGalNAc-T6 actively participates in O-glycosylation of S protein PROTEIN. Importantly, the upregulation of ppGalNAc-T6 expression can profoundly enhance the O-glycosylation level by generating new O-glycosites and increasing both O-glycan heterogeneity and intensities. Further molecular dynamics simulations reveal that the O-glycosylation on the protomer-interface regions, which are mainly modified by ppGalNAc-T6, can potentially stabilize the trimeric S protein PROTEIN structure. Our work provides deep molecular insights of how viral infection harnesses the host O-glycosyltransferases MESHD to dynamically regulate the O-glycosylation level of the viral envelope protein PROTEIN responsible for membrane fusion.

    T-cell responses as a correlate of COVID-19 MESHD vaccination. A pilot study in Health Care Workers.

    Authors: Monica Martinez-Gallo; Juliana Esperalba-Ezquerra; Ricardo Pujol-Borrell; Victor Sanda; Iria Arrese-Munoz; Candela Fernandez-Naval; Andres Anton-Pagarolas; Victoria Cardona; Moises Labrador-Horrillo; Tomas Pumarola-Sune; Manuel Hernandez-Gonzalez

    doi:10.1101/2021.03.31.21254472 Date: 2021-04-05 Source: medRxiv

    Background: Clinical trials on the different vaccines to SARS-CoV-2 have demonstrated protection efficacy, but it is urgent to assess the levels of protection generated with real-world data, especially in individuals professionally exposed. Measuring T-cell responses may complement antibody tests currently in use as correlates of protection but there are not validated T-cell responses applicable to large number of samples. Objective: To assess the feasibility of using T-cell responses to SARS-CoV-2 S MESHD peptides by commercially available whole blood interferon-gamma HGNC release assays (IGRA) as a correlate of protection. Patients: Twenty health care workers before and after vaccination. Methods: Antibody test to SARS-CoV-2 N MESHD and S proteins PROTEIN in parallel with one IGRA assay and two detection techniques than can be automated. Results: IGRA test detected T-cell responses in naturally exposed and vaccinated HCW already after first vaccination dose. the correlation by the two detection methods, CLIA and ELISA, very high (R>0.9) and sensitivity and specificity ranged between 100 and 86% and 100-73% respectively. Even though there was a very high concordance between antibody and the IGRA assay in the ability to detect immune response to SARS-CoV-2 there was a relatively low quantitative correlation. In the small group primed by natural infection, one vaccine dose was sufficient to reach immune response plateau. IGRA was positive in one Ig (S) antibody negative vaccinated immunosuppressed HCW illustrating another advantage of the IGRA test. Conclusion: Whole blood IGRA tests amenable to automation, as the one here reported, constitute a promising additional tool for measuring the state of the immune response to SARS-CoV-2; they are applicable to large number of samples and may become valuable correlates of protection to COVID-19 MESHD, particularly for vulnerable groups at risk of being re-exposed to infection, as are health care workers.

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MeSH Disease
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SARS-CoV-2 Proteins


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