Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinE (6)

ProteinM (2)

ProteinS (1)


SARS-CoV-2 Proteins
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    SARS-CoV-2 Envelope (E) Protein PROTEIN Interacts with PDZ-Domain-2 of Host Tight Junction Protein ZO1

    Authors: Ariel Shepley-McTaggart; Cari A Sagum; Isabela Oliva; Elizabeth Rybakovsky; Katie DiGuilio; Jingjing Liang; Mark T Bedford; Joel Cassel; Marius Sudol; James M Mullin; Ronald N Harty; Andreas C. W. Jenke; Jan Postberg

    doi:10.1101/2020.12.22.422708 Date: 2020-12-23 Source: bioRxiv

    Newly emerged SARS-CoV-2 is the cause of an ongoing global pandemic leading to severe respiratory disease MESHD in humans. SARS-CoV-2 targets epithelial cells in the respiratory tract and lungs, which can lead to amplified chloride secretion and increased leak across epithelial barriers, contributing to severe pneumonia MESHD and consolidation of the lungs as seen in many COVID-19 MESHD patients. There is an urgent need for a better understanding of the molecular aspects that contribute to SARS-CoV-2-induced pathogenesis and for the development of approaches to mitigate these damaging pathologies. The multifunctional SARS-CoV-2 Envelope (E) protein PROTEIN contributes to virus assembly/egress, and as a membrane protein, also possesses viroporin channel properties that may contribute to epithelial barrier damage, pathogenesis, and disease severity. The extreme C-terminal (ECT) sequence of E also contains a putative PDZ-domain binding motif (PBM), similar to that identified in the E protein PROTEIN of SARS-CoV-1. Here, we screened an array of GST-PDZ domain fusion proteins using either a biotin-labeled WT MESHD or mutant ECT peptide from the SARS-CoV-2 E protein PROTEIN. Notably, we identified a singular specific interaction between the WT E peptide and the second PDZ domain of human Zona Occludens-1 HGNC ( ZO1 HGNC), one of the key regulators of TJ formation/integrity in all epithelial tissues. We used homogenous time resolve fluorescence (HTRF) as a second complementary approach to further validate this novel modular E- ZO1 HGNC interaction. We postulate that SARS-CoV-2 E interacts with ZO1 HGNC in infected epithelial cells, and this interaction may contribute, in part, to tight junction damage and epithelial barrier compromise in these cell layers leading to enhanced virus spread and severe respiratory dysfunction MESHD that leads to morbidity. Prophylactic/therapeutic intervention targeting this virus-host interaction may effectively reduce airway barrier damage and mitigate virus spread.

    Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects

    Authors: Lucas Maldonado Sr.; Laura Kamenetzky

    doi:10.1101/2020.06.23.167072 Date: 2020-06-25 Source: bioRxiv

    In December 2019 rising pneumonia MESHD cases caused by a novel {beta}-coronavirus (SARS-CoV-2) occurred in Wuhan, China, which has rapidly spread worldwide causing thousands of deaths. The WHO declared the SARS-CoV-2 outbreak as a public health emergency of international concern therefore several scientists are dedicated to the study of the new virus. Since human viruses have codon usage biases that match highly expressed proteins in the tissues they infect MESHD and depend on host cell machinery for replication and co-evolution, we selected the genes that are highly expressed in the tissue of human lungs to perform computational studies that permit to compare their molecular features with SARS, SARS-CoV-2 and MERS genes. In our studies, we analysed 91 molecular features for 339 viral genes and 463 human genes that consisted of 677873 codon positions. Hereby, we found that A/T bias in viral genes could propitiate the viral infection MESHD favoured by a host dependant specialization using the host cell machinery of only some genes. The envelope protein E PROTEIN, the membrane glycoprotein M PROTEIN and ORF7 could have been further benefited by a high rate of A/T in the third codon position. Thereby, the mistranslation or de-regulation of protein synthesis could produce collateral effects, as a consequence of viral occupancy of the host translation machinery due tomolecular similarities with viral genes. Furthermore, we provided a list of candidate human genes whose molecular features match those of SARS-CoV-2, SARSand MERS genes, which should be considered to be incorporated into genetic population studies to evaluate thesusceptibility to respiratory viral infections MESHD caused by these viruses. The results presented here, settle the basis for further research in the field of human genetics associated with the new viral infection, COVID-19 MESHD, caused by SARS-CoV-2 and for the development of antiviral preventive methods.

    Lung ultrasound and neonatal COVID-19 MESHD pneumonia: A case report.

    Authors: Daniel Ibarra Ríos; Dina Villanueva García; Edna Patricia Vázquez Solano; Alfonso de Jesús Martínez García; María Yolotzin Valdespino-Vázquez; Addy Cecilia Helguera Repetto; Horacio Márquez González

    doi:10.21203/ Date: 2020-06-02 Source: ResearchSquare

    Introduction: Severe Novel Coronavirus Disease 2019 MESHD ( COVID-19 MESHD) infection in neonates is possible but reports are scarce.  Lung ultrasound (LUS) has been reported useful for triaging, diagnosing, and monitoring of patients with COVID-19 MESHD.Material and methods: We describe SARS-CoV-2 confirmed infection MESHD on a term newborn that developed pneumonia MESHD and pulmonary hypertension MESHD requiring mechanical ventilation. Ultrasonographic follow up of COVID-19 MESHD pneumonia MESHD and pulmonary hypertension MESHD was carried out. Histopathological and genetic study of the placenta was performed. Results: A 3,140-g male infant born at 40.3 weeks’ gestation developed progressive respiratory distress MESHD ( pulmonary hypertension MESHD) requiring mechanical ventilation. Real time PCR respiratory tract swabs for SARS COV 2 sampled on day 3 were positive for the baby and both parents. Lung ultrasound showed an irregular pleural MESHD line (shred sign), multiple confluent B-lines and bilateral ≥ 0.5 cm subpleural consolidations. Improvement of the lung and cardiac conditions were documented by ultrasound. The newborn was supported 6 days with mechanical ventilation, 3 days on CPAP and 3 HGNC days on oxygen. No antibiotics were used. The placenta showed histological findings linked to SARS-CoV-2 infection MESHD. RT-PCR from placental tissue showed amplification of viral E gene PROTEIN.Conclusion: Our case represents a severe presentation of COVID-19 MESHD pneumonia MESHD with pulmonary hypertension MESHD requiring mechanical ventilation. LUS showed to be useful for diagnosis and follow up. Transversal infection was possible. 

    Reduced Vitamin K Status as A Potentially Modifiable Prognostic Risk Factor in COVID-19 MESHD

    Authors: Anton S.M. Dofferhoff; Ianthe Piscaer; Leon J. Schurgers; Jona Walk; Jody M.W. van den Ouweland; Tilman M. Hackeng; Pim A. de Jong; Reinoud Gosens; Petra Lux; Henny van Daal; Cecile Maassen; Esther G.A. Maassen; Loes E.M. Kistemaker; Cees Vermeer; Emiel F.M. Wouters; Rob Janssen

    id:10.20944/preprints202004.0457.v2 Date: 2020-05-29 Source:

    Background: A significant proportion of SARS-CoV-2-infected MESHD patients develops respiratory failure MESHD. Thromboembolism MESHD is also prevalent in coronavirus disease 2019 MESHD ( Covid-19 MESHD). Vitamin K plays a role in coagulation and possibly also in lung diseases MESHD. We therefore hypothesized that vitamin K is implicated in Covid-19 MESHD pathogenesis. Methods: 134 Covid-19 MESHD patients and 184 controls were included. Inactive vitamin K-dependent matrix Gla protein (i.e PROTEIN.dp-ucMGP) and prothrombin (i.e. PIVKA-II) were measured, which are inversely related to respectively extrahepatic and hepatic vitamin K status. Desmosine was measured to quantify elastic fiber degradation. Lung involvement and arterial calcifications severity were assessed by computed tomography. Results Dp-ucMGP was elevated in Covid-19 MESHD patients compared to controls (P=0.001). Higher dp-ucMGP was found in Covid-19 MESHD patients with poor compared to better outcomes (P=0.002). PIVKA-II was normal in 81.8%, mildly elevated in 14.0% and moderately elevated in 4.1% of Covid-19 MESHD patients not using vitamin K antagonists. Dp-ucMGP in Covid-19 MESHD patients was correlated with desmosine (P<0.001), thoracic aortic calcification (P<0.001) but not with pneumonia MESHD severity. Conclusions: Extrahepatic vitamin K status was severely reduced in Covid-19 MESHD patients, as reflected by elevated inactive MGP HGNC, and related to poor outcome. Procoagulant prothrombin activity remained preserved in the majority of Covid-19 MESHD patients, which is compatible with the increased thrombogenicity that is frequently observed in severe Covid-19 MESHD. Impaired MGP HGNC activation was linked to accelerated elastic fiber degradation and premorbid vascular calcifications MESHD. A trial should assess whether increasing MGP HGNC and protein S PROTEIN activity by vitamin K administration improves Covid-19 MESHD outcomes.

    Pooled RNA sample reverse transcriptase real time PCR assay for SARS CoV-2 infection: a reliable, faster and economical method.

    Authors: Ekta Gupta; Abhishek Padhi; Arvind Khodare; Reshu Aggarwal; Krithiga Ramachandran; Vibha Mehta; Mousumi Kilikdar; Shantanu Dubey; Guresh Kumar; Shiv K Sarin

    doi:10.1101/2020.04.25.20079095 Date: 2020-04-29 Source: medRxiv

    Background: Corona virus disease 2019 ( COVID-19 MESHD) which initially started as a cluster of pneumonia MESHD cases in the Wuhan city of China has now become a full blown pandemic. Timely diagnosis of COVID-19 MESHD is the key in containing the pandemic and breaking the chain of In low and middle income countries availability of testing kits has become the major bottle neck in testing. Novel methods like pooling of samples are the need of the hour. Method: Extracted RNA samples were randomly placed in pools of 8 on a 96 well plate. Both individual RNA (ID) and pooled RNA RT-qPCR for the screening E gene PROTEIN were done in the same plate and the positivity for the E gene PROTEIN was seen. Results: The present study demonstrated that pool testing with 8 RNA samples can easily detect even up to a single positive sample with Ct value as high as 38. The present study also showed that the results of pool testing is not affected by number of positive samples in a pool. Conclusion: Pooling of 8 RNA samples can reduce the time and expense by one eighth, and can help expand diagnostic capabilities, especially during constrained supply of reagents and PCR kits for the diagnosis of SARS-CoV-2 infection MESHD.

    Structural modeling and conserved epitopes prediction against SARS-COV-2 structural proteins for vaccine development

    Authors: Muhammad Tahir ul Qamar; Farah Shahid; Usman Ali Ashfaq; Sidra Aslam; Israr Fatima; Muhammad Mazhar Fareed; Ali Zohaib; Ling-Ling Chen

    doi:10.21203/rs.2.23973/v1 Date: 2020-02-18 Source: ResearchSquare

    Background: Coronavirus disease 2019 MESHD ( COVID-19 MESHD) caused by Severe Acute Respiratory Syndrome MESHD Corona virus 2 (SARS-COV-2) was first diagnosed in December 2019, Wuhan, China. Little is known about this new virus and it has the potential to cause severe illness and pneumonia MESHD in some people, therefore the development of an effective vaccine is highly desired.Methods: Immunoinformatics and statistical approaches were used in this study to forecast B- and T- cell epitopes for the SARS-COV-2 structural proteins (Surface glycoprotein, Envelope protein PROTEIN Envelope protein HGNC, and Membrane glycoprotein PROTEIN) that may play a key role in eliciting immune response against COVID-19 MESHD. Different types of B cell epitopes (linear as well as discontinuous) and T cell (MHC class I and MHC class II) were determined. Moreover, their antigenicity and allergenicity were also estimated.Results: The antigenic B-cell epitopes exposed to the outer surface were screened out and 23 linear B cell epitopes were selected. “SPTKLNDLCFTNVY” had the highest antigenicity score among B cell epitopes. The T-cell epitopes bound to multiple alleles, antigenic, non-allergen, non-toxic, and conserved in the protein sequence were shortlisted. In total, 16 epitopes (9 from MHC class I and 7 from MHC class II) were selected. Among the T-cell epitopes, MHC class I (IPFAMQMAYRFN) and MHC class II (VTLACFVLAAVYRIN) were classified as strongly antigenic. Digestion analysis verified the safety and stability of the peptides predicted during this study. Furthermore, docking analyses of predicted peptides showed significant interactions with the HLA-B7 allele.Conclusion: The putative antigen epitopes identified in this study may serve as vaccine candidates and can help to eliminate/control growing health threat of COVID-19 MESHD.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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