Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinE (144)

ProteinS (39)

ProteinN (33)

ComplexRdRp (17)

ProteinM (17)


SARS-CoV-2 Proteins
    displaying 21 - 30 records in total 144
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    Host PDZ-containing proteins targeted by SARS-Cov-2

    Authors: Celia Caillet-Saguy; Fabien Durbesson; Veronica V. REZELJ; Gergo Gogl; Quang Dinh Tran; Jean-Claude Twizere; Marco Vignuzzi; Renaud Vincentelli; Nicolas Wolff; Rahaf Alharbi; Mazen Hassanain; Anwar M Hashem; Eugene B. Chang; Glenn Randall; Pablo Penaloza-MacMaster; Bozhi Tian; Maria Lucia Madariaga; Jun Huang; Dirk Jochmans; Birgit Weynand; Johan Neyts

    doi:10.1101/2021.02.01.429176 Date: 2021-02-01 Source: bioRxiv

    Small linear motif targeting protein interacting domains called PDZ have been identified at the C-terminus of the severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) proteins E PROTEIN, 3a, and N. Using a high-throughput approach of affinity-profiling against the full human PDZome, we identified sixteen human PDZ binders of SARS-CoV-2 proteins E PROTEIN, 3A and N showing significant interactions with dissociation constants values ranging from 3 M to 82 M. Six of them ( TJP1 HGNC, PTPN13 HGNC, HTRA1 HGNC, PARD3 HGNC, MLLT4 HGNC, LNX2 HGNC) are also recognized by SARS-CoV while three ( NHERF1 HGNC, MAST2 HGNC, RADIL HGNC) are specific to SARS-CoV-2 E protein PROTEIN. Most of these SARS-CoV-2 protein partners are involved in cellular junctions/polarity and could be also linked to evasion mechanisms of the immune responses during viral infection MESHD. Seven of the PDZ-containing proteins among binders of the SARS-CoV-2 proteins E PROTEIN, 3a or N affect significantly viral replication under knock-down gene expression in infected cells. This PDZ profiling identifying human proteins potentially targeted by SARS-CoV-2 can help to understand the multifactorial severity of COVID19 MESHD and to conceive effective anti-coronaviral agents for therapeutic purposes.

    Expression of human ACE2 HGNC N-terminal domain, part of the receptor for SARS-CoV-2, in fusion with maltose binding protein, E PROTEIN. coli ribonuclease I and human RNase A

    Authors: Shuang-yong Xu; Alexey Fomenkov; Tien-Hao Chen; Erbay Yigit; Yinhui Lu; Karl E Kadler

    doi:10.1101/2021.01.31.429007 Date: 2021-02-01 Source: bioRxiv

    The SARS-CoV-2 viral genome contains a positive-strand single-stranded RNA of ~30 kb. Human ACE2 HGNC protein is the receptor for SARS-CoV-2 virus attachment MESHD and initiation of infection MESHD. We propose to use ribonucleases (RNases) as antiviral agents to destroy the viral genome in vitro. In the virions the RNA is protected by viral capsid proteins, membrane proteins and nucleocapsid PROTEIN proteins. To overcome this protection we set out to construct RNase fusion with human ACE2 HGNC receptor N-terminal domain (ACE2NTD). We constructed six proteins expressed in E. coli cells: 1) MBP-ACE2NTD, 2) ACE2NTD-GFP, 3) RNase I (6xHis), 4) RNase III (6xHis), 5) RNase I-ACE2NTD (6xHis), and 6) human RNase A HGNC-ACE2NTD150 (6xHis). We evaluated fusion expression in different E. coli strains, partially purified MBP-ACE2NTD protein from the soluble fraction of bacterial cell lysate, and refolded MBP-ACE2NTD protein from inclusion body. The engineered RNase I-ACE2NTD (6xHis) and hRNase A-ACE2NTD (6xHis) fusions are active in cleaving COVID-19 MESHD RNA in vitro. The recombinant RNase I (6xHis) and RNase III (6xHis) are active in cleaving RNA and dsRNA in test tube. This study provides a proof-of-concept for construction of fusion protein between human cell receptor and nuclease that may be used to degrade viral nucleic acids in our environment.

    BRD2 HGNC inhibition blocks SARS-CoV-2 infection MESHD in vitro by reducing transcription of the host cell receptor ACE2

    Authors: Ruilin Tian; Avi J Samelson; Veronica V Rezelj; Merissa Chen; Gokul N Ramadoss; Xiaoyan Guo; Alice Mac Kain; Quang Dinh Tran; Shion A Lim; Irene Lui; James Nunez; Sarah J Rockwood; Na Liu; Jared Carlson-Stevermer; Jennifer Oki; Travis Maures; Kevin Holden; Jonathan S Weissman; James A Wells; Bruce Conklin; Marco Vignuzzi; Martin Kampmann; Roshni Patel; Juan P Dizon; Irina Shimeliovich; Anna Gazumyan; Marina Caskey; Pamela J Bjorkman; Rafael Casellas; Theodora Hatziioannou; Paul D Bieniasz; Michel C Nussenzweig

    doi:10.1101/2021.01.19.427194 Date: 2021-01-19 Source: bioRxiv

    SARS-CoV-2 infection MESHD of human cells is initiated by the binding of the viral Spike protein PROTEIN to its cell-surface receptor ACE2 HGNC. We conducted an unbiased CRISPRi screen to uncover druggable pathways controlling Spike protein PROTEIN binding to human cells. We found that the protein BRD2 HGNC is an essential node in the cellular response to SARS-CoV-2 infection MESHD. BRD2 HGNC is required for ACE2 HGNC transcription in human lung epithelial cells and cardiomyocytes, and BRD2 HGNC inhibitors currently evaluated in clinical trials potently block endogenous ACE2 HGNC expression and SARS-CoV-2 infection MESHD of human cells. BRD2 HGNC also controls transcription of several other genes induced upon SARS-CoV-2 infection MESHD, including the interferon response, which in turn regulates ACE2 HGNC levels. It is possible that the previously reported interaction between the viral E protein PROTEIN and BRD2 HGNC evolved to manipulate the transcriptional host response during SARS-CoV-2 infection MESHD. Together, our results pinpoint BRD2 HGNC as a potent and essential regulator of the host response to SARS-CoV-2 infection MESHD and highlight the potential of BRD2 HGNC as a novel therapeutic target for COVID-19 MESHD.

    Ultrasensitive RNA biosensors for SARS-CoV-2 detection in a simple color and luminescence assay

    Authors: Anirudh Chakravarthy; Anirudh K N; Geen George; Shyamsundar Ranganathan; Nishan Shettigar; Suchitta U; Dasaradhi Palakodeti; Akash Gulyani; Arati Ramesh

    doi:10.1101/2021.01.08.21249426 Date: 2021-01-08 Source: medRxiv

    The COVID-19 pandemic MESHD underlines the need for versatile diagnostic strategies. Here, we have designed and developed toehold RNA-based sensors for direct and ultrasensitive SARS-CoV-2 RNA detection. In our assay, isothermal amplification of a fragment of SARS-CoV-2 RNA coupled with activation of our biosensors leads to a conformational switch in the sensor. This leads to translation of a reporter- protein e PROTEIN.g. LacZ or Nano-lantern that is easily detected using color/luminescence. This response can be visualized by the human eye, or a simple cell phone camera as well as quantified using a spectrophotometer/luminometer. By optimizing RNA-amplification and biosensor-design, we have generated a highly-sensitive diagnostic assay; with sensitivity down to attomolar (100 copies of) SARS-CoV-2 RNA. Finally, this PHAsed NASBA-Translation Optical Method (PHANTOM) efficiently detects the presence of viral RNA in human patient samples, with clear distinction from samples designated negative for the virus. The biosensor response correlates well with Ct values from RT-qPCR tests and thus presents a powerful and easily accessible strategy for detecting Covid infection.

    Sequencing of SARS CoV2 in local transmission cases through oxford nanopore MinION platform from Karachi Pakistan

    Authors: Samina Naz Mukry; Shariq Ahmed; Ali Raza Bukhari; Aneeta Shahni; Gul Sufaida; Arshi Naz; Tahir Sultan Shamsi; Vineet D Menachery; Scott D Weaver; Philip R Dormitzer; Pei-Yong Shi

    doi:10.1101/2021.01.07.425705 Date: 2021-01-07 Source: bioRxiv

    The first case of severe acute respiratory syndrome MESHD 2 (SARS CoV2) was imported to Pakistan in February 2020 since then 10,258 deaths have been witnessed. The virus has been mutating and local transmission cases from different countries vary due to host dependent viral adaptation. Many distinct clusters of variant SARS CoV2 have been defined globally. In this study, the epidemiology of SARS CoV2 was studied and locally transmitted SARS CoV2 isolates from Karachi were sequenced to compared and identify any possible variants.The real time PCR was performed on nasopharyngeal specimen to confirm SARSCoV2 with Orf 1ab and E gene PROTEIN as targets. The viral sequencing was performed through oxford nanopore technology MinION platform. Isolates from first and second wave of COVID-19 MESHD outbreak in Karachi were compared. The overall positivity rate for PCR was 26.24% with highest number of positive cases in June. Approximately, 37.45% PCR positive subjects aged between 19-40 years. All the isolates belonged to GH clade and shared missense mutation D614G in spike protein PROTEIN linked to increased transmission rate worldwide. Another spike protein PROTEIN mutation A222V coexisted with D614G in the virus from second wave of COVID-19 MESHD. Based on the present findings it is suggested that the locally transmitted virus from Karachi vary from those reported from other parts of Pakistan. Slight variability was also observed between viruses from first and second wave. Variability in any potential vaccine target may result in failed trials therefore information on any local viral variants is always useful for effective vaccine design and/or selection. Authors summaryDespite precautionary measures the COVID-19 pandemic MESHD is causing deaths all over the world. The continuous mutations in viral genome is making it difficult to design vaccines. Variability in genome is host dependent and data sharing has revealed that variant for different geographical locations may harbor different mutations. Keeping this in mind the current study was focused on the epidemiology of SARS CoV2 in symptomatic and asymptomatic COVID -19 suspected cases with impact of age and gender. The locally transmitted SARS CoV2 isolates from Karachi were sequenced to compared and identify any possible variants. The sequenced viral genome varied from the already submitted sequences from Pakistan thereby confirming that slightly different viruses were causing infections during different time periods in Karachi. All belonged to GH clade with D614G, P323L and Q57H mutations. The virus from second wave had A222V mutation making it more different. This information can be useful in selecting or designing a vaccine.

    Structure-function investigation of a new VUI-202012/01 SARS-CoV-2 variant

    Authors: Jasdeep Singh; Nasreen Z Ehtesham; Syed Asad Rahman; Yakob G. Tsegay; Daniel S. Abebe; Mesay G. Edo; Endalkachew H. Maru; Wuletaw C. Zewde; Lydia K. Naylor; Dejen F. Semane; Menayit T. Deresse; Bereket B. Tezera; Lovisa Skoglund; Jamil Yousef; Elisa Pin; Wanda Christ; Mikaela Olausson; My Hedhammar; Hanna Tegel; Sara Mangsbo; Mia Phillipson; Anna Manberg; Sophia Hober; Peter Nilsson; Charlotte Thalin; Samuel Bates; Chevaun Morrison-Smith; Benjamin Nicholson; Edmond Wong; Leena El-Mufti; Michael Kann; Anna Bolling; Brooke Fortin; Hayden Ventresca; Wen Zhou; Santiago Pardo; Megan Kwock; Aditi Hazra; Leo Cheng; Rushdy Ahmad; James A. Toombs; Rebecca Larson; Haley Pleskow; Nell Meosky Luo; Christina Samaha; Unnati M. Pandya; Pushpamali De Silva; Sally Zhou; Zakary Ganhadeiro; Sara Yohannes; Rakiesha Gay; Jacqueline Slavik; Shibani S. Mukerji; Petr Jarolim; David R. Walt; Becky C. Carlyle; Lauren L. Ritterhouse; Sara Suliman

    doi:10.1101/2021.01.01.425028 Date: 2021-01-04 Source: bioRxiv

    The SARS-CoV-2 (Severe Acute Respiratory Syndrome-Coronavirus MESHD) has accumulated multiple mutations during its global circulation. Recently, a new strain of SARS-CoV-2 (VUI 202012/01) had been identified leading to sudden spike in COVID-19 MESHD cases in South-East England. The strain has accumulated 23 mutations which have been linked to its immune evasion and higher transmission capabilities. Here, we have highlighted structural-function impact of crucial mutations occurring in spike (S), ORF8 PROTEIN and nucleocapsid (N) protein PROTEIN of SARS-CoV-2. Some of these mutations might confer higher fitness to SARS-CoV-2 MESHD. SummarySince initial outbreak of COVID-19 MESHD in Wuhan city of central China, its causative agent; SARS-CoV-2 virus has claimed more than 1.7 million lives out of 77 million populations and still counting. As a result of global research efforts involving public-private-partnerships, more than 0.2 million complete genome sequences have been made available through Global Initiative on Sharing All Influenza Data (GISAID). Similar to previously characterized coronaviruses (CoVs), the positive-sense single-stranded RNA SARS-CoV-2 genome codes for ORF1ab PROTEIN non-structural proteins (nsp(s)) followed by ten or more structural/nsps [1, 2]. The structural proteins include crucial spike (S), nucleocapsid (N PROTEIN), membrane (M), and envelope (E) proteins PROTEIN. The S protein PROTEIN mediates initial contacts with human hosts while the E and M proteins PROTEIN function in viral assembly and budding. In recent reports on evolution of SARS-CoV-2, three lineage defining non-synonymous mutations; namely D614G in S protein PROTEIN (Clade G), G251V in ORF3a PROTEIN (Clade V) and L84S in ORF 8 (Clade S) were observed [2-4]. The latest pioneering works by Plante et al and Hou et al have shown that compared to ancestral strain, the ubiquitous D614G variant (clade G) of SARS-CoV-2 exhibits efficient replication in upper respiratory tract epithelial cells and transmission, thereby conferring higher fitness MESHD [5, 6]. As per latest WHO reports on COVID-19 MESHD, a new strain referred as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01) had been identified as a part of virological and epidemiological analysis, due to sudden rise MESHD in COVID-19 MESHD detected cases in South-East England [7]. Preliminary reports from UK suggested higher transmissibility (increase by 40-70%) of this strain, escalating Ro (basic reproduction number) of virus to 1.5-1.7 [7, 8]. This apparent fast spreading variant inculcates 23 mutations; 13 non-synonymous, 6 synonymous and 4 amino acid deletions [7]. In the current scenario, where immunization programs have already commenced in nations highly affected by COVID-19 MESHD, advent of this new strain variant has raised concerns worldwide on its possible role in disease severity and antibody responses. The mutations also could also have significant impact on diagnostic assays owing to S gene target failures.

    Acceptable Performance of the Abbott ID NOW Among Symptomatic Individuals with Confirmed COVID-19 MESHD

    Authors: William Stokes; Byron Berenger; Takshveer Singh; Ifueko Adeghe; Angela Schneider; Danielle Portnoy; Teagan King; Brittney Scott; Kanti Pabbaraju; Sandy Shokoples; Anita Ah-Ting Wong; Kara Gill; LeeAnn Turnbull; Jia Hu; Graham Tipples

    doi:10.1101/2020.12.24.20248786 Date: 2020-12-30 Source: medRxiv

    INTRODUCTION Point of care diagnostic tests for SARS-CoV-2, such as the ID NOW, have great potential to help combat the COVID-19 MESHD COVID-19 MESHD pandemic. The ID NOW is approved by the United States Food and Drug Administration (FDA) for the detection of SARS-CoV-2 in symptomatic individuals within the first 7 days of symptom onset for COVID-19 MESHD if tested within 1 hour of specimen collection. However, clinical data on the performance of the ID NOW is limited, with many studies deviating from the manufacturer instructions and/or having small sample size. METHODS Adults with COVID-19 MESHD in the community or hospital were recruited into the study. Paired throat swabs were collected, with one throat swab transported immediately in an empty sterile tube to the laboratory for ID NOW testing, and the other transported in universal transport media and tested by an in-house SARS-CoV-2 RT-PCR assay targeting the E-gene PROTEIN. Positive percent agreement (PPA) was calculated. RESULTS 133 individuals were included in the study. 129 samples were positive on either the ID NOW and/or RT-PCR. Assuming any positive result on either assay represents a true positive, PPA of the ID NOW compared to RT-PCR with 95% confidence intervals was 89.1% [82.0% - 94.1%] and 91.6% [85.1% - 95.9%], respectively. When analyzing individuals with symptoms within 7 days and who had the ID NOW performed within an hour, ID NOW PPA increased to 98.2%. DISCUSSION In this study, SARS-CoV-2 results from the ID NOW were reliable, especially when testing was adhered to manufacturer recommendations.

    Environmental Dependence of the Structure of the C-terminal Domain of the SARS-CoV-2 Envelope Protein PROTEIN

    Authors: Kundlik Gadhave; Ankur Kumar; Prateek Kumar; Shivani K Kapuganti; Neha Garg; Michele Vendruscolo; Rajanish Giri; Matthew Hall; Min Shen; Munif Haddad; Giordano Pula; Reiner Mailer; Hartmut Schlueter; Florian Langer; Klaus Pueschel; Kosta Panousis; Evi Stavrou; Coen Maas; Thomas Renne; Sachin B Surade; Omodele Ashiru; Lucia Crippa; Richard Cowan; Matthew W Bowler; Jamie I Campbell; Wing-Yiu Jason Lee; Mark D Carr; David Matthews; Paul Pfeffer; Simon E Hufton; Kovilen Sawmynaden; Jane Osbourn; John McCafferty; Aneesh Karatt-Vellatt

    doi:10.1101/2020.12.29.424646 Date: 2020-12-29 Source: bioRxiv

    The SARS-CoV-2 envelope protein (E PROTEIN) is involved in a broad spectrum of functions in the cycle of the virus, including assembly, budding, envelope formation, and pathogenesis. To enable these activities, E is likely to be capable of changing its conformation depending on environmental cues. To investigate this issue, here we characterised the structural properties of the C-terminal domain of E (E-CTD), which has been reported to interact with host cell membranes. We first studied the conformation of the E-CTD in solution, finding characteristic features of a disordered protein. By contrast, in the presence of large unilamellar vesicles and micelles, which mimic cell membranes, the E-CTD was observed to become structured. The E-CTD was also found to display conformational changes with osmolytes. Furthermore, prolonged incubation of the E-CTD under physiological conditions resulted in amyloid-like fibril formation. Taken together, these findings indicate that the E-CTD can change its conformation depending on its environment, ranging from a disordered state, to a membrane-bound folded state, and an amyloid state. Our results thus provide insight into the structural basis of the role of E in the viral infection process MESHD.

    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.

    SARS-CoV-2 RNA quantification using droplet digital RT-PCR

    Authors: Natalie N. Kinloch; Winnie Dong; Kyle D Cobarrubias; Hanwei Sudderuddin; Nancy Matic; Julio S.G. Montaner; Victor Leung; Christopher Fong Jen Lowe; Chanson J Brumme; Zabrina L. Brumme

    doi:10.1101/2020.12.21.423898 Date: 2020-12-23 Source: bioRxiv

    Quantitative viral load assays have transformed our understanding of - and ability to manage - viral diseases. They hold similar potential to advance COVID-19 MESHD control and prevention, but SARS-CoV-2 viral load tests are not yet widely available. SARS-CoV-2 molecular diagnostic tests, which typically employ real-time reverse transcriptase-polymerase chain reaction (RT-PCR), yield semi-quantitative results only. Reverse transcriptase droplet digital PCR (RT-ddPCR), a technology that partitions each reaction into 20,000 nanolitre-sized droplets prior to amplification, offers an attractive platform for SARS-CoV-2 RNA quantification. We evaluated eight primer/probe sets originally developed for real-time RT-PCR-based SARS-CoV-2 diagnostic tests for use in RT-ddPCR, and identified three (Charite-Berlin E-Sarbeco and Pasteur Institute IP2 HGNC and IP4) as the most efficient, precise and sensitive for RT-ddPCR-based SARS-CoV-2 RNA quantification. Analytical efficiency of the E-Sarbeco primer/probe set, for example, was ~83%, while assay precision, as measured by the coefficient of variation, was ~2% at 1000 input copies/reaction. Lower limits of quantification and detection for this primer/probe set were 18.6 and 4.4 input SARS-CoV-2 RNA copies/reaction, respectively. SARS-CoV-2 RNA viral loads in a convenience panel of 48 COVID-19 MESHD-positive diagnostic specimens spanned a 6.2log10 range, confirming substantial viral load variation in vivo. We further calibrated RT-ddPCR-derived SARS-CoV-2 E gene PROTEIN copy numbers against cycle threshold (Ct) values from a commercial real-time RT-PCR diagnostic platform. The resulting log-linear relationship can be used to mathematically derive SARS-CoV-2 RNA copy numbers from Ct values, allowing the wealth of available diagnostic test data to be harnessed to address foundational questions in SARS-CoV-2 biology.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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