Corpus overview


Overview

MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinN (33)

ComplexRdRp (33)

ProteinE (8)

ProteinS (8)

ORF3a (5)


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SARS-CoV-2 Proteins
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    Sewage surveillance for the presence of SARS-CoV-2 genome as a useful wastewater based epidemiology (WBE) tracking tool in India

    Authors: Sudipti Arora; Aditi Nag; Jasmine Sethi; Jayana Rajvanshi; Sonika Saxena; Sandeep Kumar Shrivastava; Akhilendra Bhushan Gupta

    doi:10.1101/2020.06.18.20135277 Date: 2020-06-20 Source: medRxiv

    The infection with SARS-CoV-2 is reported to be accompanied by the shedding of the virus in stool samples of infected MESHD patients. Earlier reports have suggested that COVID-19 MESHD agents can be present in the fecal and sewage samples and thus it can be a good indication of the pandemic extent in a community. However, no such studies have been reported in the Indian context so far. Since, several factors like local population physiology, the climatic conditions, sewage composition, and processing of samples could possibly affect the detection of the viral genome, it becomes absolutely necessary to check for the presence of the SARS-CoV-2 in the wastewater samples from wastewater treatment plants (WWTPs) serving different localities of Jaipur city, which has been under red zone (pandemic hotspots) since early April 2020. Samples from different local municipal WWTPs and hospital wastewater samples were collected and wastewater based epidemiology (WBE) studies for the presence of SARS-CoV-2 were carried out using the RT-PCR technique to confirm the presence of different COVID-19 MESHD target genes namely S gene, E PROTEIN gene, ORF1ab PROTEIN gene, RdRp PROTEIN gene and N PROTEIN gene in the viral load of wastewater samples. In the present study, the untreated wastewater samples from the municipal WWTPs and hospital wastewater samples showed the presence of SARS-CoV-2 viral genome, which was correlated with the increased number of COVID-19 MESHD positive patients from the concerned areas, as per reported in the publically available health data. This is the first study that investigated the presence of SARS-CoV-2 viral genome in wastewater, at higher ambient temperature (above 40{degrees}C), further validating WBE as a potential tool in predicting and mitigating outbreaks.

    Nucleocapsid protein PROTEIN of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

    Authors: Adriana Savastano; Alain Ibanez-de-Opakua; Marija Rankovic; Markus Zweckstetter

    doi:10.1101/2020.06.18.160648 Date: 2020-06-19 Source: bioRxiv

    The etiologic agent of the Covid-19 MESHD Covid-19 MESHD pandemic is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral membrane of SARS-CoV-2 surrounds a helical nucleocapsid in which the viral genome is encapsulated by the nucleocapsid protein PROTEIN. The nucleocapsid protein PROTEIN of SARS-CoV-2 is produced at high levels within infected cells, enhances the efficiency of viral RNA transcription and is essential for viral replication. Here we show that RNA induces cooperative liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid protein PROTEIN. In agreement with its ability to phase separate in vitro, we show that the protein associates in cells with stress granules, cytoplasmic RNA/protein granules that form through liquid-liquid phase separation and are modulated by viruses to maximize replication efficiency. Liquid-liquid phase separation generates high-density protein/RNA condensates that recruit the RNA-dependent RNA polymerase PROTEIN complex of SARS-CoV-2 providing a mechanism for efficient transcription of viral RNA. Inhibition of RNA-induced phase separation of the nucleocapsid protein PROTEIN by small molecules or biologics thus can interfere with a key step in the SARS-CoV-2 replication cycle.

    How to choose the right real-time RT-PCR primer sets for the SARS-CoV-2 genome detection? 

    Authors: Ahalieyah Anantharajah; Raphael Helaers; Jean-Philippe Defour; Nathalie Olive; Florence Kabera; Luc Croonen; Françoise Deldime; Jean-Luc Vaerman; Cindy Barbée; Monique Bodéus; Anais Scohy; Alexia Verroken; Hector Rodriguez-Villalobos; Benoît Kabamba-Mukadi

    doi:10.21203/rs.3.rs-36512/v1 Date: 2020-06-19 Source: ResearchSquare

    The SARS-CoV-2 pandemic has created an unprecedented need for rapid large-scale diagnostic testing. Currently, several quantitative reverse-transcription polymerase chain reaction (RT-qPCR) assays recommended by the World Health Organization are being used by clinical and public health laboratories and typically target regions of the RNA-dependent RNA polymerase PROTEIN ( RdRp PROTEIN), envelope (E) and nucleocapsid (N PROTEIN) coding region. However, it is currently unclear if results from different tests are comparable. The present study demonstrates substantial differences in SARS-CoV-2 RNA detection sensitivity among the primer/probe sets recommended by the World Health Organization especially for low-level viral loads. The alignment of thousands of European SARS-CoV-2 sequences against the primers/probe highlights single mismatches which might also contribute to false negatives. An understanding of the limitations depending on the targeted genes and primer/probe sets may influence the selection of molecular detection assays by clinical laboratories.

    A new system in qualitative RT-PCR detecting SARS-CoV-2 in biological samples: an Italian experience.

    Authors: Marco Favaro; Walter Mattina; Enrico Salvatore Pistoia; Roberta Gaziano; Paolo Di Francesco; Simon Middleton; Silvia D'Angelo; Tullio Altarozzi; Carla Fontana

    doi:10.1101/2020.06.17.20124396 Date: 2020-06-19 Source: medRxiv

    In the last moths the world was faced with the pandemic of a new severe acute respiratory syndrome coronavirus (SARS-CoV) MESHD and the majority of the Nations have yet to come out of it. Numerous assays have emerged to meet SARS-CoV-2 diagnostic needs. A clear knowledge of these assays parameters is essential to choose the proper test by clinical microbiologists. Unfortunately, the latter cannot be the unique criterion that guides test selection as - given the great demand - shortcomings of commercial kits is also a great issue. Aimed by the intention of overcoming both difficulties we have developed a new qualitative RT-PCR probe based for COVID-19 MESHD detection. The system detects three genes of SARS-CoV-2: RNA-dependent RNA polymerase PROTEIN ( RdRp PROTEIN), envelope (E) and nucleocapsid (N PROTEIN) and { beta}-actin HGNC gene used as endogenous internal control. The results of our assay show a total agreement with those obtained using a commercially available kit, with the exception of two specimens which did not pass the endogenous internal control. Moreover, our kit was designed to be open either for nucleic acid extraction step or on the RT-PCR assay to be carried out on several instruments. Thus, it is free from the industrial production logics of closed systems and conversely it is hypothetically available for distribution on large numbers in any microbiological laboratories. Presently, the kit is currently distributed worldwide

    Viral RNA load quantification as helpful tool to arbitrate SARS–CoV-2 detection results in respiratory samples

    Authors: Flora Marzia Liotti; Giulia Menchinelli; Simona Marchetti; Grazia Angela Morandotti; Maurizio Sanguinetti; Brunella Posteraro; Paola Cattani

    doi:10.21203/rs.3.rs-34028/v1 Date: 2020-06-08 Source: ResearchSquare

    Purpose: The increasing COVID-19 MESHD widespread has created the necessity to assess the diagnostic accuracy of newly introduced (RT-PCR based) assays for SARS–CoV-2 RNA detection in respiratory tract samples.Methods: We compared the results of the Allplex™ 2019-nCoV assay with those of the Simplexa™ COVID-19 MESHD Direct assay, both performed on 125 nasal/oropharyngeal swab samples of patients with COVID-19 MESHD suspicion.Results: Fifty-four samples tested positive (CT below 40) and 71 negative (CT above 40) with the Allplex™ 2019-nCoV assay, whereas 47 of 54 samples were also positive with the Simplexa™ COVID-19 MESHD Direct assay. Eight results were discordant, resulting in 93.6% agreement between the assays. We used the Quanty COVID-19 MESHD assay—developed to detect and quantify SARS–CoV-2 in respiratory tract samples—to arbitrate these results. One Allplex™ 2019-nCoV negative (but Simplexa™ COVID-19 MESHD positive) and seven Simplexa™ COVID-19 MESHD negative samples were truly false negative. Interestingly, a Spearman’s negative association was found between the viral RNA loads quantified by the Quanty COVID-19 MESHD assay and the CT values of RT PCRs performed with either the Allplex™ 2019–nCoV assay or the Simplexa™ COVID-19 MESHD Direct assay. However, the strength of this association was higher for the Allplex™ 2019–nCoV assay ( N gene PROTEIN, ρ = −0.92; RdRP PROTEIN gene, ρ = −0.91) than for the Simplexa™ COVID-19 MESHD Direct assay ( ORF1ab PROTEIN gene, ρ = −0.65; S gene, ρ = −0.80).Conclusion: The Allplex™ 2019–nCoV and Simplexa™ COVID-19 MESHD Direct assays yielded comparable results. However, the role these assays might play in future clinical practice warrants larger comparison studies.

    Temporal evolution and adaptation of SARS-COV 2 codon usage

    Authors: Maddalena Dilucca; Sergio Forcelloni; Andrea Giansanti; Alexandros Georgakilas; Athanasia Pavlopoulou

    doi:10.1101/2020.05.29.123976 Date: 2020-06-03 Source: bioRxiv

    The outbreak of severe acute respiratory syndrome-coronavirus-2 MESHD (SARS-CoV-2) has caused an unprecedented pandemic. Since the first sequenced whole-genome of SARS-CoV-2 on January 2020, the identification of its genetic variants has become crucial in tracking and evaluating their spread across the globe. In this study, we compared 15,259 SARS-CoV-2 genomes isolated from 60 countries since the outbreak of this novel coronavirus with the first sequenced genome in Wuhan to quantify the evolutionary divergence of SARS-CoV-2. Thus, we compared the codon usage patterns, every two weeks, of 13 of SARS-CoV-2 genes encoding for the membrane protein (M PROTEIN), envelope (E), spike surface glycoprotein (S PROTEIN), nucleoprotein (N PROTEIN), non-structural 3C-like proteinase ( 3CLpro PROTEIN), ssRNA-binding protein ( RBP HGNC), 2-O-ribose methyltransferase (OMT), endoRNase (RNase), helicase HGNC, RNA-dependent RNA polymerase PROTEIN ( RdRp PROTEIN), Nsp7, Nsp8, and exonuclease ExoN. As a general rule, we find that SARS-CoV-2 genome tends to diverge over time by accumulating mutations on its genome and, specifically, on the coding sequences for proteins N PROTEIN and S. Interestingly, different patterns of codon usage were observed among these genes. Genes S, Nsp7, NSp8, tend to use a norrower set of synonymous codons that are better optimized to the human host. Conversely, genes E PROTEIN and M consistently use a broader set of synonymous codons, which does not vary with respect to the reference genome. We identified key SARS-CoV-2 genes (S, N, ExoN, RNase, RdRp PROTEIN, Nsp7 and Nsp8) suggested to be causally implicated in the virus adaptation to the human host.

    Synonymous sites in SARS-CoV-2 genes display trends affecting translational efficiency

    Authors:

    doi:10.1101/2020.05.30.125740 Date: 2020-05-31 Source: bioRxiv

    A novel coronavirus, SARS-CoV-2, has caused a pandemic of COVID-19 MESHD. The evolutionary trend of the virus genome may have implications for infection control policy but remains obscure. We introduce an estimation of fold change of translational efficiency based on synonymous variant sites to characterize the adaptation of the virus to hosts. The increased translational efficiency of the M and N genes PROTEIN suggests that the population of SARS-CoV-2 benefits from mutations toward favored codons, while the ORF1ab PROTEIN gene has slightly decreased the translational efficiency. In the coding region of the ORF1ab PROTEIN gene upstream of the -1 frameshift site, the decreasing of the translational efficiency has been weakening parallel to the growth of the epidemic, indicating inhibition of synthesis of RNA-dependent RNA polymerase PROTEIN and promotion of replication of the genome. Such an evolutionary trend suggests that multiple infections increased virulence in the absence of social distancing.

    Molecular analysis of several in-house rRT-PCR protocols for SARS-CoV-2 detection in the context of genetic variability of the virus in Colombia.

    Authors: Diego Alejandro Alvarez-Diaz; Carlos Franco-Munoz; Katherine Laiton-Donato; Jose A Usme-Ciro; Nicolas D Franco-Sierra; Astrid C Florez; Sergio Gomez Rangel; Luz Dary Rodriguez; Juliana Barbosa-Ramirez; Erika X Ospitia-Baez; Diana M Walteros; Martha L Ospina Martinez; Marcela Mercado-Reyes

    doi:10.1101/2020.05.22.20107292 Date: 2020-05-26 Source: medRxiv

    The COVID-19 MESHD COVID-19 MESHD pandemic caused by SARS-CoV-2 is a public health problem unprecedented in the recent history of humanity. Different in-house real-time RT-PCR (rRT-PCR) methods for SARS-CoV-2 diagnosis and the appearance of genomes with mutations in primer regions have been reported. Hence, whole-genome data from locally-circulating SARS-CoV-2 strains contribute to the knowledge of its global variability and the development and fine-tuning of diagnostic protocols. To describe the genetic variability of Colombian SARS-CoV-2 genomes in hybridization regions of oligonucleotides of the main in-house methods for SARS-CoV-2 detection, RNA samples with confirmed SARS-CoV-2 molecular diagnosis were processed through next-generation sequencing. Primers/probes sequences from 13 target regions for SARS-CoV-2 detection suggested by 7 institutions and consolidated by WHO during the early stage of the pandemic were aligned with Muscle tool to assess the genetic variability potentially affecting their performance. Finally, the corresponding codon positions at the 3' end of each primer, the open reading frame inspection was identified for each gene/protein product. Complete SARS-CoV-2 genomes were obtained from 30 COVID-19 MESHD cases, representative of the current epidemiology in the country. Mismatches between at least one Colombian sequence and five oligonucleotides targeting the RdRP PROTEIN and N genes PROTEIN were observed. The 3' end of 4 primers aligned to the third codon position, showed high risk of nucleotide substitution and potential mismatches at this critical position. Genetic variability was detected in Colombian SARS-CoV-2 sequences in some of the primer/probe regions for in-house rRT-PCR diagnostic tests available at WHO COVID-19 MESHD technical guidelines; its impact on the performance and rates of false-negative results should be experimentally evaluated. The genomic surveillance of SARS-CoV-2 is highly recommended for the early identification of mutations in critical regions and to issue recommendations on specific diagnostic tests to ensure the coverage of locally-circulating genetic variants.

    In silico Proteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

    Authors: Chittaranjan Baruah; Papari Devi; Dhirendra K Sharma

    doi:10.1101/2020.05.23.104919 Date: 2020-05-24 Source: bioRxiv

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (2019-nCoV), is a positive-sense, single-stranded RNA coronavirus. The virus is the causative agent of coronavirus disease 2019 MESHD ( COVID-19 MESHD) and is contagious through human-to-human transmission. The present study reports sequence analysis, complete coordinate tertiary structure prediction and in silico sequence-based and structure-based functional characterization of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA) which is identical to GenBank entry MN908947 and MT415321. The proteome includes 12 major proteins namely orf1ab polyprotein (includes 15 proteins), surface glycoprotein, ORF3a PROTEIN protein, envelope PROTEIN envelope protein HGNC, membrane glycoprotein PROTEIN, ORF6 PROTEIN protein, ORF7a PROTEIN protein, orf7b, ORF8 PROTEIN, Nucleocapsid phosphoprotein and ORF10 PROTEIN protein. Each protein of orf1ab polyprotein group has been studied separately. A total of 25 polypeptides have been analyzed out of which 15 proteins are not yet having experimental structures and only 10 are having experimental structures with known PDB IDs MESHD. Out of 15 newly predicted structures six (6) were predicted using comparative modeling and nine (09) proteins having no significant similarity with so far available PDB structures were modeled using ab-initio modeling. Structure verification using recent tools QMEANDisCo 4.0.0 and ProQ3 for global and local (per-residue) quality estimates indicate that the all-atom model of tertiary structure of high quality and may be useful for structure-based drug designing targets. The study has identified nine major targets ( spike protein PROTEIN, envelop protein, membrane protein, nucleocapsid PROTEIN protein, 2-O-ribose methyltransferase, endoRNAse, 3-to-5 exonuclease, RNA-dependent RNA polymerase PROTEIN and helicase HGNC) for which drug design targets could be considered. There are other 16 nonstructural proteins PROTEIN (NSPs), which may also be percieved from the drug design angle. The protein structures have been deposited to ModelArchive. Tunnel analysis revealed the presence of large number of tunnels in NSP3 HGNC NSP3 PROTEIN, ORF 6 protein and membrane glycoprotein PROTEIN indicating a large number of transport pathways for small ligands influencing their reactivity.

    Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation

    Authors: Maria Jose Lista; Robert Page; Helin Sertkaya; Pedro Matos; Elena Ortiz-Zapater; Thomas J.A. Maguire; Kate Poulton; Aoife O'Byrne; Clement Bouton; Ruth E Dickenson; Mattia Ficarelli; Mark Howard; Gilberto Betancor; Rui Pedro Galao; Suzanne Pickering; Adrian W Signell; Harry Wilson; Penny Cliff; Mark Tan Kia Ik; Amita Patel; Eithne MacMahon; Emma Cunningham; Katie Doores; Monica Agromayor; Juan Martin-Serrano; Esperanza Perucha; Hannah E Mischo; Manu Shankar-Hari; Rahul Batra; Jonathan Edgeworth; Michael H Malim; Stuart Neil; Rocio Teresa Martinez-Nunez

    doi:10.1101/2020.04.22.20074351 Date: 2020-04-28 Source: medRxiv

    There is a worldwide shortage of reagents to perform detection of SARS-2. Many clinical diagnostic laboratories rely on commercial platforms that provide integrated end-to-end solutions. While this provides established robust pipelines, there is a clear bottleneck in the supply of reagents given the current situation of extraordinary high demand. Some laboratories resort to implementing kit-free handling procedures, but many other small laboratories will not have the capacity to develop those and/or will perform manual handling of their samples. In order to provide multiple workflows for SARS-CoV-2 nucleic acid detection we compared several commercially available RNA extraction methods: QIAamp Viral RNA Mini Kit (QIAgen), the recently developed RNAdvance Blood (Beckman) and Mag-Bind Viral DNA/RNA 96 Kit (Omega Bio-tek). We also compared different 1-step RT-qPCR Master Mix brands: TaqMan Fast Virus 1-Step Master Mix (ThermoFisher Scientific), qPCRBIO Probe 1-Step Go Lo-ROX (PCR Biosystems) and Luna(R) Universal Probe One-Step RT-qPCR Kit (NEB). We used the Centre for Disease Control (CDC) recommended primers that detect two regions of the viral N gene PROTEIN as well as those that detect the RdRP PROTEIN gene region as per Public Health England (PHE) guidelines (Charite/WHO/PHE). Our data show that the RNA extraction methods provide similar results. Amongst the qPCR reagents tested, TaqMan Fast Virus 1-Step Master Mix and Luna(R) Universal Probe One-Step RT-qPCR Kit proved most sensitive. The N1 and N2 primer-probes provide a more reliable detection than the RdRP PROTEIN-SARSr primer-probe set, particularly in samples with low viral titres. Importantly, we have implemented a protocol using heat inactivation and demonstrate that it has minimal impact on the sensitivity of the qPCR in clinical samples - potentially making SARS-CoV-2 testing portable to settings that do not have CL-3 facilities.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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