Corpus overview


Overview

MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ORF1 (3)

ComplexRdRp (3)

ORF1ab (1)

ProteinS (1)

ProteinN (1)


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SARS-CoV-2 Proteins
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    Temporal patterns in the evolutionary genetic distance of SARS-CoV-2 during the COVID-19 MESHD COVID-19 MESHD pandemic

    Authors: Jingzhi Lou; Shi Zhao; Lirong Cao; Zigui Chen; Renee WY Chan; Marc KC Chong; Benny CY Zee; Paul KS Chan; Maggie H Wang; Marian J Killip; Patricia A Cane; Christine B Bruce; Allen D.G Roberts; Guanghui Tian; Haji A. Aisa; Tianwen Hu; Daibao Wei; Yi Jiang; Gengfu Xiao; Hualiang Jiang; Leike Zhang; Xuekui Yu; Jingshan Shen; Shuyang Zhang; H. Eric Xu

    doi:10.1101/2020.11.01.363739 Date: 2020-11-02 Source: bioRxiv

    Background: During the pandemic of coronavirus disease 2019 MESHD ( COVID-19 MESHD), the genetic mutations occurred in severe acute respiratory syndrome coronavirus 2 MESHD (SARS-CoV-2) cumulatively or sporadically. In this study, we employed a computational approach to identify and trace the emerging patterns of the SARS-CoV-2 mutations, and quantify accumulative genetic distance across different periods and proteins. Methods: Full-length human SARS-CoV-2 strains in United Kingdom were collected. We investigated the temporal variation in the evolutionary genetic distance defined by the Hamming distance since the start of COVID-19 pandemic MESHD. Findings: Our results showed that the SARS-CoV-2 was in the process of continuous evolution, mainly involved in spike protein (S PROTEIN S protein HGNC), the RNA-dependent RNA polymerase PROTEIN ( RdRp PROTEIN) region of open reading frame 1 PROTEIN ( ORF1 PROTEIN) and nucleocapsid protein (N PROTEIN protein). By contrast, mutations in other proteins were sporadic and genetic distance to the initial sequenced strain did not show an increasing trend.

    Saliva as a potential clinical specimen for diagnosis of SARS-CoV-2

    Authors: Dr. Debdutta Bhattacharya; Dr. Debaprasad Parai; Usha Kiran Rout; Rashmi Ranjan Nanda; Dr. Srikanta Kanungo; Dr. Girish Chandra Dash; Dr. Subrat Kumar Palo; Dr. Siddharth Giri; Hari Ram Choudhary; Dr. Jaya Singh Kshatri; Dr. Jyotirmayee Turuk; Dr. Bijay Mishra; Dr. Saroj Dash; Dr. Sanghamitra Pati

    doi:10.1101/2020.09.11.20192591 Date: 2020-09-11 Source: medRxiv

    Background It is almost nine months, still there is no sign to stop the spreading of the COVID-19 pandemic MESHD COVID-19 pandemic MESHD. Rapid and early detection of the virus is the master key to cease the rapid spread and break the human transmission chain. There are very few studies in search of an alternate and convenient diagnostic tool which can substitute nasopharyngeal swab (NPS) specimen for detection of SARS-CoV-2. We aimed to analyse the comparison and agreement between the feasibility of using the saliva in comparison to NPS for diagnosis of SARS-CoV-2. Methods A total number of 74 patients were enrolled for this study. We analysed and compared the NPS and saliva specimen collected within 48 h after the symptom onset. We used real time quantitative polymerase chain reaction (RT-qPCR), gene sequencing for the detection and determination SARS-CoV-2 specific genes. Phylogenetic tree was constructed to establish the isolation of viral RNA from saliva. We use Bland-Altman model to identify the agreement between two sampling methods. Findings This study shows a lower CT mean value for the detection of SARS-CoV-2 ORF1 PROTEIN gene (27.07; 95% CI, 25.62 to 28.52) in saliva methods than that of NPS (28.24; 95% CI, 26.62 to 29.85) sampling method. Bland-Altman analysis produces relatively smaller bias and high agreement between these specimen tools. Phylogenetic analysis with the RdRp PROTEIN and Spike gene confirmed the presence of SARS-CoV-2 in the saliva samples. Interpretation: In conclusion, our study highlights that saliva represents a promising tool in COVID-19 MESHD diagnosis and would reduce the exposure risk of frontline health workers which is one of biggest concern in primary healthcare settings.

    Specific mutations in SARS-CoV2 RNA dependent RNA polymerase PROTEIN and helicase HGNC alter protein structure, dynamics and thus function: Effect on viral RNA replication

    Authors: Feroza Begum; DEBICA MUKHERJEE; SANDEEPAN DAS; DLUYA THAGRIKI; PREM PRAKASH TRIPATHI; ARUP KUMAR BANERJEE; UPASANA RAY

    doi:10.1101/2020.04.26.063024 Date: 2020-04-27 Source: bioRxiv

    1.The open reading frame PROTEIN (ORF) 1ab of SARS-CoV2 encodes non-structural proteins involved in viral RNA functions like translation and replication including nsp1-4; 3C like proteinase; nsp6-10; RNA dependent RNA polymerase PROTEIN ( RdRp PROTEIN); helicase HGNC and 3-5 exonuclease. Sequence analyses of ORF1ab PROTEIN unravelled emergence of mutations especially in the viral RdRp PROTEIN and helicase HGNC at specific positions, both of which are important in mediating viral RNA replication. Since proteins are dynamic in nature and their functions are governed by the molecular motions, we performed normal mode analyses of the SARS-CoV2 wild type and mutant RdRp PROTEIN and helicases to understand the effect of mutations on their structure, conformation, dynamics and thus function. Structural analyses revealed that mutation of RdRp PROTEIN (at position 4715 in the context of the polyprotein/ at position 323 of RdRp PROTEIN) leads to rigidification of structure and that mutation in the helicase HGNC (at position 5828 of polyprotein/ position 504) leads to destabilization increasing the flexibility of the protein structure. Such structural modifications and protein dynamics alterations might alter unwinding of complex RNA stem loop structures, the affinity/ avidity of polymerase RNA interactions and in turn the viral RNA replication. The mutation analyses of proteins of the SARS-CoV2 RNA replication complex would help targeting RdRp PROTEIN better for therapeutic intervention.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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