Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ORF1 (3)

ORF1ab (3)

ProteinN (1)

ORF1a (1)

ComplexRdRp (1)


SARS-CoV-2 Proteins
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    Translation-associated mutational U-pressure in the first ORF of SARS-CoV-2 and other coronaviruses

    Authors: Vladislav Victorovich Khrustalev; Rajanish Giri; Tatyana Aleksandrovna Khrustaleva; Shivani Krishna Kapuganti; Aleksander Nicolaevich Stojarov; Victor Vitoldovich Poboinev

    doi:10.1101/2020.05.05.078238 Date: 2020-05-05 Source: bioRxiv

    Within four months of the ongoing COVID-19 pandemic MESHD COVID-19 pandemic MESHD caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in the ORF1 PROTEIN of the virus isolated from different parts of the globe. These observations open up an obvious question about the rate and direction of mutational pressure for further vaccine and therapeutics designing. In this study, we did a comparative analysis of ORF1a PROTEIN and ORF1b by using the first isolate (Wuhan strain) as the parent sequence. We observed that most of the nucleotide mutations are C to U transitions. The rate of synonymous C to U transitions is significantly higher than the rate of nonsynonymous ones, indicating negative selection on amino acid substitutions. Further, trends in nucleotide usage bias have been investigated in 49 coronaviruses species. A strong bias in nucleotide usage in fourfold degenerated sites towards uracil residues is seen in ORF1 PROTEIN of all the studied coronaviruses. A more substantial mutational U pressure is observed in ORF1a PROTEIN than in ORF1b owing to the translation of ORF1ab PROTEIN via programmed ribosomal frameshifting. Unlike other nucleotide mutations, mutational U pressure caused by cytosine deamination, mostly occurring in the RNA-plus strand, cannot be corrected by the proof-reading machinery of coronaviruses. The knowledge generated on the direction of mutational pressure during translation of viral RNA-plus strands has implications for vaccine and nucleoside analogue development for treating covid-19 MESHD and other coronavirus infections MESHD.

    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


    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.

    Comparative analysis of primer-probe sets for the laboratory confirmation of SARS-CoV-2

    Authors: Yu Jin Jung; Gun-Soo Park; Jun Hye Moon; Keunbon Ku; Seung-Hwa Beak; Seil Kim; Edmond Changkyun Park; Daeui Park; Jong-Hwan Lee; Cheol Woo Byeon; Joong Jin Lee; Jin-soo Maeng; Seong Jun Kim; Seung Il Kim; Bum-Tae Kim; Min Jun Lee; Hong Gi Kim

    doi:10.1101/2020.02.25.964775 Date: 2020-02-27 Source: bioRxiv

    Coronavirus disease 2019 MESHD ( COVID-19 MESHD) is newly emerging human infectious diseases MESHD, which is caused by Severe Acute Respiratory Syndrome Coronavirus 2 MESHD (SARS-CoV-2, also previously known as 2019-nCoV). Within two months of the outbreak, more than 80,000 cases of COVID-19 MESHD have been confirmed worldwide. Since the human to human transmission occurred easily and the human infection is rapidly increasing, the sensitive and early diagnosis is essential to prevent the global outbreak. Recently, World Health Organization (WHO) announced various primer and probe sets for SARS-CoV-2 previously developed in China, Germany, Hong Kong, Japan, Thailand, and USA. In this study, we compared the ability to detect SARS-CoV-2 RNA among the seven primer-probe sets for N gene PROTEIN and the three primer-probe sets for Orf1 PROTEIN gene. The result of the comparative analysis represented that the 2019-nCoV_N2, N3 of USA and the ORF1ab PROTEIN of China are the most sensitive primer-probe sets for N and Orf1 PROTEIN genes, respectively. Therefore, the appropriate combination from ORF1ab PROTEIN (China), 2019-nCoV_N2, N3 (USA), and NIID_2019-nCOV_N (Japan) sets should be selected for the sensitive and reliable laboratory confirmation of SARS-CoV-2.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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