Sequence : Nsp12

Total row(s): 8
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Key Findings
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Original Article
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Phylogenetic analysis of Israeli and Non-Israeli SARS-CoV-2 sequences revealed that the Israeli SARS-CoV-2 Strain containing P681H mutation originated from the B.1.1.50 Pangolin lineage. The B.1.1.50 Pangolin lineage had the majority of the sequences are from Israel (70%), Palestine (12%), and the UK (12%)
Pre-print (medRXiv)
Date of Publishing 2021 Mar 25
Title A unique SARS-CoV-2 spike protein P681H strain detected in Israel
Author(s) nameNeta S. Zuckerman, Shay Fleishon et al.
Date of Entry 2021 Jun 14


The study reports a newly identified SARS-CoV-2 Strain from Israel. The strain included a non-synonymous mutation in the S protein: P681H (C23604A) and additional four synonymous mutations, Nsp3:C7765T, Nsp12b: C13821T, Nsp16:T21111C, and C29545A. Phylogenetic analysis was also performed to find the lineage and transmission patterns of the viral strain.
In vitro-neutralization assays were also assessed to find the effect of mutations on viral infectivity.
Pre-print (medRXiv)
Title A unique SARS-CoV-2 spike protein P681H strain detected in Israel
Author(s) name -
Date of Entry 2021 Jun 14


Indian metadata was analyzed to associate the frequent mutations and co-mutation patterns with COVID-19 patient status (deceased, symptomatic, mild, and asymptomatic groups). Patient status was reported for only 806 sequences where 95 were marked as deceased, and 631, 49, 31 were marked as symptomatic, mild, and asymptomatic, respectively
Pre-print (bioRXiv)
Date of Publishing 2021 Mar 25
Title Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India
Author(s) nameNupur Biswas, Priyanka Mallick et al.
Date of Entry 2021 Jun 14


Mutation analysis of 2213 complete genomes from six geographical regions worldwide revealed 3178 polymorphic sites. Of these polymorphic sites, 58.5% (1861 sites) were non-synonymous, compared with the reference genome, Wuhan-Hu-1. Seven frequent non-synonymous mutations were observed in the global population of SARS-CoV-2. SARS-CoV-2 from six regions around the world (United States of America (US), Latin America (LA), Europe (EU), Africa (AF), Asia (AS), and Oceania (OC)) were taken randomly from NCBI and GISAID databases up to November 13, 2020, for the analysis.
DnaSP v5.1 software was used to determine the number of polymorphisms.
The difference between synonymous and non-synonymous substitutions (dN/dS) was evaluated using the software MEGA v6.0.
dN frequencies were obtained using Jalview v2.11 software.
P323L substitution in nsp12 (replication/transcription of the SARS-CoV-2 genome) provides structural stability, S447N substitution is located in the RBM (S protein) increases the affinity for the ACE-2 receptor, G614 substitution makes the virus 2.4 times more infectious.
33572190
(Pathogens)
PMID
33572190
Date of Publishing: 2021 Feb 9
Title Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging
Author(s) nameFlores-Alanis A, Cruz-Rangel A et al.
Journal Pathogens
Impact factor
3.31
Citation count: 11


62 mutations identified, including 30 mis-sense mutations, in 22 Moroccan patient isolates showed that Spike_D614G and NSP12_P323L mutations were present in all the analyzed sequences, whereas N_G204R and N_R203K were present in 9 sequences. Link to Clock Diagram depicting Mutation Evolution Rate in Morrocan Isolates,
33558859
(Biosaf Health)
PMID
33558859
Date of Publishing: 2021 Feb 3
Title Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco
Author(s) nameBadaoui B, Sadki K et al.
Journal Biosaf Health
Impact factor
Cant find
Citation count: 3


Compared to the SARS-CoV-2 reference genome (GenBank accession number: MN996528.1), the SARS-CoV-2 genome of Bangladesh, BCSIR-NILMRC-006, (accession number: MT539159) had eight mutations. A unique mutation was observed in the non-structural protein NSP2 of the ORF1ab gene.
32972934
(Microbiol Resour Announc)
PMID
32972934
Date of Publishing: 2020 Sep 24
Title Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh
Author(s) nameAkter S, Banu TA et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 7


Compared to the SARS-CoV-2 reference genome (GenBank accession number: MN996528.1), the SARS-CoV-2 genome of Bangladesh, BCSIR-NILMRC-007, (accession number: MT539158) had six mutations.
32972934
(Microbiol Resour Announc)
PMID
32972934
Date of Publishing: 2020 Sep 24
Title Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh
Author(s) nameAkter S, Banu TA et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 7


Compared to the SARS-CoV-2 reference genome (GenBank accession number: MN996528.1), the SARS-CoV-2 genome of Bangladesh, BCSIR-NILMRC-008, (accession number: MT539160) had six mutations.
32972934
(Microbiol Resour Announc)
PMID
32972934
Date of Publishing: 2020 Sep 24
Title Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh
Author(s) nameAkter S, Banu TA et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 7



Structure : Nsp12

Total row(s): 7
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Original Article
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Structure of SARS-CoV-2 mini RTC assembly by viral RNA-dependent RNA polymerase (nsp12) with a template-primer RNA, nsp7 and nsp8, and two helicase molecules (nsp13-1 and nsp13-2). nsp13-1 stabilizes the mini RTC by contacting with nsp13-2, which anchors the 5'-extension of RNA template, and interacts with nsp7-nsp8-nsp12-RNA.
33208736
(Nat Commun)
PMID
33208736
Date of Publishing: 2020 Nov 18
Title Architecture of a SARS-CoV-2 mini replication and transcription complex
Author(s) nameYan L, Zhang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 49


Structural characterisation of SARS-CoV-2 mini replication and transcription complex
33208736
(Nat Commun)
PMID
33208736
Date of Publishing: 2020 Nov 18
Title Architecture of a SARS-CoV-2 mini replication and transcription complex
Author(s) nameYan L, Zhang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 49


The structure of the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) complex in its active form comprises the non-structural protein 12 (nsp12), nsp8, and nsp7, and more than two turns of RNA template-product duplex. The active-site cleft of nsp12 binds to the first turn of RNA. Two copies of nsp8 bind to opposite sides of the cleft and position the second turn of RNA. Long helical extensions in nsp8 protrude along exiting RNA, forming positively charged 'sliding poles'. These sliding poles help in the processivity of RdRp, required for replicating the long genome of coronaviruses. The active site of nsp12 consists of five conserved motif AE, of which the residues (D760 and D761) of motif C binds to the RNA 3 end and plays a crucial role in RNA synthesis. K58 is located in the nsp8 extension and plays an important role in interaction with RNA.
32438371
(Nature)
PMID
32438371
Date of Publishing: 2020 Aug
Title Structure of replicating SARS-CoV-2 polymerase
Author(s) nameHillen HS, Kokic G et al.
Journal Nature
Impact factor
24.36
Citation count: 218


Structural characterization of cryo-EM structure of the apo nsp12-nsp7-nsp8 complex Knowledge of viral replication mechanism as well as the structure of the protiens involved can prove to be fruitful for drug discovery against SARS-CoV-2 virus
32358203
(Science)
PMID
32358203
Date of Publishing: 2020 Jun 26
Title Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir
Author(s) nameYin W, Mao C et al.
Journal Science
Impact factor
20.57
Citation count: 404


Structural characteirzation of the nsp12-nsp7-nsp8 complex bound to the template-primer RNA and triphosphate form of Remdesivir(RTP) The structure of the template-RTP RdRp complex provides a useful model to rationalize how these drugs inhibit the activity of SARS-CoV-2 RdRp.
32358203
(Science)
PMID
32358203
Date of Publishing: 2020 Jun 26
Title Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir
Author(s) nameYin W, Mao C et al.
Journal Science
Impact factor
20.57
Citation count: 404


Structure of SARS-Cov-2 RNA-dependent RNA polymerase nsp12, in complex with nsp7 and nsp8 reports a conserved polymerase core and a β hairpin domain (residues N215 to N218) at its N-terminus. This structure aids in the study of remdesivir and other drug candidates' antiviral activity. The structure of RdRp can be used as a source for discovering broad spectrum antivirals.
32277040
(Science)
PMID
32277040
Date of Publishing: 2020 May 15
Title Structure of the RNA-dependent RNA polymerase from COVID-19 virus
Author(s) nameGao Y, Yan L et al.
Journal Science
Impact factor
20.57
Citation count: 515
Date of Entry 2021 Jul 28


Structure of SARS-CoV-2 RNA-dependent RNA polymerase nsp12 in complex with cofactors nsp7 and nsp8 under reducing condition, forms a β hairpin domain (residues N215 to N218) at its N-terminus. This structure aids in antiviral viral study of remdesivir and other antiviral drugs. The structure of RdRp can be used as a source for discovering broad spectrum antivirals.
32277040
(Science)
PMID
32277040
Date of Publishing: 2020 May 15
Title Structure of the RNA-dependent RNA polymerase from COVID-19 virus
Author(s) nameGao Y, Yan L et al.
Journal Science
Impact factor
20.57
Citation count: 515
Date of Entry 2021 Jul 28



Molecular_interactions : Nsp12

Total row(s): 3
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Key Findings
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Original Article
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Nsp13-1 stabilizes SARS-CoV-2 replication and transcription (RTC) complex by contacting with nsp13-2, which anchors the 5'-extension of RNA template, and interacting with nsp7-nsp8-nsp12-RNA. Different orientations of nsp13-1 results in different interactions with the two forms of mini RTC. Mini RTC with an nsp12R365A mutation has greater helicase activity compared to individual apsnsp13. Nsp13-1T216A mutation has a decreased helicase activity.
33208736
(Nat Commun)
PMID
33208736
Date of Publishing: 2020 Nov 18
Title Architecture of a SARS-CoV-2 mini replication and transcription complex
Author(s) nameYan L, Zhang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 49


Cryo-electron microscopy structure of the SARS-CoV-2 RdRp with non-structural protein 12 (nsp12), nsp8 and nsp7, and more than two turns of RNA template-product duplex, shows active-site cleft of nsp12 binds to the first turn of RNA and mediates RdRp activity and two copies of nsp8 bind to opposite sides of the cleft and position the second turn of RNA. Nsp8 along the exiting RNA, forms positively charged 'sliding poles' which affect the processivity of RdRp. The active site of nsp12 consists of five conserved motif AE, of which the residues (D760 and D761) of motif C binds to the RNA 3 end and plays a crucial role in RNA synthesis. K58 is located in the nsp8 extension and plays an important role in interaction with RNA.
32438371
(Nature)
PMID
32438371
Date of Publishing: 2020 Aug
Title Structure of replicating SARS-CoV-2 polymerase
Author(s) nameHillen HS, Kokic G et al.
Journal Nature
Impact factor
24.36
Citation count: 218


The complex cryo-electron microscopy structure of SARS-CoV-2 RdRp with a 50-base template-primer RNA and remdesivir, shows the partial double-stranded RNA template is present in the central channel of RdRp where remdesivir is covalently attached as the first replicated base pair and results in the termination of chain elongation. The conserved protein-RNA interactions and the catalytic active site residues, in the diverse RNA viruses, makes it possible to develop broad spectrum antiviral inhibitors.
32358203
(Science)
PMID
32358203
Date of Publishing: 2020 Jun 26
Title Structural basis for inhibition of the RNA-dependent RNA polymerase from SARS-CoV-2 by remdesivir
Author(s) nameYin W, Mao C et al.
Journal Science
Impact factor
20.57
Citation count: 404