Variants : Nsp3

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Original Article
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The study revealed that SARS-CoV-2 Delta variant genomes discovered in India by April 2021 fall into four distinct groups (Delta 1,2 3 and 4), each with its own set of characteristic spike, nucleocapsid and NSP3 changes. Delta subvariant Delta 1 was estimated to be the major pandemic driver in UK, Europe and Spain as well.
Pre-print (medRXiv)
Date of Publishing 2021 Oct 20
Title SARS-COV-2 variant drives the pandemic in India and Europe via two subvariants
Date of Entry 2021 Nov 2



Sequence : Nsp3

Total row(s): 7
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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


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


Comparative variant analysis of genome sequences of eleven Lebanese SARS-CoV-2 isolates revealed forty unique missense variants. Of forty unique variants identified, eighteen were new mutations.
33091548
(Genomics)
PMID
33091548
Date of Publishing: 2020 Oct 20
Title Variant analysis of the first Lebanese SARS-CoV-2 isolates.
Author(s) nameAbou-Hamdan M, Hamze K et al.
Journal Genomics
Impact factor
3.9
Citation count: 4


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-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



Immunology : Nsp3

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Original Article
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SARS-CoV-2 spike-specific CD8+ and CD4++ T cells were detected in 70% and 100% of COVID-19 convalescent cases, respectively. In addition to the M, spike and N protein, CD4++ T cell responses were also seen against ORF3a, ORF8, nsp3, and nsp4 proteins. SARS-CoV-2 RBD-specific IgG and IgA levels correlated with CD4++ T cell responses to spike protein. SARS-CoV-2-reactive CD4++ T cells were also detected in 40%-60% of unexposed individuals suggesting cross-reactive T cell recognition. "1.) Participant Characteristics: Table 1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237901/table/tbl1/?report=objectonly) 2.) SARS-CoV-2 IgM, IgA, and IgG Responses of Recovered COVID-19 Patients: Figure 1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237901/figure/fig1/). 3.) SARS-CoV-2-Specific CD4+ T Cell Responses of Recovered COVID-19 Patients: Figure 2 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237901/figure/fig2/) 4.) SARS-CoV-2-Specific CD8+ T Cell Responses by Recovered COVID-19 Patients: Figure 3 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237901/figure/fig3/) 5.) Correlations between SARS-CoV-2-Specific CD4+ T Cells, Antibodies, and CD8+ T Cells: Figure 4 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7237901/figure/fig4/)"
32473127
(Cell)
PMID
32473127
Date of Publishing: 2020 Jun 25
Title Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals
Author(s) nameGrifoni A, Weiskopf D et al.
Journal Cell
Impact factor
27.35
Citation count: 1309
Date of Entry 2021 Jul 24