Sequence


Last updated: 2021 Sep 13
Total hit(s): 21
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Original Article
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The frequency of mutation in the spike of the Delta variant was assessed. Eight substitution mutations( T19R, G142D, R158G, L452R, T478K, D614G, P681R, D950N )and a deletion (156-157)were observed in the N-terminal domain, Receptor binding domain, and S2 regions of the SARS-CoV-2 Delta variant spike protein.
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PMID
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Date of Publishing: 2021 Jun 28
Title Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination
Date of Entry 2021 Sep 13


Three significant mutations (L452R, W152C and S13I) were identified in the spike protein of the California variant B.1.427/B.1.429 with no particular difference from non-variant lineages (B.1.427, B.1.429, other Clade 20C lineages). Two distinct lineages, B.1.427 and B.1.429 were identified in Clade 20C after Phylogenetic analysis.
33991487
(Cell)
PMID
33991487
Date of Publishing: 2021 Jun 24
Title Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
Author(s) nameDeng X, Garcia-Knight MA et al.
Journal Cell
Impact factor
27.35
Citation count: 6
Date of Entry 2021 Sep 13


Phylogenetic analysis was performed for the RNA sequences from six patient samples which showed that they were infected with the Delta variant, despite being vaccinated. Out of 334 sequences analyzed, 328 were SARS-CoV-2 sequences designated for various variants of concern (VOC) and variant of interest (VOI), downloaded from GISAID, and 6 were the patient samples.
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PMID
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Date of Publishing: 2021 Jul 04
Title Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections
Date of Entry 2021 Aug 6


The emergent mutants L452R and Y453F had a wide range of hosts in terms of its receptor binding characteristics and participated in cross-species infection The cross-species transmission is a big threat to the pandemic.
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PMID
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Date of Publishing: 2021 Apr 05
Title An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity
Date of Entry 2021 Aug 6


The most prevalent receptor binding motif (RBM) mutation N439K was subjected to phylogenetic analysis. N439K lineage i/B.1.141 was dominant in Scotland; while N439K lineage ii/B.1.258 were first sampled in Romania and currently spread to 32 other countries. The growth rate of N439K/D614G lineage(i) was similar compared to the N439/D614 or N439/D614G WT in Scotland. The total number of N439K variants as of January 6, 2021 correspond to 764,000 of the confirmed SARS-CoV-2 infections in 34 countries.
33621484
(Cell)
PMID
33621484
Date of Publishing: 2021 Jan 28
Title Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
Author(s) nameThomson EC, Rosen LE et al.
Journal Cell
Impact factor
27.35
Citation count: 1
Date of Entry 2021 Aug 6


Whole-genome sequencing for 2 S gene target failure (SGTF) samples showed that the S deletion 21765-21770 was present in 100% of the reads. It also leads to the removal of 2 amino acids (H69/V70) in the N-terminal domain of the S1 subunit of the S protein.
33478625
(Euro Surveill)
PMID
33478625
Date of Publishing: 2021 Jan
Title Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69V70, France, August to December 2020
Author(s) nameBal A, Destras G et al.
Journal Euro Surveill
Impact factor
7.37
Citation count: 1
Date of Entry 2021 Aug 6


A rapid surge in cases of SARS-CoV-2 variant B.1.526 have been reported in New York state and, the variant spread to 32 states across the country. This variant has the E484K mutation and is resistant to neutralisation by convalescent plasma and vaccine sera. The activities of several antibodies (REGN10933 and LY-CoV555) which, are already in clinical use are either impaired or lost against E484K(NY5) pseudoviruses. The NY5(E484K) mutant also lowered the neutralizing activities of convalescent plasma or vaccine sera by 4.1 or 3.3-3.6 fold.
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PMID
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Date of Publishing: 2021 Apr 15
Title A Novel and Expanding SARS-CoV-2 Variant, B.1.526, Identified in New York
Date of Entry 18_35_03 Jul


The genomic and evolutionary charecteristics of the B.1.621 variant of interest (VOI) was assessed. Mutation of the B.1 lineage of the SARS-CoV-2 led to the rise and spread of the B.1.621 variants. These variants carry insertion 146N in the spike protein and other amino acid substitutions like Y144T, Y145Sand I95I in the N-terminal domain, R346K, E484K, N501Y in the Receptor Binding domian (RBD) and P681H in the S1/S2 cleavage site. No recombination events were reported from the whole genome.
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PMID
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Date of Publishing: 2021 May 21
Title Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2
Date of Entry 18_29_59 Jul


A sub-lineage of the Alpha variant (B.1.1.7) with a novel mutation in the Spike protein (D178H) accompanied with mutations in membrane protein (V70L) has been reported in the US. This might have accounted for the surge in the COVID-19 cases. Abrupt rise in cases can be attributed to poor sampling or super spreader events.
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PMID
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Date of Publishing: 2021 May 18
Title Rapidly emerging SARS-CoV-2 B.1.1.7 sub-lineage in the United States of America with spike protein D178H and membrane protein V70L mutations
Date of Entry 18_29_59 Jul


Whole genome sequencing and analysis showed that the Daxing strain shared 31 nucleotide substitutions when compared to the Wuhan sequence. Also, the 7 samples (from the Daxing outbreak) showed 28 nucleotide mutations which were first observed in the B.1.1.7 (Alpha variant).
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PMID
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Date of Publishing: 2021 May 08
Title COVID-19 cases from the first local outbreak of SARS-CoV-2 B.1.1.7 variant in China presented more serious clinical features: a prospective, comparative cohort study
Date of Entry 18_29_59 Jul


The evolutionary tree analysis of characteristic mutations in B.1.1.7 (alpha variant) revealed a non-coding deletion (g.a.28271) deletion mutation and its interaction with other mutations (g.gat28280cta, ORF1a:p.SGF3675-, S:p.P681H, and S:p.T716I). The 28271 nucleotide is located upstream of the start codon of the N gene. The non-coding deletion (g.a.28271), along with its interacting mutations (g.gat28280cta), alters the core KOZAK site in gene N and ORF9b. This may alters their translational efficiency thus, influencing viral transmission.
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PMID
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Date of Publishing: 2021 May 01
Title Evolutionary insights into a non-coding deletion of SARS-CoV-2 B.1.1.7
Date of Entry 18_29_59 Jul


A new variant of interest (VOI) was detected in three incoming travelers from Tanzania designated as A.VOI.V2. The A.VOI.V2 31 has 31 amino acid substitutions and 3 deletions in the spike protein. In addition, it also has 5 substitutions and 3 deletions in the N-terminal domain, some of them within the antigenic super site. 3 of 73 high quality records of SARS-CoV-2 sequenced genomes. These mutations are also present in other VOCs/VOIs like 501Y.V2/B.1.351, B.1.1.7, B.1.525 and C.16; and are suggested to be evolving under positive selection. This variant also shows high rate of transmission and resistance to neutralizing antibodies produced by both natural infection and vaccination.
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PMID
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Date of Publishing: 2021 Apr 04
Title A novel variant of interest of SARS-CoV-2 with multiple spike mutations detected through travel surveillance in Africa
Date of Entry 18_29_59 Jul


The West Coast variant had mutations in S-protein (L452R, S13I, and W152C) resulting in higher rate of transmissibility than other variants prelevant at that time. The higher transmissibility and reproductive numbers resulted in increased secondary household attacks. The other emerging variants were absent in all the samples collected. 1099 positive samples were derived from 12,124 tests
33688689
(medRxiv)
PMID
33688689
Date of Publishing: 2021 Mar 3
Title The emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco
Author(s) namePeng J, Mann SA et al.
Journal medRxiv
Impact factor
Cant find
Citation count: 1
Date of Entry 18_29_59 Jul


Novel variant 20A.EU2 was characterized by amino acid substitutions in the spike region (S447N) and nucleocapsid protein. This variant was predominant in France, Belgium, and Switzerland. Multiple variants with this S447N mutation might have emerged due to selective pressure by the host immune response.
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PMID
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Date of Publishing: 2021 Mar 24
Title Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Date of Entry 18_29_59 Jul


Novel variant 20E (EU1) was characterized by a spike mutation (A222V) as well as amino acid substitutions in the nucleocapsid protein. However, the mutations did not confer any transmission advantage on the variant. Cluster 20E (EU1) consisting of B.1.177 lineage was designated when a cluster of sequences in Clade 20A showed an additional mutation in spike (S:A222V).
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PMID
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Date of Publishing: 2021 Mar 24
Title Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Date of Entry 18_29_59 Jul


Three imported cases of the Alpha variant (B.1.1.7) from the UK to Spain with rapid household transmission related to one of the cases were reported. With reference to two UK original B.1.1.7 consensus, Imported cases (1, 2, 7 and 8) showed 4 to 6 SNPs whereas cases (3 to 6) involved in household transmission showed 1 to 4 SNPs, which were otherwise identical to the original strain. The mutations reported in the cases were consistent with the circulation of the alpha strain and import to Spain.
33685741
()
PMID
33685741
Date of Publishing: 2021 Feb 19
Title First confirmation of importation and transmission in Spain of the newly identified SARS-CoV-2 B.1.1.7 variant
Date of Entry 18_29_59 Jul


The emergent Alpha variant lineage in UK had a consistent epidemic growth and was declared as Variant of Concern(VOC).The S-gene mutations that resulted in S-gene target failures (SGTF) in RT-PCR which was characteristic to VOC lineage only. SGTF was characteristic to this lineage and was used as VOC biomarker in statistical studies of VOC and non-VOC samples.
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PMID
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Date of Publishing: 2021 Jan 04
Title Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking B.1.1.7 in England: Insights from linking epidemiological and genetic data
Date of Entry 18_29_59 Jul


Characterisation of Beta variant showed 8 lineage-defining mutations in the spike protein with 3 important mutation in the key residues (K417N, E484K and N501Y) of the Receptor binding domain (RBD). Compared to other strains circulating in South Africa, the Beta variant showed hypermutation in the whole genome and spike regions. Potential deletion of 3 amino acids at L242_244L was identified, but this site is still unresolved as it clashes with a L242H mutation in the studied sequences .
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PMID
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Date of Publishing: 2020 Dec 22
Title Emergence and rapid spread of a new severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) lineage with multiple spike mutations in South Africa
Date of Entry 18_29_59 Jul


Analysis of 12343 SARS-CoV-2 sequences from patients from 6 geographical locations led to the identification of 1234 mutations when compared to the reference sequence. ORF1ab 4715L and S protein 614G variants were postively correlated to fatality rates and number of infected cases. In BCG-vaccinated countries, the frequency of the S 614G variant was associated with higher fatality rate. Haplotype analysis using a linkage disequilibrium (LD) map for SARS-CoV-2 viral genomes showed that ORF1abP 4715L and S protein D 614G variants were in a nearly complete Linkage Disequillibrium (r^2 of LD = 0.98 and D =1.00).
32699345
(J Hum Genet)
PMID
32699345
Date of Publishing: 2020 Dec
Title SARS-CoV-2 genomic variations associated with mortality rate of COVID-19
Author(s) nameToyoshima Y, Nemoto K et al.
Journal J Hum Genet
Impact factor
2.942
Citation count: 13
Date of Entry 18_29_59 Jul


Primers and probes for multiplex RT-qPCR assay that helps in determining the N gene mutations associated with the Alpha variant (B.1.1.7 variant). The reverse primer and the probe were based on the CDC N1 reaction (https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html),
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PMID
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Date of Publishing: 2021 May 22
Title Rapid and high throughput RT-qPCR assay for identification and differentiation between SARS-CoV-2 variants B.1.1.7 and B.1.351.
Date of Entry 18_28_28 Jul


Primers and probes for multiplex RT-qPCR assay that helps in determining the spike protein mutations associated with the Beta variant (B.1.351 variant).
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PMID
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Date of Publishing: 2021 May 22
Title Rapid and high throughput RT-qPCR assay for identification and differentiation between SARS-CoV-2 variants B.1.1.7 and B.1.351.
Date of Entry 18_28_28 Jul