Mutation


Last updated: 2021 Nov 2
Total hit(s): 16
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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
Impact factor
N/A
Date of Entry 2021 Nov 2


Mutational analysis of the SARS-CoV-2 genome was carried out for better understanding of the epidemiology, transmission, and implications of mutations in the African population. ORF1ab polyprotein, spike glycoprotein, ORF3, ORF8, and nucleocapsid phosphoprotein have all been identified as mutational hotspots in the African population and may be of particular significance in SARS-adaptability CoV-2's to the human host. 1. Synonymous mutations that do not change amino acid residues were not accounted for in the current study. 2. Furthermore, because this genomic dataset only contains data from a single country in each of Central Africa and South Africa, some genomic diversity may go undetected.
Pre-print (bioRXiv)
Date of Publishing 2020 Sep 07
Title Mutational Analysis of SARS-CoV-2 Genome in African Population
Impact factor
N/A
Date of Entry 2021 Nov 2


In early 2021, routine genomic surveillance carried out in South Americadiscovered a deep-branching sublineage of Variant of Concern B.1.1.1, now known as Variant of Interest Lambda (C.37). Variants of Concern, on the other hand, were discovered less frequently in Peru over the first four months of 2021: Alpha, n=7, 0.5 percent; Gamma, n=17, 1.2 percent.
Pre-print ( medRXiv )
Date of Publishing 2021 Jul 03
Title The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America
Impact factor
N/A
Date of Entry 2021 Sep 30


In the RNA extracted from 4 waste water samples, 35 mutations were observed in the spike protein of the Delta variant. These mutations were present only in samples analyzed during second wave (Feb 2021), compared to that of first wave (Sep/Nov 2020) in India. The mutations in the present study were detected before the diagnosis of the first Delta variant case in March 2021 and were found to be similar to that of Delta variant (VOC-21APR-02; B.1.617.2 lineage). SARS-CoV-2 variant genomic surveillance in wastewater samples provides early detection of circulating new variants and their unexplained transmission.
Pre-print ( medRXiv )
Date of Publishing 2021 Jul 08
Title First detection of SARS-CoV-2 Delta variant (B.1.617.2) in the wastewater of (Ahmedabad), India
Impact factor
N/A
Date of Entry 2021 Sep 30


The establishment of a new SARS-CoV-2 lineage in South America, known as Variant of Interest (VOI) Lambda (C.37) was reported. It has seven nonsynonymous mutations in the Spike gene, as well as a deletion in the ORF1a gene, which is also present in the VOCs Alpha, Beta, and Gamma. From October to December 2020, sequencing of additional Peruvian samples is done to validate and date the origin of C.37. C.37 expansion has occurred in South America despite the existence of hundreds of circulating lineages and VOCs Alpha and Gamma, implying that this lineage is more transmissible.
Pre-print ( medRXiv )
Date of Publishing 2021 Jul 03
Title The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America
Impact factor
N/A
Date of Entry 2021 Sep 30


Six Membrane (M) gene mutations were identified in the SARS-CoV-2 B.1.575 lineage. The frequency of most mutations increased in February 2021 (upto 6.6%). Patients infected with the virus bearing one of the four M missense mutations are 4.6-6.3 years younger than those infected with the virus lacking any of the M mutations (37.138.8 vs. 43.4 years). Missense mutations were estimated to occur 3.1 times more frequently than synonymous mutations in the M gene, 2.7 times more frequently in E gene and 3.8 times in ORF6 gene.
tandfonline.com
Date of Publishing 2021 May 09
Title Emerging variants of concern in SARS-CoV-2 membrane protein: a highly conserved target with potential pathological and therapeutic implications
Impact factor
N/A
Date of Entry 2021 Sep 30


The D614G mutation was introduced into Spike-pseudotyped lentivirus and complete SARS-CoV-2 virus via site-directed mutagenesis. The D614G mutant was shown to be up to 8-fold more effective at infecting cells than wild-type. The Spike variants did not differ significantly in terms of ACE2 receptor binding, but the G614 variant is more resistant to proteolytic cleavage in vitro and in human cells than the D614. This could have an impact on the efficacy of immunizations based on spikes. The G614 variant was found to be ~2.5 fold more resistant to cleavage in the host cell than the D614 variant in cells expressing Spike by transient transfection. Virions with the G614 variant were seen to have less Spike cleavage compared to the D614 variant. No significant difference between Spike D614 and Spike G614 incorporation into pseudotyped lentiviral particles was observed.
32587969 (33570490)
(bioRxiv)
PMID
32587969 (33570490)
Date of Publishing: 2020 Jun 15
Title The Spike D614G mutation increases SARS-CoV-2 infection of multiple human cell types
Author(s) name Daniloski Z, Guo X, Sanjana NE.
Journal bioRxiv
Impact factor
N/A
Citation count: 2
Date of Entry 2021 Sep 13


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.
Pre-print ( medRXiv )
Date of Publishing 2021 Jun 28
Title Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination
Impact factor
N/A
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


Five patients with a travel history from the United Kingdom to India on December 22, 2020 who tested positive for SARS-CoV-2 had their samples sequenced. The difference in nucleotide proportion between the hCoV19/India/NIV P1 20203524/2020 and other GR clade SARS-CoV-2 sequences was 0.05 percent, indicating that isolate sequences differed. Four cases had low-grade fever with a mild headache from 2 days before testing of samples; while one case was asymptomatic. Clinical testing revealed all the samples to be positive for SARS-CoV-2.
33506252
(J Travel Med)
PMID
33506252
Date of Publishing: 2021 Feb 23
Title Isolation and characterization of the new SARS-CoV-2 variant in travellers from the United Kingdom to India: VUI-202012/01 of the B.1.1.7 lineage
Author(s) nameYadav PD, Nyayanit DA et al.
Journal J Travel Med
Impact factor
2.08
Citation count: 1
Date of Entry 2021 Aug 6


Out of 229 samples analysed, 2 different frameshift deletions were detected giving rise to 2 new variants. 6 sequences had a 34 nucleotide deletion (D34) at position 27267-27300 and 1 sequence had a 26 nucleotide deletion (D26) at position 27267- 27292. Both these deletions are in the open reading frame 6 (ORF6) of SARS CoV-2. These deletions have not been updated on the CoV-GLUE resource
33399033
(Emerg Microbes Infect)
PMID
33399033
Date of Publishing: 2021 Jan 5
Title Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster 1 during routine genomic surveillance, Lyon, France
Author(s) nameQuéromès G, Destras G et al.
Journal Emerg Microbes Infect
Impact factor
5.84
Citation count: 1
Date of Entry 2021 Aug 6


Screening for H69/V70, associated with a S-gene target failure (SGTF) was used to detect VOC 202012/01 (lineage B.1.1.7). Other mutations co-occurring with H69/V70 including S: N501Y, S477N were also identified by whole-genome sequencing. "GISAID database - (GISAID accession numbers: EPI_ISL_582112, EPI_ISL_582120) This strategy cannot identify other VOCs without H69/V70 as the variant 501Y.V2 (South Africa)"
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


The median Ct values of ORF and N-gene targets in the S-gene dropout samples was significanlty low when compared to samples with S-gene intact. This suggests high viral loads at the time of sampling.
Pre-print ( medRXiv )
Date of Publishing 2020 Dec 27
Title S-variant SARS-CoV-2 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-PCR
Impact factor
N/A
Date of Entry 2021 Aug 6


Genomic characterization of the Alpha variant revealed the presence of a lot of distinct mutations. Mutations like N501Y which increases ACE2 receptor affinity, P681H, deletion at 69-70 which is linked to immune evasion. In addition to these, there are 6 synonymous mutations-5 in ORF1b and 1 in the M gene. S1/S2 furin cleavage site of SARS-CoV-2 is not found in closely related coronaviruses, promotes entry into respiratory epithelial cells and transmission in animal models. Both N501Y and P681H have been observed independently but not to our knowledge in combination before now.
virological.org
Date of Publishing 2020 Dec 21
Title Preliminary genomic characterisation of an emergent SARS-CoV-2 lineage in the UK defined by a novel set of spike mutations
Impact factor
N/A
Date of Entry 2021 Aug 6


An engineered decoy ACE2 receptor shows high affinity to the receptor-binding domain (RBDs) in the binding site of SARS- CoV Residues. A deep mutational scan of the RBD reveals they are mutationally tolerant. The N501Y mutation found in the RBD of the alpha variant increases affinity for the wildtype ACE2 by 20-fold but remains tightly bound to the engineered ACE2. Due to its high activity and favourable properties for manufacturing, sACE22.v2.4 can be a good drug candidate for preclinical development.
33398275
(bioRxiv)
PMID
33398275
Date of Publishing: 2020 Dec 21
Title An engineered decoy receptor for SARS-CoV-2 broadly binds 2 protein S sequence variants
Author(s) nameChan KK, Tan TJC et al.
Journal bioRxiv
Impact factor
N/A
Citation count: 1
Date of Entry 2021 Aug 6


The enhanced transmissibility of viruses with deletions in the spike including, deletion H69/V7011, increases spike mediated infectivity by two-fold and stabilises other S gene mutations. This deletion mutation is usually followed by amino acid replacement in the spike (N501Y, N439K, Y453F)
Pre-print ( bioRXiv )
Date of Publishing 2020 Dec 21
Title Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion H69/V70
Impact factor
N/A
Date of Entry 2021 Aug 6