New variant


Last updated: 2021 Sep 13
Total hit(s): 103
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Original Article
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The D614G spike mutation results in increased viral transduction. However, there was no change in the binding profiles of soluble D614 and G614 spike to human ACE2. The two dissociation constants (KD) were: KD1 = 8.45 nM and KD2 = 127 nM for D614 variant, and KD1 = 18.0 nM and KD2 = 92.7 nM for G614 variant.
32587969
(bioRxiv)
PMID
32587969
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
Its not a journal
Citation count: 2
Date of Entry 2021 Sep 13


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
(bioRxiv)
PMID
32587969
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
Its not a journal
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.
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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


The goal of this investigation was to see if COVID-19 convalescent people' CD8++ T-cell responses detect SARS-CoV-2 variants. Out of 45 mutations tested, only one matched a low-prevalence CD8++ epitope from the B.1.351 Spike. This means that nearly all anti-SARS-CoV-2 CD8++ T-cell responses should be able to recognise the newly identified variations.
33594378
(medRxiv)
PMID
33594378
Date of Publishing: 2021 Feb 12
Title New research: T cells of earlier Covid-19 patients recognise all 3 major new variants
Author(s) nameRedd AD, Nardin A et al.
Journal medRxiv
Impact factor
Cant find
Citation count: 1
Date of Entry 2021 Sep 13


G-variant of the SARS-CoV-2 was highly prevalent in Brazil and the use of a SEIR model that could be used to predict future outbreaks in infected countries was highlighted in the study. The spread of COVID-19 in Brazil was taken as the first case study, where 2 lineages of SARS-CoV-2 and time-varying reproduction number were considered. Prediction of the second outbreak at end of 2020 was due to the release of NPIs across Brazil. The importance of NPIs, continuous genomic surveillance to monitor SARS-CoV-2 mutations in the development of immunological interventions was highlighted.
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PMID
-
Date of Publishing: 2020 Dec 10
Title The Impact of SARS-CoV-2 Variant to COVID-19 Epidemic in Brazil
Date of Entry 2021 Sep 13


Antibodies from vaccinated, convalescent individuals and critical COVID-19 patients was used to test the neutralising capacity aginst different SARS-CoV-2 variants. The convalescent and critical COVID-19 patients showed no significant change in the neutralsing capacity against the wild type and B.1.1.241 variant, however, a significant decrease in neutralisation against the Alpha variant (B.1.1.7) was observed. All participants showed a decrease in the neutralisation against the Beta variant (B.1.351). The large time disparities between the three examined populations in terms of post-infection or immunisation limit the interpretation of the differences in results between the three groups.
34176436
(Emerg Microbes Infect)
PMID
34176436
Date of Publishing: 2021 Dec
Title Live virus neutralisation testing in convalescent patients and subjects vaccinated against 19A, 20B, 20I/501Y.V1 and 20H/501Y.V2 isolates of SARS-CoV-2
Author(s) nameSaade C, Gonzalez C et al.
Journal Emerg Microbes Infect
Impact factor
5.84
Citation count: 3
Date of Entry 2021 Sep 13


The neutralizing ability of sera from the vaccinated individuals (Pfizer vaccine) against different SARS-CoV-2 spike variants was determined. There was no significant change in the neutralising activity against the wildtype (USA-WA1/2020), B.1.1.7-spike+ E484K and B.1.526-spike viruses. The neutralization of B.1.429-spike was slightly lower. Despite repeated alterations, the majority of newly developed SARS-CoV-2 variants are vulnerable to the vaccine-elicited immune response, emphasising the significance of widespread vaccination to combat the Covid pandemic.
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PMID
-
Date of Publishing: 2021 Jul 29
Title BNT162b2 - Elicited Neutralization against New SARS-CoV-2 Spike Variants
Date of Entry 2021 Sep 13


The disease outcomes of patients infected with B.1.1.7, B.1.351, and B.1.617.2 with those with wild-type strains were compared. B.1.617.2 infection was associated with lower PCR Ct values and longer viral shedding. B.1.617.2 infection was associated with higher chances of oxygen requirement, ICU admission or death. There were a number of vaccine breakthrough infections in the cohort, all patients infected with VOC, post-vaccination suffered from mild disease.
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PMID
-
Date of Publishing: 2021 Jun 07
Title Clinical and Virological Features of SARS-CoV-2 Variants of Concern: A Retrospective Cohort Study Comparing B.1.1.7 (Alpha), B.1.315 (Beta), and B.1.617.2 (Delta)
Date of Entry 2021 Sep 13


The NVX-CoV2373 vaccine was efficacious and induced some cross-protection against infection caused by the SARS-CoV-2 beta variant (B.1.351). Among the HIV negative participants, the post-hoc vaccine efficacy against the beta variant was 51%.
33951374
(N Engl J Med)
PMID
33951374
Date of Publishing: 2021 May 5
Title Efficacy of NVX-CoV2373 Covid-19 Vaccine against the B.1.351 Variant
Author(s) nameShinde V, Bhikha S et al.
Journal N Engl J Med
Impact factor
37.91
Citation count: 11
Date of Entry 2021 Sep 13


The efficacy of the Pfizer BNT-162b2 vaccine against SARS-CoV-2 mutants (RBD) was tested in convalescent, uninfected and vaccinated individuals. Vaccinated individuals showed a robust humoral response with high IgG antibody titers, however, they had reduced neutralizing activity against Beta variant (B.1.351) of SARS-CoV-2. Future vaccines should focus on the most prevailing RBD mutations of SARS-CoV-2 variants which are bypassing the existing strategies.
34035301
(Nat Commun)
PMID
34035301
Date of Publishing: 2021 May 25
Title Immune response to SARS-CoV-2 variants of concern in vaccinated individuals
Author(s) nameBecker M, Dulovic A et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 2
Date of Entry 2021 Sep 13


The neutralizing ability of the Sputnik V vaccine against B.1.1.7 and B.1.351 variants was determined by examining serum samples of the Sputnik V vaccine recipients. The majority of the samples showed good neutralising potency against the wild type and Alpha variants of SARS-CoV-2. However, the same set of sera showed moderate or very low activity against E484K substitution alone as well as for B.1.351 variant. Updated vaccines may be beneficial for the control of some emergent SARS-CoV-2 variants.
33851150
(Res Sq)
PMID
33851150
Date of Publishing: 2021 Apr 8
Title Neutraizing activity of Sputniv V vaccine sera against SARS-CoV-2 variants
Author(s) nameIkegame S, Siddiquey M et al.
Journal Res Sq
Impact factor
Cant find
Citation count: 1
Date of Entry 2021 Sep 13


Potential amino acid change which results in escape mutants in SARS-CoV were recreated by a mutation in the SARS-CoV-2 Spike. The 12 pseudotypes were screened against a panel of monoclonal antibodies (mAbs). Three pseudotypes encoding RFA346-8KFP, S459G, and ST477-8GK were not neutralised by the mAbs panel. Nine pseudotypes virus showed neutralisation for at least one mAb. The mAbs were mapped into clusters based on their competency to bind to the spike target site. Eight clusters comprised of neutralizing mAbs (I, III, IV, VI, VII, IX, X, XI), five of which target the RBD (I, III, VI, VII, IX), and three clusters contain only non-neutralizing mAbs (II, V and VIII).
33713594
(Cell Rep)
PMID
33713594
Date of Publishing: 2021 Mar 23
Title The impact of Spike mutations on SARS-CoV-2 neutralization
Author(s) nameRees-Spear C, Muir L et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 10
Date of Entry 2021 Aug 6


The Alpha variant B.1.1.7 pseudotype was evaluated for neutralization sensitivity to serum samples obtained from mild/asymptomatic healthcare workers and severely SARS-CoV2 affected hospitalized cohorts. The fold decrease in potency was greater for the hospitalized samples than the mild illness cohorts.
33713594
(Cell Rep)
PMID
33713594
Date of Publishing: 2021 Mar 23
Title The impact of Spike mutations on SARS-CoV-2 neutralization
Author(s) nameRees-Spear C, Muir L et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 10
Date of Entry 2021 Aug 6


The serum from 18 seropositive healthcare workers with mild or severe SARS-CoV-2 infection were assessed for neutralization potency against the 7 potential escape mutations on spike protein. All samples except one showed good neutralising potency to the spike mutations and were found to be less impacted over the spike mutations against the individual mAbs. The samples were representatives with intermediate (1:50-100), strong (1:100-1000) and potent (>1:1000) neutralizing ID50 values. The median serum ID50 for hospitalized patients selected was 1:1275, and that for selected mild/asymptomatic cases was 1:1045.
33713594
(Cell Rep)
PMID
33713594
Date of Publishing: 2021 Mar 23
Title The impact of Spike mutations on SARS-CoV-2 neutralization
Author(s) nameRees-Spear C, Muir L et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 10
Date of Entry 2021 Aug 6


The neutralising potency of a panel of monoclonal antibodies (mAbs) were assessed against the SARS-CoV-2 Alpha variant (B.1.1.7) pseudovirus. This variant lowered the potency of three mAbs- COVA2-17, COVA1-12 and COVA1-21. These mAbs belonged to distinct clusters and do not compete for binding to the same epitope.
33713594
(Cell Rep)
PMID
33713594
Date of Publishing: 2021 Mar 23
Title The impact of Spike mutations on SARS-CoV-2 neutralization
Author(s) nameRees-Spear C, Muir L et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 10
Date of Entry 2021 Aug 6


Potential amino acid change which results in escape mutants in SARS-CoV were recreated by a mutation in the SARS-CoV-2 Spike. The 12 pseudotypes were screened against a panel of monoclonal antibodies (mAbs). Pseudotype virus encoding the S494D showed absolutely no neutralization activity to both COVA2-29 (cluster I) and COVA1-12 (cluster VI) mAbs. The mAbs were mapped into clusters based on their competency to bind to the spike target site. Eight clusters comprised of neutralizing mAbs (I, III, IV, VI, VII, IX, X, XI), five of which target the RBD (I, III, VI, VII, IX), and three clusters contain only non-neutralizing mAbs (II, V and VIII).
33713594
(Cell Rep)
PMID
33713594
Date of Publishing: 2021 Mar 23
Title The impact of Spike mutations on SARS-CoV-2 neutralization
Author(s) nameRees-Spear C, Muir L et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 10
Date of Entry 2021 Aug 6


Potential amino acid change which results in escape mutants in SARS-CoV were recreated by a mutation in the SARS-CoV-2 Spike. The 12 pseudotypes were screened against a panel of monoclonal antibodies (mAbs). Pseudotype virus expressing the LF455YL showed reduced neutralization activity to a wide range of RBD-specific mAbs from different clusters- COVA2-29 (cluster I), COVA2-07 (cluster III) and COVA1-12 (cluster VI). The mAbs were mapped into clusters based on their competency to bind to the spike target site. Eight clusters comprised of neutralizing mAbs (I, III, IV, VI, VII, IX, X, XI), five of which target the RBD (I, III, VI, VII, IX), and three clusters contain only non-neutralizing mAbs (II, V and VIII).
33713594
(Cell Rep)
PMID
33713594
Date of Publishing: 2021 Mar 23
Title The impact of Spike mutations on SARS-CoV-2 neutralization
Author(s) nameRees-Spear C, Muir L et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 10
Date of Entry 2021 Aug 6


Potential amino acid change which results in escape mutants in SARS-CoV were recreated by a mutation in the SARS-CoV-2 Spike. The 12 pseudotypes were screened against a panel of monoclonal antibodies (mAbs). Pseudotype virus with L452K showed no neutralization activity to the cluster I mAb COVA2-29. The mAbs were mapped into clusters based on their competency to bind to the spike target site. Eight clusters comprised of neutralizing mAbs (I, III, IV, VI, VII, IX, X, XI), five of which target the RBD (I, III, VI, VII, IX), and three clusters contain only non-neutralizing mAbs (II, V and VIII).
33713594
(Cell Rep)
PMID
33713594
Date of Publishing: 2021 Mar 23
Title The impact of Spike mutations on SARS-CoV-2 neutralization
Author(s) nameRees-Spear C, Muir L et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 10
Date of Entry 2021 Aug 6


Potential amino acid change which results in escape mutants in SARS-CoV were recreated by a mutation in the SARS-CoV-2 Spike. The 12 pseudotypes were screened against a panel of monoclonal antibodies (mAbs). Pseudotype virus encoding the KVG444-6TST, a multiple substitution shows reduced neutralization potency (3.7-fold) for mAb COVA2-29, a cluster I RBD-specific antibody. The mAbs were mapped into clusters based on their competency to bind to the spike target site. Eight clusters comprised of neutralizing mAbs (I, III, IV, VI, VII, IX, X, XI), five of which target the RBD (I, III, VI, VII, IX), and three clusters contain only non-neutralizing mAbs (II, V and VIII).
33713594
(Cell Rep)
PMID
33713594
Date of Publishing: 2021 Mar 23
Title The impact of Spike mutations on SARS-CoV-2 neutralization
Author(s) nameRees-Spear C, Muir L et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 10
Date of Entry 2021 Aug 6


Potential amino acid change which results in escape mutants in SARS-CoV were recreated by a mutation in the SARS-CoV-2 Spike. The 12 pseudotypes were screened against a panel of monoclonal antibodies (mAbs). Pseudotype virus encoding the K417V substitution mutation showed reduced neutralising potency to the cluster III RBD-specific mAb COVA2-07. No neutralization activity was observed with mAb COVA2-04. The mAbs were mapped into clusters based on their competency to bind to the spike target site. Eight clusters comprised of neutralizing mAbs (I, III, IV, VI, VII, IX, X, XI), five of which target the RBD (I, III, VI, VII, IX), and three clusters contain only non-neutralizing mAbs (II, V and VIII).
33713594
(Cell Rep)
PMID
33713594
Date of Publishing: 2021 Mar 23
Title The impact of Spike mutations on SARS-CoV-2 neutralization
Author(s) nameRees-Spear C, Muir L et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 10
Date of Entry 2021 Aug 6


Potential amino acid change which results in escape mutants in SARS-CoV were recreated by a mutation in the SARS-CoV-2 Spike. The 12 pseudotypes were screened against a panel of monoclonal antibodies (mAbs). A complete loss of neutralising activity of the cluster III RBD-specific mAb COVA1-16 was observed with the pseudotyped virus with P384A substitution The mAbs were mapped into clusters based on their competency to bind to the spike target site. Eight clusters comprised of neutralizing mAbs (I, III, IV, VI, VII, IX, X, XI), five of which target the RBD (I, III, VI, VII, IX), and three clusters contain only non-neutralizing mAbs (II, V and VIII).
33713594
(Cell Rep)
PMID
33713594
Date of Publishing: 2021 Mar 23
Title The impact of Spike mutations on SARS-CoV-2 neutralization
Author(s) nameRees-Spear C, Muir L et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 10
Date of Entry 2021 Aug 6


The L452R and Y453F mutants were able to evade the cell-mediated HLA-A*24:02-restricted Cytotoxic T lymphocytes (CTL) responses as well as acquired immunity(humoral immunity) of the host during infection These mutants were able to escape both natural and acquired immune systems and also had a higher virulence factor proving their lethality. The increased binding affinity of the ACE2 receptor eventually increased the virulence and viral replication factors. L452R mutation increased protein stability, viral infectivity, and potentially promotes viral replication. L452R mutant also showed increased infectivity in pseudoviruses.
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PMID
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Title An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity
Date of Entry 2021 Aug 6


SARS-CoV-2 Delta variant presented the highest risk among the currently circulating strains, even in vaccinated individuals. Two Indian patients transmitted the Delta variant to 5 wedding guests in Houston, USA. The observations in the study indicate cases of vaccine breakthrough since there was no history of vaccine failure in the infected individuals.
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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


Structure analysis of SARS-CoV-2 N439K Receptor Binding Domain (RBD) in complex with hACE2 at 2.8 resolution showed strong non-covalent salt bridges. These bridges enhanced the binding for hACE2 in the N439K variant, as similar to the SARS-CoV N439R variant. Double mutants of N439K/R and K417V mutations show that salt bridge loss at RBD position 417 is compensated by the one at position 439. This results in hACE2 affinity similar to the wild type. Methods used for study: X-ray structure, Surface plasmon resonance (SPR)
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