Variants : Spike
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Original Article
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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.
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 		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
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.
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 		Pre-print ( medRXiv )
Date of Publishing 2021 Jul 03
Title The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America
Date of Entry 2021 Sep 30

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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 		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
Date of Entry 2021 Sep 13

In individuals vaccinated either with BNT162b2 or ChAdOx1, there was a significant reduction of neutralisation of B.1.617.1, B.1.617.2 and B.1.351 variants by 4.31, 5.11 and 6.29-folds respectively when compared to the Wuhan-Hu-1 variant. The mean antibody titres against the 3 VOCs analysed was higher in sera of individuals vaccinated with BNT162b2 when compared to ChAdOx1. Two doses of the Pfizer vaccine induced higher neutralising antibody titres against the Wuhan-hu-1 and the 3 VOCs compared to a single dose of BNT162b2 or two doses of the ChAdOx1 vaccine.
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 		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
Date of Entry 2021 Aug 6

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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 		Pre-print (medRXiv)
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 2021 Jul 2

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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 		Pre-print ( medRXiv )
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 2021 Jul 2

Phylogenetic analysis of a sub-lineage of SARS-CoV-2 Alpha variant (B.1.1.7) showed that this lineage emerged through sequential acquisitions of mutation in the membrane (M:V70L) in November 2020 followed by the novel spike mutation (S:D178H) in February 2021. SARS-CoV-2 viral sequencing should be carried on a widespread scale to detect new mutations of concern.
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 		Pre-print ( medRXiv )
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 2021 Jul 2

The transmission of the SARS-CoV-2 Alpha variant (B.1.1.7) was exclusive to the US where the majority of COVID-19 transmission routes were contributed by California, Washington, and Ohio as compared to the other states. Super spreader events can be one of the possible reasons of sudden rise in cases.
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 		Pre-print ( medRXiv )
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 2021 Jul 2

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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 		Pre-print ( medRXiv )
Date of Publishing 2021 May 21
Title Characterization of the emerging B.1.621 variant of interest of SARS-CoV-2
Date of Entry 2021 Jul 2

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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 		Pre-print ( medRXiv )
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 2021 Jul 2

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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 		Pre-print ( medRXiv )
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 2021 Jul 2

The new VOI detected in 3 incoming travelers from Tanzania revealed identical genomes and presented highly divergent sequences within the A lineage (PANGO lineage B.1.351). 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.
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 		Pre-print ( medRXiv )
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 2021 Jul 2

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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 		Pre-print ( medRXiv )
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 2021 Jul 2

The SARS-CoV-2 Beta variant (501Y.V2) emerged in the Nelson Mandela Bay of South Africa between July and August, which was associated with a greater number of cases by early November when compared to the three main older circulating strains. The Beta variant was the dominant circulating strain in Eastern and Western Cape, owing to the rapid surge in SARS-CoV-2 infections.
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 		Pre-print ( medRXiv )
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 2021 Jul 2

A222V mutations in the spike region do not lead to very large increases in the spike-pseudotyped lentiviruses but show a 1.3-fold higher titer than the wild type. However, the 20E (EU1) variant does not gain any transmission advantage over the variant with the D614G mutation. Lentiviral particles pseudotyped with the D614G spike mutation showed very large titers, which seem to have increased the transmission fitness of the SARS-CoV-2 variant.
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 		Pre-print (medRXiv)
Title Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Date of Entry 2021 Jul 2

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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 		Pre-print ( medRXiv )
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 2021 Jul 2

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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 		Pre-print ( medRXiv )
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 2021 Jul 2

The A222V substitution in the spike protein of the 20E (EU1) variant did not affect its antigenicity, conformation, or stability. The receptor binding domain (RBD)-specific antibodies like S309 neutralized the A222V bearing spike variant in similar capacity to that of the wild type spike protein..
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 		Pre-print ( medRXiv )
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 2021 Jul 2

The A222V substitution in the spike protein of the 20E (EU1) variant did not affect its antigenicity, conformation, or stability. The receptor binding domain (RBD)-specific antibodies like S2E12 neutralized the A222V bearing spike variant in similar capacity to that of the wild type spike protein.. S2E12 and S309 antibodies were serially diluted in a 1:3 ratio with Tris buffered saline with Tween (TBST- 1000nM).
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 		Pre-print ( medRXiv )
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 2021 Jul 2

A222V mutation in the spike neither enhance any of the antigenic properties of the 20E (EU1) variant nor showed any substantial effect on the neutralization of the N-terminal domain (NTD)-specific 4A8 antibody.
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 		Pre-print ( medRXiv )
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 2021 Jul 2

SARS-CoV-2 Delta variant has a higher replication fitness compared to Alpha variant as studied in in-vitro respiratory SARS-CoV-2 models. The Delta vs Alpha RNA ratio increased from 1.7 on day 1 to 3.1 on day 5. The furin cleavage site mutation P681R plays a key function in increasing the Delta variant's replication in basic human airway cultures.
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 		Pre-print ( bioRXiv )
Title Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant
Date of Entry 2021 Sep 30

The N501Y mutation in the Alpha variant helps in escaping from some neutralising antibodies like RBD-chAB25. However, antibodies RBD-chAb15 and 45 remained highly effective as ACE2 binding inhibitors
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 		Pre-print ( bioRXiv )
Date of Publishing 2021 May 12
Title Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations
Date of Entry 2021 Sep 30

The binding kinetics of the spike protein of alpha variant and spike of the D614G variant was compared by biolayer interferometry (BLI). A 2-fold decrease was observed in the dissociation constant (Kd) of spike in the alpha variant (Kd=1.3nM) compared to the D614G variant (Kd=3.1nM).
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 		Pre-print ( bioRXiv )
Title Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations
Date of Entry 2021 Aug 6

The T-cell responses to the wild-type spike protein were more robust in vaccinated individuals when compared to convalescent patients.
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 		Pre-print (bioRXiv)
Date of Publishing 2021 May 03
Title SARS -CoV-2 T-cell immunity to variants of concern following vaccination
Date of Entry 2021 Jul 2

Decreased T-cell responses were observed in response to the spike protein from 3 variants of the virus -B.1.1.7, B.1.351, and B.1.1.248 (when compared to wildtype spike) in vaccinated individuals
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 		Pre-print (bioRXiv)
Date of Publishing 2021 May 03
Title SARS -CoV-2 T-cell immunity to variants of concern following vaccination
Date of Entry 2021 Jul 2


Mucormycosis : Spike
Total row(s): 1
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Original Article
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The rate of cases presenting with rhino-orbital-cerebral mucormycosis (ROCM) to a tertiary care centre increased during the first wave of the coronavirus disease 2019 (COVID-19) pandemic. The number of cases identified during this interval was substantially higher than those described in the literature in other locations in the pre-pandemic era . The number of cases identified during the chosen timeframe is significantly larger than the numbers recorded in the literature in diverse contexts in the pre-pandemic era during similar intervals (range, one to two instances). Impaired host defences against the fungus due to viral-induced lymphopenia or the therapeutic use of corticosteroids and/or hydroxychloroquine, both of which are likely to impair phagocytic immune-cell response (which is the main defence mechanism against mucormycosis)could be possible forinvolvement ofCOVID-19 in the development of ROCM.
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 		34124087
(Front Med (Lausanne))
PMID
34124087
Date of Publishing: 2021
Title Spike in Rhino-Orbital-Cerebral Mucormycosis Cases Presenting to a Tertiary Care Center During the COVID-19 Pandemic
Author(s) nameFouad YA, Abdelaziz TT et al.
Journal Front Med (Lausanne)
Impact factor
3
Citation count: 15
Date of Entry 2021 Oct 30


Vaccine : Spike
Total row(s): 15
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Original Article
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A lipid nanoparticle-encapsulated and nucleoside-unmodified mRNA (mRNA-LNP) vaccine encoding the trimerized RBD (RBD trimer), elicits strong plasma B cell response. The RBD trimer mRNA vaccine modulates the antibody response toward more conserved regions on the RBD, hence overcoming the escape mutations that attenuate the efficacy of vaccines in mouse models. The vaccine protects K18-hACE2 mice from death after infection with live SARS-CoV-2 WT D614, B.1.351, and B.1.617.2 variants. B.1.351- and B.1.617.2-infected control animals demonstrated significantly higher levels of viral load than the RBD-trimer-vaccinated animals. The protectivity of the vaccine was correlated with RBD-specific B cell responses especially the long-lived plasma B cells in bone marrow, strong ability in triggering BCR clustering, and downstream signaling. Monoclonal antibodies isolated from vaccinated animals demonstrated broad and potent neutralizing activity against VOCs tested. The results suggest the existence of highly conserved and vulnerable regions within the RBD that could be precisely targeted for the development of next-generation vaccines capable of inducing broad and protective immunity against SARS-CoV-2 variants.
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 		35291264
(iScience)
PMID
35291264
Date of Publishing: 2022 Apr 15
Title RBD trimer mRNA vaccine elicits broad and protective immune responses against SARS-CoV-2 variants
Author(s) nameLiang Q, Wang Y et al.
Journal iScience
Impact factor
4.447
Citation count: 1
Date of Entry 2022 Jul 13

The median anti-S1 antibody level in the patients (median age 68 years; interquartile range (IQR), 53-76 years; 65 percent men) was 284 [IQR, 83-1190] AU/mL after the second dose and 7,554 [IQR, 2,268-11,736] AU/mL after the third dose. After receiving the second dose of the vaccine, three patients were nonresponders (anti-S1 antibody level 0.8 AU/mL) and 12 had weak responders (anti-S1 antibody level 0.8-50 AU/mL). One of the three original nonresponders produced anti-spike antibody after the third treatment, while all 12 initial weak responders had an increase in antibody levels. Antibody levels were lower after the second dosage and there was more time between the second and third doses in patients who experienced a higher increase in anti-S1 antibody levels after the third dose.
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 		34508833
(Am J Kidney Dis)
PMID
34508833
Date of Publishing: 2021 Sep 8
Title SARS-CoV-2 Antibody Response After a Third Dose of the BNT162b2 Vaccine in Patients Receiving Maintenance Hemodialysis or Peritoneal Dialysis
Author(s) nameBensouna I, Caudwell V et al.
Journal Am J Kidney Dis
Impact factor
5.59
Citation count: 25
Date of Entry 2022 Aug 26

Following two doses of AZD1222, spike-specific CD4+ T cell helper type 1 (Th1) and CD8+ T-cell responses were significantly increased in AZD1222-vaccinated persons of all ages.
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 		34189538
()
PMID
34189538
Title T-cell mediated immunity after AZD1222 vaccination: A polyfunctional spike-specific Th1 response with a diverse TCR repertoire
Date of Entry 2021 Oct 30

In a phase 1 trial, the adjuvanted sclamp subunit vaccine was found to be safe and free from severe solicited adverse reactions. Similar frequency of adverse events were observed in the placebo and the vaccine group, irrespective of the vaccine dosage. The data are reported are up unitl day 57. The MF59-adjuvanted vaccine was found to be safe and elicited a good antigen-specific immune response.
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 		33887208
(Lancet Infect Dis)
PMID
33887208
Date of Publishing: 2021 Apr 19
Title Safety and immunogenicity of an MF59-adjuvanted spike glycoprotein-clamp vaccine for SARS-CoV-2: a randomised, double-blind, placebo-controlled, phase 1 trial
Author(s) nameChappell KJ, Mordant FL et al.
Journal Lancet Infect Dis
Impact factor
21.77
Citation count: 30
Date of Entry 2021 Sep 27

In phase 1 trial, two doses of SARS-CoV-2 sclamp vaccine, at all doses (5, 15 and 45ug) induced a robust neutralising immune response and a spike glycoprotein-specific T-cell response, which indicates protection against SARS-CoV-2 infection. The presence of the glycoprotein 41 peptide in the clamp caused HIV diagnostic assay interference, posing a potential obstacle to successful implementation and highlighting the need of non-spike directed immunogenicity during vaccine development. Alternative molecular clamp trimerisation domains are being studied to improve this response.
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 		33887208
(Lancet Infect Dis)
PMID
33887208
Date of Publishing: 2021 Apr 19
Title Safety and immunogenicity of an MF59-adjuvanted spike glycoprotein-clamp vaccine for SARS-CoV-2: a randomised, double-blind, placebo-controlled, phase 1 trial
Author(s) nameChappell KJ, Mordant FL et al.
Journal Lancet Infect Dis
Impact factor
21.77
Citation count: 30
Date of Entry 2021 Sep 27

In a phase 2 placebo-controlled clinical trial, the mRNA-1273 vaccine induced good immune responses in young adults aged 18 and older. Anti-SARS-CoV-2 spike binding and neutralising antibodies were induced by both doses of the vaccine within 28 days of the first injection and increased to peak titers by 14 days after the second dose. The neutralising antibody levels were higher than levels found in convalescent sera. The mRNA-1273 vaccine was found to be safe and did not induce major adverse events. Longer the interval between the 2 doses, better the induction of antibodies.
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 		33707061
(Vaccine)
PMID
33707061
Date of Publishing: 2021 May 12
Title A preliminary report of a randomized controlled phase 2 trial of the safety and immunogenicity of mRNA-1273 SARS-CoV-2 vaccine
Author(s) nameChu L, McPhee R et al.
Journal Vaccine
Impact factor
3.31
Citation count: 64
Date of Entry 2021 Oct 30

Immunization of mice (C57BL/6 and BALB/c strains) and Pigs with RBD-SpyVLP vaccine showed strong dose-dependent neutralising antibody response. The polyclonal antibody response could recognize key epitopes on RBD (Receptor-Binding Domain). Besides, this vaccine is found to be thermostable making it easier for transportation globally.
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 		33483491
(Nat Commun)
PMID
33483491
Date of Publishing: 2021 Jan 22
Title A COVID-19 vaccine candidate using SpyCatcher multimerization of the SARS-CoV-2 spike protein receptor-binding domain induces potent neutralising antibody responses
Author(s) nameTan TK, Rijal P et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 69
Date of Entry 2021 Oct 31

Mice immunized with adjuvanted NVX-CoV2373 had significantly higher anti-S IgG titers with good neutralizing activity and blocked the hACE-2 receptor. Mice immunized with adjuvanted vaccine (both single and booster dose) were significantly protected from weight loss when compared to the palcebo treated mice.
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 		33446655
(Nat Commun)
PMID
33446655
Date of Publishing: 2021 Jan 14
Title SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice
Author(s) nameTian JH, Patel N et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 142
Date of Entry 2021 Nov 12

Olive baboons immunized with adjuvanted NVX-CoV2373 showed high titer Anti-S antibodies with good neutralizing activity and blocked the hACE-2 receptor. NVX-CoV2373 vaccine induced binding and functional antibodies in a nonhuman primate at levels comparable or higher than individuals recovered from COVID-19 and is a promisin vaccine candidate
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 		33446655
(Nat Commun)
PMID
33446655
Date of Publishing: 2021 Jan 14
Title SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice
Author(s) nameTian JH, Patel N et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 142
Date of Entry 2021 Nov 12

A prefusion-stabilized SARS-CoV-2 spike protein, S-2P was most successful in generating antibodies that neutralised pseudovirus and wild-type live virus when combined with CpG 1018 and aluminium hydroxide adjuvants, with no vaccine-related side effects.
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 		33208827
(Sci Rep)
PMID
33208827
Date of Publishing: 2020 Nov 18
Title Development of CpG-adjuvanted stable prefusion SARS-CoV-2 spike antigen as a subunit vaccine against COVID-19
Author(s) nameKuo TY, Lin MY et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 39
Date of Entry 2021 Oct 31

In a phase 1 trial, two types of RNA based vaccines were tested: a) BNT162b2, coding for membrane-bound full-length spike protein; b) BNT162b1 coding secreted domain which is trimerized. Milder systemic events were found with BNT162b2. Hence BNT162b2 was chosen for the next phase of trials. 1. 100ug dose of vaccine was included in the clinical trial study but was discontinued after one dose because of reactogenicity in the participants ( BNT162b1 vaccine and placebo)
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 		33053279
(N Engl J Med)
PMID
33053279
Date of Publishing: 2020 Dec 17
Title Safety and Immunogenicity of Two RNA-Based Covid-19 Vaccine Candidates
Author(s) nameWalsh EE, Frenck RW Jr et al.
Journal N Engl J Med
Impact factor
37.91
Citation count: 923
Date of Entry 2021 Jun 22

In a phase 1/2 trial, NVX-CoV2373, a recombinant severe acute respiratory syndrome coronavirus 2 (rSARS-CoV-2) nanoparticle vaccine was found to be safe and elicited an immune response that exceeded levels in COVID-19 convalescent serum. The adjuvanted, recombinant, full-length spike protein nanoparticle vaccine NVX-CoV2373 was found to be a safe in adult participants in the age group of 18-59 and is a promising vaccine candidate.
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 		32877576
(N Engl J Med)
PMID
32877576
Date of Publishing: 2020 Dec 10
Title Phase 1-2 Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine
Author(s) nameKeech C, Albert G et al.
Journal N Engl J Med
Impact factor
37.91
Citation count: 502

In a phase 1/2 trial, NVX-CoV2373, a recombinant severe acute respiratory syndrome coronavirus 2 (rSARS-CoV-2) nanoparticle vaccine was found to be safe and elicited an immune response that exceeded levels in COVID-19 convalescent serum. By day 35, a strong correlation was observed between neutralising antibody titres and anti-spike IgG Geometric mean ELISA units (GMEs) with adjuvanted vaccine (correlation, 0.95). This was comparable to that of convalescent serum (correlation, 0.96).
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 		32877576
(N Engl J Med)
PMID
32877576
Date of Publishing: 2020 Dec 10
Title Phase 1-2 Trial of a SARS-CoV-2 Recombinant Spike Protein Nanoparticle Vaccine
Author(s) nameKeech C, Albert G et al.
Journal N Engl J Med
Impact factor
37.91
Citation count: 502

In a phase 1/2 trial, ChAdOx1 nCoV-19 vaccine induced both cellular and humoral immune responses. Spike-specific T cells responses were detectable by day 14 and spike-specifc IgG antibodies were detectable by day 28. Both responses were boosted after the second dose. Neutralising antibody responses were seen in all participants after the booster dose.
✍
 		32702298
(Lancet)
PMID
32702298
Date of Publishing: 2020 Aug 15
Title Safety and immunogenicity of the ChAdOx1 nCoV-19 vaccine against SARS-CoV-2: a preliminary report of a phase 1/2, single-blind, randomised controlled trial
Author(s) nameFolegatti PM, Ewer KJ et al.
Journal Lancet
Impact factor
43.38
Citation count: 1005
Date of Entry 2021 Aug 3

a single dose of the INO-4800 DNA vaccine was able to induce antigen specific T cell responses and neutralising antibodies in mice and guinea pigs.
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 		32433465
(Nat Commun)
PMID
32433465
Date of Publishing: 2020 May 20
Title Immunogenicity of a DNA vaccine candidate for COVID-19
Author(s) nameSmith TRF, Patel A et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 273
Date of Entry 2021 Oct 31


Sequence : Spike
Total row(s): 52
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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%)
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 		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.
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 		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

Mutational and Co-mutational analysis of SARS-CoV-2 Sequences from India revealed different Co-mutation patterns and clade-specific mutations across seven Indian states and one union territory during term2 (April 2020 to July 2020) and term3 (August 2020 to December 2020). 70% of sequences from Telangana had 8 and above mutations within a single viral strain. 45% of sequences from Maharashtra possessed 7 co-mutations. West Bengal had a lower number of co-mutations even in ‘Term3’ (nearly 60% of sequences having 2 and 3 co-mutations per viral sequence).
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 		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

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
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 		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

Both the clusters (C1, C2) identified in the Amazon basin showed 4 mutations in the ORF1ab region and 1 mutation in the Spike gene but at different positions within the region for each cluster.
✍
 		33857136
(PLoS Negl Trop Dis)
PMID
33857136
Date of Publishing: 2021 Apr
Title Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin
Author(s) nameBallesteros N, Muñoz M et al.
Journal PLoS Negl Trop Dis
Impact factor
4.4
Citation count: 6

Mutation analysis of 469 complete Indian SARS-CoV-2 nucleotide sequences from GenBank revealed that five proteins ORF1ab, ORF3a, S, N, and M had multiple mutations in different variants. While six proteins ORF6, ORF7a, ORF7b, ORF8, ORF10, and E had a single mutation in each variant. The study focuses on constituent proteins of 469 Indian SARS-CoV-2 genome samples, collected from NCBI (as reported till August 28, 2020). Sample detail provided in Supplementary-1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7893251/#ec0005)
✍
 		33623833
(Gene Rep)
PMID
33623833
Date of Publishing: 2021 Feb 19
Title Characterizing genomic variants and mutations in SARS-CoV-2 proteins from Indian isolates
Author(s) nameDas JK, Sengupta A et al.
Journal Gene Rep
Impact factor
0.61
Citation count: 11

Mutation analysis of 59MDW SARS-CoV-2 genomes (n=37, collected from JBSA/Lackland military members and beneficiaries from May 14, 2020, to July 28, 2020) revealed 109 nucleotide changes in the coding region of the SARS-CoV-2 genome (which caused 63 unique, non-synonymous amino acid mutations), one mutation in the 5-UTR, and two mutations in the 3UTR. The biochemical properties of mutations in the SARS-CoV-2 structural proteins (S, E, and N) were studied. The effect of the mutation in viral spike protein is predicted.
✍
 		33609027
(Mil Med)
PMID
33609027
Date of Publishing: 2021 Feb 20
Title Whole-genome Sequencing of SARS-CoV-2: Using Phylogeny and Structural Modeling to Contextualize Local Viral Evolution
Author(s) name Nazario-Toole AE, Xia H, Gibbons TF.
Journal Mil Med
Impact factor
1.6
Citation count: 3

Mutation analysis of 59MDW SARS-CoV-2 genomes (n=37, collected from JBSA/Lackland military members and beneficiaries from May 14, 2020, to July 28, 2020) revealed 14 non-synonymous mutations in the structural proteins. The effect and the biochemical properties of all mutations were studied. Visualization of the mutations on the viral spike protein was done using pymol, the visualization clearly defines the mutation sites and can help in vaccine design and predicting potential spread
✍
 		33609027
(Mil Med)
PMID
33609027
Date of Publishing: 2021 Feb 20
Title Whole-genome Sequencing of SARS-CoV-2: Using Phylogeny and Structural Modeling to Contextualize Local Viral Evolution
Author(s) name Nazario-Toole AE, Xia H, Gibbons TF.
Journal Mil Med
Impact factor
1.6
Citation count: 3

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
- n/a -
Citation count: 7

Phylogenetic analysis of SARS-CoV-2 strains' whole-genome from the various regions of the world. The higher bootstrap values indicate that SARS-CoV-2 is slowly adapting to the human hosts environment in the course of COVID-19.
✍
 		33542420
(Sci Rep)
PMID
33542420
Date of Publishing: 2021 Feb 4
Title Dynamics of binding ability prediction between spike protein and human ACE2 reveals the adaptive strategy of SARS-CoV-2 in humans
Author(s) nameXue X, Shi J et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 6
Date of Entry 2021 Jul 28

Amino acid alignment of the S gene in SARS-CoV-2 and coronaviruses found in bat and pangolin. NONE
✍
 		33542420
(Sci Rep)
PMID
33542420
Date of Publishing: 2021 Feb 4
Title Dynamics of binding ability prediction between spike protein and human ACE2 reveals the adaptive strategy of SARS-CoV-2 in humans
Author(s) nameXue X, Shi J et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 6
Date of Entry 2021 Jul 28

Phylogenetic trees were also reconstructed based on the sequences of S genes Phylogenetic analysis of SARS-CoV-2 suggests that SARS-CoV-2 is probably originated from a recombination event on the spike protein between a bat coronavirus and a pangolin coronavirus that endows it humans infectivity.
✍
 		33542420
(Sci Rep)
PMID
33542420
Date of Publishing: 2021 Feb 4
Title Dynamics of binding ability prediction between spike protein and human ACE2 reveals the adaptive strategy of SARS-CoV-2 in humans
Author(s) nameXue X, Shi J et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 6
Date of Entry 2021 Jul 28

Phylogenetic analysis of deletion variants (red branches) and genetically diverse nondeletion variants revealed the origins of RDR variants and identified specific deletion clades/lineages. Variants of RDR1 and RDR3 are strongly polarized to specific clades and geographies. RDR variants have been present throughout the pandemic.
✍
 		33536258
(Science)
PMID
33536258
Date of Publishing: 2021 Feb 3
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ et al.
Journal Science
Impact factor
20.57
Citation count: 220

SARS-CoV-2 immunosuppressed patients had recurrent deletions in the spike glycoprotein. The deletions altered immunodominant epitope positions within the NTD of S glycoprotein and caused resistance to a neutralizing antibody. 3 RDR2 deletions and one RDR4 deleteion and double RDR1/2 deletion completely abolished binding of antibodies thereby concluding that the deletion mutants confer resistance to a neutralizing antibody.
✍
 		33536258
(Science)
PMID
33536258
Date of Publishing: 2021 Feb 3
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ et al.
Journal Science
Impact factor
20.57
Citation count: 220

SARS-CoV-2 sequences from the GISAID Database (deposited from 1 December 2019 to 24 October 2020) were analyzed to identify and characterize the recurrent deletion regions in the SARS-CoV-2 spike protein. Phylogenetic analysis of deletion variants and diverse nondeletion variants were performed to track the specific clades/lineages and transmission pattern of deletion variants.
✍
 		33536258
(Science)
PMID
33536258
Date of Publishing: 2021 Feb 3
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ et al.
Journal Science
Impact factor
20.57
Citation count: 220

Complete Coding Sequence of surface glycoprotein (S) gene, reported from an immunocompromised cancer patient infected with long-term SARS-CoV-2 infection (Pittsburgh long-term infection 1). The patient was named Pittsburgh long-term infection 1 (PLTI1) because the infection persisted 74 days after the COVID-19 diagnosis.
Two variants with deletions in the NTD of S glycoprotein, were identified.
✍
 		33536258
(Science)
PMID
33536258
Date of Publishing: 2021 Feb 3
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ et al.
Journal Science
Impact factor
20.57
Citation count: 220

SARS-CoV-2 sequences from the GISAID Database were analyzed to evaluate the geographic, genetic, and temporal abundance of recurrent deletion variants of S glycoprotein. RDR in the N-terminal domain of the S glycoprotein confers resistance to neutralizing antibodies
✍
 		33536258
(Science)
PMID
33536258
Date of Publishing: 2021 Feb 3
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ et al.
Journal Science
Impact factor
20.57
Citation count: 220

Most frequent and prevalent mutation reported, with reference to Wuhan sequence (hCoV-19/Wuhan/WIV04/2019), was P323L in the non-structural protein 12 (94.7%) whereas the second frequent mutation was D614G in the Spike glycoprotein region (92.6%), followed by G71S in the non-structural protein 5 (70%). SARS-CoV-2 Genome sequences generated in the study (Refer Supplementary Table 1 and 2)
✍
 		33359061
(Int J Infect Dis)
PMID
33359061
Date of Publishing: 2020 Dec 21
Title Molecular epidemiology of COVID-19 in Oman: A molecular andsurveillance study for the early transmission of COVID-19 in thecountry
Author(s) nameAl-Mahruqi S, Al-Wahaibi A et al.
Journal Int J Infect Dis
Impact factor
3.42
Citation count: 6

The in vitro mutation analysis showed that the D614G mutation changes the spike protein sorting, enhances the trafficking of spike protein to the lysosome, and thus accelerates the entry of SARS-CoV-2 in uninfected cells.
✍
 		33330866
(bioRxiv)
PMID
33330866
Date of Publishing: 2020 Dec 9
Title The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Author(s) nameGuo C, Tsai SJ et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 3

Phylogenetic analysis performed for the SARS-CoV-2 sequences taken from pharyngeal swabs of nine patients in Guangzhou, China indicated they were infected with the same viral strain since 100% identity was observed in Spike gene of SARS-CoV-2.
✍
 		33235537
(Atmos Environ (1994))
PMID
33235537
Date of Publishing: 2020 Nov 20
Title Community evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission through air
Author(s) nameLin G, Zhang S et al.
Journal Atmos Environ (1994)
Impact factor
4.3
Citation count: 10

Mutation analysis of 212 SARS-CoV-2 sequences from Israel revealed 224 unique single nucleotide variants (141 non-synonymous variants, 72 synonymous variants, 11 variants in non-coding regions) and five genomic deletions at different locations. Deletions 2,3, and 4, being a three independent deletions( i.e present in different samples) were found in the same clade which also included 18 samples. This clade is defined by a non-synonymous mutation S2430R (('A20755C', 'A23403G', 'C1059T', 'C14408T', 'C3037T', 'G25563T') in ORF1b, which affects the non-structural protein NSP16.
✍
 		33139704
(Nat Commun)
PMID
33139704
Date of Publishing: 2020 Nov 2
Title Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel
Author(s) nameMiller D, Martin MA et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 52

The in vitro and in vivo mutation analysis of Spike mutation D614G showed increased viral replication and viral infectivity in human cell lines (Calu-3), primary human airway tissue, and Syrian hamsters. Mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increase transmission
✍
 		33106671
(Nature)
PMID
33106671
Date of Publishing: 2020 Oct 26
Title Spike mutation D614G alters SARS-CoV-2 fitness
Author(s) namePlante JA, Liu Y et al.
Journal Nature
Impact factor
24.36
Citation count: 651

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

Sequence alignment of residues in the 615 to 635 loop and the corresponding NTD binding pocket of representative CoV strains belonging to lineage B of Betacoronavirus. Gaps in the interacting NTD loops and the absence of H146 at the corresponding site on SARS-CoV makes it unlikely that SARS-CoV participates in similar intertrimeric interactions.
✍
 		33082295
(Science)
PMID
33082295
Date of Publishing: 2020 Nov 27
Title Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate
Author(s) nameBangaru S, Ozorowski G et al.
Journal Science
Impact factor
20.57
Citation count: 118

In-silico analysis of the SARS-CoV-2 protein sequences from 13 different countries revealed the predicted effect of mutations on protein stability.
✍
 		32881907
(PLoS One)
PMID
32881907
Date of Publishing: 2020
Title Comparative genome analysis of novel coronavirus (SARS-CoV-2) from different geographical locations and the effect of mutations on major target proteins: An in silico insight
Author(s) nameKhan MI, Khan ZA et al.
Journal PLoS One
Impact factor
2.87
Citation count: 39


Structure : Spike
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Original Article
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Cryo-EM structure of the Omicron variant spike protein in complex with human ACE2 reveals salt bridge between RBD N417 and ACE2 D30 is lost. R493, R498 form salt bridge with ACE2 residues E35, D38, respectively and S496 forms a hydrogen bond with ACE2 residue K353. Compared to the Delta variant, new interactions are formed as a result of the mutations Q493R, G496S and Q498R, and the salt bridge between RBD K417 and ACE2 D30 is lost.
✍
 		Pre-print (bioRXiv)
Title SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
Date of Entry 2022 Jan 10

The trimer organisation of the Omicron spike protein ectodomain is similar to that of the original strain and all the earlier variants, according to cryo-EM structural study. The Omicron variant has 37 mutations in the spike protein, and 15 of which are in the receptor binding region (RBD) The Omicron variant spike protein contains 3-5 times the number of mutations found in prior SARS-CoV-2 strains. Understanding the effects of these mutations on ACE2 receptor binding and neutralising antibody evasion is critical for developing effective therapies to stop the spread of the Omicron and related variations.
✍
 		Pre-print (bioRXiv)
Title SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
Date of Entry 2022 Jan 10

Structural analysis was done to show the position of mutated residues in the Lambda spike regions (NTD and RBD). Three mutations (G75V, T76I, and RSYLTPGD246-253N) were presentin theN-terminal domain (NTD)and the deletion mutation (RSYLTPGD246-253N)mutation was observedin a loop structure(loop 5).Another protein region (Receptor binding domain) containstwo mutations (L452Q and F490S). In addition, the T859N mutation wasfound in a specificSpikesubunit (S2heptad repeat 1). Loop 5 contains 246-260 residues, which was a loop structure designated in a previous study.
✍
 		Pre-print (bioRXiv)
Title SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance
Date of Entry 2021 Dec 15

Structure of SARS-CoV-2 spike receptor binding domain (RBD) using computational methods predicts antibody RBD recognition signatures which can be used to design vaccine against Covid-19. In this study the effects from RBD substitutions on ACE2 recognition were not considered.
✍
 		Pre-print (bioRXiv)
Title Structural and energetic profiling of SARS-CoV-2 antibody recognition and the impact of circulating variants
Author(s) name -
Date of Entry 2021 Jun 14

The cryo-EM structure of the S protein of the Alpha variant in the apo form and receptor ACE-2 bound form were charecterised. The A570D mutation modulates the opening and closing of the receptor binding domain (RBD) by introducing a salt bridge. The N501Y mutation increases ACE-2 binding affinity by introducing pi-pi interaction.
✍
 		Pre-print (bioRXiv)
Title Impacts on the structure-function relationship of SARS-CoV-2 spike by B.1.1.7 mutations
Date of Entry 2021 Sep 13

Structural superimposition of the RBD region of Spike glycoprotein of SARS-CoV-2 wild and its variants - Omicron, Delta AY.1 & 2 and AY. 3, showed structural changes around the antibody binding regions. Protein structure prediction showed Omicron's polarity, non-polarity, and hydrophobicity characteristics changed from the wild SARS-CoV-2. Omicron and Delta AY.3 are expected to be more pathogenic due to their RBD structures' greater instability.
✍
 		35690234
(Microb Pathog)
PMID
35690234
Date of Publishing: 2022 Jun 8
Title The influence of new SARS-CoV-2 variant Omicron (B.1.1.529) on vaccine efficacy, its correlation to Delta variants: A computational approach
Author(s) nameRanjan P, Neha et al.
Journal Microb Pathog
Impact factor
2.64
Citation count: 1
Date of Entry 2022 Jun 27

Cryo-EM structure of monoclonal antibody - T6's Fab in complex with B.1.351 spike trimer protein shows that T6 antibody binds only to the "up" RBD, therefore the T6 epitope is buried when the RBD is in the "down" conformation in the spike trimer. Analysis of T6 epitope residues in the GISAID database revealed a high degree of conservation, thus providing a sequence and structural basis for its broad and potent neutralizing activity against a wide range of SARS-CoV-2 variants.
✍
 		35291264
(iScience)
PMID
35291264
Date of Publishing: 2022 Apr 15
Title RBD trimer mRNA vaccine elicits broad and protective immune responses against SARS-CoV-2 variants
Author(s) nameLiang Q, Wang Y et al.
Journal iScience
Impact factor
4.447
Citation count: 1
Date of Entry 2022 Jul 13

Binding of monoclonal antibody, B6-Fab to SARS-CoV/SARS-CoV-2 spike stem helix peptide, sterically interferes with the spike protein's fusion of the membrane. B6 binds to the hydrophobic core of the stem helix bundle and disrupts its quaternary structure. It prevents S2 subunit refolding from the pre- to the post-fusion state and blocks viral entry. This study unveils an unexpected target for next-generation structure-guided design of a pan-beta-coronavirus vaccine.
✍
 		33981021
(Nat Struct Mol Biol)
PMID
33981021
Date of Publishing: 2021 May 12
Title Structural basis for broad coronavirus neutralization
Author(s) nameSauer MM, Tortorici MA et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 46
Date of Entry 2021 Jul 28

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 1). Residue 501 interacts with Ser30 of Fab ab1, thus N501Y mutation would have a small effect on the antibody binding epitope. Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain. Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The comparison of neutralization profiles shows that the IC50for neutralization of the N501Y mutant is lower, suggesting that full-length spikes bearing the N501Y mutation bind ACE2-mFc to a higher extent.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 . Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The cryo-EM structures show a small but significant effect of the N501Y mutation on Fab ab1 binding and neutralization, but with no measurable effects on VH ab8 binding or neutralization.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain (focused refinement of RBD and ACE2). Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The cryo-EM methods to identify the footprints of antibodies produced byt the vaccinesis a critical tool to prevent and treact COVID-19.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8. Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity of the N501Y mutant and its increased infectivity. The cryo-EM structures show a small but significant effect of the N501Y mutation on Fab ab1 binding and neutralization, but with no measurable effects on VH ab8 binding or neutralization.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of the SARS-CoV-2 N501Y mutant spike protein ectodomain. Y501 inserts into a cavity at the binding interface near Y41 of ACE2 and this interaction causes the increased ACE2 affinity (3- to 16-fold) in ACE2 binding and its increased infectivity. The cryo-EM methods to identify the footprints of antibodies produced byt the vaccinesis a critical tool to prevent and treact COVID-19.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Structural characterization of cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to VH ab8 (focused refinement of RBD and VH ab8). Y501 shows increased ACE2 affinity and increased infectivity. Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

SARS-CoV-2 N501Y mutant spike protein ectodomain bound to human ACE2 ectodomain and Fab ab1 and VH ab8 Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Cryo-EM structure of the SARS-CoV-2 N501Y mutant spike protein ectodomain bound to Fab ab1 (class 2). IC50 for wild-type is greater than that for N501Y. IC50 of soluble ACE2-mFC neutralization is 0.066 μg/ml for unmutated pseudotyped virus and 0.0074 μg/ml for N501Y pseudotyped virus. Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

2H2 binds to T470 to T478 of the RBM within RBD of SARS-CoV-2 Spike protein. IC50 values for 2H2 is 0.0007µ/ml and has strongest neutralization capacity compared to other MAbs 2G3, 8D3, and 3C1. 2H2 is bound on the top of the RBD of S trimer
✍
 		33431876
(Nat Commun)
PMID
33431876
Date of Publishing: 2021 Jan 11
Title Development and structural basis of a two-MAb cocktail for treating SARS-CoV-2 infections
Author(s) nameZhang C, Wang Y et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 31

The conformational changes of the spike protein was studied along with the effect of D614G mutation on the soluble S ectodomain construct. The G614 variant exhibited enhanced furin cleavage efficiency and modified RBD constitution. The study used engineered soluble construct. The similarity of these to the native virion context should be studied further. Also, the effect of the D614G mutation on cleavage at the TMPRSS2 cleavage site should be studied.
✍
 		33417835
(Cell Rep)
PMID
33417835
Date of Publishing: 2021 Jan 12
Title D614G Mutation Alters SARS-CoV-2 Spike Conformation and Enhances Protease Cleavage at the S1/S2 Junction
Author(s) nameGobeil SM, Janowska K et al.
Journal Cell Rep
Impact factor
7.7
Citation count: 98
Date of Entry 2021 Oct 27

X-ray diffraction structure of SARS-CoV-2 Spike receptor binding domain binding to angiotensin-converting enzyme of Rhinolophus macrotis (bACE2-Rm), shows S-RBD binds to bACE2 with a KD = 2.78 µ;M and binds with a KD = 20.4 nM to hACE2. Y41H mutant reduces the binding capacity of bACE2 with spike RBD. The structure of the SARS-CoV-2 RBD and bACE2-Rm complex reveals a binding mode similar to that of hACE2..
✍
 		33335073
(Proc Natl Acad Sci U S A)
PMID
33335073
Date of Publishing: 2021 Jan 5
Title Cross-species recognition of SARS-CoV-2 to bat ACE2
Author(s) nameLiu K, Tan S et al.
Journal Proc Natl Acad Sci U S A
Impact factor
9.35
Citation count: 23

Monovalent hACE2 decoy CTC-445.2 binds to all the three RBDs of a single spike protein with a low nanomolar affinity and high specificity. The divalent CTC-445.2d shows about ~10 fold increase in the binding. De novo protein design approach to generate decoys is independent to traditional therapeutics and has the potential to better overcome mutational viral evasion.
✍
 		33154107
(Science)
PMID
33154107
Date of Publishing: 2020 Dec 4
Title De novo design of potent and resilient hACE2 decoys to neutralize SARS-CoV-2
Author(s) nameLinsky TW, Vergara R et al.
Journal Science
Impact factor
20.57
Citation count: 75
Date of Entry 2021 Jul 28

Structure of SARS-CoV-2 3Q-2P full-length prefusion spike trimer (C3 symmetry) of subunit vaccine candidate (NVAX-CoV2373) from Novavax, shows all three RBDs on the 3Q-2P-FL spike trimer are in the closed conformation and a shift in residues flanking the 615 to 635 loop, causes a salt bridge interaction between D614 and K854. Tight clustering of the spikes in the NVAX-CoV2373 nanoparticle formulation may lead to stronger immune responses over soluble trimers alone. Formation of a salt bridge between residue D614 on one protomer and K854 on a neighboring protomer in the vaccine candidate has a potential role in viral transmission and pathogenesis.
✍
 		33082295
(Science)
PMID
33082295
Date of Publishing: 2020 Nov 27
Title Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate
Author(s) nameBangaru S, Ozorowski G et al.
Journal Science
Impact factor
20.57
Citation count: 118

SARS-CoV-2 3Q-2P full-length dimers of spike trimers of subunit vaccine candidate (NVAX-CoV2373) from Novavax, shows residues 621-PVAIHADQ-628 in the loop interacts with neighboring NTD. Y145 and H146 switch positions and form a salt-bridge between H146 and D627. It also results in stacking between W152 and H146. NVAX-CoV2372 is stable, homogeneous, and locked in the antigenically preferred prefusion conformation.
✍
 		33082295
(Science)
PMID
33082295
Date of Publishing: 2020 Nov 27
Title Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate
Author(s) nameBangaru S, Ozorowski G et al.
Journal Science
Impact factor
20.57
Citation count: 118

Structure of SARS-CoV-2 Spike D614G variant without RBD. The current high frequency of D614G throughout the world suggests that this variant transmits person to person more efficiently than do viruses bearing D614.
✍
 		32991842
(Cell)
PMID
32991842
Date of Publishing: 2020 Oct 29
Title Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Author(s) nameYurkovetskiy L, Wang X et al.
Journal Cell
Impact factor
27.35
Citation count: 434

Structural characterization of the complex of Spike protein with Ty1, which is an antibody fragment that binds to the receptor binding domain (RBD) of the viral protein, and neutralizes the virus. Ty1 - a 12.8kDa nanobody which is capable of binding of with RBDs (both up and down) , making ACE2 interaction surface inaccessible for ACE2.
✍
 		32887876
(Nat Commun)
PMID
32887876
Date of Publishing: 2020 Sep 4
Title An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction
Author(s) nameHanke L, Vidakovics Perez L et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 124


Drugs : Spike
Total row(s): 29
Select item(s)
Key Findings
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Original Article
(hover to see details)
In silico study of quinoline-based potent inhibitors against the 3 therapeutic targets of SARS-CoV-2- 2CLpro, RdRp and Spike-ACE2 complex was carried out with already reported anti-SARS-CoV-2 drugs, lopinavir and remdesivir triphosphate as positive inhibitors. A novel phyto-quinoline and 4 other existing quinoline-based drugs were found to have the potential of being used as inhibitors for SARS-CoV-2.
✍
 		frontiersin.org
Title Quinolines-Based SARS-CoV-2 3CLpro and RdRp Inhibitors and Spike-RBD-ACE2 Inhibitor for Drug-Repurposing Against COVID-19: An in silico Analysis
Date of Entry 2021 Sep 5

We present a dockingbased screening using a quantum mechanical scoring of a library built from approved 1 drugs and compounds undergoing clinical trials, against three SARS-CoV-2 target proteins: the spike or S-protein, and two proteases, the main protease and the papain-like protease. we propose several structurally diverse compounds (either FDA-approved or in clinical trials) that could display antiviral activity against SARS-CoV-2.
✍
 		pdfs.semanticscholar.org
Title In silico Drug Repurposing for COVID-19: Targeting SARS-CoV-2 Proteins through Docking and Quantum Mechanical Scoring
Date of Entry 2021 Sep 5

In this study, we focused on the human host cell transmembrane protease serine 2 (TMPRSS2), which plays an important role in the viral life cycle by cleaving the spike protein to initiate membrane fusion. we developed an efficient pharmacophore- based approach and applied a large-scale in silico database screening for small molecule inhibitors against TMPRSS2.
✍
 		Pre-print (bioRXiv)
Title Discovery of TMPRSS2 inhibitors from virtual screening
Date of Entry 2021 Sep 5

Aim of this study was to discover the compounds that can bind to the RBD of spike protein in the prefusion conformation and to the site of the connective interface of spike-ACE2 complex protein, to prevent viral spike proteins to bind to the human ACE2 proteins in COVID-19 disease progression. Virtual screening gave 39 potential compounds from 2321 total compounds, out of which 2 showed most affinity. The protein superimposition was performed by PyMOL software to compare conformations of Spike protein in 2 states- prefusion ACE-2 free conformation and ACE-2 bound conformation. DS 2019 software with CHARM force field was used to remove substrates and add polar hydrogens and partial charges. The RBD regions of both spike proteins in the simulation models were significantly different in structural conformation
✍
 		Pre-print (bioRXiv)
Title The discovery of potential natural products for targeting SARS-CoV-2 spike protein by virtual screening
Date of Entry 2021 Sep 5

Prevalence of antibodies to Sars-Cov-2 Spike protein at baseline was higher in participants who were prescribed 800mg molnupiravir compared to participants prescribed placebo. Reduction in viral load and reduction in time to negative test was significantly reduced in participants prescribed 800mg molnupiravir compared to all other participants. Strong biological evidence of using molnupiravir as oral drug to reduce uninterrupted viral replication has been provided in this study.
✍
 		34941423
(Sci Transl Med)
PMID
34941423
Date of Publishing: 2021 Dec 23
Title A phase 2a clinical trial of molnupiravir in patients with COVID-19 shows accelerated SARS-CoV-2 RNA clearance and elimination of infectious virus
Author(s) nameFischer WA 2nd, Eron JJ Jr et al.
Journal Sci Transl Med
Impact factor
11.64
Citation count: 24
Date of Entry 2022 May 14

2466 drugs from DrugBank were used to computationally target against RBD of Spike protein in SARS-CoV-2 to obtain 18 favourable drugs with top docking scores, 6 of them formed stable complex by MD simulation, with 3 of them showing enhanced binding Residues in the predicted binding pocket exhibit conformational variability at the side-chain level. Flavin adenine dinucleotide (FAD), fondaparinux and atorvastatin showed RMSD 5 and low conformational fluctuations.
✍
 		34256255
(Comput Biol Med)
PMID
34256255
Date of Publishing: 2021 Aug
Title Drug repurposing against SARS-CoV-2 receptor binding domain using ensemble-based virtual screening and molecular dynamics simulations
Author(s) name Kumar V, Liu H, Wu C.
Journal Comput Biol Med
Impact factor
2.93
Citation count: 2
Date of Entry 2021 Sep 5

Structural modelling and binding site analysis of human host cell transmembrane protease serine 2 (TMPRSS2), a protease involved in cleaving a spike protein domain of SARS-CoV-2 to facilitate membrane fusion, was done, followed by structure-based screening of drug-like compounds for it's inhibition. Compounds Otamixaban and NCGC00386945 were shown to exhibit potent activity against TMPRSS2 with an efficient activity in the viral entry assay whereas the compound UKI-1 showed promising activity against the serine protease but was inactive in the SARS-CoV-2 PP entry assay. Out of 20,000 potential drug-like compounds, 350 were selected for experimental validation.
based on binding model analysis with known inhibitors( nafamostat, camostat, and gabexate), 4 pharmacophores were developed.
Virtual screening was done on the basis of pharmacophore based searching, 3 dimensional shape based mapping and structure band docking. Out of the 20,000 drug like compounds, only those matching atleast 2 pharmacophores were extracted.
Activity of TMPRSS2 Inhibitors in the Enzyme Assay and the SARS-COV-2 PP Entry Assay was recorded.
it was observed that most of the inhibitors possessed a benzoamidiniumhead headgroup, playing a key role in effective binding and inhibition.
✍
 		34136758
(ACS Pharmacol Transl Sci)
PMID
34136758
Date of Publishing: 2021 Jun 11
Title Discovery of TMPRSS2 Inhibitors from Virtual Screening as a Potential Treatment of COVID-19
Author(s) nameHu X, Shrimp JH et al.
Journal ACS Pharmacol Transl Sci
Impact factor
14.357
Citation count: 10
Date of Entry 2021 Sep 5

This study was performed to explore the potential of different phytochemicals as candidate inhibitors of the HR1 domain in SARS-CoV-2 spike protein. Quantum computation-based den sity functional theory (DFT) analysis was constituted to analy ze the reactivity of these compounds with the receptor. 5 phyto chemicals, i.e., SilybinC, Isopomiferin, Lycopene, SilydianinB , and Silydianin are identified as novel and potent candidates for the inhibition of HR1 domain in SARS-CoV-2 spike protein.
✍
 		34095308
(Biomed Res Int)
PMID
34095308
Date of Publishing: 2021
Title Virtual Screening of Phytochemicals by Targeting HR1 Domain of SARS-CoV-2 S Protein: Molecular Docking, Molecular Dynamics Simulations, and DFT Studies
Author(s) nameMajeed A, Hussain W et al.
Journal Biomed Res Int
Impact factor
2.14
Citation count: 3
Date of Entry 2021 Sep 5

In this study, phytochemicals (1,952 compounds) from eight potential medicinal plants used in Indian traditional medicine were meticulously collated, based on their usage in respirato ry disorders, along with immunomodulatory and anti-viral potential from contemporary literature. Further, these comp ounds were virtually screened against Receptor Binding Dom ain (RBD) of Spike protein. The potential hits in complex with spike protein were subjected to Molecular Dynamics simulati on (450 ns), to infer the stability of complex formation. Amo ng the compounds screened, Tellimagrandin-II from Syzygium aromaticum L. and O-Demethyl-demethoxy- curcumin from Curcuma longa L. were found to be highly potential due to their higher binding affinity and significant binding free energy (MM-PBSA), along with favorable ADMET properties and stable intermolecular interactions with hotspots.
✍
 		34026798
(Front Med (Lausanne).)
PMID
34026798
Title Phytochemical Moieties From Indian Traditional Medicine for Targeting Dual Hotspots on SARS-CoV-2 Spike Protein : An Integrative in-silico Approach
Journal Front Med (Lausanne).
Date of Entry 2021 Sep 5

Antiviral efficacy of Astemizole which inhibits the entry of SARS-CoV-2 Spike pseudoviruses into ACE2-expressed HEK293T cells by binding to the ACE2 receptor. SARS-COV-2 Spike pseudotype virus to enter the ACE2 cells were reduced significantly.
✍
 		33932547
(Microb Pathog)
PMID
33932547
Date of Publishing: 2021 Apr 28
Title Astemizole as a drug to inhibit the effect of SARS-COV-2 in vitro
Author(s) nameWang X, Lu J et al.
Journal Microb Pathog
Impact factor
2.64
Citation count: 2
Date of Entry 2021 Aug 10

Cytotoxicity analysis of Astemizole which inhibits the entry of SARS-CoV-2 Spike pseudoviruses into ACE2-expressed HEK293T cells by binding to the ACE2 receptor. Astemizole didn't influence the viability of ACE2 cells significantly. Astemizole can be re-used as a potential drug candidate in anti-coronavirus therapies
✍
 		33932547
(Microb Pathog)
PMID
33932547
Date of Publishing: 2021 Apr 28
Title Astemizole as a drug to inhibit the effect of SARS-COV-2 in vitro
Author(s) nameWang X, Lu J et al.
Journal Microb Pathog
Impact factor
2.64
Citation count: 2
Date of Entry 2021 Aug 10

Using computational tools to screen a library of marine seaweed compounds against the Spike protein RBD of the SARS-CoV-2 UK variant (VUI 202012/01). Dieckol cannot be used as a lead inhibitor against RBD. 1.Dieckol derivative, i.e., DK07 most potent inhibitor of RBD and was found to possess acceptable physicochemical, pharmacokinetic, drug-likeness, and ADMET properties. 2.The IUPAC name of DK07 is 8-{3-hydroxy-4-[(7-hydroxynaphthalen-2-yl)oxy]phenoxy}-1,4-benzodioxin-5-ol. DK07 binds to the RBD at the ACE2RBD interface and interacts with key amino acid residues. 3.In vitro and in vivo experiments to validate the potential of DK07 to bind UK strain of SARS-CoV-2 Spike protein RBD and prevent its interaction with ACE2.
✍
 		33922914
(Mar Drugs)
PMID
33922914
Date of Publishing: 2021 Apr 25
Title Dieckol and Its Derivatives as Potential Inhibitors of SARS-CoV-2 Spike Protein (UK Strain: VUI 202012/01): A Computational Study
Author(s) nameAatif M, Muteeb G et al.
Journal Mar Drugs
Impact factor
8
Citation count: 5
Date of Entry 2021 Sep 5

Different potential repurposed drugs, including, chloroquine , hydroxychloroquine, ivermectin, remdesivir, and favipiravir, were screened in the present study. Molecular docking of these drugs with different SARS-CoV-2 target proteins, including spike and membrane proteins, RdRp, nucleoproteins, viral proteases, and nsp14, was performed. Molecular dynamics simulation and MM-PBSA calculation were also conducted. Ivermectin and remdesivir were found to be the most promising drugs.
✍
 		33746908
(Front Microbiol)
PMID
33746908
Date of Publishing: 2020
Title Molecular Docking Reveals Ivermectin and Remdesivir as Potential Repurposed Drugs Against SARS-CoV-2
Author(s) name Eweas AF, Alhossary AA, Abdel-Moneim AS.
Journal Front Microbiol
Impact factor
4.19
Citation count: 14
Date of Entry 2021 Sep 5

In this Study the work aims to find molecules that can inhibit the attraction between the Spike proteins of the SARS-COV-2 virus and human ACE2. The results of molecular docking positioned four molecules at the interaction site Tyr-491(Spike)-Glu-37(ACE2) and one at the site Gly-488(Spike)-Lys-353(ACE2).
✍
 		33583954
(J Mol Struct)
PMID
33583954
Date of Publishing: 2021 May 15
Title Computational search for drug repurposing to identify potential inhibitors against SARS-COV-2 using Molecular Docking, QTAIM and IQA methods in viral Spike protein - Human ACE2 interface
Author(s) name Faria SHDM, Teleschi JG.
Journal J Mol Struct
Impact factor
2.19
Citation count: 2
Date of Entry 2021 Sep 5

Bisoxatin, a laxative compound can inhibit ACE2-Spike protein interactions
✍
 		33184246
(J Biosci)
PMID
33184246
Date of Publishing: 2020
Title Identification of a repurposed drug as an inhibitor of Spike protein of human coronavirus SARS-CoV-2 by computational methods
Author(s) nameUnni S, Aouti S et al.
Journal J Biosci
Impact factor
1.72
Citation count: 17
Date of Entry 2021 Jun 15

Computational screening of 19 different inhibitor molecules by Molecular docking,drug-like and ADMETprediction indicates HIV protease, anti-inflammatory and antibiotic inhibitors are potential lead drug molecules against spike protein and antimalarial drugs show less binding affinity against spike protein. Antimalarial drugs such as chloroquine, Hydroxychloroquine and Artemisinin shows weak interaction to the target receptor. The antiviral drugs such as Erythromycin and Spiramycin, anti-inflammatory drugs such as Baricitinib, Ruxolitinib, Thalidomide and HIV-protease inhibitors such as Cobicistat, Darunavir, Lopinavir and Ritonavir compounds shows strong interaction to the target receptor and these compounds are strongly recommended to the spike protein inhibitors in COVID-19.
✍
 		33152616
(J Mol Graph Model)
PMID
33152616
Date of Publishing: 2021 Jan
Title Molecular screening of antimalarial, antiviral, anti-inflammatory and HIV protease inhibitors against spike glycoprotein of coronavirus
Author(s) namePrashantha CN, Gouthami K et al.
Journal J Mol Graph Model
Impact factor
1.93
Citation count: 4
Date of Entry 2021 Sep 5

U. tomentosa can be used as a herbal supplement with the safety and efficacy parameters at both preclinical and clinical stages to evaluate its effectiveness in the treatment of novel coronavirus disease. All components discovered in U. tomentosa may work together to prevent the transmission of SARS-CoV-2 through several processes.
✍
 		33118480
(J Biomol Struct Dyn)
PMID
33118480
Date of Publishing: 2020 Oct 29
Title Uncaria tomentosa (cat's claw): a promising herbal medicine against SARS-CoV-2/ACE-2 junction and SARS-CoV-2 spike protein based on molecular modeling
Author(s) name Yepes-Pérez AF, Herrera-Calderon O, Quintero-Saumeth J.
Journal J Biomol Struct Dyn
Impact factor
3.22
Citation count: 8
Date of Entry 2022 May 14

Computational screening of more than 3800 FDA-approved drugs against RBD S1-ACE2 interface by flexible ligand docking, ADME property calculations, and protein-ligand interaction maps indicate silodosin a good inhibitor of spike protein. Ligand interaction- https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7643424/figure/F0006/
✍
 		33103586
(J Biomol Struct Dyn)
PMID
33103586
Date of Publishing: 2020 Oct 25
Title High-throughput virtual screening of drug databanks for potential inhibitors of SARS-CoV-2 spike glycoprotein
Author(s) nameAwad IE, Abu-Saleh AAA et al.
Journal J Biomol Struct Dyn
Impact factor
3.22
Citation count: 10
Date of Entry 2021 Sep 5

Virtual screening and in silico pharmacophore modelling of 764913 compounds to explore safe oral drugs against Receptor Binding Domain (RBD) of SARS-CoV-2,but only eight molecules fit the criteria for safe oral drugs. Phylogenetic analysis - https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7561340/figure/fig1/
✍
 		33083627
(Heliyon)
PMID
33083627
Date of Publishing: 2020 Oct
Title Computer-aided drug design against spike glycoprotein of SARS-CoV-2 to aid COVID-19 treatment
Author(s) name Shehroz M, Zaheer T, Hussain T.
Journal Heliyon
Impact factor
1.65
Citation count: 8
Date of Entry 2021 Sep 5

Novel peptidomimetics were designed based on crucial interacting interface residues from ACE2-SARS-CoV-2 binary interactions, the top lead peptidomimetics were screened for further validation using computational method and in that 4 lead peptidomimetic compounds shows inhibition against spike protein in cell-based assays. Novel peptidomimetics were designed based on the critically interacting residues present in the 18 aa inhibitory peptides
✍
 		33072222
(Cell Mol Bioeng)
PMID
33072222
Date of Publishing: 2020 Oct 13
Title Structure-Based Design of Novel Peptidomimetics Targeting the SARS-CoV-2 Spike Protein
Author(s) name Alagumuthu M, Rajpoot S, Baig MS.
Journal Cell Mol Bioeng
Impact factor
2.36
Citation count: 9
Date of Entry 2021 Sep 5

The anti-protease activity of three polyphenolic compounds- mangiferin, glucogallin, and phlorizin, on SARS-CoV-2 main protease (Mpro) and TMPRSS2 protein were analysed and predicted by docking studies. Molecular docking studies and MD simulation showed that all three compounds may have the potential to be used as safe protease inhibitors thus helping prevent SARS-CoV-2 spike protein priming and viral protein post-translational modification. The absorption, distribution, metabolism, and excretion (ADME) studies showed that the three compounds showed less absorption from the GI tract, no Blood brain barrier permeability, and no effect on the CYP2D6, CYP3A4, CYP1A2, CYP2C19, CYP2C9, CYP2D6, CYP3A4 cytochrome enzymes. They also showed no inhibitory effect on liver enzymes and thus no hepatotoxicity and no effect on the metabolism of other essential drugs. Solvent-accessible surface area (SASA) analysis was also carried out. All 3 compounds have sugar moities which contribute to their water solubility. MM-PBSA analysis suggested that phlorizin has the least binding free energy towars Mpro, followed by glucogallin and then mangiferin. For TMPRSS2. mangiferin showed lowest binding free energy, followed by phlorizin and glucogallin.
✍
 		33050360
(Molecules)
PMID
33050360
Date of Publishing: 2020 Oct 10
Title Protease Inhibitory Effect of Natural Polyphenolic Compounds on SARS-CoV-2: An In Silico Study
Author(s) nameSingh R, Gautam A et al.
Journal Molecules
Impact factor
3.01
Citation count: 12
Date of Entry 2021 Sep 5

Present study was aimed to target SARS-CoV-2 S-RBD with novel bioactive compounds to retrieve potential candidates that could serve as anti-coronavirus disease 2019 drugs. Discovery studio software was used to prepare two-dimensional plot of the molecular interaction network of ligands with S-RBD and PCA/essential dynamics statistical tool was used to identify similarities and dissimilarities in a particular dataset and to detect patterns in a particular dataset
✍
 		33041407
(J Mol Liq)
PMID
33041407
Date of Publishing: 2020 Dec 15
Title Promising terpenes as SARS-CoV-2 spike receptor-binding domain (RBD) attachment inhibitors to the human ACE2 receptor: Integrated computational approach
Author(s) nameMuhseen ZT, Hameed AR et al.
Journal J Mol Liq
Impact factor
4.85
Citation count: 32
Date of Entry 2021 Sep 5

In silico screening of 4015 small molecules against ACE2 specific Receptor binding domain on S-protein in SARS-CoV-2 was carried out, followed by molecular docking and molecular dynamic simulation, which suggests that Glycyrrhizic acid (GA) may potentially inhibit target activity. Sequence similarity search was conducted with whole genome of SARS-CoV-2 to reveal that it showed 96.04%, 91.64% and 82.30% identity with Bat coronavirus RaTG13 (GenBank accession number: MN996532.1), Pangolin coronavirus isolate MP789 (GenBank accession number: MT084071.1) and SARS-CoV (GenBank accession number: JX163927) Multiple sequence alignment(MSA) of RBD domains of S-protein from SARS-CoV-2 (accession number QII57328), SARS-CoV (accession number: AFR58728) and RatG13 (accession number: QHR63300) showed ACE2 receptor interaction conservation. Topological analysis of human proteins and of the human proteins targeted by SARS-CoV in the human interactome was carried out. By virtue of its degree of distribution and betweenness centrality, A2A3R6 and ACE2 were found to have identified as potential targets. But due to the fact that function of A2A3R6 is not completely understood, ACE2 was identified as the key target in SARS-CoV/host interaction.
✍
 		32765844
(F1000Res)
PMID
32765844
Date of Publishing: 2020
Title In silico screening of known small molecules to bind ACE2 specific RBD on Spike glycoprotein of SARS-CoV-2 for repurposing against COVID-19
Author(s) nameBr B, Damle H et al.
Journal F1000Res
Impact factor
2.64
Citation count: 14
Date of Entry 2021 Sep 5

High throughput virtual screening approach was used to investigate FDA approved LOPAC library drugs against both the receptor binding domain of spike protein (S-RBD) and ACE2 host cell receptor. Evidently, GR 127935 hydrochloride hydrate, GNF-5, RS504393, TNP, and eptifibatide acetate were found binding to virus binding motifs of ACE2 receptor. Additionally, KT203, BMS195614, KT185, RS504393, and GSK1838705A were identified to bind at the receptor binding site on the viral S-protein.These identified molecules may effe ctively assist in controlling the rapid spread of SARS-CoV-2 by not only potentially inhibiting the virus at entry step but are also hypothesized to act as anti-inflammatory agents, which could impart relief in lung inflammation.
✍
 		32754161
(Front Immunol)
PMID
32754161
Date of Publishing: 2020
Title Identification of SARS-CoV-2 Cell Entry Inhibitors by Drug Repurposing Using in silico Structure-Based Virtual Screening Approach
Author(s) name Choudhary S, Malik YS, Tomar S.
Journal Front Immunol
Impact factor
4.53
Citation count: 82
Date of Entry 2021 Sep 5

Virtual screening of 11 potent antimalarial compounds derived from the core structure of Artemisinin and identification of 3 compounds namely Artesunate, Artemisinin, and Artenimol to show its efficacy and potency compared to HCQ for SARS-CoV-2 through molecular dynamics study. Artenimol is recommended for clinical trials to achieve the repurposing of such class of molecules for COVID-19 treatment.
✍
 		32696720
(J Biomol Struct Dyn)
PMID
32696720
Date of Publishing: 2020 Jul 22
Title Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19
Author(s) name Sehailia M, Chemat S.
Journal J Biomol Struct Dyn
Impact factor
3.22
Citation count: 25
Date of Entry 2021 Aug 2


Diagnostics : Spike
Total row(s): 4
Select item(s)
Key Findings
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(You can add your comments too!)
Original Article
(hover to see details)
This study reports a rapid and inexpensive diagnostic test, called RAPID 1.0 (Real-time Accurate Portable Impedimetric Detection prototype 1.0) which provides a result within 4 minutes. The RAPID technology is based on electrochemical impedance spectroscopy (EIS), which transforms the binding event between the SARS-CoV-2 spike protein and receptor protein ACE2 into a detected electrical signal. The signal can be read through a desktop instrument or a smartphone. RAPID 1.0 is a good alternative to sophisticated diagnostic technique like RT-PCR. RAPID is inexpensive compared to existing methods for SARS-CoV-2 detection
✍
 		33997767
(Matter)
PMID
33997767
Date of Publishing: 2021 Jul 7
Title Low-cost Biosensor for Rapid Detection of SARS-CoV-2 at the Point-of-Care
Author(s) nameTorres MDT, de Araujo WR et al.
Journal Matter
Impact factor
- n/a -
Citation count: 16

Detection of SARS CoV-2 IgM, and IgA antibodies from Sera samples using Luminex bead-based assay by targeting SARS-CoV-2 spike and nucleocapsid antigens. The neutralizing and binding IgG, IgA, and IgM antibody levels were higher for severe than mild cases in the early convalescent phase (<6 weeks). 1/300 serum dilution showed the best signal to noise ratio for IgG and IgM and 1/150 for IgA
✍
 		33227340
(J Virol Methods)
PMID
33227340
Date of Publishing: 2021 Feb
Title Evaluating SARS-CoV-2 spike and nucleocapsid proteins as targets for antibody detection in severe and mild COVID-19 cases using a Luminex bead-based assay
Author(s) nameMariën J, Ceulemans A et al.
Journal J Virol Methods
Impact factor
1.76
Citation count: 41

A lateral flow assay that detects IgG and IgM antibody concentration against spike protein in two different cartridges with just maximum specificity Hepatitis and autoimmune samples were the main sources of limited cross reactions
✍
 		32710669
(J Med Virol)
PMID
32710669
Date of Publishing: 2021 Feb
Title Validation and performance comparision of three SARS-CoV-2 antibody assays
Author(s) namePaiva KJ, Grisson RD et al.
Journal J Med Virol
Impact factor
2.07
Citation count: 21

Development of an ELISA assay suggests that antibodies mounted upon infection of SARS-Cov-2 target full length spike protein and its receptor-binding domain(RBD). Also a high correlation between microneutraliazation assay and ELISA indicated minimal antigenic changes. This ELISA method will be very useful for serosurveys aimed at determining the real attack rate and infection fatality rate in different human populations, and to map the kinetics of the antibody response to SARS-CoV-2
✍
 		32398876
(Nat Med)
PMID
32398876
Date of Publishing: 2020 Jul
Title A serological assay to detect SARS-CoV-2 seroconversion in humans
Author(s) nameAmanat F, Stadlbauer D et al.
Journal Nat Med
Impact factor
22.66
Citation count: 874


Molecular_interactions : Spike
Total row(s): 46
Select item(s)
Key Findings
Comments
(You can add your comments too!)
Original Article
(hover to see details)
The K417N mutation of Omicron reduces ACE2 binding affinity, but new mutations Q493R, G496S and Q498R, have a compensatory effect on the strength of ACE2 binding and hence Omicron has similar binding affinities of Delta variant. The Omicron spike protein exhibits a measurable increase in affinity for ACE2 relative to the ancestral Wuhan strain, the ACE2 affinity is similar for Delta and Omicron variants.
✍
 		Pre-print (bioRXiv)
Title SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
Date of Entry 2022 Jan 10

Molecular interaction studies of SARS-CoV-2 RBD with different variants of hACE2. No major divergence of the interaction interface of SARS-CoV-2 RBD with hACE2
✍
 		PMC
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Date of Entry 2021 Jul 28

Molecular interaction studies of SARS-CoV-2 RBD with different variants of hACE2. No major divergence of the interaction interface of SARS-CoV-2 RBD with hACE2
✍
 		PMC
Title Interaction of the spike protein RBD from SARS-CoV-2 with ACE2: Similarity with SARS -Cov , hot-spot analysis and effect of the receptor polymorphism
Date of Entry 2021 Jul 28

The molecular interaction (MI) energy values between the Omicron Spike protein-RBD and ACE2 is 749.8 kcal.mol-1. This is 1.4 times delta variant MI (538.1) and 2.7 times alpha variant MI (276.9). The strong interaction can be contributed to mutations to lysine (K) at N440K, T478K and Q493K in the Omicron variant, which bind to the contact site acidic amino acids of ACE2. Covid-19 variants transmissible strength can be contributed by basic amino acids, especially lysine. Basic amino acids at the interaction site of S-RBD increased the binding affinity with ACE-2.
✍
 		35026638
(Talanta)
PMID
35026638
Date of Publishing: 2022 Apr 1
Title Quantitative in silico analysis of SARS-CoV-2 S-RBD omicron mutant transmissibility
Author(s) name Hanai T.
Journal Talanta
Impact factor
10.5
Citation count: 5
Date of Entry 2022 Feb 23

Cross-reactivity of B6 monoclonal antibody with the spike glycoproteins of SARS-CoV-2, SARS-COV, MERS and HKU4 is because of the strict conservation of 3 of the 4 hydrophobic residues in the stem helix except for the substitution of F1238MERS-CoV with Y1137SARS-CoV/Y1155SARS-CoV-2 or W1240 OC43/W1237HKU1. B6 binding sterically interferes with S fusogenic conformational changes and blocks viral entry through inhibition of membrane fusion
✍
 		33981021
(Nat Struct Mol Biol)
PMID
33981021
Date of Publishing: 2021 May 12
Title Structural basis for broad coronavirus neutralization
Author(s) nameSauer MM, Tortorici MA et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 46
Date of Entry 2021 Jul 28

Molecular docking of astemizole to ACE2 shows that it can bind to ACE2 and inhibit the invasion of SARS-CoV-2 spike pseudoviruses. Astemizole is a potential drug candidate that can be repurposed in anti-coronavirus therapies.
✍
 		33932547
(Microb Pathog)
PMID
33932547
Date of Publishing: 2021 Apr 28
Title Astemizole as a drug to inhibit the effect of SARS-COV-2 in vitro
Author(s) nameWang X, Lu J et al.
Journal Microb Pathog
Impact factor
2.64
Citation count: 2
Date of Entry 2021 Aug 10

Based on the intermolecular contact maps (COCOMAPS tool) of ACE2-S complex structure, three short peptides (pep1c, pep1d, pep1e) were designed to block virus-host interaction in the early stages of SARS-CoV-2 infection. New therapeutics for oral administration against SARS-CoV-2 infection can be developed using these peptides, which could be an alternative to traditional drug development.
✍
 		33918595
(Molecules)
PMID
33918595
Date of Publishing: 2021 Apr 9
Title Native Structure-Based Peptides as Potential ProteinProtein Interaction Inhibitors of SARS-CoV-2 Spike Protein and Human ACE2 Receptor
Author(s) nameOdolczyk N, Marzec E et al.
Journal Molecules
Impact factor
3.01
Citation count: 8
Date of Entry 2021 Aug 12

Complex of ACE2 receptor and N501Y spike protein ectodomains shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2 providing a structural explanation for the increased ACE2 affinity of the N501Y mutant, and its increased infectivity, but the mutation does note cause large structural changes. Structural studies establish the molecular basis showing the increase in ACE2 binding efficiency conferred by the N501Y mutation. Despite the higher infectivity of SARS-CoV-2 viruses carrying the N501Y mutation, the availability of the extended epitope surface on the RBD enables effective neutralization by VH ab8 and Fab ab1.
✍
 		33914735
(PLoS Biol)
PMID
33914735
Date of Publishing: 2021 Apr 29
Title Cryo-electron microscopy structures of the N501Y SARS-CoV-2 spike protein in complex with ACE2 and 2 potent neutralizing antibodies
Author(s) nameZhu X, Mannar D et al.
Journal PLoS Biol
Impact factor
7.62
Citation count: 68

Comparative analysis of the docking scores obtained by molecular docking of SARS-CoV-2 S1 RBD domain to amyloid and heparin to heparin binding proteins. This shows S1-heparin has the highest docking score and as the temperature increases from 25° C to 40° C, the binding affinity for SARS-CoV-2 S1 protein complexes decreases. Targeting the interaction of SARS-CoV-2 spike protein with the brain proteins might be a suitable way to reduce the aggregation process and thus neurodegeneration in COVID-19 patients.
✍
 		33789211
(Biochem Biophys Res Commun)
PMID
33789211
Date of Publishing: 2021 May 21
Title SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration
Author(s) name Idrees D, Kumar V.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 18
Date of Entry 2021 Aug 12

Heparin binding accelerates the aggregation of pathological amyloid proteins in the brain. Comparative study to the docking score of SARS-CoV-2 S1-heparin complex to amyloid forming proteins shows molecular interaction of the SARS-COV-2 Spike S1 RBD and Heparin shows a high docking score of -282.57. By targeting the binding and aggregation process of the S1 and Heparin, neurodegenration can be prevented.
✍
 		33789211
(Biochem Biophys Res Commun)
PMID
33789211
Date of Publishing: 2021 May 21
Title SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration
Author(s) name Idrees D, Kumar V.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 18
Date of Entry 2021 Aug 12

SARS-CoV-2 S1 RBD binds heparin binding proteins including A, -synuclein, tau, prion, and TDP-43 RRM. The heparin binding site of S1 protein assists the binding to amyloid proteins to the viral surface and initate aggregation of these proteins, leading to neurodegenration in brain. This provides a reasonable explanation for the neurodegenerative distresses caused by a COVID infection. Increase in Kd as the temperature increased from 25 C to 40 C, showed a decrease in binding affinity for SARS-CoV-2 S1 protein complexes.
Increase in temperature usually disrupts the noncovalent interactions between a protein-protein complex, but, the decrease in binding affinity across the temperatures was less apparent for the -Syn complex with S1. This anomaly suggests a stable interaction between -synuclein to SARS-CoV-2 S1 protein.
✍
 		33789211
(Biochem Biophys Res Commun)
PMID
33789211
Date of Publishing: 2021 May 21
Title SARS-CoV-2 spike protein interactions with amyloidogenic proteins: Potential clues to neurodegeneration
Author(s) name Idrees D, Kumar V.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 18
Date of Entry 2021 Aug 12

The study compares the similarities and differences in the structure of heparin sulfate (HS) in human and bat lungs. Also, discusses about the binding capacity of spike protein of SARS-CoV-2 with homosapiens and chiroptera's lung heparin sulfate. The spike glycoprotein of COVID 19 binds 3.5 times stronger to the human lung heparin(HS) sulfate than bat lung heparin sulfate. The molecular weight of the heparin sulfate is more important than the sulfation level for lung HS binding to SARS-CoV-2 virus spike protein.
✍
 		33712145
(Carbohydr Polym)
PMID
33712145
Date of Publishing: 2021 May 15
Title Heparan sulfates from bat and human lung and their binding to the spike protein of SARS-CoV-2 virus
Author(s) nameYan L, Song Y et al.
Journal Carbohydr Polym
Impact factor
6.23
Citation count: 13
Date of Entry 2021 Aug 11

Molecular interaction study between polymorphic spike protein and human ACE2 reveals affinity and stability of ACE2 to spike protein of SARS-CoV-2 for a mutants I468V, N638S, R708Q is -65.09 kcal/mol, -65.09kcal/mol and -64.99 kcal/mol, respectively. The variants in the spike protein of SARS-CoV-2 and hACE2 would provide a database for tracking the adaptive mutation of SARS-CoV-2 and potential recombination events across different species.
✍
 		33542420
(Sci Rep)
PMID
33542420
Date of Publishing: 2021 Feb 4
Title Dynamics of binding ability prediction between spike protein and human ACE2 reveals the adaptive strategy of SARS-CoV-2 in humans
Author(s) nameXue X, Shi J et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 6
Date of Entry 2021 Jul 28

Surface plasmon resonance (SPR) was used to compare the kinetics of SARS-CoV-2 S protein both D614 and D614G binding to human ACE2. D614G decreases the affinity for ACE2 by increasing the rate of dissociation. The increased infectivity of D614G is not explained by greater ACE2 binding strength.
✍
 		32991842
(Cell)
PMID
32991842
Date of Publishing: 2020 Oct 29
Title Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant
Author(s) nameYurkovetskiy L, Wang X et al.
Journal Cell
Impact factor
27.35
Citation count: 434
Date of Entry 2021 Jun 15

IgA monoclonal antibody, MAb362, competitively blocks SARS-CoV and SARS-CoV-2 spike proteins and ACE2 receptor binding. The binding affinity of IgA and IgG with RBD of SARS-CoV-2 is 0.3nM and 13nM, respectively. The study of interaction of MAb362 with other receptor blocking and neutralising antibodies against SARS-CoV-2 will help in the development of vaccines and prophylactic/therapeutic antibodies to combat future outbreaks caused by this virus family.
✍
 		32826914
(Nat Commun)
PMID
32826914
Date of Publishing: 2020 Aug 21
Title A cross-reactive human IgA monoclonal antibody blocks SARS-CoV-2 spike-ACE2 interaction
Author(s) nameEjemel M, Li Q et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 62
Date of Entry 2021 Oct 30

Seven chimeric peptides (cnCoVP-1, cnCoVP-2, cnCoVP-3, cnCoVP-4, cnCoVP-5, cnCoVP-6, and cnCoVP-7) were found to block SARS-CoV-2 Spike RBD out of 500 generated. The most promising candidates for preventing RBD of the spike are cnCoVP-1 and cnCoVP-4. Chimeric peptides cnCoVP-1 and cnCoVP-4 are found to partially block the access of SARS-CoV-2 Spike RBD to hACE2, howerver further in vitro and in vivo testing and validation is required.
✍
 		32802318
(F1000Res)
PMID
32802318
Date of Publishing: 2020
Title Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain
Author(s) nameBarh D, Tiwari S et al.
Journal F1000Res
Impact factor
2.64
Citation count: 25
Date of Entry 2021 Aug 2

Reporting 7 identifed peptides (DBP1, DBP2, DBP3, DBP4, DBP5, DBP6, DBP7) screened from 5 antimicrobial peptide databases of 20 amino acids in length to target against SARS-CoV-2 Spike RBD to exhibit their anti-SARS virus activities and recognizing DBP6 to be a potential peptide. Peptide DBP6 could be a potential drug peptide to be tested for SARS-CoV-2 Spike protein-drug development.
✍
 		32802318
(F1000Res)
PMID
32802318
Date of Publishing: 2020
Title Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain
Author(s) nameBarh D, Tiwari S et al.
Journal F1000Res
Impact factor
2.64
Citation count: 25
Date of Entry 2021 Aug 2

Reporting 3 designed stretches of hACE2 residue-based peptides (AC26, AC23, AC20) that demonstrates maximum active binding affinity with the Spike SARS-CoV RBD and identifying AC23 and AC20 to be potential sequence based peptide. AC20 and AC23 derived from hACE2 is found to probably block two key critical positions and hence can be further tested for its efficacy and therapeutics target against SARS-CoV-2 Spike RBD
✍
 		32802318
(F1000Res)
PMID
32802318
Date of Publishing: 2020
Title Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain
Author(s) nameBarh D, Tiwari S et al.
Journal F1000Res
Impact factor
2.64
Citation count: 25
Date of Entry 2021 Aug 2

SARS-CoV-2 RBD interacts with the N-linked glycan on Asn90 of ACE2 which is absent in SARS-CoV-1.MD simulation of SARS-CoV-2 with ACE2 indicate unbinding forces range from 70 to 105pN and removal of the N-linked glycan reduced unbinding forces to 50-70pN The difference in ACE2 binding between SARS-CoV-2 and SARS-CoV-1 and could help develop new strategies to block SARS-CoV-2 entry.
✍
 		32766576
(bioRxiv)
PMID
32766576
Date of Publishing: 2020 Jul 31
Title Biomechanical characterization of SARS-CoV-2 spike RBD and human ACE2 protein-protein interaction
Author(s) nameCao W, Dong C et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Oct 30

MD simulation of the glycosylated trimer spike of SARS-CoV-2 in complex with glycosylated, soluble, human ACE 2 reveals that glycan at N546 of ACE2 interacts with N0074 and N0165 in the S protein. To develop ACE2 as a possible decoy therapy, understanding the influence of ACE2 polymorphisms on glycosylation and S binding is crucial.Modifications of ACE2 glycosylation could lead to more potent biologics that are more competitive inhibitors of S binding.The study provides a foundation for the development of immunogens, vaccines, antibodies, and inhibitors, as well as new information on the mechanisms that allow for glycan microheterogeneity.In order to produce treatments, detailed investigations of the influence of new polymorphisms in S and natural and designed-for-biologics variants of ACE2 on glycosylation and binding properties are necessary.
✍
 		32743578
(bioRxiv)
PMID
32743578
Date of Publishing: 2020 Jul 24
Title Virus-Receptor Interactions of Glycosylated SARS-CoV-2 Spike and Human ACE2 Receptor
Author(s) nameZhao P, Praissman JL et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Oct 30

Structural characterization of SARS-CoV-2 spike glycoprotein (subdomain 1 to S2 quadruple mutant (u1S2q 2 Up RBD state)) construct and determing its binding with the antibody CR3022 human cell receptor ACE2 The spike glycoprotein mutant construct (u1S2q) with mutation A570L,T572I, F855Y, N856I were developed. The u1S2q 2 Up RBD Spike Protein Trimer were docked with the CR3022 Fab - RBD complex (PDB 6YLA) and potential clashes were observed in between.
✍
 		32699321
(Nat Struct Mol Biol)
PMID
32699321
Date of Publishing: 2020 Oct
Title Controlling the SARS-CoV-2 spike glycoprotein conformation
Author(s) nameHenderson R, Edwards RJ et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 150

Structural characterization of SARS-CoV-2 spike glycoprotein (subdomain 1 to S2 quadruple mutant (u1S2q 1 Up RBD)) construct. And determing its binding with the antibody CR3022 and human cell receptor ACE2. The spike glycoprotein mutant construct (u1S2q) with mutation A570L,T572I, F855Y, N856I were developed. The u1S2q 1 Up RBD Spike Protein Trimer were docked with the CR3022 Fab - RBD complex (PDB 6YLA) and potential clashes were observed in between.
✍
 		32699321
(Nat Struct Mol Biol)
PMID
32699321
Date of Publishing: 2020 Oct
Title Controlling the SARS-CoV-2 spike glycoprotein conformation
Author(s) nameHenderson R, Edwards RJ et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 150

Structural characterization of SARS-CoV-2 spike glycoprotein (RBD to S2 double mutant (rS2d)) constructs. And determing its binding with the antibody CR3022 and human cell receptor ACE2. The spike glycoprotein mutant constructs (rS2d) with double mutation S383C, D985C were developed. The RBD in the rS2d construct is locked in the 'down ' state conformation.
✍
 		32699321
(Nat Struct Mol Biol)
PMID
32699321
Date of Publishing: 2020 Oct
Title Controlling the SARS-CoV-2 spike glycoprotein conformation
Author(s) nameHenderson R, Edwards RJ et al.
Journal Nat Struct Mol Biol
Impact factor
9.8
Citation count: 150

Molecular docking studies of Hydroxychloroquine(HCQ) on the RBD of SARS-CoV-2 Spike protein produced a Vina score of −5.5 kcal mol−1 .The hydroxyl group of HCQ molecule forms a strong hydrogen bonding with Asn501 side chain residing on one part of the receptor binding motif (RBM) of the Spike protein. ~
✍
 		32696720
(J Biomol Struct Dyn)
PMID
32696720
Date of Publishing: 2020 Jul 22
Title Antimalarial-agent artemisinin and derivatives portray more potent binding to Lys353 and Lys31-binding hotspots of SARS-CoV-2 spike protein than hydroxychloroquine: potential repurposing of artenimol for COVID-19
Author(s) name Sehailia M, Chemat S.
Journal J Biomol Struct Dyn
Impact factor
3.22
Citation count: 25
Date of Entry 2021 Aug 2

Amino acid residues Asp 1165, Gly 1171, Asn 1173 of S2 subunit of spike protein of SARS-COV-2 have interactions with Lys 1648, Arg 1649, His 1672 of BRCA-1 protein. Further experimental research is required to unveil the impact of COVID-19 in cancer patients and to explore the functional role of these interactions.
✍
 		32619819
(Transl Oncol)
PMID
32619819
Date of Publishing: 2020 Oct
Title S2 Subunit of SARS-nCoV-2 Interacts with Tumor Suppressor Protein p53 and BRCA: an In Silico Study
Author(s) name Singh N, Bharara Singh A.
Journal Transl Oncol
Impact factor
3.3
Citation count: 8


Pathophysiology : Spike
Total row(s): 12
Select item(s)
Key Findings
Comments
(You can add your comments too!)
Original Article
(hover to see details)
Instilling the S1 subunit of SARS-CoV-2 Spike protein (400 µg/kg in 2ml/kg body weight) in K18-hACE2 transgenic mice exhibited a decline in body weight, increase in white blood cells and protein concentrations in bronchoalveolar lavage fluid (BALF), upregulation of multiple inflammatory cytokines in BALF and serum, histological evidence of lung injury, and activation of signal transducer and activator of transcription 3 (STAT3) and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathways in the lung. A single exposure of K18-hACE2 mice to SARS-CoV-2 Spike Protein S subunit S1 may represent a valid model of COVID-19, allow the study of the molecular mechanisms of SARS-CoV-2 induced lung injury and be useful in the investigation of potential new therapeutic approaches to the management of COVID-19 as well as future coronavirus-dependent respiratory diseases.
✍
 		34156871
(Am J Physiol Lung Cell Mol Physiol)
PMID
34156871
Date of Publishing: 2021 Jun 22
Title Single intratracheal exposure to SARS-CoV-2 S1 spike protein induces acute lung injury in K18-hACE2 transgenic mice
Author(s) nameColunga Biancatelli RML, Solopov PA et al.
Affiliations Pavel Solopov (Old Dominion University)| Ruben Colunga Biancatelli (Old Dominion University)| Elizabeth Sharlow (University of Virginia)| John Lazo (University of Virginia)| John Catravas (Old Dominion University, Old Dominion University)
Journal Am J Physiol Lung Cell Mol Physiol
Impact factor
3.78
Citation count: 27
Date of Entry 2021 Jun 15

The in vitro mutation analysis showed that the D614G mutation changes the spike protein sorting, enhances the trafficking of spike protein to the lysosome.
✍
 		33330866
(bioRxiv)
PMID
33330866
Date of Publishing: 2020 Dec 9
Title The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Author(s) nameGuo C, Tsai SJ et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 3

To understand the mechanism of lysosomal trafficking of the spike protein, the Htet1/SD614G cells were incubated with doxycycline. DMSO causes denaturation of proteins
✍
 		33330866
(bioRxiv)
PMID
33330866
Date of Publishing: 2020 Dec 9
Title The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Author(s) nameGuo C, Tsai SJ et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 3

To understand the molecular mechanism of lysosomal trafficking of the spike protein, the Htet1/SD614G cells were incubated with doxycycline and dynasore. Dynasore blocks the clathrin-dependent endocytosis pathway by inhibting dynamin-1
✍
 		33330866
(bioRxiv)
PMID
33330866
Date of Publishing: 2020 Dec 9
Title The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Author(s) nameGuo C, Tsai SJ et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 3

To understand the molecular mechanism of lysosomal trafficking of the spike protein, the Htet1/SD614G cells were incubated with doxycycline and pitstop2. Pitstop2 blocks both clathrin-dependent and clathrin-independent endocytosis pathway
✍
 		33330866
(bioRxiv)
PMID
33330866
Date of Publishing: 2020 Dec 9
Title The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Author(s) nameGuo C, Tsai SJ et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 3

To understand the molecular mechanism of lysosomal trafficking of the spike protein, the Htet1/SD614G cells were incubated with nocodazole. Nocodazole is a microtubule-inhibitor, and also disrupts motor-directed lysosome movements
✍
 		33330866
(bioRxiv)
PMID
33330866
Date of Publishing: 2020 Dec 9
Title The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Author(s) nameGuo C, Tsai SJ et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 3

To understand the molecular mechanism of lysosomal trafficking of the spike protein, the Htet1/SD614G cells were incubated with bafilomycin A1. Bafilomycin A1 is a V-ATPase inhibitor
✍
 		33330866
(bioRxiv)
PMID
33330866
Date of Publishing: 2020 Dec 9
Title The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Author(s) nameGuo C, Tsai SJ et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 3

The in vitro mutation analysis of the D614G mutation showed no effect on viral replication and viral infectivity in Vero E6 cells. The two viruses (G614 virus and the D614 virus) had similar plaque morphologies
✍
 		33106671
(Nature)
PMID
33106671
Date of Publishing: 2020 Oct 26
Title Spike mutation D614G alters SARS-CoV-2 fitness
Author(s) namePlante JA, Liu Y et al.
Journal Nature
Impact factor
24.36
Citation count: 651

Compared with the wild D614 virus, the mutant G614 virus showed increased viral replication and viral infectivity in the cell line Calu-3. Infectious viral titres and genomic RNA levels in cell culture were determined by plaque assay, and RTqPCR, respectively
✍
 		33106671
(Nature)
PMID
33106671
Date of Publishing: 2020 Oct 26
Title Spike mutation D614G alters SARS-CoV-2 fitness
Author(s) namePlante JA, Liu Y et al.
Journal Nature
Impact factor
24.36
Citation count: 651

Compared with the wild D614 virus, the mutant G614 virus showed increased viral replication and viral infectivity in the primary human airway tissue culture model. The primary human airway tissue culture model contains human tracheal and bronchial epithelial cells cultured as monolayers resembling the epithelial tissue of the respiratory tract.
✍
 		33106671
(Nature)
PMID
33106671
Date of Publishing: 2020 Oct 26
Title Spike mutation D614G alters SARS-CoV-2 fitness
Author(s) namePlante JA, Liu Y et al.
Journal Nature
Impact factor
24.36
Citation count: 651

Hamsters infected with mutant SARS-CoV-2 (G614 virus) showed higher viral load in the nasal washes and the tracheae, but not in the lungs, than those of Hamsters infected with WT SARS-CoV-2 (D614 virus). Infected hamsters from both groups showed similar weight loss.
✍
 		33106671
(Nature)
PMID
33106671
Date of Publishing: 2020 Oct 26
Title Spike mutation D614G alters SARS-CoV-2 fitness
Author(s) namePlante JA, Liu Y et al.
Journal Nature
Impact factor
24.36
Citation count: 651

The in vitro analysis of the deletion variants revealed that Var1 \(deletion of QTQTN in spike protein) reduced the viral replication during late-phase, and Var2 \(deletion of NSPRRAR in spike protein) didnt affect viral replication in Vero and Vero-E6 cells. Var1 (QTQTN deletion)is commonly detected after two rounds of cell passage
✍
 		32571797
(J Virol)
PMID
32571797
Date of Publishing: 2020 Aug 17
Title Identification of Common Deletions in the Spike Protein of Severe Acute Respiratory Syndrome Coronavirus 2
Author(s) nameLiu Z, Zheng H et al.
Journal J Virol
Impact factor
4.16
Citation count: 76


Epidemiology : Spike
Total row(s): 2
Select item(s)
Key Findings
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(You can add your comments too!)
Original Article
(hover to see details)
Out of 30 COVID-S*19 patients, 23 showed the presence of anti-S*N antibodies, 20 showed anti-S*** antibodies, and 13 had anti-S*M antibodies. S** denotes a full-length spike with a pair of trimer-stabilizing proline mutations (986KV987 to 986PP987) and a quartet of S1/S2 protease cleavage site changes (682RRAR685 to 682GSAG685)
✍
 		33330866
(bioRxiv)
PMID
33330866
Date of Publishing: 2020 Dec 9
Title The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike
Author(s) nameGuo C, Tsai SJ et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 3

SARS-CoV-2 transmission was associated with the role of D614G spike protein variant as 614G had a selective advantage when compared to 614D and it relates to higher viral load and infection of younger individuals but not higher mortality or clinical severity.
✍
 		33275900
(Cell)
PMID
33275900
Date of Publishing: 2020 Nov 19
Title Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity
Author(s) nameVolz E, Hill V et al.
Journal Cell
Impact factor
27.35
Citation count: 412


Immunology : Spike
Total row(s): 102
Select item(s)
Key Findings
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(You can add your comments too!)
Original Article
(hover to see details)
In-vitro neutralization assays revealed that Israeli strain containing the P681H mutation was not associated with higher infection rates and got neutralized by sera from vaccinated individuals. Cell lines were infected with Isolates: Israeli P681H strain (isolate hCoV-19/Israel/CVL-45176-P681H-ngs/2020), (b) non-P681H strain from Israel (isolate hCoV-19/Israel/CVL-45526-ngs/2020) and (c) B.1.1.7 strain (isolate hCoV-19/Israel/CVL-46879-ngs/2020)
✍
 		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

Peptide 2 (YYVGYLQPRTFLLKY) located at the end of the NTD of the Spike protein and upstream of the RBD is the most effective epitope for eliciting a potent antigen-specific CD8+ T response that produces IFN gamma. This important MHC-I epitope can be deliberately integrated into vaccine designs to increase the likelihood of viral eradication by immunization and be used to measure cell-mediated immunity caused by COVID-19 vaccinations.
✍
 		35171086
(Emerg Microbes Infect)
PMID
35171086
Date of Publishing: 2022 Dec
Title Identification of a promiscuous conserved CTL epitope within the SARS-CoV-2 spike protein
Author(s) nameJiang S, Wu S et al.
Journal Emerg Microbes Infect
Impact factor
5.84
Citation count: 1
Date of Entry 2022 Jun 17

In patients who had recovered from mild COVID-19 infection, the serum anti-SARS-CoV-2 Spike antibodies declined quickly within the first 4 months and then more slowly in the following 7 months. In addition, a long-lived S-specific Bone marrow plasma cells (BMPC) response was detected in COVID-19 convalescent individuals. Bone marrow aspirates were collected from 18 of the participants 7-8 months after infection.
✍
 		34030176
(Nature)
PMID
34030176
Date of Publishing: 2021 May 24
Title SARS-CoV-2 infection induces long-lived bone marrow plasma cells in humans
Author(s) nameTurner JS, Kim W et al.
Journal Nature
Impact factor
24.36
Citation count: 145

Eight months post-symptom onset, the anti-Spike and anti-receptor binding domain (RBD) IgM+ anitbodies in plasma decreases rapidly, whereas the IgG+ anitbodies decrease is less rapidly.The neutralising activity also drops rapidly. Simultaneously, the number of RBD-specific IgM+ B cells declines, while the number of RBD-specific IgG+ B cells remains stable. Long-term vaccination effectiveness is enhanced by the persistence of RBD-specific memory B cells up to 8 months following natural infection.
✍
 		33969322
(Cell Rep Med)
PMID
33969322
Date of Publishing: 2021 May 5
Title Longitudinal analysis of humoral immunity against SARS-CoV-2 Spike in convalescent individuals up to 8 months post-symptom onset
Author(s) nameAnand SP, Prévost J et al.
Journal Cell Rep Med
Impact factor
- n/a -
Citation count: 65
Date of Entry 2021 Sep 29

In convalescent patients, more than 80% of the anti-spike IgG antibody response is directed against epitopes outside the receptor binding domain (RBD). In one patient, antibodies were aimed at the amino (N)-terminal domain (NTD) that proved protective against a deadly viral attack. In a high viral load test, a cocktail of the top non-RBD plasma mAbs CM29CM31 (>85% of the IgG plasma lineages to S-ECD) provided the most effective protection and lung viral titers below the limit of detection (LOD) (10^4 PFU).
✍
 		33947773
(Science)
PMID
33947773
Date of Publishing: 2021 May 4
Title Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes
Author(s) nameVoss WN, Hou YJ et al.
Journal Science
Impact factor
20.57
Citation count: 83
Date of Entry 2021 Oct 31

Deletions at positions 144/145 and 243-244 in the NTD region of S glycoprotein disrupt the binding of antibody 4A8, which defines an immunodominant epitope within the NTD. Virus isolated from immunosuppressed patients (Pittsburgh long-term infection 1) resists neutralization by 4A8. A nondeletion variant (Munich) neutralized by 4A8. Both were neutralized by convalescent serum, and neither got neutralized by H2214 (an influenza hemagglutinin binding antibody)
✍
 		33536258
(Science)
PMID
33536258
Date of Publishing: 2021 Feb 3
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ et al.
Journal Science
Impact factor
20.57
Citation count: 220

The SARS-CoV-2 immune memory kinetics was assessed more than 6 months after infection. Spike protein-specific memory B cells were higher in number at 6 months than one month after infection. The CD4+ and CD8+ T cells decreased with a half-life of 3-5 months. "1.) Circulating antibodies to SARS-CoV-2 over time: Figure 1 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919858/figure/F1/), 2.) Kinetics of SARS-CoV-2 memory B cell responses: Figure 2(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919858/figure/F2/), 3.) SARS-CoV-2 circulating memory CD8+ T cells: Figure 3 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919858/figure/F3/), 4.) SARS-CoV-2 circulating memory CD4+ T cells: Figure 4 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7919858/figure/F4/)"
✍
 		33408181
(Science)
PMID
33408181
Date of Publishing: 2021 Jan 6
Title Immunological memory to SARS-CoV-2 assessed for up to 8 months after infection
Author(s) nameDan JM, Mateus J et al.
Journal Science
Impact factor
20.57
Citation count: 899
Date of Entry 2021 Jul 24

Using an evolutionary protein design algorithm, EvoDesign, thousands of stable S protein variants which keep the surface conformation and B cell epitopes intact were studied. The T cell epitope content and similarity score were then calculated. The newly designed S protein introduced 9 new MHC-II T cell epitopes that do not exist in the wildtype SARS-CoV-2. The computational design of the SARS-CoV-2 protein coupled with some other structural modifiactions can be used as a rational-structure-based vaccine design.
✍
 		33398234
(Comput Struct Biotechnol J)
PMID
33398234
Date of Publishing: 2020 Dec 31
Title Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering
Author(s) nameOng E, Huang X et al.
Journal Comput Struct Biotechnol J
Impact factor
5.11
Citation count: 10

During the early stages of COVID-19, total T lymphocyte count and CD4+ T cells decrease in count.
✍
 		33310028
(Int J Infect Dis)
PMID
33310028
Date of Publishing: 2020 Dec 10
Title Dynamic Anti-Spike Protein Antibody Profiles in COVID-19 Patients
Author(s) nameBao Y, Ling Y et al.
Journal Int J Infect Dis
Impact factor
3.42
Citation count: 15

Patients who had recovered showed increased anti-S IgG/IgM and high positive rates when compared to in-patients.
✍
 		33310028
(Int J Infect Dis)
PMID
33310028
Date of Publishing: 2020 Dec 10
Title Dynamic Anti-Spike Protein Antibody Profiles in COVID-19 Patients
Author(s) nameBao Y, Ling Y et al.
Journal Int J Infect Dis
Impact factor
3.42
Citation count: 15

CD8 T cell epitopes of 80 different human HLAs were generated for SARS-CoV-2 Spike protein.
✍
 		33301503
(PLoS One)
PMID
33301503
Date of Publishing: 2020
Title CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention
Author(s) name Guo E, Guo H.
Journal PLoS One
Impact factor
2.87
Citation count: 10

34 cytotoxic T cell epitopes located in spike glycoprotein, envelope protein, membrane protein, and nucleocapsid phosphoprotein were identified.
✍
 		33257716
(Sci Rep)
PMID
33257716
Date of Publishing: 2020 Nov 30
Title Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-CoV-2
Author(s) nameBehmard E, Soleymani B et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 19

14 helper T cell epitopes located in spike glycoprotein, envelope protein, and nucleocapsid phosphoprotein were identified.
✍
 		33257716
(Sci Rep)
PMID
33257716
Date of Publishing: 2020 Nov 30
Title Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-CoV-2
Author(s) nameBehmard E, Soleymani B et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 19

The neutralizing potential efficiency of anti-Spike-S1 IgYs (chicken egg yolk antibodies) that blocks the binding of various variants of SARS-CoV-2 spike protein to ACE-2 receptor was researched.
✍
 		33191178
(Int Immunopharmacol)
PMID
33191178
Date of Publishing: 2020 Nov 3
Title Chicken Egg Yolk Antibodies (IgYs) block the binding of multiple SARS-CoV-2 spike protein variants to human ACE2
Author(s) nameWei S, Duan S et al.
Journal Int Immunopharmacol
Impact factor
3.38
Citation count: 6

This study depicts distinct antibody responses following SARS-CoV-2 infection in children and adults. Anti-Spike (S) IgG, IgM and IgA antibodies, as well as anti-Nucleocapsid (N) IgG antibody were observed in adult COVID-19 patients, while children with and without multisystem inflammatory syndrome (MIS-C) exhibited reduced breadth of anti-SARS-CoV-2-specific antibodies. Children independent of whether they develop MIS-C, exhibit distinct infection course and immune response, with indications for developing age-targeted strategies for testing and safeguarding the population. Anti-SARS-CoV-2 antibody response generated in children is mainly anti-S IgG antibodies independent of clinical syndrome, whereas adults generate broader antibody responses to infection and exhibit high magnitude and breadth of the anti-S antibody response with more severe disease. The results exhibited quantitative and qualitative differences in the anti-SARS-CoV-2-specific antibody response across the spectrum of infection in children compared to adults.
✍
 		33154590
(Nat Immunol)
PMID
33154590
Date of Publishing: 2021 Jan
Title Distinct antibody responses to SARS-CoV-2 in children and adults across the COVID-19 clinical spectrum
Author(s) nameWeisberg SP, Connors TJ et al.
Journal Nat Immunol
Impact factor
18.5
Citation count: 185
Date of Entry 2021 Dec 15

Sera from hamsters infected with the WT SARS-CoV-2 (D614) virus showed higher neutralization against the G614 virus than against the D614 virus. The result suggests that the mutation wont affect the ability of vaccines
✍
 		33106671
(Nature)
PMID
33106671
Date of Publishing: 2020 Oct 26
Title Spike mutation D614G alters SARS-CoV-2 fitness
Author(s) namePlante JA, Liu Y et al.
Journal Nature
Impact factor
24.36
Citation count: 651

A monoclonal Antibody (2B04) potently inhibited SARS-CoV-2 infection with an IC50 of 3.007 ng/mL.
✍
 		33035201
(JCI Insight)
PMID
33035201
Date of Publishing: 2020 Nov 19
Title Neutralizing antibody against SARS-CoV-2 spike in COVID-19 patients, health care workers and convalescent plasma donors.
Author(s) nameZeng C, Evans JP et al.
Journal JCI Insight
Impact factor
6.014
Citation count: 35

Anti-SARS-CoV-2 antibody responses were easily detectable in serum and saliva, with peak IgG levels reaching 1630 days post-infection. Anti-SARS-CoV-2 IgA and IgM antibodies rapidly degraded in both biofluids, whereas IgG antibodies were relatively stable up to 105 days post-symptom onset (PSO). The anti-spike and anti-RBD IgG and IgM levels in the serum samples positively correlated to the levels in saliva. Saliva may be a good option for antibody testing, at least for anti-spike IgM and anti-RBD IgG readings.
✍
 		33033173
(Sci Immunol)
PMID
33033173
Date of Publishing: 2020 Oct 8
Title Persistence of serum and saliva antibody resonses to SARS-CoV-2 spike protein in COVID -19 patients
Author(s) nameIsho B, Abe KT et al.
Journal Sci Immunol
Impact factor
8.16
Citation count: 309
Date of Entry 2021 Dec 15

Studying the kinetics and antibody isotype profile to the RBD of S protein in individuals with severe infection was done along with cross-reactivity of the responses with different coronaviruses RBDs. Characterization of assay performance using the dried blood spots was done which can provide an alternative to serum or plasma. Data is skewed as majority of cohort individuals are adults having severe disease or with a high risk factors for disease progression.
✍
 		33033172
(Sci Immunol)
PMID
33033172
Date of Publishing: 2020 Oct 8
Title Persistence and decay of human antibody responses to the receptor binding domain of SARS-CoV-2 spike protein in COVID-19 patients.
Author(s) nameIyer AS, Jones FK et al.
Journal Sci Immunol
Impact factor
8.16
Citation count: 281

T cell responses towards spike, nucleocapsid and membrane proteins were compared in severe, moderate and critical COVID-19 patients. Membrane protein induced the highest number of CD4+ T cell responses. Critical COVID-19 patients had a strong T cell response that is comparable to, if not better than, non-critical patients. Critical patients had a strong SARS-CoV-2-specific T cell response, which could play a role in immunopathogenesis, but disproves the idea that a weakened T cell response is the cause of life-threatening COVID-19.
✍
 		32904468
(Cell Rep Med)
PMID
32904468
Date of Publishing: 2020 Sep 22
Title Robust T Cell Response Toward Spike, Membrane, and Nucleocapsid SARS-CoV-2 Proteins Is Not Associated with Recovery in Critical COVID-19 Patients
Author(s) nameThieme CJ, Anft M et al.
Journal Cell Rep Med
Impact factor
- n/a -
Citation count: 54
Date of Entry 2021 Sep 29

Monoclonal antibody MD67 showed neutralizing activity in the plaque reduction neutralization test (PRNT) using VeroE6 cells infected with the pathogenic SARS-CoV-2.
✍
 		32855401
(Nat Commun)
PMID
32855401
Date of Publishing: 2020 Aug 27
Title A panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes
Author(s) nameNoy-Porat T, Makdasi E et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 87

Monoclonal antibody MD29 showed neutralizing activity in the plaque reduction neutralization test (PRNT) using VeroE6 cells infected with the pathogenic SARS-CoV-2. Monoclonal antibody MD29 which recognizes the same epitope as antibody CR3022 does not inhibit the binding of RBD to human ACE2
✍
 		32855401
(Nat Commun)
PMID
32855401
Date of Publishing: 2020 Aug 27
Title A panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes
Author(s) nameNoy-Porat T, Makdasi E et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 87

Monoclonal antibody MD65 showed neutralizing activity in the plaque reduction neutralization test (PRNT) using VeroE6 cells infected with the pathogenic SARS-CoV-2. Monoclonal antibody MD65 inhibits the binding of RBD to human ACE2
✍
 		32855401
(Nat Commun)
PMID
32855401
Date of Publishing: 2020 Aug 27
Title A panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes
Author(s) nameNoy-Porat T, Makdasi E et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 87

Monoclonal antibody MD17 showed a poor neutralizing activity (NT50) in the plaque reduction neutralization test (PRNT) using VeroE6 cells infected with the pathogenic SARS-CoV-2.
✍
 		32855401
(Nat Commun)
PMID
32855401
Date of Publishing: 2020 Aug 27
Title A panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes
Author(s) nameNoy-Porat T, Makdasi E et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 87

Monoclonal antibody MD63 did not show neutralizing activity in the plaque reduction neutralization test (PRNT) using VeroE6 cells infected with the pathogenic SARS-CoV-2.
✍
 		32855401
(Nat Commun)
PMID
32855401
Date of Publishing: 2020 Aug 27
Title A panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes
Author(s) nameNoy-Porat T, Makdasi E et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 87