Variant

Last updated: 2022 Mar 3
Total hit(s): 167
Select item(s)
Key Findings
Comments
(You can add your comments too!)
Original Article
(hover to see details)
T29A, T50I, T299I, and Q613 new amino acid changes, in addition to 10 modifications of the delta variant were found in SARS-CoV-2 strains from 2 Moroccan patients with Covid-19. These sequences belong to clade GK, sub-lineage AY.33 of Delta variant B1.617.2. The emergence and transmission of novel variations originating from volatile organic compounds (VOCs) is a global issue; their resistance to vaccination is unknown, and genomic surveillance of the SARS-CoV-2 genome remains the key method for detecting variants and preventing their spread.
✍
 		35112895
(Microbiol Resour Announc)
PMID
35112895
Date of Publishing: 2022 Feb 17
Title Coding-Complete Genome Sequences of a Delta Subvariant (AY.33) of SARS-CoV-2 Obtained from Moroccan COVID-19 Patients
Author(s) nameHemlali M, Chouati T et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1
Date of Entry 2022 Mar 3

The Omicron variant's RBD and S1/S2 domain mutations boosted the spike protein's charge to +9 compared to the wild type SARS-CoV-2, while the Delta variant's charge is only +4. The spike protein interacts with the negatively charged sulfate groups present in glycosaminoglycan (GAGs) found on the cell surface and forms a stable complex. Experimentation is required to evaluate the effects of the P681H mutation on the infection potential of the Omicron form.
✍
 		35020256
(Chembiochem)
PMID
35020256
Date of Publishing: 2022 Jan 12
Title Charge Matters: Mutations in Omicron variant favor Binding to Cells
Author(s) nameNie C, Sahoo AK et al.
Journal Chembiochem
Impact factor
2.64
Citation count: 3
Date of Entry 2022 Feb 26

Serum samples from 28 COVID-19 convalescent patients infected with SARS-CoV-2 original strain, Alpha, Beta, Gamma, Delta, Lambda, and Mu variants showed 8.5, 1.2, 2.8, 1.6, 1.6, 1.7, and 4.5 folds, respectively, decreased neutralization of pseudotype SARS-CoV-2 variant Omicron (PV Omicron). Despite the fact that a third-dose enhancement method can greatly raise immunity, protection from Omicron may be reduced. Hence the effectiveness of therapeutic monoclonal antibodies against the Omicron variant must be re-evaluated.
✍
 		34890524
(Emerg Microbes Infect)
PMID
34890524
Date of Publishing: 2022 Dec
Title The significant immune escape of pseudotyped SARS-CoV-2 variant Omicron
Author(s) nameZhang L, Li Q et al.
Journal Emerg Microbes Infect
Impact factor
5.84
Citation count: 61
Date of Entry 2022 Jan 22

Sera of all convalescent patients, vaccinated cohort, Delta convalescent, Alpha convalescent and Gamma convalescent showed 8.2x, 3.4x, 4.3x, 8.6x and 10.5x, respectively, decrease in the ability to neutralize the Omicron variant relative to the Delta variant. The new mutations in the Omicron variant at residues 493, 496 and 498 appear to restore ACE2 binding efficiency that would be lost due to other mutations such as K417N. This resulted in an the increase in escape from neutralization but without compromising its ability to interact efficiently with ACE2.
✍
 		Pre-print (bioRXiv)
Title SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
Impact factor
N/A
Date of Entry 2022 Jan 10

Sera of all convalescent patients, vaccinated cohort, Delta convalescent, Alpha convalescent and Gamma convalescent showed 6.3x, 4.4x, 3.4x, 13.0x and 5.5x, respectively, decrease in the ability to neutralize the Omicron variant relative to the wild-type. Omicron variant is more resistant to neutralization than any other variant of concern. Escape from neutralization but without compromising its ability to interact efficiently with ACE2 are the key molecular features that contribute to the increase in transmissibility of the Omicron variant.
✍
 		Pre-print (bioRXiv)
Title SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
Impact factor
N/A
Date of Entry 2022 Jan 10

Monoclonal antibodies (RBD directed: ab1, ab8, S2M11; N-terminal domain (NTD directed) antibodies : 4-8 and 4A8) have lower Omicron neutralising potency, with the exception of mAb S309, which only has a 4-fold decrease in its neutralizing potency. High number of mutations in the Omicron variant spike protein appears to confer broad antibody escape relative to previously emerged variants of SARS-CoV-2.
✍
 		Pre-print (bioRXiv)
Title SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion
Impact factor
N/A
Date of Entry 2022 Jan 10

A lineage-specific single nucleotide polymorphism (SNP)-targeting allele-specific probe polymerase chain reaction (ASP-PCR) was developed. This new technique identified SARS-CoV-2 Alpha variant with an accuracy of 99.93%.
✍
 		Pre-print (medRXiv)
Date of Publishing 2021 Nov 02
Title Highly-Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe Polymerase Chain Reaction
Impact factor
N/A
Date of Entry 2021 Dec 8

A lineage-specific single nucleotide polymorphism (SNP)-targeting allele-specific probe polymerase chain reaction (ASP-PCR) was developed. This new technique identified SARS-CoV-2 Gamma (P1) variant with an accuracy of 99.42%.
✍
 		Pre-print (medRXiv)
Date of Publishing 2021 Nov 02
Title Highly-Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe Polymerase Chain Reaction
Impact factor
N/A
Date of Entry 2021 Dec 8

A lineage-specific single nucleotide polymorphism (SNP)-targeting allele-specific probe polymerase chain reaction (ASP-PCR) was developed. This new technique identified SARS-CoV-2 Zeta (P2) variant with an accuracy of 99.69%.
✍
 		Pre-print (medRXiv)
Date of Publishing 2021 Nov 02
Title Highly-Sensitive Lineage Discrimination of SARS-CoV-2 Variants through Allele-Specific Probe Polymerase Chain Reaction
Impact factor
N/A
Date of Entry 2021 Dec 8

Certain SARS-CoV-2 antibody levels (IgG) were substantially lower before vaccination, compared to post-vaccination in a serology assay (Ortho Vitros platform). Similarly, pre-vaccination Total Immunoglobin (Ig) levels were lower than thepost-vaccination levels. Most post-vaccination samples were tested again after dilutions (10- and 100-fold), since they exceeded the reported upper limit of signal-to-cutoff (S/CO) values for the assay.
✍
 		Pre-print (medRXiv)
Date of Publishing 2021 Oct 30
Title Vaccination of COVID-19 Convalescent Plasma Donors Increases Binding and Neutralizing Antibodies Against SARS-CoV-2 Variants
Impact factor
N/A
Date of Entry 2021 Dec 8

A serology assay (MSD platform) showed that there was an increase in certain binding antibodies (Anti-spike and Anti-RBD) post vaccination, compared to pre-vaccination samples. However, there was a slight decline in anti-nucleocapsid antibodies after vaccination. The antigens used in the MSD assay were SARS-CoV-2 N, SARS-CoV-2 S1 RBD, SARS-CoV-2 Spike against the ancestral Wuhan-Hu-1, SARS-CoV-2 Spike (P.1), SARS-CoV-2 Spike (D614G), SARS-CoV-2 Spike (B.1.351), SARS-CoV-2 Spike (B.1.1.7).
✍
 		Pre-print (medRXiv)
Date of Publishing 2021 Oct 30
Title Vaccination of COVID-19 Convalescent Plasma Donors Increases Binding and Neutralizing Antibodies Against SARS-CoV-2 Variants
Impact factor
N/A
Date of Entry 2021 Dec 8

Mortality rate was higher in SARS-CoV-2 infected hospitalized patients of rural America (16%) compared to the urban patients (11%). Similarly, higher hospitalization rate was reported in infected rural population (23%) than the urban inhabitants (19%). Requirement of invasive mechanical ventilation and oxygen support were also significantly higher among rural than urban patients. Rural residents showed greater rates of comorbidities in 14 of the 15 categories studied, as well as significantly higher rates of obesity. COVID-19 patients in rural locations had a 40% higher chance of being admitted to the hospital.
✍
 		Pre-print (medRXiv)
Date of Publishing 2021 Oct 07
Title Higher Hospitalization and Mortality Rates Among SARS-CoV-2 infected Persons in Rural America
Impact factor
N/A
Date of Entry 2021 Dec 8

Three important mutations of concern (N501Y, E484K, K417T/N) were identified in multiple SARS-CoV-2 variants. The mutations were primarily found in two spike regions (S1 and RBD), which are the major targets of neutralizing antibodies. SARS-CoV from the 2002 Hong Kong coronavirus outbreak and pre-emergent bat-derived WIV1-CoV were found to share around 76% spike homology to SARS-CoV-2, after comparison.
✍
 		33743213
(Cell)
PMID
33743213
Date of Publishing: 2021 Apr 29
Title Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity
Author(s) nameGarcia-Beltran WF, Lam EC et al.
Journal Cell
Impact factor
27.35
Citation count: 431
Date of Entry 2021 Dec 8

Fully vaccinated Moderna recipients had better neutralization of SARS-CoV-2 variant pseudoviruses than partially vaccinated individuals. However, the neutralization titers were lower compared to the individuals vaccinated with 2 doses of Pfizer. The amount of neutralization was associated with the overall amount of anti-RBD antibodies. Both gender and age did notseemto have a significant impact on neutralization titers.
✍
 		33743213
(Cell)
PMID
33743213
Date of Publishing: 2021 Apr 29
Title Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity
Author(s) nameGarcia-Beltran WF, Lam EC et al.
Journal Cell
Impact factor
27.35
Citation count: 431
Date of Entry 2021 Dec 8

In contrast to the partially vaccinated, sera from fully vaccinated Pfizer recipients showed significantly higher neutralization of wild type strain and SARS-CoV-2 variant pseudoviruses. However, Median titer values for partially vaccinated recipients of Pfizer (167) were slightly lower than that of Moderna (208). After two doses of vaccination, there was also an increase in pseudovirus neutralisation titers with increasing time.
✍
 		33743213
(Cell)
PMID
33743213
Date of Publishing: 2021 Apr 29
Title Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity
Author(s) nameGarcia-Beltran WF, Lam EC et al.
Journal Cell
Impact factor
27.35
Citation count: 431
Date of Entry 2021 Dec 8

Sera collected from fully vaccinated Pfizer recipients showed reduced neutralization against SARS-CoV-2 Beta pseudoviruses with spike mutations (v1, v2, v3). In contrast, higher neutralization levels similar to wild type SARS-CoV-2 virus were observed against Beta pseudoviruses without spike mutations (v1/wtRBD, v2/wtRBD, v3/wtRBD). These findings imply that although RBD mutations are responsible for the majority of vaccine-induced neutralization escapes, they are more efficient when combined with other changes, particularly those reported in B.1.351 v2 (E484K)and v3 (N501Y)variants. They are also associated with synergistic/non-additive effect of these mutations.
✍
 		33743213
(Cell)
PMID
33743213
Date of Publishing: 2021 Apr 29
Title Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity
Author(s) nameGarcia-Beltran WF, Lam EC et al.
Journal Cell
Impact factor
27.35
Citation count: 431
Date of Entry 2021 Dec 8

Seven out of twelve monoclonal antibodies directed against Receptor-binding domain (RBD) failed to neutralize the SARS-CoV-2 Beta (B.1.351) variant. In addition, none of the six monoclonal antibodies targeting the N-terminal domain (NTD) could neutralize the Beta variant. 12 additional monoclonal antibodies were tested against Beta variant of which CB6 was rendered inactive against B.1.351 because of the K417N substitution. Brii-196 and COV2-2130 were essentially unaffected by the new variants. The activities of Brii-198 and COV2-2196 were reduced by 14.6-fold and 6.3-fold. [Refer Extended data Figure 5]
✍
 		33532778
(bioRxiv)
PMID
33532778
Date of Publishing: 2021 Jan 26
Title Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
Author(s) nameWang P, Nair MS et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Dec 8

All 10 serum samples from Pfizer vaccine recipients showed a 10.3-fold reduction in neutralisation against the SARS-CoV-2 Beta (B.1.351) variant. Also, a 2.5-fold decrease in the neutralization activity was observed in the convalescent sera. In contrast, there was no significant reduction in the neutralization activity of the sera from vaccinated or convalescent individuals against the Alpha variant. There was no apparent impact of any single mutation in B.1.1.7 on the neutralizing activity of vaccinated individuals' sera.
✍
 		33532778
(bioRxiv)
PMID
33532778
Date of Publishing: 2021 Jan 26
Title Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
Author(s) nameWang P, Nair MS et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Dec 8

The neutralisation activity against the SARS-CoV-2 Beta (B.1.351) variant was reduced by 12.4-fold in the sera of Moderna vaccine recipients. Similarly, the activity also reduced by more than 2.5-fold in the convalescent sera. However, there was no loss of neutralization against the Alpha variant, either in post-vaccination sera or convalescent serum samples. The E484K substitution appears to be a key contributor to the variant's resistance to neutralisation, showing that this mutation in the RBM is located in an immunodominant epitope identified by all sera from the vaccinated individuals.
✍
 		33532778
(bioRxiv)
PMID
33532778
Date of Publishing: 2021 Jan 26
Title Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
Author(s) nameWang P, Nair MS et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Dec 8

Six monoclonal antibodies directed against the N-terminal domain (NTD) and two monoclonal antibodies targeted against the Receptor-binding domain (RBD) of the spike protein were unable to neutralise the SARS-CoV-2 Alpha variant. The Alpha variant, on the other hand, was neutralised by ten other RBD-targeted antibodies that are currently in clinical trials. 12 additional monoclonal antibodies were tested against Alpha variant of which Brii-198 (5.6-fold), Brii-196 (7.3-fold) and REGN10985 (10.5-fold) showed significant increase in neutralization whereas 1-20 (5.6-fold) and 2-30 (4.4-fold) showed reduction in neutralization activity (IC-50). [Refer Extended data Figure 5]
✍
 		33532778
(bioRxiv)
PMID
33532778
Date of Publishing: 2021 Jan 26
Title Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
Author(s) nameWang P, Nair MS et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Dec 8

The loss of neutralising activity against the pseudovirus B.1.351 was comparable to the loss of neutralising activity against the live B.1.351 virus. These diverse findings support previous studies that pseudovirus neutralisation does not always accurately replicate live viral neutralisation.
✍
 		33532778
(bioRxiv)
PMID
33532778
Date of Publishing: 2021 Jan 26
Title Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
Author(s) nameWang P, Nair MS et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Dec 8

Eight convalescent patient samples showed a decrease of >2.5-fold in neutralizing activity against B.1.1.78 pseudovirus. These diverse findings support previous studies that pseudovirus neutralisation does not always accurately replicate live viral neutralisation.
✍
 		33532778
(bioRxiv)
PMID
33532778
Date of Publishing: 2021 Jan 26
Title Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7
Author(s) nameWang P, Nair MS et al.
Journal bioRxiv
Impact factor
- n/a -
Citation count: 1
Date of Entry 2021 Dec 8

The post-vaccination sera had significantly stronger neutralizing activity than the pre-vaccination sera. In thepre-vaccination sera, however, the 50% neutralisation titres (NT50) for the wild type Wuhan-Hu-1 strain were higher than that of the SARS-CoV-2variants (Alpha, Beta, Delta). The results of the two assays, RVPN and MSD ACE2 inhibition for VOCs were substantially consistent, with r=0.8587, according to a Spearman correlation analysis.
✍
 		Pre-print (medRXiv)
Title Vaccination of COVID-19 Convalescent Plasma Donors Increases Binding and Neutralizing Antibodies Against SARS-CoV-2 Variants
Impact factor
N/A
Date of Entry 2021 Dec 8

During the second wave in Mexico, the B.1.519 variant was the most prevalent, however the Delta variant, once imported, accounted for 78 percent of all Covid-19 cases. In the third wave, the Delta variety overtookthe B.1.1519 variant in this Mexico population, demonstrating overall superior fitness. It wasfound that younger people were moreimpacted, with a mean age of 30 years old, in all COVID-19 positive samples , and there was no gender bias in this cohort.
✍
 		Pre-print (medRXiv)
Date of Publishing 2021 Oct 20
Title SARS-CoV-2 variant transmission in a community-health population (Mexico City, Mexico)
Impact factor
N/A
Date of Entry 2021 Dec 15

Neutralisation assay showed that Lambda variant is highly infectious and resistant to the vaccine-induced humoral immunity. The variant is resistant to Pfizer vaccine-induced neutralisation due to the characteristic 7-amino-acid deletion mutation in the N-terminal domain of the Lambda spike protein.
✍
 		Pre-print (bioRXiv)
Date of Publishing 28 Jul 21
Title SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance
Impact factor
N/A
Date of Entry 2021 Dec 15