Variant


Last updated: 2021 Nov 2
Total hit(s): 136
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Original Article
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Mortality rate was 2 times higher in unvaccinated (3.45%) and partially vaccinated people (vaccinated with COVISHIELD (ChAdOx1) or COVAXIN (BBV-152)) (3.35%) when compared to the fully vaccinated group (1.5%). Additional booster doses or a modification in vaccine type for these non-responders to vaccination should be investigated further.
Pre-print (medRXiv)
Date of Publishing 2021 Jul 16
Title Clinical outcomes in vaccinated individuals hospitalized with Delta variant of SARS-CoV-2
Impact factor
N/A
Date of Entry 2021 Nov 2


An examination of the number of reported deaths in Africa reveals significant disparities throughout the continent. In terms of case fatality rate, South Africa reported the highest number with 20241 deaths. Egypt, Sudan, Chad, and Niger, all of which share borders, were found to have the largest number of COVID-19-related deaths, indicating that more research is needed to understand the variables that contributed to this public health burden.
34031660
(medRxiv)
PMID
34031660
Date of Publishing: 2021 May 19
Title Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa
Author(s) nameOkoh OS, Nii-Trebi NI et al.
Journal medRxiv
Impact factor
Cant find
Citation count: 1
Date of Entry 2021 Nov 2


The mutation P681R greatly improved furin's efficiency to cleave the spike peptide, indicating that the arginine substitution is responsible for the B.1.617 lineage spike protein's enhanced cleavage. This might play a role in increased transmissibility and pathogenicity. This study speculates that the higher transmissibility of these SARS-CoV-2 variants is due to increased S1/S2 cleavage found in B.1.617 and B.1.1.7 lineages. Therefore, they must be closely monitored for any early signs of faster transmission or increased pathogenesis.
Pre-print (bioRXiv)
Title The SARS-CoV-2 variants associated with infections in India, B.1.617, show enhanced spike cleavage by furin
Impact factor
N/A
Date of Entry 2021 Nov 2


The generation time of the Delta variant (4.6 days) between two infections was shorter than that of the Alpha variant (5.5 days), resulting in faster transmission of the Delta variant. Effect of SARS-CoV-2 variants on household generation time was more prominent than effect of vaccination status or age of patients.
Pre-print (medRXiv)
Date of Publishing 2021 Oct 23
Title Generation time of the Alpha and Delta SARS-CoV-2 variants
Impact factor
N/A
Date of Entry 2021 Nov 2


Phylogenetic analysis showed that by March 9 2021, all the SARS-CoV-2 Delta genomes discovered around the world had formed five distinct clusters: Delta1, Delta 2, pre-delta 3, Delta 3, and Delta 4. Since May 2021,Delta1 has gradually surpassed all other subvariants and emerged as the primary pandemic driver, with Delta 2 playing a minor role and the remaining two (delta 3 and delta 4) being inconsequential.
Pre-print (medRXiv)
Date of Publishing 2021 Oct 20
Title SARS-COV-2 variant drives the pandemic in India and Europe via two subvariants
Impact factor
N/A
Date of Entry 2021 Nov 2


In early 2021, the emergence of the Delta variant was 37-163 % faster than the Alpha variant. Across New England, the Delta variant was estimated to be 58-120 % more transmissible than Alpha. A multiplicative increase in Rt estimates indicates that Delta had the greatest advantage in Maine (1.99x increase) and Vermont (1.87x increase), and the lowest advantage in New Hampshire (1.51x) and Massachusetts (1.45x).
Pre-print (medRXiv)
Date of Publishing 2021 Oct 07
Title Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
Impact factor
N/A
Date of Entry 2021 Nov 2


Phylogenetic analysis of 43 sequenced genomes identified 3 Pango lineages: SARS-CoV-2 Alpha (B.1.1.7), Kappa (B.1.617.1) and Delta (B.1.61.7.2) variants among the 146 flight passengers from New Delhi to Hong Kong in April 2021. Additional neighbouring cases could not be sequenced due to low viral load, and those cases could be missing links in the hypothesised transmission chains.
Pre-print (medRXiv)
Date of Publishing 2021 Jul 23
Title Air travel-related outbreak of multiple SARS-CoV-2 variants
Impact factor
N/A
Date of Entry 2021 Nov 2


Out of 46 COVID-19 positive individuals on a flight from New Delhi to Hong Kong, the Kappa variant (B.1.617.1) was linked to a cluster of 39 cases (84.8%), while the Delta variant (B.1.617.2) was reported in two passengers (4.3%). The Alpha variant (B.1.1.7) was detected in five passengers including a crew member (10.9%). One parent tested positive for Alpha whereas the infant tested positive for Kappa in a family of 3 (Travel group A). Similary, in a famly of 6 (Travel group B), a child tested positive for Alpha while2 children and 3 adults were infected with Kappa during travel.
Pre-print (medRXiv)
Date of Publishing 2021 Jul 23
Title Air travel-related outbreak of multiple SARS-CoV-2 variants
Impact factor
N/A
Date of Entry 2021 Nov 2


African viruses cluster closely with viruses from all continents, but especially with viruses from Europe, according to phylogenetic study. Only 143 of the 782 Pango lineages discovered around the world circulated in Africa, with five different lineages dominating at different times during the pandemic. The phylogenetic topological linkages revealed that African genomes tended to cluster with those from Europe, which is consistent with the continents' considerable cultural and commercial connectivity. Many notable outbreaks were foundin Egypt, the Democratic Republic of the Congo, Gambia, and South Africa, which reflects the greater number of sequences available in these countries.
34031660
(medRxiv)
PMID
34031660
Date of Publishing: 2021 May 19
Title Epidemiology and genetic diversity of SARS-CoV-2 lineages circulating in Africa
Author(s) nameOkoh OS, Nii-Trebi NI et al.
Journal medRxiv
Impact factor
Cant find
Citation count: 1
Date of Entry 2021 Nov 2


Neutralising activity of REGN-COV2 therapeutic monoclonal antibodies was studied. REGN10987 retained the majority of its neutralising action against the variant spike proteins, but REGN10933 lost the majority of its activity against the B.1.351, B.1.1.248, and mink cluster 5 variant spike proteins. E406W mutation was seen to allow escape from both antibodies, but is not located in either of the epitopes bound by the antibodies.
34060334
(mBio)
PMID
34060334
Date of Publishing: 2021 Jun 1
Title Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes
Author(s) nameTada T, Dcosta BM et al.
Journal mBio
Impact factor
6.5
Citation count: 1
Date of Entry 2021 Nov 2


Amongst the 20 monoclonal antibodies tested against the beta variant, 14 showed >10-fold decrease in the neutralisation titers.
33730597
(Cell)
PMID
33730597
Date of Publishing: 2021 Apr 29
Title Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera
Author(s) nameZhou D, Dejnirattisai W et al.
Journal Cell
Impact factor
27.35
Citation count: 36
Date of Entry 2021 Nov 2


The kinetics of binding of soluble ACE2 to recombinant RBD was assessed by biolayer interferometry (BLI). The affinity of the B.1.351 RBD to ACE2 was 19-fold higher when compared to the wildtype and 2.7-fold higher when compared to the alpha variant.
33730597
(Cell)
PMID
33730597
Date of Publishing: 2021 Apr 29
Title Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera
Author(s) nameZhou D, Dejnirattisai W et al.
Journal Cell
Impact factor
27.35
Citation count: 36
Date of Entry 2021 Nov 2


B.1.526 variant is associated with lowered antibody neutralisation which is already in clinical use, thereby raising concerns against the risk of re-infection and efficacy of antibody therapy. The S477N mutation did not have any antigenic impact, as the NY5(S477N) pseudoviruses did not show any neutralizing activity against 12 monoclonal antibodies covering all epitopes on RBD.
Pre-print (medRXiv)
Date of Publishing 2021 Apr 15
Title A Novel and Expanding SARS-CoV-2 Variant, B.1.526, Identified in New York
Impact factor
N/A
Date of Entry 2021 Nov 2


The study revealed that SARS-CoV-2 Delta variant genomes discovered in India by April 2021 fall into four distinct groups (Delta 1,2 3 and 4), each with its own set of characteristic spike, nucleocapsid and NSP3 changes. Delta subvariant Delta 1 was estimated to be the major pandemic driver in UK, Europe and Spain as well.
Pre-print (medRXiv)
Date of Publishing 2021 Oct 20
Title SARS-COV-2 variant drives the pandemic in India and Europe via two subvariants
Impact factor
N/A
Date of Entry 2021 Nov 2


Antibody neutralization of the UK, South Africa, Europe, Columbus, Ohio and mink spike variants by the sera of convalescent individuals and those vaccinated with BNT162b2 was assessed. Both convalescent and vaccinated patients' sera were able to neutralise the variants. The sera from vaccinated individuals was able to neutralise the alpha variant spike protein which was comparable to the original D614G virus, while the beta variant spike was neutralised with a 3-4-fold lower IC50 than the D614G virus. Convalescent plasma was obtained from donors who had been infected before April 2020 (before the emergence of variants). Vaccinated donor serum was collected from individuals 7 days after administration of vaccine, after confirming that there were no neutralising antibodies in the serum prior to vaccination. Serum collected was titrated against lentivirus samples pseudotyped with spike protein variants.
34060334
(mBio)
PMID
34060334
Date of Publishing: 2021 Jun 1
Title Convalescent-Phase Sera and Vaccine-Elicited Antibodies Largely Maintain Neutralizing Titer against Global SARS-CoV-2 Variant Spikes
Author(s) nameTada T, Dcosta BM et al.
Journal mBio
Impact factor
6.5
Citation count: 1
Date of Entry 2021 Nov 2


For the Beta variant, the neutralizing ability of convalescent sera was reduced by 13.3-fold (infected with wild type) and 3.1-fold (infected with Alpha variant) when compared to the wild strain. The neutralization titres for Beta variant were reduced by 9-fold and 7.6-fold for the Oxford-AstraZeneca and Pfizer vaccines respectively. The previous infection or vaccination with the ancestral strain of SARS-CoV-2 may not provide signigicant protection against Beta variant and even for other emerging variants with predominant mutations in the RBD region. Next generation vaccines should concentrate on major mutations like E484K in order to provide sufficient protection. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7901269/figure/fig2/?report=objectonly
33730597
(Cell)
PMID
33730597
Date of Publishing: 2021 Apr 29
Title Evidence of escape of SARS-CoV-2 variant B.1.351 from natural and vaccine-induced sera
Author(s) nameZhou D, Dejnirattisai W et al.
Journal Cell
Impact factor
27.35
Citation count: 36
Date of Entry 2021 Nov 2


B.1.526 variant is associated with lowered antibody neutralisation which is already in clinical use, thereby raising concerns against the risk of re-infection and efficacy of antibody therapy. The S477N mutation didnot have any antigenic impact, as the NY5(S477N) pseudoviruses didnot show any neutralizing activity against 12 monoclonal antibodies covering all epitopes on RBD.
Pre-print (medRXiv)
Date of Publishing 2021 Apr 15
Title A Novel and Expanding SARS-CoV-2 Variant, B.1.526, Identified in New York
Impact factor
N/A
Date of Entry 2021 Nov 2


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


As of April 2021, the Lambda Variant of Interest (C.37), which was initially discovered in South America in late 2020, accounted for 97% of Peruvian public genomes. It has been found in Colombia, Ecuador, Mexico, the United States, Germany, and Israel, and evidence of transmission has been found in Chile and Argentina. To assess its transmission, pathogenicity, and immune escape qualities, more epidemiological data and analysis are required.
Pre-print ( medRXiv )
Date of Publishing 2021 Jul 03
Title The Emergence of SARS-CoV-2 Variant Lambda (C.37) in South America
Impact factor
N/A
Date of Entry 2021 Sep 30


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.
Pre-print ( bioRXiv )
Title Delta spike P681R mutation enhances SARS-CoV-2 fitness over Alpha variant
Impact factor
N/A
Date of Entry 2021 Sep 30


For SARS-CoV-2 cused by Delata variant, the time interval between symptom onset of consecutive COVID-19 cases in a transmission chain was reduced from 4 days to 2.5 days. Faster spread of Delta variant was indicated since Reproductive number was above 1 during the study period. Factors such as Increased travel and impact of COVID-19 vaccination was not considered in the study.
Pre-print ( medRXiv )
Date of Publishing 2021 Aug 20
Title Changes in the serial interval and transmission dynamics associated with the SARS-CoV-2 Delta variant in South Korea
Impact factor
N/A
Date of Entry 2021 Sep 30


Delta (B.1.617.2) variant of concern (VOC) and Gamma variant (P.1) had replaced the Alpha (B.1.1.7) variant of concern (VOC) as the major variant responsible for spread of SARS-CoV-2 in United States. Of these 2, Delta variantwas the most dominant variant responsible for spread of SARS-CoV-2. The transmission of Delta variant is higher in countries where vaccination is low. 1. The number of positive cases being tested reduced in last two months of study due to low test positivity rates. 2. Lack of homogeneity in the data across United States was noted.
Pre-print ( medRXiv )
Date of Publishing 2021 Jun 21
Title Rapid displacement of SARS-CoV-2 variant B.1.1.7 by B.1.617.2 and P.1 in the United States
Impact factor
N/A
Date of Entry 2021 Sep 30


The study focuses on the prevalence of COVID 19 caused by Delta VOC or Alpha VOC in the population of Scotland. The Delta VOC was found to be mostly prevalent in younger, wealthier people.
thelancet.com
Date of Publishing 2021 Jun 14
Title SARS-CoV-2 Delta VOC in Scotland: demographics, risk of hospital admission, and vaccine effectiveness
Impact factor
N/A
Date of Entry 2021 Sep 30


Rapid displacement of SARS-CoV-2 Alpha variant by the Delta variant in June-July 2021 was detected in Lebanon. The study confirmed international travel and community spread to be the transmission routes for this displacement. Travel restrictions and Public health measures were insufficient to prevent the spread of the SARS-CoV-2 variants. Rapid genomic sequencing was necessary to detect the otherwise silent transmisson of Delta variant in the community.
Pre-print ( medRXiv )
Date of Publishing 2021 Aug 11
Title Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
Impact factor
N/A
Date of Entry 2021 Sep 30


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