Sequence

Last updated: 2022 Mar 3
Total hit(s): 27
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Original Article
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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.
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 		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

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.
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 		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

Phylogenetic analysis showed that all the Lambda variant isolates descended from a single ancestor, indicating monophyletic origin. The study also discovered that the Lambda variant with the deletion (RSYLTPGD246-253N) mutation first emerged around July 12, 2020 but was detected only on 8th November 2020 in Argentina. Through neutralisation assay, the study showed that the Lambda S is more resistant to the vaccine-induced antisera than the Lambda S derivative (Lambda+N246-253RSYLTPGD) which had recovered the RSYLTPGD246-253N deletion mutation. This supports the suggestion that the deletion mutation was a driving force behind the spread of the variant.
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 		Pre-print (bioRXiv)
Date of Publishing 2021 Jul 28
Title SARS-CoV-2 Lambda variant exhibits higher infectivity and immune resistance
Impact factor
N/A
Date of Entry 2021 Dec 15

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.
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 		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

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.
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 		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.
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 		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
- n/a -
Citation count: 1
Date of Entry 2021 Nov 2

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
Impact factor
N/A
Date of Entry 2021 Sep 13

Three significant mutations (L452R, W152C and S13I) were identified in the spike protein of the California variant B.1.427/B.1.429 with no particular difference from non-variant lineages (B.1.427, B.1.429, other Clade 20C lineages). Two distinct lineages, B.1.427 and B.1.429 were identified in Clade 20C after Phylogenetic analysis.
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 		33991487
(Cell)
PMID
33991487
Date of Publishing: 2021 Jun 24
Title Transmission, infectivity, and neutralization of a spike L452R SARS-CoV-2 variant
Author(s) nameDeng X, Garcia-Knight MA et al.
Journal Cell
Impact factor
27.35
Citation count: 162
Date of Entry 2021 Sep 13

Phylogenetic analysis was performed for the RNA sequences from six patient samples which showed that they were infected with the Delta variant, despite being vaccinated. Out of 334 sequences analyzed, 328 were SARS-CoV-2 sequences designated for various variants of concern (VOC) and variant of interest (VOI), downloaded from GISAID, and 6 were the patient samples.
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 		Pre-print ( medRXiv )
Date of Publishing 2021 Jul 04
Title Transmission event of SARS-CoV-2 Delta variant reveals multiple vaccine breakthrough infections
Impact factor
N/A
Date of Entry 2021 Aug 6

The emergent mutants L452R and Y453F had a wide range of hosts in terms of its receptor binding characteristics and participated in cross-species infection The cross-species transmission is a big threat to the pandemic.
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 		doi
Date of Publishing 2021 Apr 05
Title An emerging SARS-CoV-2 mutant evading cellular immunity and increasing viral infectivity
Impact factor
N/A
Date of Entry 2021 Aug 6

The most prevalent receptor binding motif (RBM) mutation N439K was subjected to phylogenetic analysis. N439K lineage i/B.1.141 was dominant in Scotland; while N439K lineage ii/B.1.258 were first sampled in Romania and currently spread to 32 other countries. The growth rate of N439K/D614G lineage(i) was similar compared to the N439/D614 or N439/D614G WT in Scotland. The total number of N439K variants as of January 6, 2021 correspond to 764,000 of the confirmed SARS-CoV-2 infections in 34 countries.
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 		33621484
(Cell)
PMID
33621484
Date of Publishing: 2021 Jan 28
Title Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
Author(s) nameThomson EC, Rosen LE et al.
Journal Cell
Impact factor
27.35
Citation count: 259
Date of Entry 2021 Aug 6

Whole-genome sequencing for 2 S gene target failure (SGTF) samples showed that the S deletion 21765-21770 was present in 100% of the reads. It also leads to the removal of 2 amino acids (H69/V70) in the N-terminal domain of the S1 subunit of the S protein.
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 		33478625
(Euro Surveill)
PMID
33478625
Date of Publishing: 2021 Jan
Title Two-step strategy for the identification of SARS-CoV-2 variant of concern 202012/01 and other variants with spike deletion H69V70, France, August to December 2020
Author(s) nameBal A, Destras G et al.
Journal Euro Surveill
Impact factor
7.37
Citation count: 90
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.
Impact factor
N/A
Date of Entry 2021 Jul 2

Primers and probes for multiplex RT-qPCR assay that helps in determining the N gene mutations associated with the Alpha variant (B.1.1.7 variant). The reverse primer and the probe were based on the CDC N1 reaction (https://www.cdc.gov/coronavirus/2019-ncov/lab/rt-pcr-panel-primer-probes.html),
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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.
Impact factor
N/A
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
Impact factor
N/A
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
Impact factor
N/A
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
Impact factor
N/A
Date of Entry 2021 Jul 2

The evolutionary tree analysis of characteristic mutations in B.1.1.7 (alpha variant) revealed a non-coding deletion (g.a.28271) deletion mutation and its interaction with other mutations (g.gat28280cta, ORF1a:p.SGF3675-, S:p.P681H, and S:p.T716I). The 28271 nucleotide is located upstream of the start codon of the N gene. The non-coding deletion (g.a.28271), along with its interacting mutations (g.gat28280cta), alters the core KOZAK site in gene N and ORF9b. This may alters their translational efficiency thus, influencing viral transmission.
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 		Pre-print ( bioRXiv )
Date of Publishing 2021 May 01
Title Evolutionary insights into a non-coding deletion of SARS-CoV-2 B.1.1.7
Impact factor
N/A
Date of Entry 2021 Jul 2

A rapid surge in cases of SARS-CoV-2 variant B.1.526 have been reported in New York state and, the variant spread to 32 states across the country. This variant has the E484K mutation and is resistant to neutralisation by convalescent plasma and vaccine sera. The activities of several antibodies (REGN10933 and LY-CoV555) which, are already in clinical use are either impaired or lost against E484K(NY5) pseudoviruses. The NY5(E484K) mutant also lowered the neutralizing activities of convalescent plasma or vaccine sera by 4.1 or 3.3-3.6 fold.
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 		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 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
Impact factor
N/A
Date of Entry 2021 Jul 2

The West Coast variant had mutations in S-protein (L452R, S13I, and W152C) resulting in higher rate of transmissibility than other variants prelevant at that time. The higher transmissibility and reproductive numbers resulted in increased secondary household attacks. The other emerging variants were absent in all the samples collected. 1099 positive samples were derived from 12,124 tests
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 		33688689
(medRxiv)
PMID
33688689
Date of Publishing: 2021 Mar 3
Title The emergent SARS-CoV-2 variants detected by genomic surveillance at a community-based testing site in San Francisco
Author(s) namePeng J, Mann SA et al.
Journal medRxiv
Impact factor
- n/a -
Citation count: 1
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
Impact factor
N/A
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
Impact factor
N/A
Date of Entry 2021 Jul 2

Three imported cases of the Alpha variant (B.1.1.7) from the UK to Spain with rapid household transmission related to one of the cases were reported. With reference to two UK original B.1.1.7 consensus, Imported cases (1, 2, 7 and 8) showed 4 to 6 SNPs whereas cases (3 to 6) involved in household transmission showed 1 to 4 SNPs, which were otherwise identical to the original strain. The mutations reported in the cases were consistent with the circulation of the alpha strain and import to Spain.
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 		33685741
(Enferm Infecc Microbiol Clin (Engl Ed).)
PMID
33685741
Date of Publishing: 2021 Feb 19
Title First confirmation of importation and transmission in Spain of the newly identified SARS-CoV-2 B.1.1.7 variant
Journal Enferm Infecc Microbiol Clin (Engl Ed).
Impact factor
N/A
Date of Entry 2021 Jul 2

The emergent Alpha variant lineage in UK had a consistent epidemic growth and was declared as Variant of Concern(VOC).The S-gene mutations that resulted in S-gene target failures (SGTF) in RT-PCR which was characteristic to VOC lineage only. SGTF was characteristic to this lineage and was used as VOC biomarker in statistical studies of VOC and non-VOC samples.
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 		doi
Date of Publishing 2021 Jan 04
Title Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking B.1.1.7 in England: Insights from linking epidemiological and genetic data
Impact factor
N/A
Date of Entry 2021 Jul 2