Sequence

Last updated: 2022 Mar 3
Total hit(s): 279
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Original Article
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SARS-CoV-2 strains from 2 Moroccan patients with Covid-19 were sequenced. They belong to clade GK, sublineage AY.33 of Delta variant B1.617.2 (Delta 2). Both samples had T29A, T50I, T299I, and Q613 new amino acid changes, in addition to 10 modifications which characterised it as a Delta variant. 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

Phylogenetic analysis of RBD 2019-nCoV spike glycoprotein and SARS-CoV RBD shows relatively high identity of about 73%. (1)According to the findings, several SARS-CoV-specific monoclonal antibodies may be successful at neutralising 2019-nCoV.
(2) It is essential to test anti-SARS-CoV antibodies for cross-reactivity with 2019-nCoV spike protein, since this might have consequences for the fast development of vaccines and therapeutic antibodies against 2019-nCoV.
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 		32065055
(Emerg Microbes Infect)
PMID
32065055
Date of Publishing: 2020
Title Potent binding of 2019 novel coronavirus spike protein by a SARS coronavirus-specific human monoclonal antibody
Author(s) nameTian X, Li C et al.
Journal Emerg Microbes Infect
Impact factor
5.84
Citation count: 655
Date of Entry 2021 Nov 20

A209C mutation in the nsp16 of SARS-CoV-2, in the adenosine binding pocket might influence the RNA cap binding. A distant (25 ) ligand-binding site unique to SARS-CoV-2 was discovered which can be targeted for antiviral development.
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 		32709886
(Nat Commun)
PMID
32709886
Date of Publishing: 2020 Jul 24
Title Structural basis of RNA cap modification by SARS-CoV-2
Author(s) nameViswanathan T, Arya S et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 92
Date of Entry 2021 Oct 27

Phylogenetic analysis shows that SARS-CoV-2 is more similar to SARS-CoV than MERS-CoV. A 90% genetic similarity was observed in the M, N and E proteins of SARS-CoV and SARS-CoV-2. Zaria Bat coronavirus strain (accession ID: HQ166910.1) is used as an outgroup.
✍
 		32106567
(Viruses)
PMID
32106567
Date of Publishing: 2020 Feb 25
Title Preliminary Identification of Potential Vaccine Targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies.
Author(s) name Ahmed SF, Quadeer AA, McKay MR.
Journal Viruses
Impact factor
3.76
Citation count: 507
Date of Entry 2021 Sep 4

Reporting multiple sequence analysis of Envelope protein (E) C-terminal domain sequence extracted from 13 genomes considered for study of SARS-CoV and SARS-CoV-2. 2 phylogenetic clades observed with the full genome is confirmed by SARS-CoV and SARS-CoV-2 E proteins.
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 		32891874
(Microbes Infect)
PMID
32891874
Date of Publishing: 2020 Nov-Dec
Title Improved binding of SARS-CoV-2 Envelope protein to tight junction-associated PALS1 could play a key role in COVID-19 pathogenesis
Author(s) nameDe Maio F, Lo Cascio E et al.
Journal Microbes Infect
Impact factor
2.373
Citation count: 28
Date of Entry 2021 Aug 2

Sequence analysis of RNA dependent RNA polymerase protein of SARS-CoV-2, SARS-CoV, MERS-CoV RNA shows Val 557 common in the active site. Similarity in the active site of the RdRp can help in the discovery of new inhibitors similar to Remdesivir (broad spectrum antiviral activity), a RdRp inhibitor.
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 		32167173
(J Med Virol)
PMID
32167173
Date of Publishing: 2020 Jun
Title The potential chemical structure of anti-SARS-CoV-2 RNA-dependent RNA polymerase
Author(s) nameLung J, Lin YS et al.
Journal J Med Virol
Impact factor
2.07
Citation count: 99
Date of Entry 2021 Aug 11

Phylogenetic analysis based on full genomes and RBDs from the different isolates. Phylogeny trees of genome and RBD are simliar.
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 		32410735
(Biochem Biophys Res Commun)
PMID
32410735
Date of Publishing: 2020 Jun 30
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
Author(s) nameOthman H, Bouslama Z et al.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 69
Date of Entry 2021 Jul 28

Sequence analysis of whole genome sequences and the protein sequences of viral RBDs NONE
✍
 		32410735
(Biochem Biophys Res Commun)
PMID
32410735
Date of Publishing: 2020 Jun 30
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
Author(s) nameOthman H, Bouslama Z et al.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 69
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
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 		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 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

Korber et al. present evidence that there are now more SARS-CoV-2 viruses circulating in the human population globally that have the G614 form of the Spike protein versus the D614 form that was originally identified from the first human cases in Wuhan, China. Follow-up studies show that patients infected with G614 shed more viral nucleic acid compared with those with D614, and G614-bearing viruses show significantly higher infectious titers in vitro than their D614 counterparts.
✍
 		32697968
(Cell)
PMID
32697968
Date of Publishing: 2020 Aug 20
Title Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus
Author(s) nameKorber B, Fischer WM et al.
Journal Cell
Impact factor
27.35
Citation count: 1755
Date of Entry 2021 Jul 13

Virus mutagenic capability depends upon several factors, including the fdelity of viral enzymes that replicate nucleic acids, as SARS-CoV-2 RNA dependent RNA polymerase (RdRp) According to the observations of the authors, after February 2020, when the first locally transmitted SARS-CoV-2 cases out of Asia were reported, viral genomes presented diferent point mutations, clearly distinguishable within different geographic areas. Over time, it was observed that they were able to identify three recurrent mutations in Europe (in positions 3036, 14408 and 23403) and 3 other different mutations in North America (in positions 17746, 17857 and 18060). So far, these mutations have not been detected in Asia. The number and the occurrence, as well as the median value of virus point mutations registered out of Asia, increase over time. In the preset study, they found that the RdRp mutation, located at position 14408, which is present in European viral genomes starting from February 20th, 2020, is associated with a higher number of point mutations compared to viral genomes from Asia.
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 		32321524
(J Transl Med)
PMID
32321524
Date of Publishing: 2020 Apr 22
Title Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant
Author(s) namePachetti M, Marini B et al.
Journal J Transl Med
Impact factor
4.2
Citation count: 414
Date of Entry 2021 Jul 13

Whole Genome sequencing of the WH-Human 1 corona virus (WHCV) was reported The order of genes (5 to 3) was as follows: replicase ORF1ab, spike (S), envelope (E), membrane (M) and nucle- ocapsid (N). WHCV has 5 and 3 terminal sequences that are typical of betacoronaviruses, with 265 nt at the 5 terminal end and 229 nt at the 3 terminal end. The predicted replicase ORF1ab gene of WHCV is 21,291 nt in length and contained 16 predicted non-structural proteins. highly conserved domain (LLRKNGNKG: amino acids 122130) in nsp1 with SARS-CoV. The predicted S, ORF3a, E, M and N genes of WHCV are 3,822, 828, 228, 669 and 1,260 nt in length, respectively.
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 		32015508
(Nature)
PMID
32015508
Date of Publishing: 2020 Mar
Title A new coronavirus associated with human respiratory disease in China
Author(s) nameWu F, Zhao S et al.
Journal Nature
Impact factor
24.36
Citation count: 4209
Date of Entry 2021 Jul 12

Metagenomic sequencing of RNA from a single patient in Wuhan led to the identification of a new virus belonging to the Coronaviridae family and designated as 'WH-Human 1' virus. The longest (30,474 nucleotides) had highest abundance and closely resembled the SARS-like coronavirus (CoV) isolate--bat SL-CoVZC45 (GenBank accession number MG772933) with 89.1% identity.
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 		32015508
(Nature)
PMID
32015508
Date of Publishing: 2020 Mar
Title A new coronavirus associated with human respiratory disease in China
Author(s) nameWu F, Zhao S et al.
Journal Nature
Impact factor
24.36
Citation count: 4209
Date of Entry 2021 Jul 12

Sequences analysis of Indian SARS-CoV-2 sequences revealed clade-specific mutations and co-mutations patterns across Indian states and Union Territories. The network was constructed for each state and UT showing co-occurrence between frequent mutations of that state/UT.
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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.
Impact factor
N/A
Date of Entry 2021 Jun 14

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.
Impact factor
N/A
Date of Entry 2021 Jun 14

Sequence analysis of Indian SARS-CoV-2 sequences (3277 from GISAID) revealed that GR, GH, and G (GISAID) or 20B and 20A (Nextstrain) clades were the prevalent clades in India during the middle and later half of the year 2020. SARS-CoV2 sequences from North America, South America, Europe, Africa, Oceania, and Asia (without Indian sequences) were also analyzed to find the clade dynamics. Other than North America and Europe, all the other continents showed the prevalence of GR clade in the middle and later half of the year 2020. North America showed a consistent prevalence of GH clade throughout the year. And a massive increase in GV clade sequences was observed in Europe during the latter part of 2020.
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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.
Impact factor
N/A
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.
Impact factor
N/A
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
✍
 		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.
Impact factor
N/A
Date of Entry 2021 Jun 14

Whole Genome Sequences of 54 SARS-CoV-2 Strains (from August to October 2020), reported from Kolkata, West Bengal. The age of the patients ranges from 6 to 88 years with a maximum peak in the range of 51-60 years.
The majority of sequences clustered into O clade or Nextstrain 20A clade.
The clade-specific mutations and the co-mutation patterns across states and union territories of India over the time course were studied.
✍
 		Pre-print (bioRXiv)
Title Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India
Author(s) name -
Impact factor
N/A
Date of Entry 2021 Jun 14

Primer and Probe sequence specific for E gene of SARS-CoV-2 used in wastewater RT- ddPCR assay. Amplicon Length: 100
Genomic Location of forward primer: 26260-26279,
Genomic Location of reverse primer: 26359-26340,
Genomic location of probe sequence: 26290-26317
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 		Pre-print (medRXiv)
Title Redesigning SARS-CoV-2 clinical RT-qPCR assays for wastewater RT-ddPCR
Author(s) name -
Impact factor
N/A
Date of Entry 2021 Jun 14

Primer and Probe sequence specific for N gene of SARS-CoV-2 used in wastewater RT- ddPCR assay. Amplicon Length: 95
Genomic Location of forward primer: 20131-29150,
Genomic Location of reverse primer: 29225-29206,
Genomic location of probe sequence: 29185-29204
✍
 		Pre-print (medRXiv)
Title Redesigning SARS-CoV-2 clinical RT-qPCR assays for wastewater RT-ddPCR
Author(s) name -
Impact factor
N/A
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 -
Impact factor
N/A
Date of Entry 2021 Jun 14

Of 3080 SARS-CoV-2 genomes analyzed, ~1.5% genome had a rare missense mutation in three accessory proteins ORF6, ORF7b, and ORF10. The mutation caused several changes in the R-group properties of amino acids. Of 3080 genomes analyzed, 2126 genomes were from the USA, 306 genomes were from Asia, 281 genomes were from Europe, 365 genomes were from Oceania, and one genome from Africa. Mutations in putative diacidic motif- may affect the suppression of the expression of co-transfected myc-nsp8.
Mutated ORF7b(F(19)L)-Retention in Golgi complex is affected.
Mutated ORF7b (L(20)STOP)-Non-functional protein.
Nonsense mutation in ORF10- Non-functional protein.
Mutated ORF10 (V(6)I)-synonymous change of R-group property (Functions not affected).
Mutation may have potential role in viral rapid replications, virulence and pathogenicity.
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 		33619452
(Meta Gene)
PMID
33619452
Date of Publishing: 2021 Jun
Title Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes
Author(s) name Hassan SS, Choudhury PP, Roy B.
Journal Meta Gene
Impact factor
0.88
Citation count: 3