Sequence Analysis

Last updated: 2021 Aug 2
Total hit(s): 33
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Original Article
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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

Sequence analysis of whole genome sequences and the protein sequences of viral RBDs NONE
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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

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

Sequences analysis of 2213 complete genomes from six geographical regions worldwide revealed that the nucleotide diversity of SARS-CoV-2 had increased over time. SARS-CoV-2 sequences from six regions around the world (United States of America (US), Latin America (LA), Europe (EU), Africa (AF), Asia (AS), and Oceania (OC)) were taken randomly from NCBI and GISAID databases up to November 13, 2020, for the analysis.
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 		33572190
(Pathogens)
PMID
33572190
Date of Publishing: 2021 Feb 9
Title Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging
Author(s) nameFlores-Alanis A, Cruz-Rangel A et al.
Journal Pathogens
Impact factor
3.31
Citation count: 15

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
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 		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.
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 		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

Sequence alignment of 22164 SARS-CoV-2 genomes from the GISAID database with the reference genome revealed 9210 single nucleotide changes (C>U being the most abundant), resulting in CpG loss. The CpG reduction was linked to two known host molecular defense mechanisms the APOBEC, and ZAP proteins. APOBEC protein catalyze cytosine to uracil (C>U) deamination in ssDNA and ssRNA and ZAP selectively binds to viral CpG regions. High amount of APOBEC and ZAP was found in COVID-19 patients.Selective pressure driving the adaptation of SARS-CoV-2 to its host. Absence of APOBEC enhances zinc-finger antiviral protein (ZAP) activity leading to viral degradation.
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 		33630074
(J Mol Cell Biol)
PMID
33630074
Date of Publishing: 2021 Feb 25
Title Short sequence motif dynamics in the SARS-CoV-2 genome suggest a role for cytosine deamination in CpG reduction
Author(s) nameSadykov M, Mourier T et al.
Journal J Mol Cell Biol
Impact factor
4.4
Citation count: 9

This study reports a sequencing and bioinformatics workflow for stand-alone, real-time tracking of pathogen evolution at Lackland Air Force Base, TX (JBSA/Lackland).
✍
 		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

Conservation analysis report of the residues involved in ACE2 binding to SARS CoV 2 RBD among 32 bats species Y41 plays a crucial role in the binding of SARS-CoV-2 RBD with bACE2-Rm.
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 		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

Sequence and structural similarity between the ORF7a proteins of SARS-CoV1 and SARS-CoV2 The genomic and proteomic data generated over the last decade since SARS-CoV1 outbreak can be useful to test and develop treatment strategies for the current pandemic caused by SARS-CoV2.
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 		33305306
(Biosci Rep)
PMID
33305306
Date of Publishing: 2020 Dec 11
Title Structural assessment of SARS-CoV2 accessory protein ORF7a predicts LFA-1 and Mac-1 binding potential
Author(s) nameNizamudeen ZA, Xu ER et al.
Journal Biosci Rep
Impact factor
2.51
Citation count: 7

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

Metagenomics analysis revealed the changes in respiratory microbial diversity associated with SARS-CoV-2. It was observed that in many cases, a single organism comprised the vast majority of sequencing reads detected among the SARS-CoV-2-positive patients
✍
 		33219095
(mBio)
PMID
33219095
Date of Publishing: 2020 Nov 20
Title Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients
Author(s) nameMostafa HH, Fissel JA et al.
Journal mBio
Impact factor
6.5
Citation count: 39

Antigenicity study of spike protein SARSCoV sequence was analyzed to look for the abundance of antigenic peptide.
✍
 		32383269
(J Med Virol)
PMID
32383269
Date of Publishing: 2020 Oct
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) name Choudhury A, Mukherjee S.
Journal J Med Virol
Impact factor
2.07
Citation count: 162

Antigenicity study of spike glycoprotein SARSCoV-2 sequence was analyzed to look for the abundance of antigenic peptide.
✍
 		32383269
(J Med Virol)
PMID
32383269
Date of Publishing: 2020 Oct
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) name Choudhury A, Mukherjee S.
Journal J Med Virol
Impact factor
2.07
Citation count: 162

Antigenicity study of spike protein SARS-CoV-2 sequence was analyzed to look for the abundance of antigenic peptide
✍
 		32383269
(J Med Virol)
PMID
32383269
Date of Publishing: 2020 Oct
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) name Choudhury A, Mukherjee S.
Journal J Med Virol
Impact factor
2.07
Citation count: 162

Sequence alignment of RBDs of SARS-CoV-1 and SARS-CoV-2 shows a highly conserved epitope Neutralizers like CR3022 ( first identified as a neutralizing antibody against SARS-CoV-1) can be used to neutralise SARS-CoV-2.
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 		32585135
(Cell Host Microbe)
PMID
32585135
Date of Publishing: 2020 Sep 9
Title Neutralization of SARS-CoV-2 by destruction of the Prefusion Spike
Author(s) nameHuo J, Zhao Y et al.
Journal Cell Host Microbe
Impact factor
10.45
Citation count: 144

Comparative In silico analyses of SARS-CoV-2 genomic features (codon, codon pair, dinucleotide usage, and RNA structure around the frameshift region) was performed to find out the best potential target gene for codon pair deoptimization. Genes N and S are suggested as best targets because of high codon pair bias (CPB) compared to that of other viral genes. 5,064 complete SARS-CoV-2 genomes were analyzed. The codon and codon pair usage was calculated for all the genes coded by SARS-CoV-2. Relative synonymous codon usage (RSCU) and codon pair score (CPS) are the metrics that describe the codon and codon pair usage bias, respectively. The codon pair bias (CPB) is the average CPS across a gene.
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 		32973171
(Sci Rep)
PMID
32973171
Date of Publishing: 2020 Sep 24
Title Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
Author(s) nameKames J, Holcomb DD et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 22

Multiple characteristics features of the SARS-CoV-2 genome, particularly in terms of the codon bias, have been established. 5,064 complete SARS-CoV-2 genomes were analyzed The codon and codon pair usage was calculated for all the genes coded by SARS-CoV-2. Relative synonymous codon usage (RSCU) and codon pair score (CPS) are the metrics that describe the codon and codon pair usage bias, respectively. The codon pair bias (CPB) is the average CPS across a gene.
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 		32973171
(Sci Rep)
PMID
32973171
Date of Publishing: 2020 Sep 24
Title Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
Author(s) nameKames J, Holcomb DD et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 22

The feature of the SARS-CoV-2 genome, in terms of the CpG composition, have been characterized. E ORF and ORF10 did not suppress the UpA dinucleotide, while other SARS-CoV-2 ORFs does. E ORF and ORF10 showed negative CPB scores, indicating the usage of under-represented codon pairs
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 		33029383
(Virus Evol)
PMID
33029383
Date of Publishing: 2020 Jul
Title Intra-genome variability in the dinucleotide composition of SARS-CoV-2
Author(s) nameDigard P, Lee HM et al.
Journal Virus Evol
Impact factor
1
Citation count: 23

The feature of the human-infecting coronavirus (HCoV-229E, HCoV-HKU1, HCoV-NL63, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2), in terms of the CpG composition, have been characterized. The coronaviruses from most of the host species showed CpG suppression in the E ORF, while bat E ORF showed a diverse range from total suppression to overrepresentation, and notably avian coronaviruses and Human SARS-CoV and SARS-CoV-2 showed high CpG ratios in E ORF.
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 		33029383
(Virus Evol)
PMID
33029383
Date of Publishing: 2020 Jul
Title Intra-genome variability in the dinucleotide composition of SARS-CoV-2
Author(s) nameDigard P, Lee HM et al.
Journal Virus Evol
Impact factor
1
Citation count: 23

Sequence alignment of SARS-CoV-2 Nsp15 with SARS-Co-V, MERS-Co-V, HCoV229E, MHV show that the active site residues are conserved both in terms of sequence and conformation. Structural comparisons suggest that inhibitors of SARS-CoV Nsp15 have good chance to inhibit the SARS-CoV-2 homolog, but inhibitors of MERS-CoV NendoU are unlikely to inhibit the enzyme.
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 		32304108
(Protein Sci)
PMID
32304108
Date of Publishing: 2020 Jul
Title Crystal structure of Nsp15 endoribonuclease NendoU from SARSCoV2
Author(s) nameKim Y, Jedrzejczak R et al.
Journal Protein Sci
Impact factor
2.4
Citation count: 153

N protein-encoding region of SARS-CoV-2, SARS-CoV, MERS-CoV, and HCoV-OC43 have 89.74%, 48.59%, 35.62%, sequence identity respectively. None
✍
 		32363136
(Acta Pharm Sin B)
PMID
32363136
Date of Publishing: 2020 Jul
Title Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites
Author(s) nameKang S, Yang M et al.
Journal Acta Pharm Sin B
Impact factor
6.15
Citation count: 271

Sequence alignment of RBDs of SARS-CoV and SARS-CoV-2 shows a highly conserved epitope. Conserved epitopes helps in structure-based design of a SARS-CoV-2 vaccine and also in cross-protective antibody responses against future coronavirus epidemics and pandemics.
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 		32245784
(Science)
PMID
32245784
Date of Publishing: 2020 May 8
Title A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV
Author(s) nameYuan M, Wu NC et al.
Journal Science
Impact factor
20.57
Citation count: 731

Sequence alignment of 42 mammal ACE2 protein sequences from wild animal protection lists of Hubei Province and Jiangxi Province, including the human ACE2 protein, to predict the RBD binding capacity of mammalian ACE2. The key amino acids in hACE2 for interacting with RBM are K31, E35, D38, M82 and K353. K31 and K353 in hACE2 are most critical residues for RBM recognition.
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 		32201080
(Biochem Biophys Res Commun)
PMID
32201080
Date of Publishing: 2020 May 21
Title Spike protein recognition of mammalian ACE2 predicts the host range and an optimized ACE2 for SARS-CoV-2 infection
Author(s) nameLuan J, Lu Y et al.
Journal Biochem Biophys Res Commun
Impact factor
2.73
Citation count: 181