Sequence Analysis


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Sequences analysis of Indian SARS-CoV-2 sequences revealed clade-specific mutations and co-mutations patterns across Indian states and Union Territories.
PMID
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, Sujay Krishna Maity, Debaleena Bhowmik, Arpita Ghosh Mitra, Soumen Saha, Aviral Roy, Partha Chakrabarti, Sandip Paul, Saikat Chakrabarti
Journal
Impact factor
Citation count
Date of publishing2021 Mar 25
Sequences analysis of 2213 complete genomes from six geographical regions worldwide revealed that the nucleotide diversity of SARS-CoV-2 had increased over time.
PMID 33572190
Title Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging
Author(s) nameFlores-Alanis A, Cruz-Rangel A, Rodríguez-Gómez F, González J, Torres-Guerrero CA, Delgado G, Cravioto A, Morales-Espinosa R.
Journal Pathogens
Impact factor3.31
Citation count1
Date of publishing2021 Feb 9
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.
PMID 33536258
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ, Nambulli S, Robinson-McCarthy LR, Bain WG, Haidar G, Duprex WP.
Journal Science
Impact factor20.57
Citation count6
Date of publishing2021 Feb 3
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.
PMID 33536258
Title Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
Author(s) nameMcCarthy KR, Rennick LJ, Nambulli S, Robinson-McCarthy LR, Bain WG, Haidar G, Duprex WP.
Journal Science
Impact factor20.57
Citation count6
Date of publishing2021 Feb 3
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.
PMID 33630074
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, Guan Q, Pain A.
Journal J Mol Cell Biol
Impact factor4.4
Citation count1
Date of publishing2021 Feb 25
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).
PMID 33609027
Title Whole-genome Sequencing of SARS-CoV-2: Using Phylogeny and Structural Modeling to Contextualize Local Viral Evolution
Author(s) nameNazario-Toole AE, Xia H, Gibbons TF.
Journal Mil Med
Impact factor
Citation count1
Date of publishing2021 Feb 20
Conservation analysis report of the residues involved in ACE2 binding to SARS CoV 2 RBD among 32 bats species
PMID 33335073
Title Cross-species recognition of SARS-CoV-2 to bat ACE2
Author(s) nameLiu K, Tan S, Niu S, Wang J, Wu L, Sun H, Zhang Y, Pan X, Qu X, Du P, Meng Y, Jia Y, Chen Q, Deng C, Yan J, Wang HW, Wang Q, Qi J, Gao GF.
Journal Proc Natl Acad Sci U S A
Impact factor9.35
Citation count1
Date of publishing2021 Jan 5
Sequence and structural similarity between the ORF7a proteins of SARS-CoV1 and SARS-CoV2
PMID 33305306
Title Structural assessment of SARS-CoV2 accessory protein ORF7a predicts LFA-1 and Mac-1 binding potential
Author(s) nameNizamudeen ZA, Xu ER, Karthik V, Halawa M, Arkill KP, Jackson AM, Bates DO, Emsley J.
Journal Biosci Rep
Impact factor2.51
Citation count1
Date of publishing2020 Dec 11
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.
PMID 33082295
Title Structural analysis of full-length SARS-CoV-2 spike protein from an advanced vaccine candidate
Author(s) nameBangaru S, Ozorowski G, Turner HL, Antanasijevic A, Huang D, Wang X, Torres JL, Diedrich JK, Tian JH, Portnoff AD, Patel N, Massare MJ, Yates JR 3rd, Nemazee D, Paulson JC, Glenn G, Smith G, Ward AB.
Journal Science
Impact factor20.57
Citation count12
Date of publishing2020 Nov 27
Metagenomics analysis revealed the changes in respiratory microbial diversity associated with SARS-CoV-2.
PMID 33219095
Title Metagenomic Next-Generation Sequencing of Nasopharyngeal Specimens Collected from Confirmed and Suspect COVID-19 Patients
Author(s) nameMostafa HH, Fissel JA, Fanelli B, Bergman Y, Gniazdowski V, Dadlani M, Carroll KC, Colwell RR, Simner PJ.
Journal mBio
Impact factor6.5
Citation count2
Date of publishing2020 Nov 20
Antigenicity study of spike protein SARSCoV sequence was analyzed to look for the abundance of antigenic peptide.
PMID 32383269
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) nameChoudhury A, Mukherjee S.
Journal J Med Virol
Impact factor2.07
Citation count32
Date of publishing2020 Oct
Antigenicity study of spike protein SARS-CoV-2 sequence was analyzed to look for the abundance of antigenic peptide
PMID 32383269
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) nameChoudhury A, Mukherjee S.
Journal J Med Virol
Impact factor2.07
Citation count32
Date of publishing2020 Oct
Antigenicity study of spike glycoprotein SARSCoV-2 sequence was analyzed to look for the abundance of antigenic peptide.
PMID 32383269
Title In silico studies on the comparative characterization of the interactions of SARSCoV2 spike glycoprotein with ACE2 receptor homologs and human TLRs
Author(s) nameChoudhury A, Mukherjee S.
Journal J Med Virol
Impact factor2.07
Citation count32
Date of publishing2020 Oct
Sequence alignment of RBDs of SARS-CoV-1 and SARS-CoV-2 shows a highly conserved epitope
PMID 32585135
Title Neutralization of SARS-CoV-2 by destruction of the Prefusion Spike
Author(s) nameHuo J, Zhao Y, Ren J, Zhou D, Duyvesteyn HME, Ginn HM, Carrique L, Malinauskas T, Ruza RR, Shah PNM, Tan TK, Rijal P, Coombes N, Bewley KR, Tree JA, Radecke J, Paterson NG, Supasa P, Mongkolsapaya J, Screaton GR, Carroll M, Townsend A, Fry EE, Owens RJ, Stuart DI.
Journal Cell Host Microbe
Impact factor10.45
Citation count39
Date of publishing2020 Sep 9
Multiple characteristics features of the SARS-CoV-2 genome, particularly in terms of the codon bias, have been established.
PMID 32973171
Title Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
Author(s) nameKames J, Holcomb DD, Kimchi O, DiCuccio M, Hamasaki-Katagiri N, Wang T, Komar AA, Alexaki A, Kimchi-Sarfaty C.
Journal Sci Rep
Impact factor4.12
Citation count2
Date of publishing2020 Sep 24
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.
PMID 32973171
Title Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design
Author(s) nameKames J, Holcomb DD, Kimchi O, DiCuccio M, Hamasaki-Katagiri N, Wang T, Komar AA, Alexaki A, Kimchi-Sarfaty C.
Journal Sci Rep
Impact factor4.12
Citation count2
Date of publishing2020 Sep 24
Multiple sequence alignment of nucleocapsid protein of coronaviruses N-terminal domain
PMID 32363136
Title Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites
Author(s) nameKang S, Yang M, Hong Z, Zhang L, Huang Z, Chen X, He S, Zhou Z, Zhou Z, Chen Q, Yan Y, Zhang C, Shan H, Chen S.
Journal Acta Pharm Sin B
Impact factor6.15
Citation count72
Date of publishing2020 Jul
The feature of the SARS-CoV-2 genome, in terms of the CpG composition, have been characterized.
PMID 33029383
Title Intra-genome variability in the dinucleotide composition of SARS-CoV-2
Author(s) nameDigard P, Lee HM, Sharp C, Grey F, Gaunt E.
Journal Virus Evol
Impact factor1
Citation count7
Date of publishing2020 Jul
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.
PMID 33029383
Title Intra-genome variability in the dinucleotide composition of SARS-CoV-2
Author(s) nameDigard P, Lee HM, Sharp C, Grey F, Gaunt E.
Journal Virus Evol
Impact factor1
Citation count7
Date of publishing2020 Jul
Sequence alignment of SARSCoV2 Nsp15 coronaviral homologs with SARSCoV2, SARSCoV, MERSCoV, HCoV229E, MHV
PMID 32304108
Title Crystal structure of Nsp15 endoribonuclease NendoU from SARSCoV2
Author(s) nameKim Y, Jedrzejczak R, Maltseva NI, Wilamowski M, Endres M, Godzik A, Michalska K, Joachimiak A.
Journal Protein Sci
Impact factor2.4
Citation count58
Date of publishing2020 Jul
Sequence alignment of RBDs of SARS-CoV and SARS-CoV-2 shows a highly conserved epitope.
PMID 32245784
Title A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV
Author(s) nameYuan M, Wu NC, Zhu X, Lee CD, So RTY, Lv H, Mok CKP, Wilson IA.
Journal Science
Impact factor20.57
Citation count269
Date of publishing2020 May 8
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.
PMID 32201080
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, Jin X, Zhang L.
Journal Biochem Biophys Res Commun
Impact factor2.73
Citation count80
Date of publishing2020 May 21
Sequence analysis of Receptor binding motif (RBM) of Spike protein of SARS-CoV and SARS-CoV-2.
PMID 32201080
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, Jin X, Zhang L.
Journal Biochem Biophys Res Commun
Impact factor2.73
Citation count80
Date of publishing2020 May 21
Amino acid sequence alignment analysis of the ganglioside-binding domain (GBD) of SARS-CoV-2 and related coronavirus.
PMID 32251731
Title Structural and molecular modelling studies reveal a new mechanism of action of chloroquine and hydroxychloroquine against SARS-CoV-2 infection
Author(s) nameFantini J, Di Scala C, Chahinian H, Yahi N.
Journal Int J Antimicrob Agents
Impact factor4.6
Citation count118
Date of publishing2020 May
Sequence alignment of the RBDs from SARS-CoV and SARS-like viruses.
PMID 32225175
Title Structural basis of receptor recognition by SARS-CoV-2
Author(s) nameShang J, Ye G, Shi K, Wan Y, Luo C, Aihara H, Geng Q, Auerbach A, Li F.
Journal Nature
Impact factor24.36
Citation count599
Date of publishing2020 May