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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.
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 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
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.
PMID
Title A unique SARS-CoV-2 spike protein P681H strain detected in Israel
Author(s) nameNeta S. Zuckerman, Shay Fleishon, Efrat Bucris, Dana Bar-Ilan, Michal Linial, Itay Bar-Or, Victoria Indenbaum, Merav Weil,Ella Mendelson, Michal Mandelboim, Orna Mor
Journal
Impact factor
Citation count
Date of publishing2021 Mar 25
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).
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
Metadata was analyzed to associate the frequent mutations and co-mutation patterns with COVID-19 patient status (deceased, symptomatic, mild, and asymptomatic groups).
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
Primer and Probe sequence specific for E gene of SARS-CoV-2 used in wastewater RT- ddPCR assay.
PMID
Title Redesigning SARS-CoV-2 clinical RT-qPCR assays for wastewater RT-ddPCR
Author(s) name-
Journal
Impact factor
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Date of publishing-
Whole Genome Sequences of 54 SARS-CoV-2 Strains (from August to October 2020), reported from Kolkata, West Bengal.
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) name-
Journal
Impact factor
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Date of publishing-
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.
PMID
Title A unique SARS-CoV-2 spike protein P681H strain detected in Israel
Author(s) name-
Journal
Impact factor
Citation count
Date of publishing-
Primer and Probe sequence specific for N gene of SARS-CoV-2 used in wastewater RT- ddPCR assay.
PMID
Title Redesigning SARS-CoV-2 clinical RT-qPCR assays for wastewater RT-ddPCR
Author(s) name-
Journal
Impact factor
Citation count
Date of publishing-
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.
PMID 33619452
Title Rare mutations in the accessory proteins ORF6, ORF7b, and ORF10 of the SARS-CoV-2 genomes
Author(s) nameHassan SS, Choudhury PP, Roy B.
Journal Meta Gene
Impact factor0.88
Citation count1
Date of publishing2021 Jun
Both the clusters (C1, C2) identified in the Amazon basin showed 4 mutations in the ORF1ab region and 1 mutation in the Spike gene but at different positions within the region for each cluster.
PMID 33857136
Title Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin
Author(s) nameBallesteros N, Muñoz M, Patiño LH, Hernández C, González-Casabianca F, Carroll I, Santos-Vega M, Cascante J, Angel A, Feged-Rivadeneira A, Palma-Cuero M, Flórez C, Gomez S, van de Guchte A, Khan Z, Dutta J, Obla A, Alshammary HA, Gonzalez-Reiche AS, Hernandez MM, Sordillo EM, Simon V, van Bakel H, Paniz-Mondolfi AE, Ramírez JD.
Journal PLoS Negl Trop Dis
Impact factor4.4
Citation count
Date of publishing2021 Apr
The SARS-CoV-2 isolates collected from the Amazon basin was distributed into two clades: G, GH and further into two independent clusters: C1, C2 with 10 Pangolin lineages in circulation.
PMID 33857136
Title Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin
Author(s) nameBallesteros N, Muñoz M, Patiño LH, Hernández C, González-Casabianca F, Carroll I, Santos-Vega M, Cascante J, Angel A, Feged-Rivadeneira A, Palma-Cuero M, Flórez C, Gomez S, van de Guchte A, Khan Z, Dutta J, Obla A, Alshammary HA, Gonzalez-Reiche AS, Hernandez MM, Sordillo EM, Simon V, van Bakel H, Paniz-Mondolfi AE, Ramírez JD.
Journal PLoS Negl Trop Dis
Impact factor4.4
Citation count
Date of publishing2021 Apr
Mutation analysis of 2213 complete genomes from six geographical regions worldwide revealed 3178 polymorphic sites. Of these polymorphic sites, 58.5% (1861 sites) were non-synonymous, compared with the reference genome, Wuhan-Hu-1. Seven frequent non-synonymous mutations were observed in the global population of SARS-CoV-2.
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
The Nexstrain phylogenetic analysis of 2213 complete genomes (December 2019-November 2020, from NCBI and GISAID) from six geographical regions worldwide revealed that the genomes were grouped into seven clusters based on seven non-synonymous mutations. Among seven mutations, G614 (clade 19A) and L323 (clade 20A) had the highest global frequencies (>75%).
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
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
Phylogenetic analysis of deletion variants (red branches) and genetically diverse nondeletion variants revealed the origins of RDR variants and identified specific deletion clades/lineages.
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
Complete Coding Sequence of surface glycoprotein (S) gene, reported from an immunocompromised cancer patient infected with long-term SARS-CoV-2 infection (Pittsburgh long-term infection 1).
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 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
SARS-CoV-2 immunosuppressed patients had recurrent deletions in the spike glycoprotein. The deletions altered immunodominant epitope positions within the NTD of S glycoprotein and caused resistance to a neutralizing antibody.
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
62 mutations identified, including 30 mis-sense mutations, in 22 Moroccan patient isolates showed that Spike_D614G and NSP12_P323L mutations were present in all the analyzed sequences, whereas N_G204R and N_R203K were present in 9 sequences.
PMID 33558859
Title Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco
Author(s) nameBadaoui B, Sadki K, Talbi C, Salah D, Tazi L.
Journal Biosaf Health
Impact factorCant find
Citation count1
Date of publishing2021 Feb 3
22 SARS-CoV-2 genome sequences from Morocco shows diversity in the virus lineage and multiple, unrelated introductions in Morocco via different routes, giving rise to various SARS-CoV-2 strains with mutations.
PMID 33558859
Title Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco
Author(s) nameBadaoui B, Sadki K, Talbi C, Salah D, Tazi L.
Journal Biosaf Health
Impact factorCant find
Citation count1
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.
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
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
Isolate UF-8 (GenBank accession No. MW221275.1) had 12-nucleotide in-frame deletion within ORF3a that encodes viroporin 3a protein.
PMID 33632859
Title In-Frame 12-Nucleotide Deletion within Open Reading Frame 3a in a SARS-CoV-2 Strain Isolated from a Patient Hospitalized with COVID-19
Author(s) nameLednicky JA, Cherabuddi K, Tagliamonte MS, Elbadry MA, Subramaniam K, Waltzek TB, Morris JG Jr.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2021 Feb 25