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Last updated: 2021 Jul 28
Total hit(s): 37
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Original Article
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Phylogenetic analysis based on full genomes and RBDs from the different isolates. Phylogeny trees of genome and RBD are simliar.
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: 27
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: 1
Date of Entry 2021 Jul 28


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%)
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.
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.
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.
Date of Entry 2021 Jun 14


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%). The study helps to detect and describe the transmission dynamics of new variants of the virus with clinical relevance.
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: 1


Phylogenetic analysis of deletion variants (red branches) and genetically diverse nondeletion variants revealed the origins of RDR variants and identified specific deletion clades/lineages. Variants of RDR1 and RDR3 are strongly polarized to specific clades and geographies. RDR variants have been present throughout the pandemic.
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: 6


Phylogenetic analysis of 302 sequences (including 30 UF sequences, University of Florida) from GISAID revealed that UF-8 Isolate (GenBank accession No. MW221275.1) was closely related to early SARS-CoV-2 strains that circulated locally. 2,452 genomes that also includes 30 new UF isolates (UF1 to UF30), were retained and aligned using MAFFT v7.407.
Isolate UF-8 had 12-nucleotide in-frame deletion within ORF3a, which encodes viroporin 3a.
33632859
(Microbiol Resour Announc)
PMID
33632859
Date of Publishing: 2021 Feb 25
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 et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1


Phylogenetic analysis of 59MDW SARS-CoV-2 genomes (n=41, collected from JBSA/Lackland military members and beneficiaries from May 14, 2020, to July 28, 2020) with 301 other SARSCoV-2 genomes (collected worldwide) revealed that all 59MDW SARS-CoV-2 genomes belong to the clade 20C cluster. Global strains were classifed into one of the five clades:19A, 19B, 20A, 20B, and 20C
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: 1


Phylogenetic analysis of ten SARS-CoV-2 genome sequences (GenBank accession no. MW079418- MW079427) from Malta along with 50 representative GISAID sequences revealed that all genomes clustered together to the B.1 lineage. All genomes except Hu-1 belong to the B.1 cluster
33509993
(Microbiol Resour Announc)
PMID
33509993
Date of Publishing: 2021 Jan 28
Title Genome Sequences of 10 SARS-CoV-2 Viral Strains Obtained by Nanopore Sequencing of Nasopharyngeal Swabs in Malta
Author(s) nameBiazzo M, Madeddu S et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1


Phylogenetic analysis of two SARS-CoV-2 genome sequences (accession no. EPI_ISL_492181, EPI_ISL_492182) from Arkansas with other GISAID sequences available till 7 July 2020 revealed that both genomes grouped in different subclusters of clade G. Clade G is defined by S protein D614G mutation. The color (clade) of the dots was classified according to the mutation marks from the GISAID database nomenclature
33334896
(Microbiol Resour Announc)
PMID
33334896
Date of Publishing: 2020 Dec 17
Title Two SARS-CoV-2 Genome Sequences of Isolates from Rural U.S. Patients Harboring the D614G Mutation, Obtained Using Nanopore Sequencing
Author(s) nameJenjaroenpun P, Wanchai V et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1


Phylogenetic analysis of two SARS-CoV-2 genomes from Tunisia along with other SARS-CoV-2 genomes from different countries reveals that sample MHT_1 (accession number: MT559037) grouped in clade 20A, and sample MHT_2 (accession number: MT559038 ) grouped in clade 19B. Nextstrain clade 20A is marked by the mutations C3037T, C14408T and A23403G. Clade 19 B is defined by T28144C mutations.
33034798
(Virus Genes)
PMID
33034798
Date of Publishing: 2020 Dec
Title Whole genome sequencing and phylogenetic classification of Tunisian SARS-CoV-2 strains from patients of the Military Hospital in Tunis
Author(s) nameHandrick S, Bestehorn-Willmann M et al.
Journal Virus Genes
Citation count 2


Phylogenetic analysis of Taiwanese SARS-CoV-2 genomes with global SARS-CoV-2 strains reveals that they clustered to four different clades, Clade I, II, III, and IV. Clade I, II, III, and IV are marked by ORF8-L84S mutation, ORF3a-G251V mutation, S-D614G mutation, and ORF1ab-V378I mutation, respectively. Taiwanese isolates were found in different lineages, showing various variants circulating in Taiwan.
32543353
(Emerg Microbes Infect)
PMID
32543353
Date of Publishing: 2020 Dec
Title SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East
Author(s) nameGong YN, Tsao KC et al.
Journal Emerg Microbes Infect
Impact factor
5.84
Citation count: 22


Phylogenetic analysis of 214 SARS-CoV-2 sequences of Israel, with 4693 SARS-CoV-2 genomes from all around the world, showed the origin, timing of the introductions and, the transmission patterns of multiple circulating clades of viruses in Israel. The time-resolved phylogeny confirmed most of the viral introductions and transmissions in the country from the passengers traveling from the United States of America. Many introductions from Europe, U.K., France, and Belgium were noticed. Phylodynamic Analysis was performed to understand the epidemiology of the disease inside the country. The reproduction number of circulating virus was inferred before and after the implementation of social distancing to track the transmission heterogeneity. The patterns of disease incidence and prevalence were also estimated to determine the timing and level of viral superspreading. The reproduction number ( R0) was found to be between 2.1 and 2.3, increasing toward R0=3.0 indicating high levels of superspreading. After the implementation of social distancing and following quarantine measures, R0 is found to be reduced by more than two-thirds.
33139704
(Nat Commun)
PMID
33139704
Date of Publishing: 2020 Nov 2
Title Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel
Author(s) nameMiller D, Martin MA et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 9


Phylogenetic analysis of twenty-three SARS-CoV-2 genomes (accession number: MT919768 - MT919790) from the Philippines reveals that twenty genomes are grouped in Clade GR/lineage B.1.1, two genomes grouped in Clade GR/lineage B.1.1.28, and a genome grouped in Clade O/lineage B.6. SARS-CoV-2 clade GR (both lineages B.1.1 and B.1.1.28) are defined by 4 amino acid substitutions (ORF1b-P314L, S-D614G, N-R203K, and N-G204R) clade GR/lineage B.1.1, frequently found in Europe clade GR/lineage B.1.1.28, found in Brazil (89%), the United Kingdom (8%), and China (2%) clade O/lineage B.6, a global lineage mostly found in Singapore and India
33093050
(Microbiol Resour Announc)
PMID
33093050
Date of Publishing: 2020 Oct 22
Title Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines
Author(s) nameVelasco JM, Chinnawirotpisan P et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 2


The phylogenetic analysis of the 29 SARS-CoV-2 genomes from Hangzhou, along with 196 sequences, revealed that the genomes were grouped into three different clades, L, V, and G, and two subclades GR, and GH. Thus revealed multiple sources of SARS-CoV-2 introduction and different transmission patterns.
33060796
(Sci Rep)
PMID
33060796
Date of Publishing: 2020 Oct 15
Title Rapid genomic characterization of SARSCoV2 viruses from clinical specimens using nanopore sequencing
Author(s) nameLi J, Wang H et al.
Journal Sci Rep
Impact factor
4.12
Citation count: 1


Phylogenetic analysis of the SARS-CoV-2 genome from Siena (accession numbers: MT531537) reveals that it is grouped in the B1.1 lineage with European SARS-CoV-2 isolates. Lineage B.1.1, mostly found in Europe and are defined by 4 amino acid substitutions (ORF1b-P314L, S-D614G, N-R203K, and N-G204R)
32972948
(Microbiol Resour Announc)
PMID
32972948
Date of Publishing: 2020 Sep 24
Title Whole-Genome Sequence of SARS-CoV-2 Isolate Siena-1/2020
Author(s) nameCusi MG, Pinzauti D et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1


Phylogenetic analysis of three SARS-CoV-2 genomes from Bangladesh (accession number: EPI_ISL_455458, EPI_ISL_455420, and EPI_ISL_455459), along with other GISAID SARS-CoV-2 sequences, reveal that three genomes belong to Clade 20B. Nextstrain clade 20B is defined by three consecutive mutations: G28881A, G28882A, and G28883C
32972934
(Microbiol Resour Announc)
PMID
32972934
Date of Publishing: 2020 Sep 24
Title Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh
Author(s) nameAkter S, Banu TA et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1


Phylogenetic analysis of SARS-CoV-2 Isolates GZ69 and AP66 (from Brescia), along with 3171 other SARS-CoV-2 sequences, reveals that the SARS-CoV-2 AP66 belongs to 'clade B1', and the SARS-CoV-2 GZ69 belongs to 'sub-lineage B.1.1'. The B1 clade and B.1.1 sub-lineage mostly includes genome sequences from Italy, Europe and United States.
32967693
(J Transl Med)
PMID
32967693
Date of Publishing: 2020 Sep 23
Title A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual
Author(s) nameCaccuri F, Zani A et al.
Journal J Transl Med
Impact factor
4.2
Citation count: 4


Phylogenetic analysis of a Mexican SARS-CoV-2 genome (accession number: EPI_ISL_412972), with other GISAID sequences, reveals that it is grouped in the subclade A2a of clade A2. The isolate from Mexico is closely related to the isolates from Finland, Italy, and Germany, Brazil. Clade A2 (subclade A2a) also called lineage G which is defined by D614G mutation in the S gene. Subclade A2a is marked by ORF1b-P314L mutation.
32556599
(Arch Virol)
PMID
32556599
Date of Publishing: 2020 Sep
Title Full genome sequence of the first SARS-CoV-2 detected in Mexico
Author(s) nameGarcés-Ayala F, Araiza-Rodríguez A et al.
Journal Arch Virol
Impact factor
2.23
Citation count: 4


Phylogenetic analysis of six SARS-CoV-2 isolates, Morocco/RMPS-01 (accession number: MT731285), Morocco/RMPS-02 (accession number: MT731292), Morocco/RMPS-03 (accession number: MT731673 ), Morocco/RMPS-04 (accession number: MT731327 ), Morocco/RMPS-05 (accession number: MT731468), Morocco/RMPS-06 (accession number: MT731764), along with 250 other genome sequences, reveal that all genomes clustered into "clade A2a", except Morocco/RMPS-03 which is grouped in clade A2. Nextstrain clade A2 is defined by D614G mutations in spike proteins and A2a is defined by ORF1b-P314L mutation.
32763945
(Microbiol Resour Announc)
PMID
32763945
Date of Publishing: 2020 Aug 6
Title Genome Sequences of Six SARS-CoV-2 Strains Isolated in Morocco, Obtained Using Oxford Nanopore MinION Technology
Author(s) nameLaamarti M, Chemao-Elfihri MW et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1


Phylogenetic analysis of the SARS-CoV-2 genome of Bangladesh (accession number: MT509958), with twenty-four other GISAID SARS-CoV-2 genome sequences, reveals that it is grouped with three isolates of the United States. The genome was found to be closest with isolate (MT476385.1 SARS-CoV-2/human/BGD/CHRF), among 17 Bangladesh isolates under study.
32646908
(Microbiol Resour Announc)
PMID
32646908
Date of Publishing: 2020 Jul 9
Title Coding-Complete Genome Sequence of SARS-CoV-2 Isolate from Bangladesh by Sanger Sequencing
Author(s) nameMoniruzzaman M, Hossain MU et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 2


Phylogenetic analysis of two Israel SARS-CoV-2 genomes along with all Asian SARS-CoV-2 genomes from Nextstrain datasets reveal that the ISR_JP0320 isolate (accession number: MT276597) belongs to clade 19A, while the ISR_IT0320 isolate (accession number: MT276598) belongs to the 20B clade. Nextstrain clade 19A is marked by mutation C8782T which is primarly seen in Asian countries. And 20B is defined by three consecutive mutations: G28881A, G28882A, and G28883C primarily seen in Europian countries.
32646911
(Microbiol Resour Announc)
PMID
32646911
Date of Publishing: 2020 Jul 9
Title Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Early Manifestations of COVID-19 in Israel
Author(s) nameCohen-Gihon I, Israeli O et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1


Phylogenetic analysis of three SARS-CoV-2 genomes from Hong Kong (accession number: EPI_ISL_430018, EPI_ISL_430063, EPI_ISL_451957), with other GISAID SARS-CoV-2 genome sequences, reveals that they descended from European samples. All the three cases from Hong Kong were imported, cases 1, 2 had 88% similarity with European Samples, case 3 had 100% similarity with European Samples. Case 1 and 2 were related to each other and had a similar SARS-CoV-2 genomes. While case 3 phlogeny consistent with international travel.
32732237
(Microbiol Resour Announc)
PMID
32732237
Date of Publishing: 2020 Jul 30
Title Genome Sequences of SARS-CoV-2 Strains Detected in Hong Kong
Author(s) nameAu CH, Chan WS et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1


Phylogenetic analysis of a Moroccan SARS-CoV-2 genome (accession number: EPI_ISL_451400) along with 53 other SARS-CoV-2 sequences reveal that it is grouped in SARS-CoV-2 clade G. Clade G is defined by D614G mutation in the S gene
32616647
(Microbiol Resour Announc)
PMID
32616647
Date of Publishing: 2020 Jul 2
Title Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Morocco
Author(s) nameLemriss S, Souiri A et al.
Journal Microbiol Resour Announc
Impact factor
0.88
Citation count: 1


The phylogenetic analysis of the E gene of human and bat coronaviruses revealed that the CpG composition in E ORF is an ancestrally derived trait and is closely related to the bat relatives. 7 human coronavirus (HCoV-229E, HCoV-HKU1, HCoV-NL63, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2) and 96 bat coronavirus E genes were analyzed
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: 7