Phylogenetic Analysis


Last updated: 2021 Sep 4
Total hit(s): 58
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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: 263
Date of Entry 2021 Sep 4


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


Amino acid alignment of the S gene in SARS-CoV-2 and coronaviruses found in bat and pangolin. NONE
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 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: 1
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 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. Introduction of SARS-CoV-2 into the Amazonas is likely caused due to multiple, distict events.
33857136
(PLoS Negl Trop Dis)
PMID
33857136
Date of Publishing: 2021 Apr
Title Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin
Author(s) nameBallesteros N, Muñoz M et al.
Journal PLoS Negl Trop Dis
Impact factor
4.4
Citation count: 1


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


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. Link to Radial Phylogenetic Tree
33558859
(Biosaf Health)
PMID
33558859
Date of Publishing: 2021 Feb 3
Title Genetic diversity and genomic epidemiology of SARS-CoV-2 in Morocco
Author(s) nameBadaoui B, Sadki K et al.
Journal Biosaf Health
Impact factor
Cant find
Citation count: 1


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


A total of 67 events reported 6 independent transmissions resulting in a transmission lineage, 39 leading to singletons as well as 22 transmissions causing stem clusters, finally giving rise to 143 introductions in Russia. GISAID
33510171
(Nat Commun)
PMID
33510171
Date of Publishing: 2021 Jan 28
Title Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia
Author(s) nameKomissarov AB, Safina KR et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 1


Most of the SARS-CoV-2 genome sequences found in Oman were closely related to each other and was defined in the B.1.1 (GR) clade. Wuhan Reference genome (GenBank: MN908947)
33359061
(Int J Infect Dis)
PMID
33359061
Date of Publishing: 2020 Dec 21
Title Molecular epidemiology of COVID-19 in Oman: A molecular andsurveillance study for the early transmission of COVID-19 in thecountry
Author(s) nameAl-Mahruqi S, Al-Wahaibi A et al.
Journal Int J Infect Dis
Impact factor
3.42
Citation count: 1


All sequences were closely related to each other and belonged to B.1.1.27 (GH) clade and B.1.1 lineage. Wuhan Reference genome (GenBank: MN908947)
33359061
(Int J Infect Dis)
PMID
33359061
Date of Publishing: 2020 Dec 21
Title Molecular epidemiology of COVID-19 in Oman: A molecular andsurveillance study for the early transmission of COVID-19 in thecountry
Author(s) nameAl-Mahruqi S, Al-Wahaibi A et al.
Journal Int J Infect Dis
Impact factor
3.42
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 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 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


Out of 125 samples evaluated in Milwaukee county, 148 distinct single-nucleotide-variants (SNVs) were identified and 75 sequences (60%) were clustered in 19A clade and 31 (24.8%) clustered in 20A clade. SARS-CoV-2 viruses clustered close together in Milwaukee county with less introductions leading to community transmission.
33144575
(Nat Commun)
PMID
33144575
Date of Publishing: 2020 Nov 3
Title Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread
Author(s) nameMoreno GK, Braun KM et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 1


Out of 122 SARS-CoV-2 samples evaluated in Dane county, 155 distinct single-nucleotide-variants (SNVs) were identified and 63 sequences (51.6%) were clustered in 20A clade. There was excess diversity between SARS-CoV-2 viruses introduced in Dane and Milwaukee county with higher introductions in Dane.
33144575
(Nat Commun)
PMID
33144575
Date of Publishing: 2020 Nov 3
Title Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread
Author(s) nameMoreno GK, Braun KM et al.
Journal Nat Commun
Impact factor
11.8
Citation count: 1


38 (73%) specimens, including 23 [61%] from primary and 15 [39%] from secondary and tertiary cases, were successfully sequenced, covering at least 98% of the SARS-CoV-2 genome. Six genetically similar clusters with known epidemiologic links were identified, five of which demonstrated secondary or tertiary transmission.
33237891
(MMWR Morb Mortal Wkly Rep)
PMID
33237891
Date of Publishing: 2020 Nov 27
Title COVID-19 Outbreak Associated with a 10-Day Motorcycle Rally in a Neighboring State Minnesota, AugustSeptember
Author(s) nameFirestone MJ, Wienkes H et al.
Journal MMWR Morb Mortal Wkly Rep
Impact factor
14.4
Citation count: 1


Phylogenetic analysis performed for the SARS-CoV-2 sequences taken from pharyngeal swabs of nine patients in Guangzhou, China indicated they were infected with the same viral strain since 100% identity was observed in Spike gene of SARS-CoV-2.
33235537
(Atmos Environ (1994))
PMID
33235537
Date of Publishing: 2020 Nov 20
Title Community evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission through air
Author(s) nameLin G, Zhang S et al.
Journal Atmos Environ (1994)
Impact factor
4.3
Citation count: 1


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