Phylogenetic Analysis


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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
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
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
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
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
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
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.
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
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.
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
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.
PMID 33510171
Title Genomic epidemiology of the early stages of the SARS-CoV-2 outbreak in Russia
Author(s) nameKomissarov AB, Safina KR, Garushyants SK, Fadeev AV, Sergeeva MV, Ivanova AA, Danilenko DM, Lioznov D, Shneider OV, Shvyrev N, Spirin V, Glyzin D, Shchur V, Bazykin GA.
Journal Nat Commun
Impact factor11.8
Citation count1
Date of publishing2021 Jan 28
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.
PMID 33509993
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, Elnifro E, Sultana T, Muscat J, Scerri CA, Santoro F, Pinzauti D.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2021 Jan 28
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.
PMID 33359061
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, Khan AL, Al-Jardani A, Asaf S, Alkindi H, Al-Kharusi S, Al-Rawahi AN, Al-Rawahi A, Al-Salmani M, Al-Shukri I, Al-Busaidi A, Al-Abri SS, Al-Harrasi A.
Journal Int J Infect Dis
Impact factor3.42
Citation count1
Date of publishing2020 Dec 21
All sequences were closely related to each other and belonged to B.1.1.27 (GH) clade and B.1.1 lineage.
PMID 33359061
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, Khan AL, Al-Jardani A, Asaf S, Alkindi H, Al-Kharusi S, Al-Rawahi AN, Al-Rawahi A, Al-Salmani M, Al-Shukri I, Al-Busaidi A, Al-Abri SS, Al-Harrasi A.
Journal Int J Infect Dis
Impact factor3.42
Citation count1
Date of publishing2020 Dec 21
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.
PMID 33334896
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, Ono-Moore KD, Laudadio J, James LP, Adams SH, Prior F, Nookaew I, Ussery DW, Wongsurawat T.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2020 Dec 17
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.
PMID 33034798
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, Eckstein S, Walter MC, Antwerpen MH, Naija H, Stoecker K, Wölfel R, Ben Moussa M.
Journal Virus Genes
Impact factor
Citation count2
Date of publishing2020 Dec
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.
PMID 32543353
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, Hsiao MJ, Huang CG, Huang PN, Huang PW, Lee KM, Liu YC, Yang SL, Kuo RL, Chen KF, Liu YC, Huang SY, Huang HI, Liu MT, Yang JR, Chiu CH, Yang CT, Chen GW, Shih SR.
Journal Emerg Microbes Infect
Impact factor5.84
Citation count22
Date of publishing2020 Dec
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.
PMID 33144575
Title Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread
Author(s) nameMoreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC.
Journal Nat Commun
Impact factor11.8
Citation count1
Date of publishing2020 Nov 3
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.
PMID 33144575
Title Revealing fine-scale spatiotemporal differences in SARS-CoV-2 introduction and spread
Author(s) nameMoreno GK, Braun KM, Riemersma KK, Martin MA, Halfmann PJ, Crooks CM, Prall T, Baker D, Baczenas JJ, Heffron AS, Ramuta M, Khubbar M, Weiler AM, Accola MA, Rehrauer WM, O'Connor SL, Safdar N, Pepperell CS, Dasu T, Bhattacharyya S, Kawaoka Y, Koelle K, O'Connor DH, Friedrich TC.
Journal Nat Commun
Impact factor11.8
Citation count1
Date of publishing2020 Nov 3
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.
PMID 33237891
Title COVID-19 Outbreak Associated with a 10-Day Motorcycle Rally in a Neighboring State Minnesota, AugustSeptember
Author(s) nameFirestone MJ, Wienkes H, Garfin J, Wang X, Vilen K, Smith KE, Holzbauer S, Plumb M, Pung K, Medus C, Yao JD, Binnicker MJ, Nelson AC, Yohe S, Como-Sabetti K, Ehresmann K, Lynfield R, Danila R.
Journal MMWR Morb Mortal Wkly Rep
Impact factor14.4
Citation count1
Date of publishing2020 Nov 27
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.
PMID 33235537
Title Community evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission through air
Author(s) nameLin G, Zhang S, Zhong Y, Zhang L, Ai S, Li K, Su W, Cao L, Zhao Y, Tian F, Li J, Wu Y, Guo C, Peng R, Wu X, Gan P, Zhu W, Lin H, Zhang Z.
Journal Atmos Environ (1994)
Impact factor4.3
Citation count1
Date of publishing2020 Nov 20
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.
PMID 33139704
Title Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel
Author(s) nameMiller D, Martin MA, Harel N, Tirosh O, Kustin T, Meir M, Sorek N, Gefen-Halevi S, Amit S, Vorontsov O, Shaag A, Wolf D, Peretz A, Shemer-Avni Y, Roif-Kaminsky D, Kopelman NM, Huppert A, Koelle K, Stern A.
Journal Nat Commun
Impact factor11.8
Citation count9
Date of publishing2020 Nov 2
In a molecular epidemiological study conducted in Thailand, WU5 was identified as Type L which was closely related to Wuhan-Hu-1. 10 strains of Type G including 7 GH and 3 GR strains, 2 strains of Type O as well as 27 out of 40 samples with Type T cluster were identified.
PMID 33024144
Title Molecular epidemiology of the first wave of severe acute respiratory syndrome coronavirus 2 infection in Thailand in 2020
Author(s) namePuenpa J, Suwannakarn K, Chansaenroj J, Nilyanimit P, Yorsaeng R, Auphimai C, Kitphati R, Mungaomklang A, Kongklieng A, Chirathaworn C, Wanlapakorn N, Poovorawan Y.
Journal Sci Rep
Impact factor4.12
Citation count1
Date of publishing2020 Oct 6
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.
PMID 33093050
Title Coding-Complete Genome Sequences of 23 SARS-CoV-2 Samples from the Philippines
Author(s) nameVelasco JM, Chinnawirotpisan P, Joonlasak K, Manasatienkij W, Huang A, Valderama MT, Diones PC, Leonardia S, Timbol ML, Navarro FC, Villa V 2nd, Tabinas H Jr, Chua D Jr, Fernandez S, Jones A, Klungthong C.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count2
Date of publishing2020 Oct 22
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.
PMID 33060796
Title Rapid genomic characterization of SARSCoV2 viruses from clinical specimens using nanopore sequencing
Author(s) nameLi J, Wang H, Mao L, Yu H, Yu X, Sun Z, Qian X, Cheng S, Chen S, Chen J, Pan J, Shi J, Wang X.
Journal Sci Rep
Impact factor4.12
Citation count1
Date of publishing2020 Oct 15
Phylogenetic analysis of human ACE2 receptor (accession number: AAT45083.1), with ACE2 receptor protein sequences from other genera of the animal kingdom.
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
Phylogenetic analysis of SARS-CoV-2 Spike glycoprotein protein (accession number: QIC53213.1), with ten other spike glycoprotein sequences from all the selected organisms.
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