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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 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
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
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
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 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
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 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
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 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.
PMID 32972934
Title Coding-Complete Genome Sequences of Three SARS-CoV-2 Strains from Bangladesh
Author(s) nameAkter S, Banu TA, Goswami B, Osman E, Uzzaman MS, Habib MA, Jahan I, Mahmud ASM, Sarker MMH, Hossain MS, Shamsuzzaman AKM, Nafisa T, Molla MMA, Yeasmin M, Ghosh AK, Al Din SMS, Ray UC, Sajib SA, Hossain M, Khan MS.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2020 Sep 24
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.
PMID 32972948
Title Whole-Genome Sequence of SARS-CoV-2 Isolate Siena-1/2020
Author(s) nameCusi MG, Pinzauti D, Gandolfo C, Anichini G, Pozzi G, Santoro F.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2020 Sep 24
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'.
PMID 32967693
Title A persistently replicating SARS-CoV-2 variant derived from an asymptomatic individual
Author(s) nameCaccuri F, Zani A, Messali S, Giovanetti M, Bugatti A, Campisi G, Filippini F, Scaltriti E, Ciccozzi M, Fiorentini S, Caruso A.
Journal J Transl Med
Impact factor4.2
Citation count4
Date of publishing2020 Sep 23
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.
PMID 32556599
Title Full genome sequence of the first SARS-CoV-2 detected in Mexico
Author(s) nameGarcés-Ayala F, Araiza-Rodríguez A, Mendieta-Condado E, Rodríguez-Maldonado AP, Wong-Arámbula C, Landa-Flores M, Del Mazo-López JC, González-Villa M, Escobar-Escamilla N, Fragoso-Fonseca DE, Esteban-Valencia MDC, Lloret-Sánchez L, Arellano-Suarez DS, Nuñez-García TE, Contreras-González NB, Cruz-Ortiz N, Ruiz-López A, Fierro-Valdez MÁ, Regalado-Santiago D, Martínez-Velázquez N, Mederos-Michel M, Vázquez-Pérez J, Martínez-Orozco JA, Becerril-Vargas E, Salas J, Hernández-Rivas L, López-Martínez I, Alomía-Zegarra JL, López-Gatell H, Barrera-Badillo G, Ramírez-González JE.
Journal Arch Virol
Impact factor2.23
Citation count4
Date of publishing2020 Sep
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.
PMID 32763945
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, Kartti S, Laamarti R, Allam L, Ouadghiri M, Smyej I, Rahoui J, Benrahma H, Diawara I, Alouane T, Essabbar A, Siah S, Karra M, El Hafidi N, El Jaoudi R, Sbabou L, Nejjari C, Amzazi S, Mentag R, Belyamani L, Ibrahimi A.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2020 Aug 6
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.
PMID 32646908
Title Coding-Complete Genome Sequence of SARS-CoV-2 Isolate from Bangladesh by Sanger Sequencing
Author(s) nameMoniruzzaman M, Hossain MU, Islam MN, Rahman MH, Ahmed I, Rahman TA, Bhattacharjee A, Amin MR, Rashed A, Keya CA, Das KC, Salimullah M.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count2
Date of publishing2020 Jul 9
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.
PMID 32646911
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, Shifman O, Stein D, Achdout H, Weiss S, Mandelboim M, Erster O, Regev-Yochay G, Segal G, Yitzhaki S, Shapira SC, Beth-Din A, Zvi A.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2020 Jul 9
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.
PMID 32732237
Title Genome Sequences of SARS-CoV-2 Strains Detected in Hong Kong
Author(s) nameAu CH, Chan WS, Lam HY, Ho DN, Lam SYM, Zee JST, Chan TL, Ma ESK.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2020 Jul 30
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.
PMID 32616647
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, Amar N, Lemzaoui N, Mestoui O, Labioui M, Ouaariba N, Jibjibe A, Yartaoui M, Chahmi M, El Rhouila M, Sellak S, Kandoussi N, El Kabbaj S.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count1
Date of publishing2020 Jul 2
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.
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
Phylogenetics analysis of 89 SARS-CoV-2 genome sequence including three Colombian isolates (Cali-01, Antioquia, Bogot) revealed that Cali-01 and Bogota grouped into G clade, while Antioquia clustered into S clade.
PMID 32586872
Title Genome Sequence of SARS-CoV-2 Isolate Cali-01, from Colombia, Obtained Using Oxford Nanopore MinION Sequencing
Author(s) nameLopez-Alvarez D, Parra B, Cuellar WJ.
Journal Microbiol Resour Announc
Impact factor0.88
Citation count3
Date of publishing2020 Jun 25
Phylogenetic analysis of four SARS-CoV-2 genomes from Ecuador (HEE-01, HGSQ-USFQ-018, HGSQ-USFQ-007, HGSQ-USFQ-010), along with other GISAID SARS-CoV-2 genomes, reveals that the variant HEE-01, HGSQ-USFQ-007, and HGSQ-USFQ-010 belongs to the B lineage and HGSQ-USFQ-018 belongs to the B.1 lineage.
PMID 32588004
Title Genome sequencing of the first SARS-CoV-2 reported from patients with COVID-19 in Ecuador
Author(s) nameMarquez S, Prado-Vivar B, Guadalupe JJ, Gutierrez Granja B, Jibaja M, Tobar M, Mora F, Gaviria J, Garcia M, Ligna E, Espinosa F, Reyes J, Barragan V, Rojas-Silva P, Trueba G, Grunauer M, Cardenas P.
Journal medRxiv
Impact factorCant find
Citation count1
Date of publishing2020 Jun 14