¿Cuál es el resultado del análisis filogenético de la secuencia del genoma del SARS-CoV-2?
(What is the result of phylogenetic analysis of sars-cov-2 genome sequence?)
Primeras 5 respuestas:
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Phylogenetic analysis of SARS-CoV-2 and its 20 closely related coronaviruses formed four well supported clades (Fig. 2) .
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Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan.
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Phylogenetic analysis was carried out with 178 representative that a clade can be also determined by one or more mutations.
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Phylogenetic analysis, natural selection investigation and genome recombination analysis were performed.
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The phylogenetic tree results demonstrate that all the CoVs responsible for the outbreak of concentrated pneumonia belong to the genera Betacoronavirus ( Figure 2 ).
Phylogenetic analysis of SARS-CoV-2 and its 20 closely related coronaviruses formed four well supported clades (Fig. 2) .
... further compared their alterations of nucleotides and amino acids in comparison to other representative coronaviruses. Phylogenetic analysis of SARS-CoV-2 and its 20 closely related coronaviruses formed four well supported clades (Fig. 2) . The two SARS-CoV-2 strain WIV04 (from Wuhan) and SNU01 (from Korea patient) were clustered with ...
Ref: Comparative genomic analysis revealed specific mutation pattern between human coronavirus SARS-CoV-2 and Bat-SARSr-CoV RaTG13 [bioRxiv, 2020-03-02]Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan.
... cell cultures were confluent 3 days after the first blind passage of the sample. Coronavirus was confirmed with spherical particle having a fringe reminiscent of crown on transmission electron microscopy. Phylogenetic analyses of whole genome sequences showed that it clustered with other SARS-CoV-2 reported from Wuhan. ...
Ref: Virus Isolation from the First Patient with SARS-CoV-2 in Korea [J Korean Med Sci, 2020-02-18]Phylogenetic analysis was carried out with 178 representative that a clade can be also determined by one or more mutations.
Phylogenetic analysis was carried out with 178 representative that a clade can be also determined by one or more mutations.
Ref: cord_uid shn7vx3d Genome-Wide Identification and Characterizatio... shn7vx3d Genome-Wide Identification and Characterizatio... Name: title, dtype: object [J Korean Med Sci, cord_uid shn7vx3d 2020 shn7vx3d 2020-06-19 Name: publish_time, dtype: object]Phylogenetic analysis, natural selection investigation and genome recombination analysis were performed.
... sequences of SARS-CoV, bat SARS-like CoVs and MERS-CoV, the latter currently detected in this region. Phylogenetic analysis, natural selection investigation and genome recombination analysis were performed. Our analysis showed that all Saudi SARS-CoV-2 sequences are of the same origin and closer ...
Ref: Insights into molecular evolution recombination of pandemic SARS-CoV-2 using Saudi Arabian sequences [bioRxiv, 2020-05-13]The phylogenetic tree results demonstrate that all the CoVs responsible for the outbreak of concentrated pneumonia belong to the genera Betacoronavirus ( Figure 2 ).
... CoVs whole-genome sequences obtained from National Center for Biotechnology Information (NCBI) ( Table S1 ). The phylogenetic tree results demonstrate that all the CoVs responsible for the outbreak of concentrated pneumonia belong to the genera Betacoronavirus ( Figure 2 ). All the SARS-CoV-2 clade grouped with the cluster of SARS/SARS-like CoVs, with bat CoVs HKU9-1, ...
Ref: Evolutionary Trajectory for the Emergence of Novel Coronavirus SARS-CoV-2 [Pathogens, 2020-03-23]Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple, independent but isolated introductions mainly from Europe and other parts of the United States.
... sequenced the virus causing COVID-19 in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV2 genomes indicates multiple, independent but isolated introductions mainly from Europe and other parts of the United States. Moreover, we find evidence for community transmission of SARS-CoV-2 as suggested by clusters of related ...
Ref: Introductions and early spread of SARS-CoV-2 in the New York City area [Science, 2020-05-29]Phylogenetic analysis was carried out on the core gene clusters to produce a species tree and similarly for each gene cluster to produce gene trees.
... on. Gene sequences were compared to each other for sequence similarity, followed by gene clustering. Phylogenetic analysis was carried out on the core gene clusters to produce a species tree and similarly for each gene cluster to produce gene trees. For this pangenome analysis we used panX 12 (Ding et al., 2018 ) that takes ...
Ref: Functional pangenome analysis suggests inhibition of the protein E as a readily available therapy for COVID-2019 [bioRxiv, 2020-02-21]SARS-CoV-2 clustering was different depending on whether the whole genome or specific genes were used in the analysis.
... identified coronaviruses based on their whole-genome sequences, main structural protein genes, and non-structural protein genes. SARS-CoV-2 clustering was different depending on whether the whole genome or specific genes were used in the analysis. For example, SARS-CoV-2 clustered with the members of the subgenus Sarbecovirus including the SARS-CoV (79.5% ...
Ref: The COVID-19 Pandemic: A Comprehensive Review of Taxonomy, Genetics, Epidemiology, Diagnosis, Treatment, and Control [J Clin Med, 2020-04-24]We observed an uneven distribution of genetic variants, and a statistically significant spatial phylogenetic structure.
... analysis of SARS-CoV-2 genomes collected from the beginning of the pandemic to April 25, 2020. We observed an uneven distribution of genetic variants, and a statistically significant spatial phylogenetic structure. As discussed below, this suggests that long-distance dispersal can favor the establishment of otherwise rare, ...
Ref: Mega-phylogeny sheds light on SARS-CoV-2 spatial phylogenetic structure [bioRxiv, 2020-06-05]Based on phylogenetic and taxonomy data, SARS-CoV-2 was recently shown to form a sister clade with SARS coronavirus [4] .
... Based on phylogenetic and taxonomy data, SARS-CoV-2 was recently shown to form a sister clade with SARS coronavirus [4] . Since SARS-CoV-2 and SARS genomes have been shown to be similar, we sought to investigate the pathogenesis of SARS-CoV-2 by predicting miRNAs regulating their pathogenesis as well as taking clues ...
Ref: In-silico analysis of SARS-CoV-2 genomes: Insights from SARS encoded non-coding RNAs [bioRxiv, 2020-04-04]The study was concluded with the introduction of a properly designed vaccine from the most suitable of epitopes.
... their antigenicity and surface accessibility. Epitope-allele interaction was investigated through molecular docking. A phylogenetic analysis was undertaken to identify molecular evolutionary relationship of the selected S, E and M proteins. The study was concluded with the introduction of a properly designed vaccine from the most suitable of epitopes. ...
Ref: Multi-epitope Based Peptide Vaccine Design Using Three Structural Proteins (S, E, and M) of SARS-CoV-2: An In Silico Approach [bioRxiv, 2020-06-13]Results The phylogenetic analysis showed the strain in Nigeria clustered in a monophyletic clade with a Wuhan sublineage.
... Time Reversible model. Phylogenetic tree was constructed to determine the common ancestor of each strain. Results The phylogenetic analysis showed the strain in Nigeria clustered in a monophyletic clade with a Wuhan sublineage. Nucleotide alignment also showed a 100% similarity indicating a common origin of evolution. Comparative analysis ...
Ref: Phyloevolutionary analysis of SARS-CoV-2 in Nigeria [New Microbes New Infect, 2020-06-14]The phylogenetic analysis demonstrated that SARS-CoV-2 formed a cluster with the bat CoV isolate RaTG13.
... genomic regions which may have permitted the adaptation of SARS-CoV-2 to the human host. RESULTS: The phylogenetic analysis demonstrated that SARS-CoV-2 formed a cluster with the bat CoV isolate RaTG13. Possible CoV interspecies jumps among bat isolates were also observed. The phylogenetic tree reconstructed from ...
Ref: The Novel Coronavirus SARS-CoV-2: From a Zoonotic Infection to Coronavirus Disease-19 (COVID19) [J. med. virol, 2020]Our analysis showed that all Saudi SARS-CoV-2 sequences are of the same origin and closer proximity to bat SARS-like CoVs,
... detected in this region. Phylogenetic analysis, natural selection investigation and genome recombination analysis were performed. Our analysis showed that all Saudi SARS-CoV-2 sequences are of the same origin and closer proximity to bat SARS-like CoVs, followed by SARS-CoVs, however quite distant to MERS-CoV. Moreover, genome recombination analysis revealed two recombination ...
Ref: Insights into molecular evolution recombination of pandemic SARS-CoV-2 using Saudi Arabian sequences [bioRxiv, 2020-05-13]These results reveal at least three major clades circulating in the Chicago region as of mid-March 2020.
... phylogenetic and phylodynamic analyses of 88 SARS-CoV-2 genomes from COVID-19 patients in Chicago, Illinois, USA. These results reveal at least three major clades circulating in the Chicago region as of mid-March 2020. Two of the three clades are broadly representative of the major circulating clades that expanded ...
Ref: A Unique Clade of SARS-CoV-2 Viruses is Associated with Lower Viral Loads in Patient Upper Airways [medRxiv : the preprint server for health sciences, 2020-05-26]This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format.
... software application to quickly and accurately assemble all known virus genomes from next-generation sequencing datasets. This application allows the identification of phylogenetic clusters and genotypes from assembled genomes in FASTA format. Since its release in 2019, we have produced a number of typing tools for emergent ...
Ref: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes [Bioinformatics, 2020]we estimated the time to the most recent common ancestor and evolutionary rate of SARS‐CoV‐2,
... comparative analyses of the genomes. Based on Bayesian time‐scaled phylogenetic analysis using the tip‐dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS‐CoV‐2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10(−3) substitutions ...
Ref: Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2 [J Med Virol, 2020-03-11]Phylogenetic analysis showed that the view, pangolin acted as an intermediate host, may be controversial.
... SARS-CoV-2, which may be explaining the existing widespread and high adaptation of the deadly virus. Phylogenetic analysis showed that the view, pangolin acted as an intermediate host, may be controversial. The network indicated that, in the original haplotype (H14), one patient sample lived near the ...
Ref: Genome-wide data inferring the evolution and population demography of the novel pneumonia coronavirus (SARS-CoV-2) [bioRxiv, 2020-03-07]Our phylogenetic reconstructions suggest possible multiple introduction of SARS‐CoV‐2.
... dynamics in Italy, we analyzed complete genomes of SARS‐CoV‐2 isolates, obtained directly from clinical samples. Our phylogenetic reconstructions suggest possible multiple introduction of SARS‐CoV‐2. Continued genomic surveillance strategies are needed to improve monitoring and understanding of the current SARS‐CoV‐2 ...
Ref: A doubt of multiple introduction of SARS‐CoV‐2 in Italy: A preliminary overview [J Med Virol, 2020-03-27]This divergence away from the SARS-CoV-2 sequences broadly mirrors the phylogenetic relationships obtained from the whole-genome alignments.
... responses. MERS and the milder symptom viruses showed greater differences and even significant sequence gaps. This divergence away from the SARS-CoV-2 sequences broadly mirrors the phylogenetic relationships obtained from the whole-genome alignments. Therefore, patterns of mutation, occurring during sequence divergence from the longer established human viruses to ...
Ref: The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities [Viruses, 2020]country-specific data still present severe limitations and should be interpreted with caution.
... available genome sequences of SARS-CoV-2 is growing daily and the sequences show increasing phylogenetic information, country-specific data still present severe limitations and should be interpreted with caution. OBJECTIVE: The objective of this study was to determine the quality of the currently available ...
Ref: A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis [JMIR Public Health Surveill, 2020-06-01]phylogenetic analysis reveals that they are very closely related to viruses sampled from the earliest Wuhan patients.
... first suspected. Genome sequences of ""environmental samples""-likely surfaces-from the market have now been obtained, and phylogenetic analysis reveals that they are very closely related to viruses sampled from the earliest Wuhan patients. While this again suggests that the market played an important role in virus emergence, it ...
Ref: A Genomic Perspective on the Origin and Emergence of SARS-CoV-2 [Cell, 2020-04-16]We confirm high sequence similarity (>99%) between all sequenced 2019‐nCoVs genomes available,
... also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and severe acute respiratory syndrome. We confirm high sequence similarity (>99%) between all sequenced 2019‐nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic ...
Ref: Genomic variance of the 2019‐nCoV coronavirus [J Med Virol, 2020-02-19]We identified a missense mutation, D614G, in the spike protein of SARS-CoV-2,
... phylogenetic analysis of over 1,225 SARS-CoV-2 genomes spanning from late December 2019 to mid-March 2020. We identified a missense mutation, D614G, in the spike protein of SARS-CoV-2, which has emerged as a predominant clade in Europe (954 of 1,449 (66%) sequences) and ...
Ref: Evolutionary and structural analyses of SARS-CoV-2 D614G spike protein mutation now documented worldwide [bioRxiv, 2020-06-08]The phylogenetic study has confirmed close relatedness of SARS-CoV-2 to bats' coronaviruses.
... relationship between spike glycoproteins from different coronaviruses. This was done with a combination of the phylogenetic tree analysis (reconstructed from the translated sequences) and a comparison of the structural models. The phylogenetic study has confirmed close relatedness of SARS-CoV-2 to bats" coronaviruses. ...
Ref: SARS‐CoV‐2: Structural diversity, phylogeny, and potential animal host identification of spike glycoprotein [J Med Virol, 2020-05-17]The phylogenetic tree showed that SARS-CoV-2 was 96.2% identical to bat β-coronaviruses from lineage B.
... several patients who traveled to Wuhan or went to a seafood wholesale market in Wuhan. The phylogenetic tree showed that SARS-CoV-2 was 96.2% identical to bat β-coronaviruses from lineage B. Also, several studies reported that SARS-CoV-2 uses the SARS-CoV receptor, angiotensin-converting enzyme 2, for entry ...
Ref: Comparison of the COVID-2019 (SARS-CoV-2) pathogenesis with SARS-CoV and MERS-CoV infections [J Med Virol, 2020-05-20]we found a similarity rate of 96% between RaTG13 and SARS-CoV-2 (Wuhan isolate).
... After carrying out the analyzes using BRIG software, we found a similarity rate of 96% between RaTG13 and SARS-CoV-2 (Wuhan isolate). However, the mutations which were present in the human strain were randomly distributed along the S gene and not concentrated in a ...
Ref: The Novel Coronavirus SARS‐CoV‐2: From a Zoonotic Infection to Coronavirus Disease‐19 (COVID19) [J Med Virol, 2020-05-29]Viral genome sequences are quality benchmarked by counting the missing bases,
... the transmission of SARS-CoV-2 (Shen et al., in submission). Phylogenetic Analysis and Reference Phylogenetic Trees. Viral genome sequences are quality benchmarked by counting the missing bases, the length deviation from the reference sequence (NC_045512.2), and the quality scores (if available). When ...
Ref: Children’s Hospital Los Angeles COVID-19 Analysis Research Database (CARD) - A Resource for Rapid SARS-CoV-2 Genome Identification Using Interactive Online Phylogenetic Tools [bioRxiv, 2020-05-23]SARS-CoV genome was found to be 99.8% similar to that from civet cats.
... SARS-CoV genome was found to be 99.8% similar to that from civet cats. The similarity of whole genome sequence of SARS CoV2 to pangolins is only 92% and 96.2% similarity to a bat SARS-related Coronavirus (SARSr-CoV; RaTG13) which is insufficient to prove beyond ...
Ref: SARS-CoV-2: Camazotz's Curse [Med J Armed Forces India, 2020-04-27]Consensus viral genome sequences from the Houston isolates were generated using the ARTIC nCoV-2019 bioinformatics pipeline.
... exploited to facilitate an enhanced public health response to this pandemic. SARS-CoV-2 genome sequence analysis. Consensus viral genome sequences from the Houston isolates were generated using the ARTIC nCoV-2019 bioinformatics pipeline. Publicly available genomes and metadata were acquired through GISAID on April 13, 2020 (16) . ...
Ref: Molecular Architecture of Early Dissemination and Evolution of the SARS-CoV-2 Virus in Metropolitan Houston, Texas [bioRxiv, 2020-05-03]We suggest that the first introduction of the virus to the country is earlier than the first reported case of infection.
... performed a phylogenetic analysis of the first thirty SARS-CoV-2 genomes isolated and sequenced in Turkey. We suggest that the first introduction of the virus to the country is earlier than the first reported case of infection. Virus genomes isolated from Turkey are dispersed among most types in the phylogenetic tree. We ...
Ref: Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey [bioRxiv, 2020-06-10]Results Phylogenetic analyses revealed the evolution of “genome-type clusters” and adaptive selection of “L” type SARS-CoV-2 strains
... strains. Secondary structure of RdRP/NSP12 protein was predicted with respect to the novel A97V mutation. Results Phylogenetic analyses revealed the evolution of “genome-type clusters” and adaptive selection of “L” type SARS-CoV-2 strains with genetic closeness to the bat SARS-like coronaviruses than pangolin or MERS-CoVs. With regards to ...
Ref: The novel Coronavirus enigma: Phylogeny and mutation analyses of SARS-CoV-2 viruses circulating in India during early 2020 [bioRxiv, 2020-05-26]In a phylogenetic tree, the Italian patient's sequence clustered with sequences from Germany while the tourist's sequence clustered with other European sequences.
... Chinese tourist visiting Rome and an Italian, were compared with sequences from Europe and elsewhere. In a phylogenetic tree, the Italian patient"s sequence clustered with sequences from Germany while the tourist"s sequence clustered with other European sequences. Some additional European sequences in the tree segregated outside the two clusters containing the patients" ...
Ref: Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe [Euro surveill, 2020]The analysis showed that the viral pp1ab has not changed in most isolates throughout the outbreak time,
... sarbecoviruses. In this short communication, we performed phylogenetic‐structural sequence analysis of pp1ab protein of SARS‐CoV‐2. The analysis showed that the viral pp1ab has not changed in most isolates throughout the outbreak time, but interestingly a deletion of 8 aa in the virulence factor nonstructural protein 1 was ...
Ref: An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human‐pathogenic coronavirus (SARS‐CoV‐2) [J Med Virol, 2020-03-20]The phylogenetic tree showed that the protein gene sequences were clearly clustered into three groups;
... The phylogenetic tree showed that the protein gene sequences were clearly clustered into three groups; SARS-152 CoV-2 related, SARS-CoV related and HKU3 related groups (Fig. 1A) . SARS-CoV and SARS-CoV-2 groups 153 formed a rigid monophyletic group with their own closest bat SARS-CoV related strains, ...
Ref: Spike protein binding prediction with neutralizing antibodies of SARS-CoV-2 [bioRxiv, 2020-02-27]Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2.
... insertions were identified in the spike protein of SARS-CoV-2 in comparison with that of SARS-CoV. Phylogenetic analyses of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of ...
Ref: Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach [Infect Genet Evol, 2020]Whole genome analysis of SARS-CoV-2 revealed ~96% genomic similarity with bat CoV (RaTG13)
... (COVID-19) by coronavirus (SARS-CoV-2) has threatened global public health and urged to investigate its source. Whole genome analysis of SARS-CoV-2 revealed ~96% genomic similarity with bat CoV (RaTG13) and clustered together in phylogenetic tree. Furthermore, RaTGl3 also showed 97.43% spike protein similarity with ...
Ref: Evidence of the Recombinant Origin and Ongoing Mutations in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) [bioRxiv, 2020-03-19]Phylogenetic analysis revealed that the six SARS-CoV-2 sequences found cluster within two clades representing the Washington state and European outbreaks.
Phylogenetic analysis revealed that the six SARS-CoV-2 sequences found cluster within two clades representing the Washington state and European outbreaks.
Ref: Metagenomic analysis reveals clinical SARS-CoV-2 infection and bacterial or viral superinfection and colonization [Clin Chem, 2020-05-07]SARS-CoV-2 is closely related to the Bat coronavirus isolate RaTG13, due to its homology in phylogenetics analysis 3 .
... on Taxonomy of Viruses named it as SARS-CoV-2 2 based on genomic and phylogenetics analysis. SARS-CoV-2 is closely related to the Bat coronavirus isolate RaTG13, due to its homology in phylogenetics analysis 3 . Hence, SARS-CoV-2 is a betacoronavirus with more homology to RATG13 (around 96% sequence identity) and ...
Ref: Genetic variants and source of introduction of SARS‐CoV‐2 in South America [J Med Virol, 2020-05-13]The phylogenies were estimated using MrBayes approach employing the GTR+I+G nucleotide substitution model.
... gene sequences depicting the evolutionary relationship among SARS-CoV-2, pangolin-CoV-2020, and other coronaviruses from different hosts. The phylogenies were estimated using MrBayes approach employing the GTR+I+G nucleotide substitution model. three individuals by mapping clean reads without ribosomes and host sequences to an inhouse virus ...
Ref: Are pangolins the intermediate host of the 2019 novel coronavirus (SARS-CoV-2)? [PLoS Pathog, 2020-05-14]NGS analysis from the TS specimens retrieved two complete genome sequences from case 1 and case 3.
... NGS of SARS-CoV-2 from India -Phylogenetic analysis and molecular characterization: NGS analysis from the TS specimens retrieved two complete genome sequences from case 1 and case 3. The complete genomic sequence data for case 2 could not be recovered due to the lower kappa concentration of the ...
Ref: Full-genome sequences of the first two SARS-CoV-2 viruses from India [Indian J Med Res, 2020-04-28]The phylogeny of the genomes yields some interesting results.
... family genomes, conferring unique infection, facilitation of transmission, virulence and immunogenic features to the virus. The phylogeny of the genomes yields some interesting results. Systematic gene level mutational analysis of the genomes has enabled us to identify several unique ...
Ref: Comparative analyses of SAR-CoV2 genomes from different geographical locations and other coronavirus family genomes reveals unique features potentially consequential to host-virus interaction and pathogenesis [bioRxiv, 2020-03-21]The first classification analysis subjects a query sequence to BLAST and AGA analysi.
... enables virus species assignments and the second, which is restricted to SARSr-CoV, includes phylogenetic analysis. The first classification analysis subjects a query sequence to BLAST and AGA analysi. AGA is a novel alignment method for nucleic acid sequences against annotated genomes from NCBI ...
Ref: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes [bioRxiv, 2020-02-02]A total of four breakpoints were detected in the F46 genome with strong P-values (o10 -30 ).
... of F46, we conducted recombination analysis using available genome sequences of human/civet and bat SARS-like CoVs. A total of four breakpoints were detected in the F46 genome with strong P-values (o10 -30 ). The results showed that F46 is a recombinant from Rs3367, LYRa11 and BJ01 lineages. ...
Ref: Discovery and genetic analysis of novel coronaviruses in least horseshoe bats in southwestern China [Emerg Microbes Infect, 2017-03-29]Phylogenetic Analysis 201 genome sequences were obtained from Gisaid and Genbank.
... Phylogenetic Analysis 201 genome sequences were obtained from Gisaid and Genbank. Specifically, we obtained 8 pangolin coronavirus sequences, 6 bat coronavirus sequences, 6 SARS coronavirus sequences, 3 MERS coronavirus sequences and all 177 SARS-nCoV-2 genome sequences available on 25 February 2020. ...
Ref: Master Regulator Analysis of the SARS-CoV-2/Human interactome [bioRxiv, 2020-03-17]A maximum-likelihood phylogenetic analysis based on the multiple sequence alignment of ORF were performed under the condition of separating each codon position.
... A maximum-likelihood phylogenetic analysis based on the multiple sequence alignment of ORF were performed under the condition of separating each codon position. Blue, green, and yellow branches indicate group TCT, TCC, and CTC respectively. Substitutions on the parsimony-informative sites were mapped to the corresponding branches. SARS-CoV-2 isolated from human formed a monophyletic ...
Ref: Phylogenetic analyses of the severe acute respiratory syndrome coronavirus 2 reflected the several routes of introduction to Taiwan, the United States, and Japan [bioRxiv, 2020-02-20]The SARS-CoV-2/Wuhan genome presented 708 75 UUU ssRNA fragments,
... at 4,012, with more than 113,702 confirmed cases in China, as well Table 1 ). The SARS-CoV-2/Wuhan genome presented 708 75 UUU ssRNA fragments, which represents 17.4% more fragments than the SARS-CoV 76 genome (1.17-fold change) and 8.1% more ...
Ref: Bioinformatic analysis and identification of single-stranded RNA sequences recognized by TLR7/8 in the SARS-CoV-2, SARS-CoV, and MERS-CoV genomes [Microbes Infect, 2020-04-30]RESULTS: The phylogenetic analysis demonstrated that SARS-CoV-2 formed a cluster with the bat CoV isolate RaTG13.
... suggest genomic regions which may have permitted the adaptation of SARS-CoV-2 to the human host. RESULTS: The phylogenetic analysis demonstrated that SARS-CoV-2 formed a cluster with the bat CoV isolate RaTG13. Possible CoV interspecies jumps among bat isolates were also observed. The phylogenetic tree reconstructed from ...
Ref: The Novel Coronavirus SARS-CoV-2: From a Zoonotic Infection to Coronavirus Disease-19 (COVID19) [J. med. virol, 2020]Analysis of evolutionary rates derived from comparative genomics, including insertions and deletions, can pinpoint functionally interesting sections of the viral genome.
... (white: no difference, red:nonsynonymous, green:synonymous, blue:noncoding, yellow:missing data due to unalignable, absent or unknown sequence). Analysis of evolutionary rates derived from comparative genomics, including insertions and deletions, can pinpoint functionally interesting sections of the viral genome. For instance, comparisons of SARS-CoV-2 with less pathogenic coronaviruses suggest features of the genome that ...
Ref: The UCSC SARS-CoV-2 Genome Browser [bioRxiv, 2020-05-04]the estimated Ka/Ks ratio is 1.008 or 1.094,
... In the evolution analysis of 622 or 3624 complete SARS-CoV-2 genomes, the estimated Ka/Ks ratio is 1.008 or 1.094, which is higher than that of SARS-CoV and MERS-CoV, and the time to the most recent common ancestor (tMRCA) ...
Ref: Evolution and molecular characteristics of SARS-CoV-2 genome [bioRxiv, 2020-05-15]In a few months, SARS-CoV-2 has caused thousands of disease cases and deaths in several countries.
... In December 2019, a novel human-infecting coronavirus (SARS-CoV-2) was recognized in China. In a few months, SARS-CoV-2 has caused thousands of disease cases and deaths in several countries. Phylogenetic analyses indicated that SARS-CoV-2 clusters with SARS-CoV in the Sarbecovirus subgenus and viruses related to SARS-CoV-2 were ...
Ref: Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses [Infect Genet Evol, 2020]Phylogenetic analyses revealed the cryptic introduction of at least 7 different SARS-CoV-2 lineages into California,
... 2020, using samples from 36 patients spanning 9 counties and the Grand Princess cruise ship. Phylogenetic analyses revealed the cryptic introduction of at least 7 different SARS-CoV-2 lineages into California, including epidemic WA1 strains associated with Washington State, with lack of a predominant lineage and ...
Ref: Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California [Science, 2020-06-08]Phylogenetic analysis showed two major clusters of SARS patients in Taiwan.
... two loci (positions 26203 and 27812) were segregated together as a specific genotype-T:T or C:C. Phylogenetic analysis showed two major clusters of SARS patients in Taiwan. CONCLUSION: We developed a very economical and rapid method to sequence the whole genome of ...
Ref: SARS-CoV Infection Was from at Least Two Origins in the Taiwan Area [Intervirology, 2005-03-24]Phylogenetic analysis showed the eight new sequences have close relationships with existing strains detected in camels and humans in Arabian Gulf countries.
... 3D structure of MERS-CoV spike glycoprotein to predict MERS-CoV epitopes and assess antibody binding affinity. Phylogenetic analysis showed the eight new sequences have close relationships with existing strains detected in camels and humans in Arabian Gulf countries. The 2019-nCov strain appears to have higher homology to both bat coronavirus and SARS-CoV than ...
Ref: Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia. [Viruses, 2020-06-03]In a phylogenetic tree, the Italian patient’s sequence clustered with sequences from Germany while the tourist’s sequence clustered with other European sequences.
... Chinese tourist visiting Rome and an Italian, were compared with sequences from Europe and elsewhere. In a phylogenetic tree, the Italian patient’s sequence clustered with sequences from Germany while the tourist’s sequence clustered with other European sequences. Some additional European sequences in the tree segregated outside the two clusters containing the patients’ ...
Ref: Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe [Euro Surveill, 2020-04-02]The analysis of SARS-CoV-2 genomes shows that numerous links among samples are still missing ( Figure S5 ).
... there are in the putative transmission chain connecting them, using a transmission matrix (16) . The analysis of SARS-CoV-2 genomes shows that numerous links among samples are still missing ( Figure S5 ). In such a scenario, it is not advisable to extrapolate conclusions on the origin and ...
Ref: A snapshot of SARS-CoV-2 genome availability up to 30th March, 2020 and its implications [bioRxiv, 2020-04-05]Our phylogenetic tree also clearly shows the separation of the two types (Fig. 5) .
... Our phylogenetic tree also clearly shows the separation of the two types (Fig. 5) . Viruses of the L type (blue) first clustered together, and likewise, viruses of the S type (red) were also more closely related to each other. Therefore, our whole-genome comparisons further ...
Ref: On the origin and continuing evolution of SARS-CoV-2 [Natl Sci Rev, 2020-03-03]The phylogenetic analysis of a total of 66 sequences (26 unique SARS-CoV-2 and 40 different coronavirus S glycoprotein sequences) was performed.
... The phylogenetic analysis of a total of 66 sequences (26 unique SARS-CoV-2 and 40 different coronavirus S glycoprotein sequences) was performed. The evolutionary distances showed that all the SARS-CoV-2 spike proteins cluster in the same node of the phylogenetic tree confirming the sequences are similar to Refseq YP_009724390 (Fig. 2) . ...
Ref: Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: a computational biology approach [bioRxiv, 2020-04-11]A phylogenetic tree was constructed from all genbank sequences and depict a mixed clustering of sequences between Asia, Europe and North America,
... Europe and North America origin, respectively and we aligned them against the SARS-CoV-2 reference genome. A phylogenetic tree was constructed from all genbank sequences and depict a mixed clustering of sequences between Asia, Europe and North America, supporting the existance of different viral signatures. (Fig. S1 ). Variant calling from these alignment ...
Ref: Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions [PeerJ, 2020-05-21]Our bioinformatic analysis showed a group of only six crRNAs can target more than 90% of all coronaviruses.
... cleaving SARS-CoV-2. The approach is effective in reducing respiratory cell viral replication for H1N1 IAV. Our bioinformatic analysis showed a group of only six crRNAs can target more than 90% of all coronaviruses. The PAC-MAN approach is potentially a rapidly implementable pan-coronavirus strategy to deal with emerging pandemic ...
Ref: Development of CRISPR as a prophylactic strategy to combat novel coronavirus and influenza [bioRxiv, 2020-03-14]Five clades could be identified and labelled, corresponding to the Full genome tree delivered by GISAID (see Figure 1 ).
... that occur during viral cultivation or the infection by multi-strain of coronavirus. Table S1 ). Five clades could be identified and labelled, corresponding to the Full genome tree delivered by GISAID (see Figure 1 ). In Figure 2 , we found two peaks in genome sequencing depths, one covering the ...
Ref: A High-Coverage SARS-CoV-2 Genome Sequence Acquired by Target Capture Sequencing [bioRxiv, 2020-04-15]We performed phylogenetic, split network, transmission network, likelihood‐mapping, and comparative analyses of the genomes.
... representative SARS‐related coronaviruses isolates from bats, with particular attention paid to the spike glycoprotein gene. We performed phylogenetic, split network, transmission network, likelihood‐mapping, and comparative analyses of the genomes. Based on Bayesian time‐scaled phylogenetic analysis using the tip‐dating method, we estimated the time to ...
Ref: Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2 [J Med Virol, 2020-03-11]Using MegaX (version 10.1.7) [27], we inferred all maximum likelihood (ML) phylogenetic trees.
... Sequence alignment was carried out using MUSCLE software [25] . Alignment accuracy was checked manually base by base. Gblocks [26] was used to process the gap in the aligned sequence. Using MegaX (version 10.1.7) [27], we inferred all maximum likelihood (ML) phylogenetic trees. ...
Ref: Probable Pangolin Origin of SARS-CoV-2 Associated with the COVID-19 Outbreak [Curr Biol, 2020-03-19]Phylogenetic study and analyses of mutation were based on the nine structural and non-structural genes of SARS-CoV-2 strains.
... sequences submitted from India were downloaded from the GISAID (39/46) or from NCBI (7/46) database. Phylogenetic study and analyses of mutation were based on the nine structural and non-structural genes of SARS-CoV-2 strains. Secondary structure of RdRP/NSP12 protein was predicted with respect to the novel A97V mutation. Results ...
Ref: The novel Coronavirus enigma: Phylogeny and mutation analyses of SARS-CoV-2 viruses circulating in India during early 2020 [bioRxiv, 2020-05-26]To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 sequences was assembled.
... 2 (SARS-CoV-2) has motivated an intensive analysis of its molecular epidemiology following its worldwide spread. To understand the early evolutionary events following its emergence, a dataset of 985 complete SARS-CoV-2 sequences was assembled. Variants showed a mean 5.5-9.5 nucleotide differences from each other, commensurate with a mid-range coronavirus ...
Ref: Rampant C->U hypermutation in the genomes of SARS-CoV-2 and other coronaviruses – causes and consequences for their short and long evolutionary trajectories [bioRxiv, 2020-05-01]This effort has allowed us to present novel phylogeographic inferences on the origin and dynamics of SARS-CoV-2 strains.
... high-quality (HQ) genomes, we devoted great effort to elucidate the most parsimonious phylogeny of SARS-CoV-2. This effort has allowed us to present novel phylogeographic inferences on the origin and dynamics of SARS-CoV-2 strains. In particular, we discovered a few dozen genomes (representing > 1/3 of the total database) ...
Ref: The impact of super-spreaders in COVID-19: mapping genome variation worldwide [bioRxiv, 2020-06-12]The resulting phylogeny reveals that RaTG13 is the closest relative of SARS-COV-2,
... The resulting phylogeny reveals that RaTG13 is the closest relative of SARS-COV-2, followed by pangolin_2019 and pangolin_2017, then CoVZC45 and CoVZXC21, and other SARS-related sequences as outgroups (Supplementary Fig. 1 ). According to general time reversible model, transition occurred more frequent than ...
Ref: The origin and underlying driving forces of the SARS-CoV-2 outbreak [J Biomed Sci, 2020-06-07]Results Our analysis suggests that Indian SARS-CoV-2 isolates are closely related to isolates reported from other parts of the world.
... sequences of isolates reported from other countries to identify the mutations occurred in Indian isolates. Results Our analysis suggests that Indian SARS-CoV-2 isolates are closely related to isolates reported from other parts of the world. Most ORFs are highly conserved; mutations were also detected in some ORFs. We found that ...
Ref: Genome analysis of SARS-CoV-2 isolates occurring in India: Present scenario. [Indian journal of public health, 2020-06-01]phylogenetic analysis indicated the isolate exhibited greater than 99.99% sequence identity with other publicly available SARS-CoV-2 genomes.
... characteristic of viruses of the family Coronaviridae. Whole genome sequencing of the viral isolate and phylogenetic analysis indicated the isolate exhibited greater than 99.99% sequence identity with other publicly available SARS-CoV-2 genomes. Within 24 hours of isolation, the first Australian SARS-CoV-2 isolate was shared with local and ...
Ref: Isolation and rapid sharing of the 2019 novel coronavirus (SARS-CoV-2) from the first patient diagnosed with COVID-19 in Australia [Med J Aust, 2020]Viral genome sequences are quality benchmarked by counting the missing bases, the length deviation from the reference sequence (NC_045512.2),
... the transmission of SARS-CoV-2 (Shen et al., in submission). Phylogenetic Analysis and Reference Phylogenetic Trees. Viral genome sequences are quality benchmarked by counting the missing bases, the length deviation from the reference sequence (NC_045512.2), and the quality scores (if available). When constructing different subsets of global or country-specific FASTA ...
Ref: Children’s Hospital Los Angeles COVID-19 Analysis Research Database (CARD) - A Resource for Rapid SARS-CoV-2 Genome Identification Using Interactive Online Phylogenetic Tools [bioRxiv, 2020-05-23]Clustering outcomes of the DBSCAN method via phylogenetic trees using Set 3 of reference sequences (Table 3) are presented in Fig. 8 .
... Clustering outcomes of the DBSCAN method via phylogenetic trees using Set 3 of reference sequences (Table 3) are presented in Fig. 8 . We first apply DBSCAN to reference sequences only, which results in 3 clusters and several outliers (Fig. 8A) . The search radius parameter ε is set equal to 0.55. As ...
Ref: Origin of Novel Coronavirus (COVID-19): A Computational Biology Study using Artificial Intelligence [bioRxiv, 2020-05-15]Our phylogenetic analysis revalidated the bat origin of the SARS-CoV-2 (Andersen et al., 2020) .
... bats and the majority of human infectious coronaviruses like SARS, MERS and also recent SARS-CoV-2. Our phylogenetic analysis revalidated the bat origin of the SARS-CoV-2 (Andersen et al., 2020) . While the clade 5 has sequences from Bovine coronaviruses, it also has subclades that are ...
Ref: Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease [J Biomol Struct Dyn, 2020-05-05]This study reports for the first time the natural infection of a cat in France (near Paris) probably through their owners.
... cat SARS-CoV-2 belongs to the phylogenetic clade A2a like most of the French human SARS-CoV-2. This study reports for the first time the natural infection of a cat in France (near Paris) probably through their owners. There is currently no evidence that cats can spread COVID-19 and owners should not abandon ...
Ref: First detection and genome sequencing of SARS-CoV-2 in an infected cat in France [J Biomol Struct Dyn, 2020]Phylogenetic analysis was performed using maximum likelihood (ML) and Bayesian trees, lineage classification and molecular clock calculations.
... from patients in KZN using ARCTIC protocols and assembling whole genomes using meticulous alignment methods. Phylogenetic analysis was performed using maximum likelihood (ML) and Bayesian trees, lineage classification and molecular clock calculations. Findings: The epidemic in South Africa has been very heterogeneous. Two of the largest provinces, ...
Ref: Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report [medRxiv : the preprint server for health sciences, 2020-05-30]we built a 172 phylogenetic tree based on the aa sequences of all the ACE2s (Figure 3A) .
... shown in Figure 1B To evaluate the phylogenetic relationship of the 20 ACE2s assessed above, we built a 172 phylogenetic tree based on the aa sequences of all the ACE2s (Figure 3A) . In the tree, 173 we observed the obvious branches of mammalian, bird, reptilia and fish ...
Ref: Receptor utilization of angiotensin converting enzyme 2 (ACE2) indicates a narrower host range of SARS-CoV-2 than that of SARS-CoV [bioRxiv, 2020-06-13]The tool has been able to correctly classify all the recently released SARS-CoV-2 genomes,
... Moreover, it can easily be updated to add new phylogenetic clusters if new outbreaks arise or if the classification nomenclature changes. The tool has been able to correctly classify all the recently released SARS-CoV-2 genomes, as well as all the 2002-2003 SARS outbreak sequences. ...
Ref: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes [Bioinformatics, 2020-02-28]Phylogenetic analyses of consensus genomes have enabled tracking of patterns of viral spread, both regionally 6 and across the globe 7 .
... Phylogenetic analyses of consensus genomes have enabled tracking of patterns of viral spread, both regionally 6 and across the globe 7 . Clear lineage-defining single nucleotide polymorphisms (SNPs) have emerged 8 , and it has been postulated that some of these might represent mutations that increase the fitness of the virus, raising ...
Ref: Shared SARS-CoV-2 diversity suggests localised transmission of minority variants [bioRxiv, 2020-06-02]the virus is not showing any sign of severing mutation or diversification rapidly.
... phylogenetic analysis of the available genomes of SARS-CoV-2 isolated from different sources also reveals that the virus is not showing any sign of severing mutation or diversification rapidly. Therefore the repurposed drug combinations could be used against SARS-CoV-2 on the pan-community level. Furthermore ...
Ref: In silico prediction of potential inhibitors for the Main protease of SARS-CoV-2 using molecular docking and dynamics simulation based drug-repurposing [J Infect Public Health, 2020-06-16]The genomic characteristics of SARS-CoV-2 have been elucidated using phylogenetic, 57 structural and mutational analyses by scientists across the globe [4] .
... The genomic characteristics of SARS-CoV-2 have been elucidated using phylogenetic, 57 structural and mutational analyses by scientists across the globe [4] . High-throughput 58 sequencing revealed that SARS-CoV-2 was a novel betacoronavirus which resembled CoV at around 79.5% sequence identity [5, 6] . A recent study indicated that SARS-CoV-2 was 60 96% ...
Ref: Identification of super-transmitters of SARS-CoV-2 [J Infect Public Health, 2020-04-22]it was found that SARS-CoV-2 felled within the subgenus Sarbecovirus of the genus Betacoronavirus
... was closer to SARS-like coronavirus in bat [19] . By analyzing genome sequence of SARS-CoV-2, it was found that SARS-CoV-2 felled within the subgenus Sarbecovirus of the genus Betacoronavirus and was closely related to two bat-derived SARS-like coronaviruses, bat-SL-CoVZC45 and bat-SL-CoVZXC21, but were relatively ...
Ref: SARS-CoV-2: an Emerging Coronavirus that Causes a Global Threat [Int J Biol Sci, 2020-03-15]The analysis confirmed that all SARS-CoV-2 S sequences clustered very closely with bat SARS-like sequences,
... and various export locations worldwide were analyzed along with representative members of lineages A-D betacoronaviruses. The analysis confirmed that all SARS-CoV-2 S sequences clustered very closely with bat SARS-like sequences, with the closest matching sequence corresponding to a bat coronavirus (bat-CoV) strain named Bat-SL-RaTG13. Other ...
Ref: Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop [J Mol Biol, 2020-04-19]For this analysis, we curated high quality genomes spanning ~3-month periods for the following groups:
... genome is, we first performed a side-by-side comparison of evolutionary dynamics between SARS-CoV-2 and SARS-CoV. For this analysis, we curated high quality genomes spanning ~3-month periods for the following groups: 11 genomes for early-to-mid epidemic SARS-CoV, 32 genomes for late epidemic SARS-CoV, and 46 genomes ...
Ref: SARS-CoV-2 is well adapted for humans. What does this mean for re-emergence? [bioRxiv, 2020-05-02]Phylogenetic analysis of the samples was performed as detailed previously following the standard protocol for analysis of SARS-CoV-2 genomes provided by Nextstrain.
... Phylogenetic analysis of the samples was performed as detailed previously following the standard protocol for analysis of SARS-CoV-2 genomes provided by Nextstrain. 13 , 14 The sequences were clustered using Augur, the phylodynamic pipeline provided by Nextstrain. 15 The sequences were aligned against the WH1 reference genome using MAFFT and spurious variant ...
Ref: A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates [bioRxiv, 2020-05-31]we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2,
... comparative analyses of the genomes. Based on Bayesian time-scaled phylogenetic analysis using the tip-dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS-CoV-2, which ranged from 22 to 24 November 2019 and 1.19 to 1.31 × 10-3 substitutions ...
Ref: Evolutionary history, potential intermediate animal host, and cross-species analyses of SARS-CoV-2 [J. med. virol, 2020]The phylogenetic tree was constructed by MEGA7 using the neighbour-joining (NJ) method with 1000 bootstrap replicates and visualized using FigTree.
... of 248 vertebrate species were downloaded from GenBank (File S1). Multiple sequence alignment was performed for the whole aa sequences of ACEs using MAFFT with a local alignment strategy FFT-NS-2. The phylogenetic tree was constructed by MEGA7 using the neighbour-joining (NJ) method with 1000 bootstrap replicates and visualized using FigTree. ...
Ref: Predicting the angiotensin converting enzyme 2 (ACE2) utilizing capability as the receptor of SARS-CoV-2 [Microbes Infect, 2020-03-19]Molecular phylogenetic analysis revealed that these RBD mutations cluster into distinct phyletic clades among global subtypes of SARS-CoV-2
... mutations were located in the Receptor Binding Domain (RBD) region that directly engages host ACE2. Molecular phylogenetic analysis revealed that these RBD mutations cluster into distinct phyletic clades among global subtypes of SARS-CoV-2 implying possible emergence of novel sublineages of the strain. Structure-guided homology modelling and docking analysis ...
Ref: Structural and Functional Implications of Spike Protein Mutational Landscape in SARS-CoV-2 [bioRxiv, 2020-06-13]our analysis results reflect clearly the chronological spread of SARS-CoV-2 around the globe.
... directly model the evolutionary relationship of the different SARS-CoV-2 genomes, e.g. via phylogenetic analysis. Nevertheless, our analysis results reflect clearly the chronological spread of SARS-CoV-2 around the globe. The advantages of our methodology compared to existing network analyses are twofold: First, our unsupervised ...
Ref: Unsupervised cluster analysis of SARS-CoV-2 genomes reflects its geographic progression and identifies distinct genetic subgroups of SARS-CoV-2 virus [bioRxiv, 2020-05-06]Nevertheless, our analysis results reflect clearly the chronological spread of SARS-CoV-2 around the globe.
... to directly model the evolutionary relationship of the different SARS-CoV-2 genomes, e.g. via phylogenetic analysis. Nevertheless, our analysis results reflect clearly the chronological spread of SARS-CoV-2 around the globe. The advantages of our methodology compared to existing network analyses are twofold: First, our unsupervised ...
Ref: Unsupervised cluster analysis of SARS-CoV-2 genomes reflects its geographic progression and identifies distinct genetic subgroups of SARS-CoV-2 virus [bioRxiv, 2020-05-06]The result of the phylogenetic and mutational analysis performed by AGA is available in a detailed report.
... The result of the phylogenetic and mutational analysis performed by AGA is available in a detailed report. This report contains an interactive phylogenetic tree and genome mapper (Supplementary Figure 1) . It also presents the virus species and cluster assignments and a detailed table that provides information ...
Ref: Genome Detective Coronavirus Typing Tool for rapid identification and characterization of novel coronavirus genomes [bioRxiv, 2020-02-02]This result revealed a significant degree of genetic diversification of SARS-CoV-2 strains.
... of SARS-CoV-2 genomes were analyzed, three distinct genetic clades were found (see Fig. 3 ). This result revealed a significant degree of genetic diversification of SARS-CoV-2 strains. Moreover, co-circulation of strains from different genetic clades was observed in different countries (Fig. 3) ...
Ref: Evidence of Increasing Diversification of Emerging SARS‐CoV‐2 Strains [J Med Virol, 2020-05-15]The evolutionary structure of the 181 isolates as determined by the phylogenetic tree reveals three major clusters (C1-C3) ( Figure 2 ).
... The evolutionary structure of the 181 isolates as determined by the phylogenetic tree reveals three major clusters (C1-C3) ( Figure 2 ). The C1 cluster mainly represents Wuhan and isolates captured early on; C2 and C3 contain later isolates, such as Sydney/3, Australia/VIC01 and France/IDF0372 in C2 and Australia/NSW01, Australia/QLD01-3, Australia/VIC02 and ...
Ref: Supporting pandemic response using genomics and bioinformatics: A case study on the emergent SARS‐CoV‐2 outbreak [Transbound Emerg Dis, 2020-05-25]We generated multiple sequence alignments and phylogenetic trees for representative spike proteins of SARS CoV and SARS CoV-2 from various host sources
... SARS CoV-2 via their glycosylated spike proteins recognize the human angiotensin converting enzyme-2 (ACE-2) receptor. We generated multiple sequence alignments and phylogenetic trees for representative spike proteins of SARS CoV and SARS CoV-2 from various host sources in order to analyze the specificity in SARS CoV-2 spike proteins required for causing infection ...
Ref: Evolutionary relationships and sequence-structure determinants in human SARS coronavirus-2 spike proteins for host receptor recognition. [Proteins, 2020-06-16]The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis.
... of spike protein revealed that Bat coronavirus have a close evolutionary relationship with circulating SARS-CoV-2. The genetic variation analysis data presented in this study can help a better understanding of SARS-CoV-2 pathogenesis. Based on results reported herein, potential inhibitors against S protein can be designed by considering ...
Ref: Exploring the genomic and proteomic variations of SARS-CoV-2 spike glycoprotein: A computational biology approach [Infect Genet Evol, 2020]Phylogenetic analysis, natural selection investigation and genome recombination analysis 23 were performed.
... region. Phylogenetic analysis, natural selection investigation and genome recombination analysis 23 were performed. Our analysis showed that all Saudi SARS-CoV-2 sequences are of the same origin 24 and closer proximity to bat SARS-like CoVs, followed by SARS-CoVs, however quite distant to 25 ...
Ref: Insights into molecular evolution recombination of pandemic SARS-CoV-2 using Saudi Arabian sequences [bioRxiv, 2020-05-13]Our phylogenetic tree shows that all camel and human MERS-CoVs are clustered together.
... we performed the phylogenetic analysis for these sequences with two SRAS-CoVs serving as the outgroup. Our phylogenetic tree shows that all camel and human MERS-CoVs are clustered together. The bat and hedgehog MERS-CoVs formed a basal paraphyletic group to all camel and human ...
Ref: Evolutionary Dynamics of MERS-CoV: Potential Recombination, Positive Selection and Transmission [Sci Rep, 2016-05-04]The performed study reveals the phylogenetic relationships between SARS-CoV-2 and CoV genomes obtained from bats from different parts of the world.
... The performed study reveals the phylogenetic relationships between SARS-CoV-2 and CoV genomes obtained from bats from different parts of the world. Moreover, we The performed mutation analysis demonstrated several AA changes which were localized in the S region of the SARS-CoV-2 genome compared to RaTG13 bat strain. ...
Ref: The Novel Coronavirus SARS‐CoV‐2: From a Zoonotic Infection to Coronavirus Disease‐19 (COVID19) [J Med Virol, 2020-05-29]phylogenetic relationship with other selected high-quality samples from The Genome Variation Map (GVM).
... these high-quality sequences, we discuss the heterozygosity and viral expression during coronavirus replication, and its phylogenetic relationship with other selected high-quality samples from The Genome Variation Map (GVM). Therefore, this universal SARS-CoV-2 enrichment probe system can capture and enrich SARS-CoV-2 viral sequences selectively ...
Ref: High-Coverage SARS-CoV-2 Genome Sequences Acquired by Target Capture Sequencing. [Journal of medical virology, 2020-06-03]Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained.
... Results: Three cases with a travel history from Wuhan, China, were confirmed positive for SARS-CoV-2. Almost complete (29,851 nucleotides) genomes of case 1, case 3 and a fragmented genome for case 2 were obtained. The sequences of Indian SARS-CoV-2 though not identical showed high (~99.98%) identity with Wuhan seafood ...
Ref: Full-genome sequences of the first two SARS-CoV-2 viruses from India [Indian J Med Res, 2020]This analysis required over 150 hours to obtain enough samples from the joint posterior,
... on a smaller SARS-CoV-2 data set (2,795 genomic sequences) using BEAST 1.10 (data not shown). This analysis required over 150 hours to obtain enough samples from the joint posterior, while using the latest GPU accelerated implementations 17 on 15 parallel runs. With a combined ...
Ref: A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages [bioRxiv, 2020-05-09]Early phylogenetic studies on SARS-CoV-2 genomic sequences revealed that it clustered closely with sequences originating from SARS-like sequences from bats,
... Early phylogenetic studies on SARS-CoV-2 genomic sequences revealed that it clustered closely with sequences originating from SARS-like sequences from bats, within lineage B of the Betacoronavirus genus. Lineage A groups prototypical coronaviruses such as murine hepatitis virus (MHV) and human coronaviruses HCoV-HKU1 and HCoV-OC43. The other highly pathogenic coronavirus, MERS-CoV ...
Ref: Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop [J Mol Biol, 2020-04-19]