nucleotide identity matrix  (Bioedit Company)

Journal: Frontiers in Microbiology

Article Title: The genetic and proliferation characterization analysis of novel coxsackievirus A12 in Beijing, China

doi: 10.3389/fmicb.2025.1665461

Figure Lengend Snippet: Viral nucleotide loads in growth curve cultures. (A) The dynamic range and linearity of the CVA12 real-time assay. The threshold cycle (Ct) values (x-axis) were plotted against tenfold dilutions of CVA12. The parameters of the slope and y-intercept are given by the equation. R 2 , regression coefficient. (B) The levels of CVA12 RNA in the culture supernatants at 6, 12, 24, 48 and 72 hpi were determined by qRT-PCR ( n = 3 biological replicates). The 100 TCID 50 of CVA12 stock were used to infect RD and Hep-2 cell lines, respectively. (C) The levels of CVA12 RNA in the cell lysates at 6, 12, 24, 48 and 72 hpi were determined by qRT-PCR ( n = 3 biological replicates). The 100 TCID 50 of CVA12 stock were used to infect RD and Hep-2 cell lines, respectively. (D) Virus titer detection in RD and Hep-2 cell lines infected with 100 TCID 50 of CVA12 stock. The culture were collected at 6, 12, 24, 48 and 72 h post-infection (hpi). All the data are expressed as the mean ± SD of three biological replicates. Statistical significance was determined by ordinary one-way analysis of variance (ANOVA) with multiple comparisons methods using the GraphPad Prism software. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001.

Article Snippet: A nucleotide identity matrix was generated using BioEdit software.

Techniques: Quantitative RT-PCR, Virus, Infection, Software

Journal: Frontiers in Microbiology

Article Title: The genetic and proliferation characterization analysis of novel coxsackievirus A12 in Beijing, China

doi: 10.3389/fmicb.2025.1665461

Figure Lengend Snippet: The phylogenetic characteristics of CVA12. (A) Nucleotide distances between the different groups and within each group. (B) Principal components of CVA12 sequences with genogroups used as prior groups based on VP1 coding region. Different colors represent prior genogroups, and individual sequences are marked as dots. Results of eigenvalues analysis (PCA and DA) displayed in the inset. Axes represent the frst two principles. PCA, principal components analysis; DA, discriminant analysis. (C) Maximum likelihood phylogenetic tree based on the full-length VP1 coding region, with 1,000 bootstraps and SH-like approximate likelihood ratio tests (SH-aLRT) replicates at each node. The scale bar indicates nucleotide substitutions per site per year. The red colors represent the five CVA12 strains in this study.

Article Snippet: A nucleotide identity matrix was generated using BioEdit software.

Techniques:

Journal: Viruses

Article Title: Epidemiology of Hand, Foot, and Mouth Disease and Genetic Characterization of Coxsackievirus A16 in Shenyang, Liaoning Province, China, 2013–2023

doi: 10.3390/v16111666

Figure Lengend Snippet: ( A ) Maximum likelihood tree constructed based on 240 CVA16 VP1 sequences in Shenyang from 2013 to 2023. Bootstrap values are indicated by solid circles, and the circle size represents the size of the bootstrap value. The outer circle represents CVA16 from different years, and CVA16 sequences from Shenyang are marked with an asterisks. The inner circle represents different genogroups/sub-genogroups marked with different colors. ( B ) Time-scaled phylogenetic tree based on complete VP1 nucleotide sequences of CVA16 strains in Shenyang. ( C ) Genetic distance matrix of CVA16 nucleotide sequences from different years.

Article Snippet: The identity matrix of nucleotide sequences was generated using BioEdit (version 7.0.9.0) [ ].

Techniques: Construct

Journal: PLoS ONE

Article Title: Insights into the genetic diversity, recombination, and systemic infections with evidence of intracellular maturation of hepadnavirus in cats

doi: 10.1371/journal.pone.0241212

Figure Lengend Snippet: ( A ) The DCH CP54S THA/2016 isolated in this study and DCH Sydney2016 (MH307903) from Australia served as the putative major and minor parents. ( B ) The potential recombination event was detected in the core protein gene and was supported by similarity and bootscan analysis, which indicated that DCH CP54S THA/2016 (blue line) served as the main template of the whole DCH genome, and then the genome sequence was replaced by the sequence from the DCH Sydney2016 at most of the C gene. The DCH CP23S/2016 isolate served as the query. The y-axis indicated the percentage of nucleotide identity and permutated trees for the similarity plot and boot scanning, respectively, within a 200 bp-wide window with a 20-bp step size between plots. ( C ) The ML phylogenetic trees of the recombinant DCH23S THA/2016 strains (●) and its major (▲) and minor (▼) putative parent strains over three different segments. Bootstrap (1000 replications) values over 50% are shown for each node.

Article Snippet: The sequences of the nine obtained Thai DCH strains were then compared with the three available DCH strains using a pairwise nucleotide identity matrix software embedded in BioEdit.

Techniques: Isolation, Sequencing, Recombinant