Journal: Scientific Reports

Article Title: Whole-genome analysis of CVA4 in children with herpangina in two cities of Shandong, China

doi: 10.1038/s41598-026-39455-x

Figure Lengend Snippet: Similarity plot and bootscan analyses of the CVA4 strains in this study with the reference strains. Similarity plot and bootscan profiles were indistinguishable among isolates YT13, LY10, LY25, LY32 and LY36; therefore, only the representative plots for LY10 are shown.

Article Snippet: To validate these events and precisely map the recombination breakpoints, similarity plot and bootscan analyses were subsequently performed using Simplot (v3.5.1) (Fig. ).

Techniques:

Journal: Microbial Genomics

Article Title: Full-genome analysis of emerging Coxsackievirus B4 genotype D strains associated with herpangina in eastern China

doi: 10.1099/mgen.0.001656

Figure Lengend Snippet: ( a ) Recombination detection plot of Z168 by using RDP4. ( b ) Recombination detection plot of Z296 by using RDP4. ( c ) Simplot of general recombination events identified in P2 and P3 regions of the Coxsackievirus B4 full-length sequence Z168 isolated in the study, as compared to dataset CVB4+CVB-like CDS, by using SimPlot. ( d ) Simplot of general recombination events identified in the P2 and P3 regions of the Coxsackievirus B4 full-length sequence Z296 isolated in the study, as compared to dataset CVB4+CVB-like CDS, by using SimPlot. ( e ) Bootscan plot of Z168 and its inferred major and minor parental strains as determined by RDP4 analysis. ( f ) Bootscan plot of Z296 and its inferred major and minor parental strains as determined by RDP4 analysis.

Article Snippet: To validate the recombination signals, bootscan analysis was performed using SimPlot software v3.5.1.

Techniques: Sequencing, Isolation

Journal: Microorganisms

Article Title: Phylogenetic Characteristics and High Prevalence of a Merbecovirus in Hedgehogs from Greenspace of a Metropolis, China

doi: 10.3390/microorganisms14010083

Figure Lengend Snippet: Analysis of the BJ-HKU31 spike (S) protein. ( A ) Detection of a possible recombination event was conducted using bootscan analysis. A whole genome sequence similarity plot was performed using Simplot (v3.5.1), with a window size of 1000 bp and a step size of 200 bp. A bat coronavirus (GenBank accession no. KC869678 ) served as the query sequence and was compared against other coronaviruses, including Ea -HedCoV HKU31 (red, this study), BtVs-BetaCoV/SC2013 (green), and bat coronavirus HKU4 (yellow). ( B ) Amino acid sequence alignments of receptor-binding domain (RBD) sequences of hedgehog coronaviruses. The sequence of MERS-CoV (GenBank accession no. NC_019843 ) was used as the reference sequence. Different colors are used to highlight distinct residues, red asterisks mark conserved residues (functionally critical in MERS-CoV).

Article Snippet: To assess potential recombination events in the genomes of hedgehog CoVs identified in this study, Bootscan analysis was performed using SimPlot (v3.5.1; SCRoftware, Johns Hopkins University School of Medicine, Baltimore, MD, USA) with a 1000 bp sliding window and 200 bp step size, based on the Kimura two-parameter model and the Neighbor-Joining method.

Techniques: Sequencing, Binding Assay