Journal: Poultry Science

Article Title: Recombination with a vaccine strain drives the evolution of a more virulent phenotype in avian infectious bronchitis virus

doi: 10.1016/j.psj.2026.106747

Figure Lengend Snippet: Genomic characterization and recombination analysis of IBV. (A) Schematic diagram of the IBV genome. (B-D) Recombination analysis of the complete genome sequences of SX/2407 (B), SX/2409 (C), and SX/2410 (D) was performed using BootScan. The analysis was conducted with SimPlot v3.5.1, using a window size of 500 bp and a step size of 50 bp. The identified recombination sites correspond to the full genome map in (A).

Article Snippet: To validate the results, credible recombination events inferred by RDP4 were re-analyzed using the BootScan method in SimPlot software to verify the recombination relationships between the recombinant strain, major parent, and minor parent.

Techniques:

Journal: Viruses

Article Title: Next-Generation Sequencing Reveals Continued Circulation of Rare HIV-1 Subtypes in the Democratic Republic of the Congo and Refines the Estimate of the Emergence Dates of Three Subtypes

doi: 10.3390/v18020268

Figure Lengend Snippet: ( A ) Subtype H branch of the ML tree from B. The red dot and number indicate the basal node of the branch with bootstrap value. ( B ) Similarity plot of the genome from specimen 146 (most basal H on the tree) comparing similarity between subtypes. ( C ) Bootscan of the genome from specimen 146 showing no evidence of recombination between subtypes. For SimPlot analysis in ( B , C ), all pure H subtypes from this study were included as references, and a window of 500 bp and step of 50 bp were used. For bootscanning, 1000 bootstrap replicates were used. To more clearly indicate sequences generated in this study, “_drc” was added to the specimen IDs in the figure. Subtype reference consensus sequences were used for SimPlot and Bootscan analyses.

Article Snippet: Sequences branching basal to reference subtypes/CRFs were analyzed for evidence of recombination using Simplot v3.5.1 ( https://sray.med.som.jhmi.edu/SCRoftware/SimPlot/ , accessed on 15 July 2025) for similarity plot and bootscanning analyses as previously described [ , ].

Techniques: Generated

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: