Journal: Microorganisms

Article Title: A New Gilliam Genotypic Variant of Orientia tsutsugamushi in Human Scrub Typhus Cases from South India

doi: 10.3390/microorganisms13122670

Figure Lengend Snippet: Bootscan analysis of 56-kDa with the following parameters: Kimura 2-parameter (K2P) model, 200 bp window, 20 bp step size, and 500 bootstrap replicates. ( a ). Ot-TJTN isolate demonstrated evidence of sequence transfer involving TA716 and Kato strains; ( b ) Karp clade carries recombinant segments derived from both Karp and Ikeda lineages. Together, these patterns highlight the genetic exchange contributing to antigenic diversity in the 56-kDa protein. The dashed vertical lines mark the recombination breakpoints within the 56-kDa gene region.

Article Snippet: The two clades in 56-kDa were further investigated for potential genetic exchange breakpoints by using the bootscan analysis in Simplot++.

Techniques: Sequencing, Recombinant, Derivative Assay

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:

Journal: Scientific Reports

Article Title: Emerging recombination of the C2 sub-genotype of HFMD-associated CV-A4 is persistently and extensively circulating in China

doi: 10.1038/s41598-019-49859-7

Figure Lengend Snippet: Similarity plot and bootscan analysis of representative CV-A4 strains of HFMD circulating in China with the EV-A prototype strains. A sliding window of 500 nucleotides moving in 20 nucleotide increments was used in this analysis. ( A ) Mild case of C2, 11–60-CQ-CHN-2011. ( B ) Severe case of C2, 16–5-HuN-CHN-2016. ( C ) C5, 14–41-JX-CHN-2014. ( D ) C5, 16–128-JX-CHN-2016.

Article Snippet: Potential recombination between CV-A4 and other HEV-A strains was determined with similarity plots and the bootscan method (version 3.5.1; Stuart Ray, Johns Hopkins University, Baltimore, Maryland, USA) .

Techniques: