Journal: Viruses

Article Title: Genetic Analysis of the Complete S1 Gene in Japanese Infectious Bronchitis Virus Strains

doi: 10.3390/v14040716

Figure Lengend Snippet: Similarity analysis ( a ) and BootScan analysis ( b ) on the putative recombinant JP/Nagasaki/2013 strain. Reference strains JP/Wakayama/2003 (GI-13, green) and JP/Shimane/98 (GI-19, blue) strains were used as putative parental strains. Additionally, the M41 strain (G1-1, red) was used as an outlier sequence. The y -axis indicates the percentage of identity within a 200-bp wide sliding window centered on the plotted position, with a step size of 20 bp between plots.

Article Snippet: Subsequently, BootScan analysis was conducted, employing a subprogram embedded in SimPlot, in addition to signals of 70% or more of the observed permuted trees to indicate potential recombination events [ , ].

Techniques: Recombinant, Sequencing

Journal: Viruses

Article Title: Clinical, Laboratory, and Molecular Epidemiology of an Outbreak of Aseptic Meningitis Due to a Triple-Recombinant Echovirus in Ashburton, New Zealand

doi: 10.3390/v14040658

Figure Lengend Snippet: Whole genome Simplot BootScan analysis with the query sequence of strain NZ/Ashburton/17WQ2027G/2017-08-20 (accession number MW586892) compared to Echovirus E6 (accession number KP289439), E11 (accession number KP294524), and E30 (accession number KY888274) reference sequences. ( A ) Similarity plot analysis, ( B ) Bootscanning analysis on the putative recombinant strain and its parental sequences. The enterovirus genomic organization is shown in the top.

Article Snippet: An additional Simplot BootScan analysis of an alignment of the NZ Echovirus E30 MW586892 with available whole genome sequences of the enterovirus prototype strains described in [ ] is presented in .

Techniques: Sequencing, Recombinant

Journal: Virus Evolution

Article Title: The tissue virome of black-spotted frogs reveals a diversity of uncharacterized viruses

doi: 10.1093/ve/veae062

Figure Lengend Snippet: Genomic structure, recombination prediction, and phylogenetic analyses of FV3/CHN2022/Frog/JKCDN22. (a) Genomic structure comparison of FV3/JKCDN22 with a FV3 representative. The highlighted ORFs are DNAp and MCP genes, which were used in the phylogenetic analyses. (b) Recombination analysis of FV3/JKCDN22 and its three closest relatives. Similarity plots (the upper inset) and bootscan analyses (the lower inset) were conducted with FV3/JKCDN22 as the query. The gray portion indicates the location where recombination happened. (c) The ML phylogenies of FV3/JKCDN22 based on DNAp and NTPase genes.

Article Snippet: The significant recombination event was exhibited using similarity plot and bootscan analyses using SimPlot version 3.5.1.

Techniques: Comparison

Journal: Viruses

Article Title: Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada

doi: 10.3390/v12101096

Figure Lengend Snippet: Bootscan analysis of recombinant CAstV sequences for confirming recombination was performed using Simplot program v3.5.1. Each analysis considers different parent sequences (different colors) plotted in a graph considering in the vertical-axis Percentage of permuted trees, and on the horizontal axis, position on the genome of the query sequence. Recombinant CAstV query sequences are 19-0981/CA-SK/19 ; Biii-ANAND/IN/2016 ; Bi-GDYHTJ718-6/CN/2018 ; 18-0942/CA-SK/18 ; 19-0935/CA-SK/19 ; CC_CkAstV/US/2014 ; and Bii-GA2011/US/2011 .

Article Snippet: Putative recombination sequences were further investigated by using Bootscan analysis within the Simplot program version 3.5.1 [ ], using the following parameters: window size = 400 bp; step size = 40 bp; GapStrip = On; Repetitions = 100; Kimura 2-parameter substitution model; T/t = 2; and using the neighbor-joining method [ , , ].

Techniques: Recombinant, Sequencing

Journal: Viruses

Article Title: Chicken Astrovirus (CAstV) Molecular Studies Reveal Evidence of Multiple Past Recombination Events in Sequences Originated from Clinical Samples of White Chick Syndrome (WCS) in Western Canada

doi: 10.3390/v12101096

Figure Lengend Snippet: CAstV recombinant sequences and parents/parent-like sequences detected by 6 recombination methods in RDP5, ML phylogenetic trees, and Bootscan analysis in SimPlot software.

Article Snippet: Putative recombination sequences were further investigated by using Bootscan analysis within the Simplot program version 3.5.1 [ ], using the following parameters: window size = 400 bp; step size = 40 bp; GapStrip = On; Repetitions = 100; Kimura 2-parameter substitution model; T/t = 2; and using the neighbor-joining method [ , , ].

Techniques: Recombinant, Software, Sequencing