Journal: Virulence

Article Title: Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men

doi: 10.1080/21505594.2022.2106021

Figure Lengend Snippet: Recombination analyses of the near-full-length HIV-1 genome sequence (790–8795 in the HXB2 genome) of sample CY533 used as a representative sample to illustrate the intersubtype mosaic structure of the CRF91_cpx strain. The recombination analyses were conducted against a reference dataset of HIV-1 group M subtypes (A, B, C, D, F, G, H, J and K) and CRF02_AG downloaded from the Los Alamos HIV Sequence Database ( http://www.hiv.lanl.gov ) as well as the top two CRF02_AG BLAST hits. (A) The upper left diagram in this scheme illustrates the genomic map of sample CY533, which was generated by the Recombinant HIV-1 Drawing Tool ( https://www.hiv.lanl.gov/content/sequence/DRAW_CRF/recom_mapper.html ). The numbers above the diagram indicate the intersubtype recombination breakpoints in accordance with the HXB2 numbering. The near full-length HIV-1 genome was divided into seven fragments based on the six recombination breakpoints, showing its unique mosaic structure. The subtype origin of each fragment is colour coded in accord with informative analyses, and the colour coding is defined in the middle of the scheme. The middle left diagram displays the similarity plot analysis, in which the y-axis represents the percent similarity of the query sequence to the reference dataset. The bottom left diagram displays the bootscan analysis, where the y-axis represents the bootstrap support value. The x-axes of both diagrams represent the nucleotide positions in accordance with HXB2 numbering. The dotted horizontal line specifies the 70% bootstrap support value, which was considered to be definitive for subtype origin. The colour coding used for the similarity plot and bootscan analyses is identical to the colour coding of the genomic map. The similarity plot and bootscan analyses were performed in SimPlot v3.5.1 software. The parameters included a sliding window of 400 nucleotides, overlapped by 40 nucleotides, with 1,000 bootstrap replicates. (B) The right diagram illustrates the subregion confirmatory neighbour-joining tree analyses performed with MEGA X software. The neighbour-joining trees were constructed for each of the seven fragments characterized by the similarity plot and bootscan analyses. The phylogenetic analyses employed the Kimura two-parameter nucleotide substitution model with 1,000 bootstrap replicates to assess the reliability of the phylogenetic clustering results. A bootstrap support value of 70% was considered definitive for subtype origin. The region of the nucleotide sequences encoding each of the seven fragments is denoted above each tree with respect to HXB2 numbering. The dotted line ending with a black dot represents the query sequence of each tree. The colour coding used for the neighbour-joining trees is identical to the colour coding of the genomic map, similarity plot and bootscan analyses.

Article Snippet: The three fragments were separated by the two putative intersubtype recombination breakpoints, as identified with SimPlot v3.5.1 software [ ].

Techniques: Sequencing, Generated, Recombinant, Software, Construct

Journal: Virulence

Article Title: Characterization of a novel HIV-1 circulating recombinant form, CRF91_cpx, comprising CRF02_AG, G, J, and U, mostly among men who have sex with men

doi: 10.1080/21505594.2022.2106021

Figure Lengend Snippet: Recombination analyses of the near-full-length HIV-1 genome sequence (790–8795 in the HXB2 genome) of sample CY467 used to illustrate the intersubtype mosaic structure of the URF of the CRF91_cpx strain, “Rec. of 91_cpx, B.” The recombination analyses were conducted against a reference dataset of HIV-1 group M subtypes (A, B, C, D, F, G, H, J and K) and CRF02_AG downloaded from the Los Alamos HIV Sequence Database ( http://www.hiv.lanl.gov ) as well as the top two CRF02_AG BLAST hits. (A) The upper left diagram in this scheme illustrates the genomic map of sample CY467, which was generated by the Recombinant HIV-1 Drawing Tool ( https://www.hiv.lanl.gov/content/sequence/DRAW_CRF/recom_mapper.html ). The numbers above the diagram indicate the intersubtype recombination breakpoints in accordance with HXB2 numbering. The near full-length HIV-1 genome was divided into nine fragments based on the eight recombination breakpoints presenting its unique mosaic structure. The subtype origin of each fragment is colour coded in accord with informative analyses, and the colour coding is defined in the middle of the scheme. The middle left diagram displays the similarity plot analysis, where the y-axis represents the percent similarity of the query sequence to the reference dataset. The bottom left diagram displays the bootscan analysis, where the y-axis represents the bootstrap support value. The x-axes of both diagrams represent the nucleotide positions in accordance with HXB2 numbering. The dotted horizontal line specifies the 70% bootstrap support value, which was considered to be definitive for subtype origin. The colour coding used for the similarity plot and bootscan analyses is identical to the colour coding of the genomic map. The similarity plot and bootscan analyses were performed with SimPlot v3.5.1 software. The parameters included a sliding window of 400 nucleotides, overlapped by 40 nucleotides, with 1,000 bootstrap replicates. (B) The right diagram illustrates the subregion confirmatory neighbour-joining tree analyses performed with MEGA X software. The neighbour-joining trees were constructed for each of the nine fragments characterized by the similarity plot and bootscan analyses. The phylogenetic analyses employed the Kimura two-parameter nucleotide substitution model with 1,000 bootstrap replicates to assess the reliability of the phylogenetic clustering results. A bootstrap support value of 70% was considered to be definitive for subtype origin. The region of the nucleotide sequences encoding each of the nine fragments is denoted above each tree with respect to HXB2 numbering. The dotted line ending with a black dot represents the query sequence of each tree. The colour coding used for the neighbour-joining trees is identical to the colour coding of the genomic map, similarity plot and bootscan analyses.

Article Snippet: The three fragments were separated by the two putative intersubtype recombination breakpoints, as identified with SimPlot v3.5.1 software [ ].

Techniques: Sequencing, Generated, Recombinant, Software, Construct

Journal: Viruses

Article Title: Recombination and Mutation in a New HP-PRRSV Strain (SD2020) from China

doi: 10.3390/v15010165

Figure Lengend Snippet: Recombination analyses on SD2020 genome. ( A ) Recombination analysis was conducted and a similarity map was generated by Simplot 3.5.1 software with window size of 200 bp and step size of 20 bp. SD2020 as query sequence, was used in similarity plot analysis. ( B ) Schematic diagram of SD2020 PRRSV genomes. ( C ) Recombination regions were shown with segments of different colors and the four recombination breakpoints were detected by RDP v4.1016. Red segments represent the sequence of VR-2332 strain. Blue segment represents the sequence of JXA1-P80 strain. Green segment represents the sequence of JXA1 strain. ( D ) Individual phylogenies reconstructed from non-recombinant fragments identified by RDP v4.1016, with the JXA1-like strain labelled with a blue background and the VR2332 strain labelled with a red background. The phylogenetic tree was constructed by using the neighbor-joining method with 1000 bootstrap replicates in the PHYLIP 3.65 software package.

Article Snippet: The recombination analysis (similarity plot in SIMPLOT v3.5.1) supported that the SD2020 has a recombinant genome ( A).

Techniques: Generated, Software, Sequencing, Recombinant, Construct

Journal: PLoS ONE

Article Title: Analysis of HIV-1 Protease Gene Reveals Frequent Multiple Infections Followed by Recombination among Drug Treated Individuals Living in São Paulo and Santos, Brazil

doi: 10.1371/journal.pone.0084066

Figure Lengend Snippet: We used the Neighbor-Joining method with K2P and 1000 bootstrap replicates. This analysis was performed using the software Simplot v3.5.1, with a window of 75 bp and 5 bp increments.

Article Snippet: Inter-subtype recombinants and breakpoints were investigated using Bootscan as implemented in the Simplot package v3.5.1 .

Techniques: Software