Journal: Poultry Science

Article Title: Isolation and characterization of a duck reovirus strain from mature ducks in China

doi: 10.1016/j.psj.2022.102345

Figure Lengend Snippet: Sequence and analysis of the entire GL18 strain genome. (A) Phylogenetic analysis of σC gene sequences of ARVs isolates with the maximum-likelihood method. (B) Amino acid sequence alignment of the σC protein of GL18 with Chinese DRV isolates. (C) Gene recombination event prediction by RDP. (D) Verification of gene recombination by Simplot.

Article Snippet: The Recombination Detection Program ( RDP ) and SimPlot program analyses suggested potential genetic recombination events in the M2 segments.

Techniques: Sequencing

Journal: Indian Journal of Medical Microbiology

Article Title: TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2

doi: 10.1016/j.ijmmb.2021.01.003

Figure Lengend Snippet: (A &B): Genomic organization and similarity analysis: (A): Genomic Organization of SARS-CoV-2, +ssRNA 29,903 bp genome. (B): Similarity plot (SimPlot version 3.5.1 software) analysis of five full genomes of closely related genomes of SARS-CoV-2 including strain Bat/RaTG13 (closest), SARS-CoV, bat-SL-CoVZC45 and Pangolin-CoV strain from Guangdong province, China.

Article Snippet: In our recombination event analysis in SimPlot version 3.5.1 software using the whole genome sequences of nearest animal and human coronaviruses, no significant recombination events with SARS-CoV-2 was detected.

Techniques: Software

Journal: Indian Journal of Medical Microbiology

Article Title: TSP-based PCR for rapid identification of L and S type strains of SARS-CoV-2

doi: 10.1016/j.ijmmb.2021.01.003

Figure Lengend Snippet: Bootscan Plot: Recombination event analysis was performed for full genome sequences of five closely related strains of SARS-CoV-2 including strain Bat/RaTG13, SARS-CoV, bat-SL-CoVZC45 and Pangolin-CoV strains from Guangdong province, China. Analysis was performed in SimPlot version 3.5.1 software, keeping a bootscan window of 800 bp, a 20 bp Step using Kimura 2-parameter algorithm and a 100 bootstrap replicates. No significant recombination event detected during the analysis.

Article Snippet: In our recombination event analysis in SimPlot version 3.5.1 software using the whole genome sequences of nearest animal and human coronaviruses, no significant recombination events with SARS-CoV-2 was detected.

Techniques: Software

Journal: bioRxiv

Article Title: Molecular characterization of the viral structural gene of the first dengue virus type 1 outbreak in Xishuangbanna, a border area of China, Burma and Laos

doi: 10.1101/423152

Figure Lengend Snippet: ( a ) amino acid mutations of the DV-Jinghong, DV-Myanmar, DV-Mengla strain compared with the DEN1SS. DV-j, DV-m, DV-M indicated DV-Jinghong, DV-Mengla, DV-Myanmar respectively. ▲ Indicates that the mutation existed in all sample strains. ( b ) Homologous recombination prediction of the structural proteins for DEN1SS and DV-Jinghong, DV-Myanmar, DV-Mengla. MG523256 represents the DV-Jinghong, MG523190 represents the DV-Mengla, MG696653 represents the DV-Myanmar. No obvious homologous recombination signal among these stains.

Article Snippet: To reveal the role of genetic mechanisms, such as gene recombination in genetic evolution, the structural protein of DENV-1SS DV-Jinghong, DV-Mengla, and DV-Myanmar were analyzed by homologous recombination software SimPlot.

Techniques: Mutagenesis, Homologous Recombination