Journal: Poultry Science

Article Title: Pathogen identification and analysis of broiler bronchial obstruction syndrome using high-throughput sequencing technology

doi: 10.1016/j.psj.2026.107032

Figure Lengend Snippet: Recombination analysis of CK/CH/HBBD/BD6 and CK/CH/HBBD/BD3. The genomic characteristics of IBV and the whole-genome recombination analysis were conducted using the Simplot software for Bootscan analysis (window size: 200 bp, step size: 20 bp).

Article Snippet: Bootscan analysis performed using Simplot software ( ) further validated the recombination events identified by RDP4 software and no recombination events were found in the S gene.

Techniques: Software

Journal: Scientific Reports

Article Title: Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand

doi: 10.1038/s41598-025-16816-6

Figure Lengend Snippet: Maximum likelihood trees of five GI.6 strains. (A) Complete RdRp and (B) complete VP1 genes were analyzed. The trees were constructed using the GTR best-fit model, with 1,000 bootstrap replications for branch support as implemented in MEGA X. The scale bar indicates nucleotide substitutions per site, and selected bootstrap values greater than 80 are shown. The five norovirus GI.6 strains identified in Thailand are denoted in bold and with green (GI.6[P6]) and red (GI.6[P11]) circles.

Article Snippet: Simplot nucleotide pairwise analysis of the complete genome sequence of norovirus GI.6[P6] and reference strains was performed using the prototype of GI.6[P6] strain ( AF093797 ) as the query, revealing nucleotide sequence identity percentages consistent with the prototype strain and showing a similar trend in similarity percentages to closely related strains, ranging from 81 to 99% (Fig. A) with the most diversity observed in p48 gene.

Techniques: Construct

Journal: Scientific Reports

Article Title: Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand

doi: 10.1038/s41598-025-16816-6

Figure Lengend Snippet: Genetic analysis of five norovirus GI.6 strains. (A) Pairwise nucleotide similarities compared the complete genome sequence of a norovirus GI.6[P6] strain from this study (GI/Hu/TH/2022/GI.6[P6]/B8203) with other GI.6[P6] reference strains (shown in different colors). The genome of strain GI/Hu/DE/1997/GI.6[P6]/BS5 (Hesse) ( AF093797 ) serves as the query sequence. The positions of the complete genome region are indicated. (B) Amino acid residues of the complete genome sequence of Thai norovirus GI.6[P11] strains were compared with other GI.6[P11] sequences. The Thai strain is shown in the bottom four row (red bold), with unique amino acid changes labeled in red. Amino acids are colored by the properties of their side-chains: purple for basic – R, H, K; pink for acidic – D, E; Green for nonpolar – G, A, V, L, I, M, F, W, and P; blue for polar – S, T, C, Y, N, and Q.

Article Snippet: Simplot nucleotide pairwise analysis of the complete genome sequence of norovirus GI.6[P6] and reference strains was performed using the prototype of GI.6[P6] strain ( AF093797 ) as the query, revealing nucleotide sequence identity percentages consistent with the prototype strain and showing a similar trend in similarity percentages to closely related strains, ranging from 81 to 99% (Fig. A) with the most diversity observed in p48 gene.

Techniques: Sequencing, Labeling

Journal: Scientific Reports

Article Title: Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand

doi: 10.1038/s41598-025-16816-6

Figure Lengend Snippet: Genetic analysis of the Thai EV-A76 strain. (A) A Maximum likelihood tree of EV-A76 strains was inferred for complete nucleotide sequences using the GTR best-fit model, with 1,000 bootstrap replications for branch support as implemented in MEGA X. The scale bar indicates nucleotide substitutions per site, and selected bootstrap values greater than 80 are shown. The rare EV-A76 strain identified in Thailand is denoted with bold black and a red circle. The genome of strain Enterovirus_A76_FRA_FRA91-10369_1991 ( AY697458 ) as prototype EV-A76 strain is highlighted in green. (B) Amino acid residues of the complete genome sequence of the Thai EV-A76 strain (red bold) was compared with other full genome EV-A76 strains, with unique amino acid changes labeled in red. Amino acids are colored by the properties of their side-chains: purple for basic – R, H, K; pink for acidic – D, E; Green for nonpolar – G, A, V, L, I, M, F, W, and P; blue for polar – S, T, C, Y, N, and Q.

Article Snippet: Simplot nucleotide pairwise analysis of the complete genome sequence of norovirus GI.6[P6] and reference strains was performed using the prototype of GI.6[P6] strain ( AF093797 ) as the query, revealing nucleotide sequence identity percentages consistent with the prototype strain and showing a similar trend in similarity percentages to closely related strains, ranging from 81 to 99% (Fig. A) with the most diversity observed in p48 gene.

Techniques: Sequencing, Labeling

Journal: Scientific Reports

Article Title: Metagenomic analysis and genomic characterization of enterovirus A76 and Norovirus GI.6[P11] co-infection in a patient with acute gastroenteritis in Thailand

doi: 10.1038/s41598-025-16816-6

Figure Lengend Snippet: Similarity Plot and BootScan analyses of EV-A76 genome. (A) Similarity plot analysis comparing the complete genome of the Thai EV-A76 strain (B9955), used as the query, against four reference strains, consisting of the EV-A76 prototype strain and three other EV-A76 strains obtained from GenBank (represented by different colors). The X-axis indicates the nucleotide positions across the genome, and the Y-axis represents the percentage similarity. (B) BootScan analysis using the Thai EV-A76 strain (EV-A76/THA/B9955/2023) as the query and comparing it with two other EV-A76 refence strains and one EV-A89 reference strain (shown in different colors). Both analyses were performed using SimPlot version 3.5.1, applying the Kimura 2-parameter model with a 200 bp window size and a 20 bp step size.

Article Snippet: Simplot nucleotide pairwise analysis of the complete genome sequence of norovirus GI.6[P6] and reference strains was performed using the prototype of GI.6[P6] strain ( AF093797 ) as the query, revealing nucleotide sequence identity percentages consistent with the prototype strain and showing a similar trend in similarity percentages to closely related strains, ranging from 81 to 99% (Fig. A) with the most diversity observed in p48 gene.

Techniques:

Journal: Virulence

Article Title: Novel Taiwan-I-type infectious bronchitis virus: First evidence of testicular atrophy and efficacious protection with strain-matched oil-emulsified inactivated vaccine

doi: 10.1080/21505594.2026.2664950

Figure Lengend Snippet: Prediction of B-cell antigen epitopes in the GX-NN200723 strain and commonly administered domestic vaccine strains.

Article Snippet: The recombination result of the GX-NN200723 strain was analyzed by SimPlot software.

Techniques:

Journal: Virulence

Article Title: Novel Taiwan-I-type infectious bronchitis virus: First evidence of testicular atrophy and efficacious protection with strain-matched oil-emulsified inactivated vaccine

doi: 10.1080/21505594.2026.2664950

Figure Lengend Snippet: Clinical symptom scores (a) and percentage survival (b) of the SPF chickens challenged with the GX-NN200723 strain.

Article Snippet: The recombination result of the GX-NN200723 strain was analyzed by SimPlot software.

Techniques:

Journal: Virulence

Article Title: Novel Taiwan-I-type infectious bronchitis virus: First evidence of testicular atrophy and efficacious protection with strain-matched oil-emulsified inactivated vaccine

doi: 10.1080/21505594.2026.2664950

Figure Lengend Snippet: Clinical symptoms of the trachea, kidney, testis, ovary, and oviduct in the GX-NN200723 group and the control group.

Article Snippet: The recombination result of the GX-NN200723 strain was analyzed by SimPlot software.

Techniques: Control

Journal: Virulence

Article Title: Novel Taiwan-I-type infectious bronchitis virus: First evidence of testicular atrophy and efficacious protection with strain-matched oil-emulsified inactivated vaccine

doi: 10.1080/21505594.2026.2664950

Figure Lengend Snippet: Clinical symptom scores (a) and percentage survival (b) of the Three-Yellow chickens in all experimental groups challenged with the GX-NN200723 strain.

Article Snippet: The recombination result of the GX-NN200723 strain was analyzed by SimPlot software.

Techniques:

Journal: Virulence

Article Title: Novel Taiwan-I-type infectious bronchitis virus: First evidence of testicular atrophy and efficacious protection with strain-matched oil-emulsified inactivated vaccine

doi: 10.1080/21505594.2026.2664950

Figure Lengend Snippet: Clinical symptoms of the trachea and kidney in Three-Yellow chickens from all experimental groups challenged with the GX-NN200723 strain.

Article Snippet: The recombination result of the GX-NN200723 strain was analyzed by SimPlot software.

Techniques:

Journal: Virulence

Article Title: Novel Taiwan-I-type infectious bronchitis virus: First evidence of testicular atrophy and efficacious protection with strain-matched oil-emulsified inactivated vaccine

doi: 10.1080/21505594.2026.2664950

Figure Lengend Snippet: Histopathological analysis of the trachea and kidney in Three-Yellow chickens from all experimental groups challenged with the GX-NN200723 strain.

Article Snippet: The recombination result of the GX-NN200723 strain was analyzed by SimPlot software.

Techniques:

Journal: Virulence

Article Title: Novel Taiwan-I-type infectious bronchitis virus: First evidence of testicular atrophy and efficacious protection with strain-matched oil-emulsified inactivated vaccine

doi: 10.1080/21505594.2026.2664950

Figure Lengend Snippet: Trachea ciliostasis scores in Three-Yellow chickens from all experimental groups challenged with the GX-NN200723 strain.

Article Snippet: The recombination result of the GX-NN200723 strain was analyzed by SimPlot software.

Techniques:

Journal: Virulence

Article Title: Novel Taiwan-I-type infectious bronchitis virus: First evidence of testicular atrophy and efficacious protection with strain-matched oil-emulsified inactivated vaccine

doi: 10.1080/21505594.2026.2664950

Figure Lengend Snippet: Virus copy-number of the trachea (a), kidney (a), oral swabs (b) and cloacal swabs (C) from all experimental groups challenged with the GX-NN200723 strain.

Article Snippet: The recombination result of the GX-NN200723 strain was analyzed by SimPlot software.

Techniques: Virus