Journal: iScience

Article Title: In silico reconstruction of a salmonid alphavirus virion reveals distinctive molecular features implicated in virulence

doi: 10.1016/j.isci.2026.115070

Figure Lengend Snippet: Aquatic and terrestrial alphavirus phylogeny and E2 envelope protein alignment (A) Phylogenetic tree of alphavirus structural protein sequences. The amino acid sequence of 17 representative terrestrial and aquatic alphaviruses were aligned and a maximum-likelihood (ML) phylogenetic tree was generated (LG [G + I] substitution model). Numbers at nodes indicate percent bootstrap support from 1,000 replicates. Tree drawn to scale with branch lengths measured in number of substitutions per site (scale bar). For each alphavirus, the known host range and vectors are indicated by animal diagrams. Experimentally determined virion structures are depicted for the following terrestrial alphaviruses: VEEV (PDB: 3j0c ); EEEV (PDB: 6odf ); SINV (PDB: 6imm ); WEEV (PDB: 8dec ); RRV (PDB: 6vyv ); MAYV (PDB: 7ko8 ); CHIKV (PDB: 3j2w ). (B) Amino acid sequence alignment of the N-term region of alphavirus E2. Protein sequences of the 17 aquatic and terrestrial alphaviruses in (A) were aligned and the region corresponding to E2 N-term is shown. The alignment reveals an amino acid insert present only in fish alphavirus E2 proteins (Indel, top). Salmonid alphavirus (SAV) is unique in harboring an additional stretch of three residues herein referred to as 7-8-9 triplet based on SAV E2 amino acid numbering.

Article Snippet: Cryo-EM structure of the mature and infective Mayaro virus , Protein DataBank (PDB) , 7ko8.

Techniques: Sequencing, Generated

Journal: iScience

Article Title: In silico reconstruction of a salmonid alphavirus virion reveals distinctive molecular features implicated in virulence

doi: 10.1016/j.isci.2026.115070

Figure Lengend Snippet: Aquatic and terrestrial alphavirus phylogeny and E2 envelope protein alignment (A) Phylogenetic tree of alphavirus structural protein sequences. The amino acid sequence of 17 representative terrestrial and aquatic alphaviruses were aligned and a maximum-likelihood (ML) phylogenetic tree was generated (LG [G + I] substitution model). Numbers at nodes indicate percent bootstrap support from 1,000 replicates. Tree drawn to scale with branch lengths measured in number of substitutions per site (scale bar). For each alphavirus, the known host range and vectors are indicated by animal diagrams. Experimentally determined virion structures are depicted for the following terrestrial alphaviruses: VEEV (PDB: 3j0c ); EEEV (PDB: 6odf ); SINV (PDB: 6imm ); WEEV (PDB: 8dec ); RRV (PDB: 6vyv ); MAYV (PDB: 7ko8 ); CHIKV (PDB: 3j2w ). (B) Amino acid sequence alignment of the N-term region of alphavirus E2. Protein sequences of the 17 aquatic and terrestrial alphaviruses in (A) were aligned and the region corresponding to E2 N-term is shown. The alignment reveals an amino acid insert present only in fish alphavirus E2 proteins (Indel, top). Salmonid alphavirus (SAV) is unique in harboring an additional stretch of three residues herein referred to as 7-8-9 triplet based on SAV E2 amino acid numbering.

Article Snippet: Cryo-EM structure of Chikungunya virus asymmetric unit , Protein DataBank (PDB) , 8fcg.

Techniques: Sequencing, Generated

Journal: iScience

Article Title: In silico reconstruction of a salmonid alphavirus virion reveals distinctive molecular features implicated in virulence

doi: 10.1016/j.isci.2026.115070

Figure Lengend Snippet: In vitro biochemical analysis and in silico modeling of SAV E3E2 furin cleavage and comparison with CHIKV (A) SAV E3 C-term furin cleavage site (FCS) and E2 N-term. Position of the FCS, amino acid composition, triplet 7-8-9 and E2 N-term insert α-helix are shown. The residues involved in the E2 N-term α-helix predicted by AlphaFold3, RoseTTAFold, and PsiPred are depicted as helical cartoons. (B) Biochemical analysis of cleavage status of p62 in infected cells and purified SAV virions. Western blot analysis was performed on lysates of mock-infected (lane 1) or SAV2-infected BF-2 cells at an m.o.i. of 1 (lane 2) or 5 (lane 3) or on sucrose cushion-purified SAV2 virions (lane 4). Western blot analyses performed using anti-E2 (17H23) or anti-E1 (78K5) mAbs. GAPDH detection was used as loading control for cell lysates. (C) Structural modeling of SAV p62 (E3E2) cleavage by furin. SAV E1 ecto , E2 ecto , and E3 were modeled as complexes using AlphaFold 3. Top corresponds to uncleaved p62 (E3E2), middle corresponds to E3 cleaved from E2 with E3 remaining non-covalently linked, and bottom corresponds to E1 and E2 ectodomains after E3 release. Arrows indicate location of E2 N-term ɑ-helix and 7-8-9 triplet. The models are colored using AlphaFold pLDDT confidence scoring. (D) Structural alignment of CHIKV and SAV uncleaved p62. The uncleaved model of SAV p62 (pink) was structurally aligned with the crystal structure of CHIKV p62 (gold, PDB: 3n40 ) using MatchMaker in ChimeraX. For panels C and D, structure labeling, representation, and scale bars were visualized using ChimeraX.

Article Snippet: Cryo-EM structure of Chikungunya virus asymmetric unit , Protein DataBank (PDB) , 8fcg.

Techniques: In Vitro, In Silico, Comparison, Infection, Purification, Western Blot, Control, Labeling

Journal: iScience

Article Title: In silico reconstruction of a salmonid alphavirus virion reveals distinctive molecular features implicated in virulence

doi: 10.1016/j.isci.2026.115070

Figure Lengend Snippet: Structural and evolutionary analyses of aquatic and terrestrial alphavirus proteins (A) E2-E1-Cp subunit of SAV predicted by AlphaFold 3. (B) Detailed view of E2 ectodomain with N-term insert helix and 7-8-9 triplet highlighted (arrows). (C) E2-E1-Cp subunit of VEEV (PDB: 3j0c ) and CHIKV (PDB: 8fcg ) terrestrial alphaviruses and E2-E1-Cp subunit of mammalian aquatic alphaviruses SESV and AHPV predicted by AlphaFold 3. (D) E2-E1-Cp subunit of WHAV, CAV, WCFAV, and WSFAV fish alphaviruses predicted by AlphaFold 3. For Cp, only the ordered C-term region of the respective proteins was modeled. The known host range and vectors are indicated by animal diagrams. For (C and D), a focused view of the E2 N-term of each model is shown in each box. Structure labeling, representation, and scale bars were visualized using ChimeraX. (E) Comparative analyses between alphavirus proteins using structure-based protein alignment and phylogenetic analysis. FoldMason was used to perform multiple protein structure alignments (MSTA) of alphavirus E1 and E2 ectodomains and Cp protein (C-term domain). In each structural alignment, the blue (E1), green (E2), and red (Cp) protein corresponds to SAV while the superimposed proteins in gold are from the other species analyzed. The structure-based protein sequence alignments were used to build Maximum-Likelihood phylogenetic trees using WAG+G+I substitution model for E1 and WAG+G for E2 and Cp. Numbers at nodes indicate percent bootstrap support from 1,000 replicates. Trees drawn to scale with branch lengths measured in number of substitutions per site (scale bars).

Article Snippet: Cryo-EM structure of Chikungunya virus asymmetric unit , Protein DataBank (PDB) , 8fcg.

Techniques: Labeling, Sequencing

Journal: iScience

Article Title: In silico reconstruction of a salmonid alphavirus virion reveals distinctive molecular features implicated in virulence

doi: 10.1016/j.isci.2026.115070

Figure Lengend Snippet: Aquatic and terrestrial alphavirus phylogeny and E2 envelope protein alignment (A) Phylogenetic tree of alphavirus structural protein sequences. The amino acid sequence of 17 representative terrestrial and aquatic alphaviruses were aligned and a maximum-likelihood (ML) phylogenetic tree was generated (LG [G + I] substitution model). Numbers at nodes indicate percent bootstrap support from 1,000 replicates. Tree drawn to scale with branch lengths measured in number of substitutions per site (scale bar). For each alphavirus, the known host range and vectors are indicated by animal diagrams. Experimentally determined virion structures are depicted for the following terrestrial alphaviruses: VEEV (PDB: 3j0c ); EEEV (PDB: 6odf ); SINV (PDB: 6imm ); WEEV (PDB: 8dec ); RRV (PDB: 6vyv ); MAYV (PDB: 7ko8 ); CHIKV (PDB: 3j2w ). (B) Amino acid sequence alignment of the N-term region of alphavirus E2. Protein sequences of the 17 aquatic and terrestrial alphaviruses in (A) were aligned and the region corresponding to E2 N-term is shown. The alignment reveals an amino acid insert present only in fish alphavirus E2 proteins (Indel, top). Salmonid alphavirus (SAV) is unique in harboring an additional stretch of three residues herein referred to as 7-8-9 triplet based on SAV E2 amino acid numbering.

Article Snippet: Cryo-EM Structure of Western Equine Encephalitis Virus , Protein DataBank (PDB) , 8dec.

Techniques: Sequencing, Generated