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. 2016 Apr 4;9(Suppl 2):43-58.
doi: 10.4137/BBI.S37223. eCollection 2015.

Bioinformatics and Molecular Analysis of the Evolutionary Relationship between Bovine Rhinitis A Viruses and Foot-And-Mouth Disease Virus

Devendra K Rai  1 , Paul Lawrence  2 , Steve J Pauszek  2 , Maria E Piccone  2 , Nick J Knowles  3 , Elizabeth Rieder  2
Affiliations

Bioinformatics and Molecular Analysis of the Evolutionary Relationship between Bovine Rhinitis A Viruses and Foot-And-Mouth Disease Virus

Devendra K Rai et al. Bioinform Biol Insights. .

Abstract

Bovine rhinitis viruses (BRVs) cause mild respiratory disease of cattle. In this study, a near full-length genome sequence of a virus named RS3X (formerly classified as bovine rhinovirus type 1), isolated from infected cattle from the UK in the 1960s, was obtained and analyzed. Compared to other closely related Aphthoviruses, major differences were detected in the leader protease (L(pro)), P1, 2B, and 3A proteins. Phylogenetic analysis revealed that RS3X was a member of the species bovine rhinitis A virus (BRAV). Using different codon-based and branch-site selection models for Aphthoviruses, including BRAV RS3X and foot-and-mouth disease virus, we observed no clear evidence for genomic regions undergoing positive selection. However, within each of the BRV species, multiple sites under positive selection were detected. The results also suggest that the probability (determined by Recombination Detection Program) for recombination events between BRVs and other Aphthoviruses, including foot-and-mouth disease virus was not significant. In contrast, within BRVs, the probability of recombination increases. The data reported here provide genetic information to assist in the identification of diagnostic signatures and research tools for BRAV.

Keywords: BRAV RS3X; bioinformatics; evolution; phylogeny; sequence.

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Figures

Figure 1
Figure 1
(A) Alignment of polyprotein of Aphthoviruses: FMDV A24 Cruzeiro strain was used as a template for alignment and feature annotation and marked as FMDV A24 Cruz. BRAV RS3X (GeneBank: KT948520), BRBV EC-11 (GeneBank: EU236594) and ERAV (GeneBank: DQ272578) were aligned to FMDV A24 Cruz (GeneBank: AY 593768). Marks the start of a protein sequence (N-terminus of), and the text following it identifies the protein. Yellow highlights suggest functionally critical (active site residue). (·) denotes a conserved residue in comparison to FMDV A24 Cruz. (−) denotes a gap introduced in the alignment. Cyan highlights indicate functionally important residues of a protein other than active site residues. Green highlights denote the RGD cell surface receptor. (B) Alignment of polyprotein of BRVs: Color code of highlighting and feature marking is the same as (A). Text at the beginning of each line is the sequence identifier for the given virus strain. For example, BRAV RS3X indicates BRAV RS3X sequence. The GeneBank accession numbers of the sequences used in the alignment are KT948520, KP236128, KP236129, JN936206, KP264974, EU236594, KP236130, KP264975, and KP264980 for BRAV RS 3X, BRAV Sd-1, BRAV 140032-1, BRAV H-1, BRAV BSRI4, BRBV EC-11, BRBV 140032-2, BRAV BSRI3, and BRAV BSRI1, respectively.
Figure 1
Figure 1
(A) Alignment of polyprotein of Aphthoviruses: FMDV A24 Cruzeiro strain was used as a template for alignment and feature annotation and marked as FMDV A24 Cruz. BRAV RS3X (GeneBank: KT948520), BRBV EC-11 (GeneBank: EU236594) and ERAV (GeneBank: DQ272578) were aligned to FMDV A24 Cruz (GeneBank: AY 593768). Marks the start of a protein sequence (N-terminus of), and the text following it identifies the protein. Yellow highlights suggest functionally critical (active site residue). (·) denotes a conserved residue in comparison to FMDV A24 Cruz. (−) denotes a gap introduced in the alignment. Cyan highlights indicate functionally important residues of a protein other than active site residues. Green highlights denote the RGD cell surface receptor. (B) Alignment of polyprotein of BRVs: Color code of highlighting and feature marking is the same as (A). Text at the beginning of each line is the sequence identifier for the given virus strain. For example, BRAV RS3X indicates BRAV RS3X sequence. The GeneBank accession numbers of the sequences used in the alignment are KT948520, KP236128, KP236129, JN936206, KP264974, EU236594, KP236130, KP264975, and KP264980 for BRAV RS 3X, BRAV Sd-1, BRAV 140032-1, BRAV H-1, BRAV BSRI4, BRBV EC-11, BRBV 140032-2, BRAV BSRI3, and BRAV BSRI1, respectively.
Figure 1
Figure 1
(A) Alignment of polyprotein of Aphthoviruses: FMDV A24 Cruzeiro strain was used as a template for alignment and feature annotation and marked as FMDV A24 Cruz. BRAV RS3X (GeneBank: KT948520), BRBV EC-11 (GeneBank: EU236594) and ERAV (GeneBank: DQ272578) were aligned to FMDV A24 Cruz (GeneBank: AY 593768). Marks the start of a protein sequence (N-terminus of), and the text following it identifies the protein. Yellow highlights suggest functionally critical (active site residue). (·) denotes a conserved residue in comparison to FMDV A24 Cruz. (−) denotes a gap introduced in the alignment. Cyan highlights indicate functionally important residues of a protein other than active site residues. Green highlights denote the RGD cell surface receptor. (B) Alignment of polyprotein of BRVs: Color code of highlighting and feature marking is the same as (A). Text at the beginning of each line is the sequence identifier for the given virus strain. For example, BRAV RS3X indicates BRAV RS3X sequence. The GeneBank accession numbers of the sequences used in the alignment are KT948520, KP236128, KP236129, JN936206, KP264974, EU236594, KP236130, KP264975, and KP264980 for BRAV RS 3X, BRAV Sd-1, BRAV 140032-1, BRAV H-1, BRAV BSRI4, BRBV EC-11, BRBV 140032-2, BRAV BSRI3, and BRAV BSRI1, respectively.
Figure 1
Figure 1
(A) Alignment of polyprotein of Aphthoviruses: FMDV A24 Cruzeiro strain was used as a template for alignment and feature annotation and marked as FMDV A24 Cruz. BRAV RS3X (GeneBank: KT948520), BRBV EC-11 (GeneBank: EU236594) and ERAV (GeneBank: DQ272578) were aligned to FMDV A24 Cruz (GeneBank: AY 593768). Marks the start of a protein sequence (N-terminus of), and the text following it identifies the protein. Yellow highlights suggest functionally critical (active site residue). (·) denotes a conserved residue in comparison to FMDV A24 Cruz. (−) denotes a gap introduced in the alignment. Cyan highlights indicate functionally important residues of a protein other than active site residues. Green highlights denote the RGD cell surface receptor. (B) Alignment of polyprotein of BRVs: Color code of highlighting and feature marking is the same as (A). Text at the beginning of each line is the sequence identifier for the given virus strain. For example, BRAV RS3X indicates BRAV RS3X sequence. The GeneBank accession numbers of the sequences used in the alignment are KT948520, KP236128, KP236129, JN936206, KP264974, EU236594, KP236130, KP264975, and KP264980 for BRAV RS 3X, BRAV Sd-1, BRAV 140032-1, BRAV H-1, BRAV BSRI4, BRBV EC-11, BRBV 140032-2, BRAV BSRI3, and BRAV BSRI1, respectively.
Figure 2
Figure 2
(A) Prediction of the transmembrane domain in: (i) FMDV A24 Cruz 2B and (ii) BRAV RS3X 2B. Color codes for different features are explained adjacent to each image. (B) Modeled structures of VP1 structural proteins of (i) FMDV A24 Cruz and BRAV RS3X are colored cyan, the G–H loop is marked with a yellow oval, and the RGD tripeptide is marked with cyan text. N- and C-terminus of the proteins in the structure are marked. (ii) The prediction of the 2B viroporin of: FMDV A24 Cruz (purple) and BRAV RS3X (cyan) were superimposed on HCV p7. N- and C-terminus of the proteins in the structure are marked. Structure-based sequence alignments are positioned to the left of each image. All structures are rendered in cartoon representation using UCSF-Chimera ver 1.10
Figure 2
Figure 2
(A) Prediction of the transmembrane domain in: (i) FMDV A24 Cruz 2B and (ii) BRAV RS3X 2B. Color codes for different features are explained adjacent to each image. (B) Modeled structures of VP1 structural proteins of (i) FMDV A24 Cruz and BRAV RS3X are colored cyan, the G–H loop is marked with a yellow oval, and the RGD tripeptide is marked with cyan text. N- and C-terminus of the proteins in the structure are marked. (ii) The prediction of the 2B viroporin of: FMDV A24 Cruz (purple) and BRAV RS3X (cyan) were superimposed on HCV p7. N- and C-terminus of the proteins in the structure are marked. Structure-based sequence alignments are positioned to the left of each image. All structures are rendered in cartoon representation using UCSF-Chimera ver 1.10
Figure 3
Figure 3
Neighbor-joining phylogeny trees of the P1 structural protein region (A) and 3Dpol non-structural protein (B) of family Picornaviridae including BRAV RS3X. Neighbor-joining phylogeny trees involving BRAV RS3X and all known members of Picornaviridae were constructed with the JTT model for amino acid substitution (pairwise deletions only) for (A) P1 structural proteins and (B) 3Dpol non-structural protein. As shown, 1,000 bootstraps with only those of 70% and above are displayed. Scale of resolution is indicated at the bottom of each figure. Note: “ ” indicate proposed new species and genera in Picornaviridae.
Figure 3
Figure 3
Neighbor-joining phylogeny trees of the P1 structural protein region (A) and 3Dpol non-structural protein (B) of family Picornaviridae including BRAV RS3X. Neighbor-joining phylogeny trees involving BRAV RS3X and all known members of Picornaviridae were constructed with the JTT model for amino acid substitution (pairwise deletions only) for (A) P1 structural proteins and (B) 3Dpol non-structural protein. As shown, 1,000 bootstraps with only those of 70% and above are displayed. Scale of resolution is indicated at the bottom of each figure. Note: “ ” indicate proposed new species and genera in Picornaviridae.
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