Mapping of antigenic sites of foot-and-mouth disease virus serotype Asia 1 and relationships with sites described in other serotypes

Grazioli, Santina; Fallacara, Francesca; Brocchi, Emiliana

doi:10.1099/vir.0.048249-0

Cited by 48 publications

(50 citation statements)

References 29 publications

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“…In the FMDV serotypes, both SAT1 and SAT2 are known to share one major antigenic region, the highly flexible VP1 G-H loop (Crowther et al 1993b), a cord of connected amino acid residues. Additional residues have also been identified on the SAT serotypes (Crowther et al 1993b;Grazioli et al 2006), as well as others on related serotypes A, O, C and Asia1 which may also occur within the SAT serotypes (Grazioli et al 2013;Kitson et al 1990;Lea et al 1994;Saiz et al 1991). For the H1N1 virus, experimental studies have identified four major antigenic sites (Caton et al 1982), as well as a number of other sites known to be important (McDonald et al 2007).…”

Section: Introductionmentioning

confidence: 99%

“…The VP2 B-C loop is antigenic in all serotypes and contains the highly antigenic VP2 72 residue, which has been experimentally validated in all of the FMDV serotypes except SAT2 (Aktas and Samuel 2000;Crowther et al 1993a;Grazioli et al 2006Grazioli et al , 2013Kitson et al 1990;Lea et al 1994;Saiz et al 1991). The VP1 C-terminus has been proven to be antigenic in all but the Asia1 serotype, although it is almost certainly antigenic there also (Aktas and Samuel 2000;Baxt et al 1989;Grazioli et al 2006;Mateu 1995).…”

Section: Sat1 Datamentioning

confidence: 99%

“…Additionally in the VP1 G-H loop, an antigenic loop in every FMDV serotype (Bolwell et al 1989;Crowther et al 1993b;Grazioli et al 2006Grazioli et al , 2013Kitson et al 1990;Lea et al 1994) known to distract the host immune systems, the conjugate SABRE method has also identified VP1 143 and VP1 150. These residues are next to the experimentally validated residues in the protein alignment and confirm that the VP1 G-H loop is a highly antigenic part of the SAT1 serotype.…”

Section: Sat1 Datamentioning

confidence: 99%

“…6.2.1, the conjugate SABRE method has selected VP2 74 from the VP2 B-C loop. However in addition it has also selected VP2 72 which is antigenic in all FMDV serotypes and VP2 79 which has been experimentally validated in the A, O, Asia1 and SAT2 serotypes (Grazioli et al 2006(Grazioli et al , 2013Mateu 1995). The conjugate SABRE model also again selects several residues from the VP1 C-terminus; VP1 209, VP1 211 and VP1 218.…”

Section: Extended Sat1 Datamentioning

confidence: 99%

“…Firstly we include any residues which have been experimentally validated as important within the SAT1 serotype by monoclonal antibody escape mutant studies (MAbs) (Grazioli et al 2006). Secondly, we include those residues which are part of cords of connected experimentally validated antigenic residues for four or more different serotypes; VP1 140-169 (part of the VP1 G-H loop), VP1 200-224 (VP1 C terminus), VP2 70-82 (VP2 B-C loop) and VP3 56-61 (VP3 B-B knob) (Aktas and Samuel 2000;Barnett et al 1989;Crowther et al 1993a;Baxt et al 1989;Bolwell et al 1989;Grazioli et al 2006Grazioli et al , 2013Lea et al 1994;Kitson et al 1990;Mateu 1995;Saiz et al 1991;Thomas et al 1988a, b). As antigenic sites have been found in a large number of different individual locations, we include additional information from other serotypes when classifying whole loops due the similar structure of the different serotypes.…”

Section: Real Data With Partial Ground Truthmentioning

confidence: 99%

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A sparse hierarchical Bayesian model for detecting relevant antigenic sites in virus evolution

et al. 2017

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Understanding how viruses offer protection against closely related emerging strains is vital for creating effective vaccines. For many viruses, multiple serotypes often co-circulate and testing large numbers of vaccines can be infeasible. Therefore the development of an in silico predictor of cross-protection between strains is important to help optimise vaccine choice. Here we present a sparse hierarchical Bayesian model for detecting relevant antigenic sites in virus evolution (SABRE) which can account for the experimental variability in the data and predict antigenic variability. The method uses spike and slab priors to identify sites in the viral protein which are important for the neutralisation of the virus. Using the SABRE method we are able to identify a number of key antigenic sites within several viruses, as well as providing estimates of significant changes in the evolutionary history of the serotypes. We show how our method outperforms alternative established methods; standard mixed effects models, the mixed effects LASSO, and the mixed effects elastic nets. We also propose novel proposal mechanisms for the Markov chain Monte Carlo simulations, which Keywords Spike and slab prior · Foot-and-mouth disease virus · Influenza virus · Antigenic variability · Bayesian hierarchical models · Mixed-effects models · LASSO · Markov chain Monte Carlo

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Section: Introductionmentioning

confidence: 99%

Section: Sat1 Datamentioning

confidence: 99%

Section: Sat1 Datamentioning

confidence: 99%

Section: Extended Sat1 Datamentioning

confidence: 99%

Section: Real Data With Partial Ground Truthmentioning

confidence: 99%

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A sparse hierarchical Bayesian model for detecting relevant antigenic sites in virus evolution

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Capsid coding region diversity of re-emerging lineage C foot-and-mouth disease virus serotype Asia1 from India

et al. 2015

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Foot-and-mouth disease virus (FMDV) serotype Asia1 was first reported in India in 1951, where three major genetic lineages (B, C and D) of this serotype have been described until now. In this study, the capsid protein coding region of serotype Asia1 viruses (n = 99) from India were analyzed, giving importance to the viruses circulating since 2007. All of the isolates (n = 50) recovered during 2007-2013 were found to group within the re-emerging cluster of lineage C (designated as sublineage C(R)). The evolutionary rate of sublineage C(R) was estimated to be slightly higher than that of the serotype as a whole, and the time of the most recent common ancestor for this cluster was estimated to be approximately 2001. In comparison to the older isolates of lineage C (1993-2001), the re-emerging viruses showed variation at eight amino acid positions, including substitutions at the antigenically critical residues VP279 and VP2131. However, no direct correlation was found between sequence variations and antigenic relationships. The number of codons under positive selection and the nature of the selection pressure varied widely among the structural proteins, implying a heterogeneous pattern of evolution in serotype Asia1. While episodic diversifying selection appears to play a major role in shaping the evolution of VP1 and VP3, selection pressure acting on codons of VP2 is largely pervasive. Further, episodic positive selection appears to be responsible for the early diversification of lineage C. Recombination events identified in the structural protein coding region indicates its probable role in adaptive evolution of serotype Asia1 viruses.

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Single-cell analysis reveals the relevance of foot-and-mouth disease virus persistence to emopamil-binding protein gene expression in host cells

et al. 2017

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Foot-and-mouth disease virus (FMDV) infects host cells in either an acute or persistent manner. In this study, we examined the relevance of the establishment of FMDV persistence to the expression of the emopamil-binding protein (EBP) gene in 231 individual persistently infected baby hamster kidney (BHK-21) cells after passages 28, 38, and 68 (PI28, PI38, and PI68). At PI28, the stage at which persistent infection of FDMV becomes unstable, the percentage of cells carrying FMDV was 66.7%, while 80.2% of cells were EBP positive. Additionally, in 55.6% of the EBP-positive cells at PI28, EBP expression was upregulated approximately 149.9% compared to uninfected BHK-21 cells. This was the highest expression level among all cell passages measured. Interestingly, in a parallel experiment, the average EBP expression level in the whole cell population at PI28 was only slightly higher (108.2%) than that in uninfected BHK-21 cells. At PI38, 98.7% of the cells were positive for FMDV 3D (an RNA-dependent RNA polymerase enzyme gene), and its maximum expression level observed at this passage. The expression level of EBP in 78.2% of the total cells, however, was reduced significantly. At PI68, 95.8% of the cells were 3D positive, and the expression of both the EBP and 3D genes were at the lowest levels of all the passages. Our studies using single cells yielded data that are otherwise inaccessible a using whole cell population. These results suggest that the establishment of persistent infection by FMDV is a dynamic process that results from the continuous adaptation and coevolution of viruses and cells to reach an equilibrium.

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Mapping of antigenic sites of foot-and-mouth disease virus serotype Asia 1 and relationships with sites described in other serotypes

Cited by 48 publications

References 29 publications

A sparse hierarchical Bayesian model for detecting relevant antigenic sites in virus evolution

A sparse hierarchical Bayesian model for detecting relevant antigenic sites in virus evolution

Capsid coding region diversity of re-emerging lineage C foot-and-mouth disease virus serotype Asia1 from India

Single-cell analysis reveals the relevance of foot-and-mouth disease virus persistence to emopamil-binding protein gene expression in host cells

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