Sequence analysis of monoclonal antibody resistant mutants of type O foot and mouth disease virus: Evidence for the involvement of the three surface exposed capsid proteins in four antigenic sites

Kitson, Jeremy; McCahon, D.; Belsham, Graham J.

doi:10.1016/0042-6822(90)90269-w

Cited by 204 publications

(196 citation statements)

References 27 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: 83%

“…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: 83%

Section: Real Data With Partial Ground Truthmentioning

confidence: 99%

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

et al. 2017

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“…The amino acid comparison of the type O viruses analysed showed a good correlation between the genotype and the residues present in the 140-160 region and the carboxyterminus of VP1, which contribute to an important antigenic site in this serotype [16] (Fig. 6).…”

Section: Discussionmentioning

confidence: 91%

“…The comparison of the amino acid sequences deduced from the nt sequences showed that non-synonymous substitutions were accumulated around positions 140-160, which span a major antigenic site in this and other serotypes [2,16,25,32]. In addition, substitutions were also found in the last residues of the protein, which constitute an additional antigenic site (Fig.…”

Section: Discussionmentioning

confidence: 95%

“…This is highly desirable, in view of the additional information that will be derived from these analyses. However, the results reported here, indicated that, for phylogenetic purposes, the use of windows of the 250 3' end nt allowed derivation of trees similar to those obtained with the whole VP1 gene of serotypes A, O and C. This sequence window also offered the possibility of deducing the amino acid sequence corresponding to VP1 residues around positions 140-160 and those at the carboxyterminus, which contribute to important antigenic sites in the three serotypes [2,16,25]. These results may provide additional information on the antigenic properties of the viral isolates.…”

Section: Discussionmentioning

confidence: 95%

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Identification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses

Núñez

Martı́n

Piccone³

et al. 2001

Vet. Res.

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-An analysis of the informative content of sequence stretches on the foot-and-mouth disease virus (FMDV) VP1 gene was applied to two important viral serotypes: A and O. Several sequence regions were identified to allow the reconstruction of phylogenetic trees equivalent to those derived from the whole VP1 gene. The optimal informative regions for sequence windows of 150 to 250 nt were predicted between positions 250 and 550 of the gene. The sequences spanning the 250 nt of the 3' end (positions 400 to 650), extensively used for FMDV phylogenetic analyses, showed a lower informative content. In spite of this, the use of sequences from this region allowed the derivation of phylogenetic trees for type A and type O FMDVs which showed topologies similar to those previously reported for the whole VP1 gene. When the sequences determined for viruses isolated in Argentina, between 1990 and 1993, were included in these analyses, the results obtained revealed features of the circulation of type A and type O viruses in the field, in the months that preceded the eradication of the disease in this country. Type A viruses were closely related to an Argentinean vaccine strain, and defined an independent cluster within this serotype. Among the type O viruses analysed, two groups were distinguished; one was closely related to the South American vaccine strains, while the other was grouped with viruses of the O3 subtype. In addition, a detailed phylogeny for type A FMDV is presented.foot-and-mouth disease virus / phylogenetic analysis / informative region / molecular epidemiology Vet. Res. 32 (2001) [31][32][33][34][35][36][37][38][39][40][41][42][43][44][45] 31

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Comparative studies of the capsid precursor polypeptide P1 and the capsid protein VP1 cDNA vectors for DNA vaccination against foot‐and‐mouth disease virus

Yang

Wang

Lin

et al. 2005

The Journal of Gene Medicine

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This strategy of using the whole capsid precursor protein P1 cDNA for vaccination, intentionally without the use of virus-specific protease or other encoding genes for safety reasons, may thus be employed as a relevant experimental system for induction or upgrading of effective neutralizing antibody response, and as a convenient surrogate test system for DNA vaccination studies of FMDV and presumably other viral diseases.

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Sequence analysis of monoclonal antibody resistant mutants of type O foot and mouth disease virus: Evidence for the involvement of the three surface exposed capsid proteins in four antigenic sites

Cited by 204 publications

References 27 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

Identification of optimal regions for phylogenetic studies on VP1 gene of foot-and-mouth disease virus: analysis of types A and O Argentinean viruses

Comparative studies of the capsid precursor polypeptide P1 and the capsid protein VP1 cDNA vectors for DNA vaccination against foot‐and‐mouth disease virus

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