Molecular epidemiology of foot-and-mouth disease virus

Knowles, Nick J.; Samuel, A. R.

doi:10.1016/s0168-1702(02)00260-5

Cited by 612 publications

(581 citation statements)

References 74 publications

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“…Differences exist in the selection forces shaping the evolution of the serotypes with, for example, type C and SAT 3 major antigenic regions reported to be under no positive Darwinian selection when VP1-coding sequences were analysed [24]. However, the low level of sequence divergence observed in this study is comparable to that observed in C 1 subtype strains from Europe, which showed very little change from 1953 to 1989 [4]. The absence of significant sequence divergence in type C strains has also been reported in India [25].…”

Section: Discussioncontrasting

confidence: 45%

Low diversity of foot-and-mouth disease serotype C virus in Kenya: evidence for probable vaccine strain re-introductions in the field

Sangula

Siegismund²,

Belsham

et al. 2010

Epidemiol. Infect.

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SUMMARYMost viruses are maintained by complex processes of evolution that enable them to survive but also complicate efforts to achieve their control. In this paper, we study patterns of evolution in foot-and-mouth disease (FMD) serotype C virus isolates from Kenya, one of the few places in the world where serotype C has been endemic and is suspected to remain. The nucleotide sequences encoding the capsid protein VP1 from eight isolates collected between 1967 and 2004 were analysed for patterns of sequence divergence and evolution. Very low nucleotide diversity (π=0·0025) and remarkably little change (only five segregating sites and three amino-acid changes) were observed in these isolates collected over a period of almost 40 years. We interpret these results as being suggestive of re-introductions of the vaccine strain into the field. The implications of these results for the maintenance of serotype C FMD virus and the use of vaccination as a control measure in Kenya are discussed.

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Section: Discussioncontrasting

confidence: 45%

Low diversity of foot-and-mouth disease serotype C virus in Kenya: evidence for probable vaccine strain re-introductions in the field

Sangula

Siegismund²,

Belsham

et al. 2010

Epidemiol. Infect.

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“…As a rule of thumb, distances of Ͻ5% are considered to indicate the same "strain" (30,31). At the other end of the spectrum, distances of more than 15% have been considered sufficient to classify isolates as unrelated (26,32), although because of the greater variation in the SATs, a higher threshold of 20% has been suggested (20). However, this leaves a range of 5 to 15% phylogenetic distances that are undefined.…”

Section: Discussionmentioning

confidence: 99%

Molecular Epidemiology of Foot-and-Mouth Disease Viruses in the Adamawa Province of Cameroon

et al. 2004

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Foot-and-mouth disease virus (FMDV) causes a highly contagious viral disease of even-toed ungulates and is one of the most important economic diseases of livestock. Most studies of FMDV are done in countries where control measures are being implemented. In contrast, in areas such as sub-Saharan Africa, where FMDV is endemic and new strains are likely to emerge, there are only sporadic submissions to the World Reference Laboratory, Pirbright, United Kingdom. This paper describes the molecular epidemiology of FMDV in the Adamawa province of Cameroon based on a population sample of cattle herds. Serotypes SAT2 and A were isolated in the cross-sectional study. SAT2 isolates were all similar, with phylogenetic distances of <6%, and were most closely related to published sequences of isolates from Eritrea and Saudi Arabia. Serotype A isolates were more variable, with phylogenetic distances of 0 to 11%, and were most closely related to historic isolates from Cameroon. Use of a population-based sample gives a representative sample of virus diversity and will improve our understanding of the evolution of FMDV and its epidemiology. A supplementary study of pigs passing through the railhead collection yard at Ngaoundere detected a serotype O virus. A third pilot longitudinal study monitored viral persistence in three cattle herds over 12 months, and serotype O and A viruses were recovered from a herd 12 months after it was first recorded as being infected with SAT2 virus. The pig type O isolate was not closely related to that recovered from the cattle, suggesting that the pigs had not introduced the O virus into the cattle herds.

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“…The accumulation of these changes in geographically isolated virus lineages allows for the division of serotypes into topotypes, groups of genetically similar viruses associated with a particular geographic area (Knowles and Samuel 2003). Strains within topotypes share a common evolutionary history that is distinct from strains within other topotypes.…”

Section: Introductionmentioning

confidence: 99%

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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Molecular epidemiology of foot-and-mouth disease virus

Cited by 612 publications

References 74 publications

Low diversity of foot-and-mouth disease serotype C virus in Kenya: evidence for probable vaccine strain re-introductions in the field

Low diversity of foot-and-mouth disease serotype C virus in Kenya: evidence for probable vaccine strain re-introductions in the field

Molecular Epidemiology of Foot-and-Mouth Disease Viruses in the Adamawa Province of Cameroon

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

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