About: The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus

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About: The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus
Creator	Soubeyrand, Samuel Valdazo-González, Begoña Wadsworth, Jemma Haydon, Daniel Knowles, Nick King, Donald Kim, Jan
Source	Elsevier; Medline; PMC
abstract	Full-genome sequences have been used to monitor the fine-scale dynamics of epidemics caused by RNA viruses. However, the ability of this approach to confidently reconstruct transmission trees is limited by the knowledge of the genetic diversity of viruses that exist within different epidemiological units. In order to address this question, this study investigated the variability of 45 foot-and-mouth disease virus (FMDV) genome sequences (from 33 animals) that were collected during 2007 from eight premises (10 different herds) in the United Kingdom. Bayesian and statistical parsimony analysis demonstrated that these sequences exhibited clustering which was consistent with a transmission scenario describing herd-to-herd spread of the virus. As an alternative to analysing all of the available samples in future epidemics, the impact of randomly selecting one sequence from each of these herds was used to assess cost-effective methods that might be used to infer transmission trees during FMD outbreaks. Using these approaches, 85% and 91% of the resulting topologies were either identical or differed by only one edge from a reference tree comprising all of the sequences generated within the outbreak. The sequence distances that accrued during sequential transmission events between epidemiological units was estimated to be 4.6 nucleotides, although the genetic variability between viruses recovered from chronic carrier animals was higher than between viruses from animals with acute-stage infection: an observation which poses challenges for the use of simple approaches to infer transmission trees. This study helps to develop strategies for sampling during FMD outbreaks, and provides data that will guide the development of further models to support control policies in the event of virus incursions into FMD free countries.
has issue date	2015-04-08(xsd:dateTime)
bibo:doi	10.1016/j.meegid.2015.03.032
bibo:pmid	25861750
has license	no-cc
sha1sum (hex)	5b3dc04ff123b8aa8bca8f0caa665376bd16f6f9
schema:url	https://doi.org/10.1016/j.meegid.2015.03.032
resource representing a document's title	The impact of within-herd genetic variation upon inferred transmission trees for foot-and-mouth disease virus
has PubMed Central identifier	PMC7106308
has PubMed identifier	25861750
schema:publication	Infect Genet Evol
resource representing a document's body	covid:5b3dc04ff123b8aa8bca8f0caa665376bd16f6f9#body_text
is schema:about of	named entity 'infer' named entity 'recovered' named entity 'assess' named entity 'viruses' named entity 'estimated' named entity 'samples' named entity 'exist' named entity 'development' named entity 'foot-and-mouth disease virus' covid:arg/5b3dc04ff123b8aa8bca8f0caa665376bd16f6f9 named entity 'TRANSMISSION' named entity 'STRATEGIES' named entity 'ADDRESS' named entity 'RECONSTRUCT' named entity 'NUCLEOTIDES' named entity 'FOOT-AND-MOUTH DISEASE VIRUS' named entity 'INFERRED' named entity 'ESTIMATED' named entity 'DESCRIBING' named entity 'OBSERVATION' named entity 'FREE' named entity 'INVESTIGATED' named entity 'GENOME' named entity 'EDGE' named entity 'ASSESS' named entity 'CONSISTENT WITH' named entity 'IMPACT' named entity 'SCENARIO' named entity 'SAMPLES' named entity 'COLLECTED' named entity 'GENETIC DIVERSITY' named entity 'SCALE' named entity 'DATA' named entity 'ANIMALS' named entity 'TO SUPPORT' named entity 'THESE' named entity 'ACUTE' named entity 'RECOVERED' named entity 'HERD' named entity 'HAVE' named entity 'APPROACHES' named entity 'CHRONIC CARRIER' named entity 'STATISTICAL' named entity 'SELECTING' named entity 'GUIDE' named entity 'CAUSED BY' named entity 'CONTROL' named entity 'APPROACH' named entity 'COUNTRIES' named entity 'RNA VIRUSES' named entity 'USING' named entity 'GENETIC VARIATION' named entity 'ORDER' named entity 'KNOWLEDGE' named entity 'TREES' named entity 'DYNAMICS' named entity 'IMPACT' named entity 'IDENTICAL' named entity 'HELPS' named entity 'ALTERNATIVE' named entity 'STAGE' named entity 'EPIDEMIOLOGICAL' named entity 'SEQUENCES' named entity 'MONITOR' named entity 'DEVELOPMENT' named entity 'USED' named entity 'TREES' named entity 'HERD' named entity 'OUTBREAK' named entity 'SEQUENCE' named entity 'PROVIDES' named entity 'GENERATED' named entity 'OUTBREAKS' named entity 'TRANSMISSION' named entity 'HIGHER'

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