Sequence data and evidence of possible airborne spread in the 2001 foot‐and‐mouth disease epidemic in the UK

König, Guido; Cottam, Eleanor M.; Upadhyaya, Sasmita; Gloster, J.; Mansley, L. M.; Haydon, Daniel T.; King, Donald P.

doi:10.1136/vr.165.14.410

Cited by 10 publications

(7 citation statements)

References 6 publications

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“…Although next-generation sequencing was not available at the time of the epidemic, collection of viral samples across the epidemic has allowed retrospective analysis. Konig et al [48] used consensus WGS to test specific hypotheses regarding the airborne spread of FMDV. Cottam et al [30] used genetic data as a filter to identify a subset of the trees that were then ranked based on their likelihood given the associated space-time data.…”

Section: Reviewmentioning

confidence: 99%

Supersize me: how whole-genome sequencing and big data are transforming epidemiology

Kao

Haydon

Lycett

et al. 2014

Trends in Microbiology

117

111

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In epidemiology, the identification of 'who infected whom' allows us to quantify key characteristics such as incubation periods, heterogeneity in transmission rates, duration of infectiousness, and the existence of high-risk groups. Although invaluable, the existence of many plausible infection pathways makes this difficult, and epidemiological contact tracing either uncertain, logistically prohibitive, or both. The recent advent of next-generation sequencing technology allows the identification of traceable differences in the pathogen genome that are transforming our ability to understand high-resolution disease transmission, sometimes even down to the host-to-host scale. We review recent examples of the use of pathogen whole-genome sequencing for the purpose of forensic tracing of transmission pathways, focusing on the particular problems where evolutionary dynamics must be supplemented by epidemiological information on the most likely timing of events as well as possible transmission pathways. We also discuss potential pitfalls in the over-interpretation of these data, and highlight the manner in which a confluence of this technology with sophisticated mathematical and statistical approaches has the potential to produce a paradigm shift in our understanding of infectious disease transmission and control.

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Section: Reviewmentioning

confidence: 99%

Supersize me: how whole-genome sequencing and big data are transforming epidemiology

Kao

Haydon

Lycett

et al. 2014

Trends in Microbiology

117

111

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“…It lacks an envelope and is grouped under the family of Picornaviridae, genus Aphthovirus [11]. It is 25 to 30 nm diameter in size, being a very simple and small in structure, which accelerates the air transmission of the virus, allowing it to spread over long distances in a very short time by following the nature of the wind speed and direction [12,13].…”

Section: Introductionmentioning

confidence: 99%

Review on Outbreak Dynamics, the Endemic Serotypes, and Diversified Topotypic Profiles of Foot and Mouth Disease Virus Isolates in Ethiopia from 2008 to 2018

Wubshet

Dai

et al. 2019

Viruses

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Foot and mouth disease (FMD) endemicity in Ethiopia’s livestock remains an ongoing cause for economic concern, with new topotypes still arising even in previously unaffected areas. FMD outbreaks occur every year almost throughout the country. Understanding the outbreak dynamics, endemic serotypes, and lineage profiles of FMD in this country is very critical in designing control and prevention programs. For this, detailed information on outbreak dynamics in Ethiopia needs to be understood clearly. In this article, therefore, we review the spatial and temporal patterns and dynamics of FMD outbreaks from 2008 to 2018. The circulating serotypes and the topotypic profiles of the virus are also discussed. FMD outbreak data were obtained from; reports of MoARD (Ministry of Agriculture and Rural Development)/MoLF (Ministry of livestock and Fishery, NVI (National Veterinary Institute), and NAHDIC (National Animal Health Diagnostic and Investigation Center); published articles; MSc works; PhD theses; and documents from international organizations. To effectively control and prevent FMD outbreaks, animal health agencies should focus on building surveillance systems that can quickly identify and control ongoing outbreaks and implement efficient preventive measures.

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“…These reports are based on consensus genomes sequenced directly from epithelial lesions, blood or oesophageal–pharyngeal scrapings (probang samples) collected from individual animals on infected premises (IPs). The 2001 post-outbreak investigation retrospectively resolved inter-farm transmission of FMDV (Cottam et al , 2006, 2008a; König et al , 2009). In 2007, full-genome sequencing was used in ‘real time’ to identify the initial outbreak virus and to connect the first and second temporal clusters of IPs (Cottam et al , 2008b).…”

Section: Introductionmentioning

confidence: 99%

Accumulation of nucleotide substitutions occurring during experimental transmission of foot-and-mouth disease virus

Juleff

Valdazo-González

Wadsworth

et al. 2013

Journal of General Virology

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Analysis of full-genome sequences was previously used to trace the origin and transmission pathways of foot-and-mouth disease virus (FMDV) outbreaks in the UK in 2001 and 2007. Interpretation of these data was sometimes at variance with conventional epidemiological tracing, and was also used to predict the presence of undisclosed infected premises that were later discovered during serological surveillance. Here we report the genome changes associated with sequential passage of a highly BHK-21-cell-adapted (heparan sulphate-binding) strain of FMDV arising from two independent transmission chains in cattle. In vivo virus replication rapidly selected for a wild-type variant with an amino acid substitution at VP356. Full-genome sequence analysis clearly demonstrated sequence divergence during parallel passage. The genetic diversity generated over the course of infection and the rate at which these changes became fixed and were transmitted between cattle occurred at a rate sufficient to enable reliable tracing of transmission pathways at the level of the individual animal. However, tracing of transmission pathways was only clear when sequences from epithelial lesions were compared. Sequences derived from oesophageal–pharyngeal scrapings were problematic to interpret, with a varying number of ambiguities suggestive of a more diverse virus population. These findings will help to correctly interpret full-genome sequence analyses to resolve transmission pathways within future FMDV epidemics.

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Sequence data and evidence of possible airborne spread in the 2001 foot‐and‐mouth disease epidemic in the UK

Abstract: * Dates as estimated by Gloster and others (2005) † Ideal meteorological conditions for airborne transmission of FMDV to the farms involved in this study occurred on the nights of

Cited by 10 publications

References 6 publications

Supersize me: how whole-genome sequencing and big data are transforming epidemiology

Supersize me: how whole-genome sequencing and big data are transforming epidemiology

Review on Outbreak Dynamics, the Endemic Serotypes, and Diversified Topotypic Profiles of Foot and Mouth Disease Virus Isolates in Ethiopia from 2008 to 2018

Accumulation of nucleotide substitutions occurring during experimental transmission of foot-and-mouth disease virus

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