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Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus ☆

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ABSTRACT

Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT–PCR method was developed to amplify a 7.6 kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal.

No MeSH data available.


Related in: MedlinePlus

Statistical parsimony analysis of consensus sequences generated in relation to the estimated lesion age of each sample. Grey triangles represent samples that were sequenced as part of this study, white triangles (i.e. UKG/95 and UKG/93) indicate samples from IP2b sequenced previously by Sanger methods (Valdazo-González et al., 2015). Black lines represent single nucleotide substitutions. Closest consensus sequences for viruses recovered from other farms infected in sequence (IP1b and IP5) are indicated.
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f0010: Statistical parsimony analysis of consensus sequences generated in relation to the estimated lesion age of each sample. Grey triangles represent samples that were sequenced as part of this study, white triangles (i.e. UKG/95 and UKG/93) indicate samples from IP2b sequenced previously by Sanger methods (Valdazo-González et al., 2015). Black lines represent single nucleotide substitutions. Closest consensus sequences for viruses recovered from other farms infected in sequence (IP1b and IP5) are indicated.

Mentions: Statistical parsimony analysis was used to generate a transmission network to investigate the genetic relatedness between FMDV sequences recovered on IP2b (Fig. 2). The consensus sequence of Sample 341 was most genetically similar to FMD viruses collected from IP1b (1 nucleotide difference) and IP2c (2 nucleotide differences) (data not shown in figure). Sample 341 and 147 (both 6 days old) were identical to previously published consensus sequences derived from the same animals on IP2b (GenBank accession numbers: KJ560280 and KJ560282 respectively). Sample 238 exhibited a single nucleotide difference to sample 341, but also demonstrated close nucleotide identify to the consensus sequences derived from IP5 and later IPs (Fig. 2). Over the amplicon region compared in this study, the consensus sequence of sample 004 was also found to be identical to a previously published sequence from IP2b (EU448373; data not shown); however original records at The Pirbright Institute show that these sequences derive from different animals.


Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus ☆
Statistical parsimony analysis of consensus sequences generated in relation to the estimated lesion age of each sample. Grey triangles represent samples that were sequenced as part of this study, white triangles (i.e. UKG/95 and UKG/93) indicate samples from IP2b sequenced previously by Sanger methods (Valdazo-González et al., 2015). Black lines represent single nucleotide substitutions. Closest consensus sequences for viruses recovered from other farms infected in sequence (IP1b and IP5) are indicated.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5036933&req=5

f0010: Statistical parsimony analysis of consensus sequences generated in relation to the estimated lesion age of each sample. Grey triangles represent samples that were sequenced as part of this study, white triangles (i.e. UKG/95 and UKG/93) indicate samples from IP2b sequenced previously by Sanger methods (Valdazo-González et al., 2015). Black lines represent single nucleotide substitutions. Closest consensus sequences for viruses recovered from other farms infected in sequence (IP1b and IP5) are indicated.
Mentions: Statistical parsimony analysis was used to generate a transmission network to investigate the genetic relatedness between FMDV sequences recovered on IP2b (Fig. 2). The consensus sequence of Sample 341 was most genetically similar to FMD viruses collected from IP1b (1 nucleotide difference) and IP2c (2 nucleotide differences) (data not shown in figure). Sample 341 and 147 (both 6 days old) were identical to previously published consensus sequences derived from the same animals on IP2b (GenBank accession numbers: KJ560280 and KJ560282 respectively). Sample 238 exhibited a single nucleotide difference to sample 341, but also demonstrated close nucleotide identify to the consensus sequences derived from IP5 and later IPs (Fig. 2). Over the amplicon region compared in this study, the consensus sequence of sample 004 was also found to be identical to a previously published sequence from IP2b (EU448373; data not shown); however original records at The Pirbright Institute show that these sequences derive from different animals.

View Article: PubMed Central - PubMed

ABSTRACT

Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT–PCR method was developed to amplify a 7.6 kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal.

No MeSH data available.


Related in: MedlinePlus