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

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.


A pairwise comparison of the relationships between consensus sequences (genomic distance) and shared variants in the viral swarm populations. Each of the samples was compared to the other samples in turn, giving a total of 42 data points. Firstly the genome distance (number of nucleotide substitutions in the consensus sequences) between the samples was calculated. Secondly, the observed number of shared variants between the samples was divided by the total number of observed variants in one of the samples (as a consequence, a different value was generated when comparing samples X and Y than when comparing sample Y to X, to address differences in depth of coverage between the samples).
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f0020: A pairwise comparison of the relationships between consensus sequences (genomic distance) and shared variants in the viral swarm populations. Each of the samples was compared to the other samples in turn, giving a total of 42 data points. Firstly the genome distance (number of nucleotide substitutions in the consensus sequences) between the samples was calculated. Secondly, the observed number of shared variants between the samples was divided by the total number of observed variants in one of the samples (as a consequence, a different value was generated when comparing samples X and Y than when comparing sample Y to X, to address differences in depth of coverage between the samples).

Mentions: The hypothesis that as a virus disseminates through multiple hosts, the number of shared variants from the source of infection decreases, was investigated by a comparative analysis of each of the 7 samples to the other 6. No correlation between similarities in the swarm structure and the relatedness of consensus sequences was identified, suggesting that variation within a viral population is unique to the individual infected host (Fig. 4).


Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus ☆
A pairwise comparison of the relationships between consensus sequences (genomic distance) and shared variants in the viral swarm populations. Each of the samples was compared to the other samples in turn, giving a total of 42 data points. Firstly the genome distance (number of nucleotide substitutions in the consensus sequences) between the samples was calculated. Secondly, the observed number of shared variants between the samples was divided by the total number of observed variants in one of the samples (as a consequence, a different value was generated when comparing samples X and Y than when comparing sample Y to X, to address differences in depth of coverage between the samples).
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

f0020: A pairwise comparison of the relationships between consensus sequences (genomic distance) and shared variants in the viral swarm populations. Each of the samples was compared to the other samples in turn, giving a total of 42 data points. Firstly the genome distance (number of nucleotide substitutions in the consensus sequences) between the samples was calculated. Secondly, the observed number of shared variants between the samples was divided by the total number of observed variants in one of the samples (as a consequence, a different value was generated when comparing samples X and Y than when comparing sample Y to X, to address differences in depth of coverage between the samples).
Mentions: The hypothesis that as a virus disseminates through multiple hosts, the number of shared variants from the source of infection decreases, was investigated by a comparative analysis of each of the 7 samples to the other 6. No correlation between similarities in the swarm structure and the relatedness of consensus sequences was identified, suggesting that variation within a viral population is unique to the individual infected host (Fig. 4).

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.