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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: The distribution of variants across the FMDV genome. The variants belonging to each sample are indicated by a difference in colour. Sample 147 – red; sample 161A – orange; sample 004 – yellow; sample 241 – green; sample 161B – dark blue; sample 341 – black, and sample 238 – grey. b: A Circos histogram showing the relationship between FMDV consensus and sub-consensus variants. Only variants that were called by Lofreq in both duplicates and shared between 2 of more samples are represented here. The histogram is split into 7 sections, with each representing a different sample. Each genome region is represented by a different colour (light grey – 5′UTR, dark grey – leader, dark blue – VP4, dark green – VP2, red – VP3, dark purple – VP1, dark orange – 2A, light blue – 2B, light green – 2C, light orange – 3A, light purple – 3B, yellow – 3C, black – 3D, grey – 3′UTR). Variants which are shared between 2 or more samples are indicated with links, with the colour correlating to the coding region the variant is present in. The inner circles represent the variant frequencies across the genome. In pseudo log scale, the first gridline represents variants from 0% to 1%, the second gridline represents variants from 1% to 10%, the third gridline represents variants from 10% to 50% and the fourth gridline represents variants from 50% to 100%. For visual purposes, variants were scaled up, 0% to 1% was scaled up to 1%, 1% to 10% was scaled up to 10%, 10% to 50% was scaled up to 50% and 50% to 100% was scaled up to 100%.
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f0015: a: The distribution of variants across the FMDV genome. The variants belonging to each sample are indicated by a difference in colour. Sample 147 – red; sample 161A – orange; sample 004 – yellow; sample 241 – green; sample 161B – dark blue; sample 341 – black, and sample 238 – grey. b: A Circos histogram showing the relationship between FMDV consensus and sub-consensus variants. Only variants that were called by Lofreq in both duplicates and shared between 2 of more samples are represented here. The histogram is split into 7 sections, with each representing a different sample. Each genome region is represented by a different colour (light grey – 5′UTR, dark grey – leader, dark blue – VP4, dark green – VP2, red – VP3, dark purple – VP1, dark orange – 2A, light blue – 2B, light green – 2C, light orange – 3A, light purple – 3B, yellow – 3C, black – 3D, grey – 3′UTR). Variants which are shared between 2 or more samples are indicated with links, with the colour correlating to the coding region the variant is present in. The inner circles represent the variant frequencies across the genome. In pseudo log scale, the first gridline represents variants from 0% to 1%, the second gridline represents variants from 1% to 10%, the third gridline represents variants from 10% to 50% and the fourth gridline represents variants from 50% to 100%. For visual purposes, variants were scaled up, 0% to 1% was scaled up to 1%, 1% to 10% was scaled up to 10%, 10% to 50% was scaled up to 50% and 50% to 100% was scaled up to 100%.

Mentions: The majority of the diversity characterised by Lofreq in all samples was sub-consensus, with 104 unique variants identified with a frequency between 0.24% and 50%. Overall, the mean number of variants for each sample was 19.7, with sample 341 having the highest number (37) and sample 147 having the lowest number (7). The total number and frequency of variants found within each coding region can be found in Table 2 and in Fig. 3a. For this sample set, the highest and lowest relative mutational frequencies were observed in the sequences that encode 2A and 2C, respectively; however, analyses of more samples may be required to properly determine whether these fluctuations across the genome are reproducible and reflect an aspect of FMDV replication and transmission.


Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus ☆
a: The distribution of variants across the FMDV genome. The variants belonging to each sample are indicated by a difference in colour. Sample 147 – red; sample 161A – orange; sample 004 – yellow; sample 241 – green; sample 161B – dark blue; sample 341 – black, and sample 238 – grey. b: A Circos histogram showing the relationship between FMDV consensus and sub-consensus variants. Only variants that were called by Lofreq in both duplicates and shared between 2 of more samples are represented here. The histogram is split into 7 sections, with each representing a different sample. Each genome region is represented by a different colour (light grey – 5′UTR, dark grey – leader, dark blue – VP4, dark green – VP2, red – VP3, dark purple – VP1, dark orange – 2A, light blue – 2B, light green – 2C, light orange – 3A, light purple – 3B, yellow – 3C, black – 3D, grey – 3′UTR). Variants which are shared between 2 or more samples are indicated with links, with the colour correlating to the coding region the variant is present in. The inner circles represent the variant frequencies across the genome. In pseudo log scale, the first gridline represents variants from 0% to 1%, the second gridline represents variants from 1% to 10%, the third gridline represents variants from 10% to 50% and the fourth gridline represents variants from 50% to 100%. For visual purposes, variants were scaled up, 0% to 1% was scaled up to 1%, 1% to 10% was scaled up to 10%, 10% to 50% was scaled up to 50% and 50% to 100% was scaled up to 100%.
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f0015: a: The distribution of variants across the FMDV genome. The variants belonging to each sample are indicated by a difference in colour. Sample 147 – red; sample 161A – orange; sample 004 – yellow; sample 241 – green; sample 161B – dark blue; sample 341 – black, and sample 238 – grey. b: A Circos histogram showing the relationship between FMDV consensus and sub-consensus variants. Only variants that were called by Lofreq in both duplicates and shared between 2 of more samples are represented here. The histogram is split into 7 sections, with each representing a different sample. Each genome region is represented by a different colour (light grey – 5′UTR, dark grey – leader, dark blue – VP4, dark green – VP2, red – VP3, dark purple – VP1, dark orange – 2A, light blue – 2B, light green – 2C, light orange – 3A, light purple – 3B, yellow – 3C, black – 3D, grey – 3′UTR). Variants which are shared between 2 or more samples are indicated with links, with the colour correlating to the coding region the variant is present in. The inner circles represent the variant frequencies across the genome. In pseudo log scale, the first gridline represents variants from 0% to 1%, the second gridline represents variants from 1% to 10%, the third gridline represents variants from 10% to 50% and the fourth gridline represents variants from 50% to 100%. For visual purposes, variants were scaled up, 0% to 1% was scaled up to 1%, 1% to 10% was scaled up to 10%, 10% to 50% was scaled up to 50% and 50% to 100% was scaled up to 100%.
Mentions: The majority of the diversity characterised by Lofreq in all samples was sub-consensus, with 104 unique variants identified with a frequency between 0.24% and 50%. Overall, the mean number of variants for each sample was 19.7, with sample 341 having the highest number (37) and sample 147 having the lowest number (7). The total number and frequency of variants found within each coding region can be found in Table 2 and in Fig. 3a. For this sample set, the highest and lowest relative mutational frequencies were observed in the sequences that encode 2A and 2C, respectively; however, analyses of more samples may be required to properly determine whether these fluctuations across the genome are reproducible and reflect an aspect of FMDV replication and transmission.

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.