Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing

Biology – Quantitative Biology – Genomics

Scientific paper

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

Scientific paper

The sequence diversity of viral populations within individual hosts is the starting material for selection and subsequent evolution of RNA viruses such as foot-and-mouth disease virus (FMDV). Using next-generation sequencing (NGS) performed on a Genome Analyzer platform (Illumina), this study compared the viral populations within two bovine epithelial samples (foot lesions) from a single animal with the Inoculum used to initiate experimental infection. Genomic sequences were determined in duplicate sequencing runs, and the consensus sequence determined by NGS, for the Inoculum, was identical to that previously determined using the Sanger method. However, NGS reveals the fine polymorphic sub-structure of the viral population, from nucleotide variants present at just below 50% frequency to those present at fractions of 1%. Some of the higher frequency polymorphisms identified encoded changes within codons associated with heparan sulphate binding and were present in both feet lesions revealing intermediate stages in the evolution of a tissue-culture adapted virus replicating within a mammalian host. We identified 2,622, 1,434 and 1,703 polymorphisms in the Inoculum, and in the two foot lesions respectively: most of the substitutions occurred only in a small fraction of the population and represent the progeny from recent cellular replication prior to onset of any selective pressures. We estimated an upper limit for the genome-wide mutation rate of the virus within a cell to be 7.8 x 10-4 per nt. The greater depth of detection, achieved by NGS, demonstrates that this method is a powerful and valuable tool for the dissection of FMDV populations within-hosts.

No associations

LandOfFree

Say what you really think

Search LandOfFree.com for scientists and scientific papers. Rate them and share your experience with other people.

Rating

Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.

If you have personal experience with Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus using next-generation genome sequencing will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFWR-SCP-O-546314

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.