Circular sequencing (CirSeq) is a genetic sequencing technique which was developed at UCSF by the Andino lab and is published in Nature has become the preeminent sequencing technique due to its high accuracy. CirSeq provides accurate detection of virus genome mutations by identifying and correcting sequencing errors. CirSeq allows for the identification of individual viral strains within a population, through highly accurate sequence data. In parallel, the utilization of our innovative sequencing platform allows for a new genetic approach to study the evolution of viruses within the context of their host. CirSeq works by creating a large number of copies of each virus through rolling circle replication, a process in which hundreds of copies are made of each individual virus. In this way each individual virus is represented by a large number of copies, which allows researchers to see if that individual virus had a mutation. (If only one virus in a population has a mutation according to sequencing data, it is not clear whether that mutation is real or perhaps a sequencing error. If 100 copies of the virus all have that mutation, it is clear that it is indeed a mutation and not a sequencing error.)
Frequencies of the detected mutations across polio virus passages were mapped over time, allowing the viruses to infect multiple cells and then estimating the rate and type of mutations that occurred. From the clustering methods, the 2B segment of the polio genome looks to have mutations that are highly associated with fitness (better ability to survive, reproduce, etc.). Other clusters of mutations were found in the protease and polymerase region of the polio genome, which are also important regions.
Above is the TbioInfo Virology Modeling Pipeline that includes 3 main sections: Cirseq, Regular NGS and Integration.
In the big scheme this could mean that changes in certain regions of the virus could prevent it from properly infecting a cell. Understanding the mutations that occur and how those different viruses are able to adapt give researchers an understanding of areas for potential drug or vaccine targets.
In light of ongoing research using CirSeq, computational approaches have been implemented as parts of the T-BioInfo Platform. The platform offers a visual and intuitive interface to connect algorithms into pipelines, making the computational approach more user friendly. The virology pipeline on T-BioInfo integrates visualization as an output, allowing researchers to see their data in a clear and meaningful way. The use of visualization allows for identification of significant biological insights without overwhelming the user with informatics complexities that are not necessary for a biologist to understand.
See the link below for a more detailed description of Pine Biotech’s vision for virology research using CirSeq and the T-BioInfo platform.
For an interactive demo of the output, you can view this link: http://www.pine-biotech.com/viz/views/poliotest.html