Wed 14th March 2018
Time: 3pm, UK time
Other timings: 4pm CET, 8am PST, 11am EST, 11pm CST
*The webinar will be available on-demand after this date
Join Andrew Routh for a webinar, where he will discuss:
- What defective viral genomes are and how they affect the outcome of viral infections
- What sequencing strategies exist for the discovery and chacterisation of defective viral genomes and what their limitations are
- How nanopore sequencing provides a powerful and unique tool to identify defective viral genomes
An online Q&A session with Andrew will follow his talk.
Register to receive notifications about his talk.
Defective RNAs are copies of RNA viruses that naturally arise during viral infections due to viral recombination. Despite losing critical portions of the viral genome, defective RNAs retain the functional genomic elements required for replication and encapsidation and as a result can essentially ‘parasitize’ the wild-type viral infection. Defective RNAs have important roles in viral pathology as they can attenuate viral replication, alter the outcome of viral infection, induce viral persistence, and have been proposed as anti-viral therapeutics. Due to their complex genetic structure involving recombination, large insertions, deletions and duplications, nanopore sequencing provides a unique and powerful platform to characterise defective RNAs.
Using a combination of long- and short-read Next-Generation Sequencing, we have characterized defective RNAs that arise during serial passaging of Flock House virus (FHV) in cell-culture over a period of 30 days in order to elucidate the pathways and potential mechanisms defective RNA formation and evolution (Jaworski et al, PLoS Path, 2017). For short-read RNAseq, we employed ‘ClickSeq’ for its ability to sensitively and confidently detect RNA recombination events with nucleotide resolution. In parallel, we used the Oxford Nanopore Technologies’s (ONT) MinION to resolve full-length defective and wild-type viral genomes. Together, these accurately resolve both rare and common RNA recombination events, determine the correlation between recombination events, and quantify the relative abundance of different defective RNAs throughout passaging.
We are extending these studies using direct RNA and cDNA nanopore sequencing to characterize defective RNAs of enteroviruses and alphaviruses. These are important human pathogens, but the role or presence of defective RNAs in their lifecycles and pathology is currently unclear. I will present our on-going work characterising the abundance and genomic-makeup of defective viral genomes of these viruses both in cell-culture and biological specimens.
Andrew Routh, Assistant Professor, University of Texas Medical Branch obtained his under-graduate degrees in Cellular and Molecular Biochemistry from the University of Oxford, UK. Subsequently he moved to the Medical Research Council Laboratory of Molecular Biology (MRC-LMB) Cambridge, UK, obtaining his PhD under the supervision of Dr. Daniela Rhodes. Here, he studied the impact and roles of linker histones, nucleosome repeat length and histone post-transcriptional modifications upon the compaction and structure of the ‘30nm’ chromatin fibre. Andrew then moved to The Scripps Research Institute (La Jolla, California) as an EMBO post-doctoral fellow to study RNA virus replication, recombination and virion assembly under the mentorships of Prof. Jack Johnson and Prof. Bruce Torbett.
Andrew took up his current position as Assistant Professor at the University of Texas Medical Branch, Galveston, in the department of Biochemistry and Molecular Biology in 2015. In his lab, they combine molecular and cellular virology, next-generation sequencing and computational biology to study model RNA viruses such as Flock House virus, as well as human pathogens including human rhinoviruses, Coxsackievirus, chikungunya virus, and zika virus. Together, these provide clinically important and experimentally tractable model systems for the exploration of the principles of RNA virus biology and evolution.
Andrew Routh, Assistant Professor, University of Texas Medical Branch
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