Rapid and sensitive direct detection and identification of poliovirus using nanopore sequencing
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Global poliovirus surveillance involves the identification of the virus from both the stool samples of potential cases and from environmental samples (sewage) that can reveal transmission of the virus within a population. The current detection algorithm requires the culture of the virus within cell lines and can take 2-3 weeks to progress from sample receipt to a sequencing result, with confirmation of poliovirus being established through the genetic sequence of the VP1 capsid region. Rapid detection and identification of the virus is however essential in informing the correct response to a potential virus outbreak. We have developed a rapid poliovirus amplification and sequencing method using the Oxford Nanopore MinION that has allowed us to provide viral identification in under three days. We can rapidly and accurately determine between the three poliovirus serotypes, identifying both wildtype and Sabin (vaccine) strains. We were also able to resolve samples containing mixtures of polioviruses, including vaccine-derived polioviruses (VDPVs) which can deviate from vaccine (Sabin) strains by as little as six nucleotides over the ~900 bp VP1 region.