Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Environmental Samples v1 Article Swipe

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Erika Bujáki , Alison Tedcastle , Thomas Wilton , khurshida not provided , Yasir Arshad , alammu not provided , Joyce Akello , Nick Grassly , Javier Martín , Catherine Troman , Alex Shaw , Andrew Rambaut , Áine O’Toole , c.ansley not provided , rachel.colquhoun not provided , Dimitra Klapsa ·

YOU? · · 2024 · Open Access · · DOI: https://doi.org/10.17504/protocols.io.8epv5r1wjg1b/v1

This protocol covers amplification of poliovirus nucleic acid from concentrated sewage samples and the subsequent sequencing of barcoded VP1 amplicons. The protocol was successfully tested on concentrates prepared with two-phase separation method, spin-column concentration and bag-mediated filtration system. Poliovirus molecular detection sensitivity will inherently depend on what viral content had been successfully captured in the starting wastewater concentrate sample. Viral RNA should be purified in duplicates from each concentrate following the method for MagMAX Viral RNA Isolation Large volume extraction protocol using 1.2 mL of concentrate for each extraction. It is recommended to perform the extraction fresh so the RNA can be used immediately after purification. Each RNA sample is then subjected to two step amplification in triplicates using a semi-nested PCR approach. Once controls are confirmed by gel electrophoresis, the PCR products are carried forward for nanopore sequencing library preparation. The PCR amplicons are pooled and purified before end-repair and dA-tailing. Following sequencing adapter ligation, the sequencing mix is prepared and loaded onto the flow cell. This protocol is for use with Oxford Nanopore kit14 chemistry ligation sequencing reagents and the prepared sequencing mix can be run on MinION Mk1B or GridION sequencer.

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Poliovirus Nanopore Biology Nanopore sequencing Evolutionary biology Virology Nanotechnology Genetics DNA sequencing Materials science Virus DNA

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Type: preprint
Language: en
Landing Page: https://doi.org/10.17504/protocols.io.8epv5r1wjg1b/v1
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DOI: https://doi.org/10.17504/protocols.io.8epv5r1wjg1b/v1

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Title: Direct Detection of poliovirus and Nanopore Sequencing (DDNS) - Environmental Samples v1

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Type: preprint

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Language: en

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Publication year: 2024

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Publication date: 2024-04-19

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Authors: Erika Bujáki, Alison Tedcastle, Thomas Wilton, khurshida not provided, Yasir Arshad, alammu not provided, Joyce Akello, Nick Grassly, Javier Martín, Catherine Troman, Alex Shaw, Andrew Rambaut, Áine O’Toole, c.ansley not provided, rachel.colquhoun not provided, Dimitra Klapsa

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Landing page: https://doi.org/10.17504/protocols.io.8epv5r1wjg1b/v1

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Concepts: Poliovirus, Nanopore, Biology, Nanopore sequencing, Evolutionary biology, Virology, Nanotechnology, Genetics, DNA sequencing, Materials science, Virus, DNA

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