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A. Shaw - Complete genome sequencing of FMDV using Nanopore sequencing

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A. Shaw - Complete genome sequencing of FMDV using Nanopore sequencing

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Session III
The benefits of complete genome sequencing have become increasingly clear, for example the identification of emergent lineages with altered phenotypic characteristics or the fine scale tracking of virus movements. Indeed, in the UK in 2007 complete genome sequencing enabled the tracing of an outbreak of foot-and-mouth disease virus (FMDV), in turn allowing the identification of a missing premises.
Previously, we showed that it was possible to sequence the capsid-coding region of the FMDV genome using nanopore sequencing technology (Oxford Nanopore Technologies) following amplification of the P1 region by RT-PCR. Here, we designed a universal RT-PCR based amplification strategy for the amplification of complete FMDV genomes prior to nanopore sequencing using the MinION sequencer.

Session III
The benefits of complete genome sequencing have become increasingly clear, for example the identification of emergent lineages with altered phenotypic characteristics or the fine scale tracking of virus movements. Indeed, in the UK in 2007 complete genome sequencing enabled the tracing of an outbreak of foot-and-mouth disease virus (FMDV), in turn allowing the identification of a missing premises.
Previously, we showed that it was possible to sequence the capsid-coding region of the FMDV genome using nanopore sequencing technology (Oxford Nanopore Technologies) following amplification of the P1 region by RT-PCR. Here, we designed a universal RT-PCR based amplification strategy for the amplification of complete FMDV genomes prior to nanopore sequencing using the MinION sequencer.

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A. Shaw - Complete genome sequencing of FMDV using Nanopore sequencing

  1. 1. EuFMD OS22 Andrew Shaw, Antonello Di Nardo, Ugo Ihearahu, Kebaneilwe Lebani, Nick Knowles, Jemma Wadsworth, Natasha Edwards, Donald King Complete genome sequencing of FMDV using Nanopore sequencing
  2. 2. #OS22 Digitalization and innovation applied to the prevention and control of foot-and-mouth and similar transboundary animal diseases (FAST) OS22 2 Introduction Why generate complete FMDV genomes? FMDV phylogenies are classically based upon the 1D region encoding VP1 due to its information dense nature and lack of recombination However… ● Complete genomes are required for fine-scale mapping of outbreaks ● Certain phenotypic traits are encoded outside of 1D, e.g. antigenic sites Andrew Shaw Nanopore sequencing of FMDV
  3. 3. #OS22 Digitalization and innovation applied to the prevention and control of foot-and-mouth and similar transboundary animal diseases (FAST) OS22 3 Genome tiling strategy Andrew Shaw Nanopore sequencing of FMDV Adapted from Grubman and Baxt 2004 RT-PCR amplification of genomes followed by nanopore sequencing
  4. 4. #OS22 Digitalization and innovation applied to the prevention and control of foot-and-mouth and similar transboundary animal diseases (FAST) OS22 4 Outcome Pan-FMDV oligo pools amplify entire genomes Andrew Shaw Nanopore sequencing of FMDV O/ZAM/8/2019 (MZ486070) O/ZAM/57/2019 (OM259994) O/ZAM/18/2019 (OM259984) O/ZAM/3/2019 (MZ486067) O/ZAM/7/2019 (MZ486069) O/ZAM/24/2019 (OM259987) O/ZAM/55/2019 (OM259992) O/ZAM/2/2019 (MZ486066) O/ZAM/4/2019 (MZ486068) O/ZAM/56/2019 (OM259993) O/ZAM/2/2020 (OM259999) O/ZAM/1/2020 (OM259998) O/ZAM/21/2019 (OM259986) O/ZAM/20/2019 (OM259985) O/ZAM/27/2019 (OM259989) O/ZAM/26/2019 (OM259988) O/ZAM06/2019* (MZ486071) O/ZAM07/2019* (MZ486072) O/ZAM/58/2019 (OM259995) O/ZAM/28/2019 (OM259990) O/ZAM/16/2019 (OM259983) O/ZAM/15/2019 (OM259982) O/ZAM/62/2019 (OM259997) O/ZAM/6/2020 (OM260002) O/ZAM/7/2020 (OM260003) O/ZAM/4/2020 (OM260001) O/ZAM/11/2020 (OM260007) O/ZAM/12/2020 (OM260008) O/ZAM/3/2020 (OM260000) O/ZAM/8/2020 (OM260004) O/ZAM/9/2020 (OM260005) O/ZAM/10/2020 (OM260006) O/ZAM/7/2021 (OM260012) O/ZAM/11/2021 nanopore O/ZAM/11/2021 (OM260014) O/ZAM/9/2021 (OM260013) O/NMB/1/2021 O/UGA/3/2002 (DQ165077) O/KEN/5/2002 (DQ165073) O/TAN/2/2004 (KF561679) O/MAL/1/98 (DQ165074) EA-2 EA-1 O/K40/84* (KY091280)
  5. 5. Thank you !.. www. https://www.pirbright.ac.uk/ andrew.shaw@pirbright.ac.uk @VirusMuser

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