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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Exotic & Emerging Avian Viral Diseases Research » Research » Publications at this Location » Publication #350343
Research Project: Intervention Strategies to Prevent and Control Disease Outbreaks Caused by Emerging Strains of Avian Influenza Viruses

Location: Exotic & Emerging Avian Viral Diseases Research

Title: Use of the Minion nanopore sequencer for rapid sequencing of avian influenza virus isolates

Author
item GORAICHUK, IRYNA - Consultant
item DIMITROV, KIRIL - Consultant
item Afonso, Claudio
item Suarez, David

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 3/15/2018
Publication Date: 4/15/2018
Citation: Goraichuk, I., Dimitrov, K., Afonso, C.L., Suarez, D.L. 2018. Use of the Minion nanopore sequencer for rapid sequencing of avian influenza virus isolates. Meeting Abstract. 10th International Symposium on Avian Influenza, April 15-18, 2018, Brighton, United Kingdom. p. 71.

Interpretive Summary:

Technical Abstract: A relatively new sequencing technology, the MinION nanopore sequencer, provides a platform that is smaller, faster, and cheaper than existing Next Generation Sequence (NGS) technologies. The MinION sequences of individual strands of DNA and can produce millions of sequencing reads. The cost of the sequencer itself is around $1000, which is considerable less than other NGS sequencers. The reagents for NGS are expensive, but different methods of processing multiple samples on a single run allow for reasonable costs per sample. Efforts to use Barcoding, which provides unique 24 nucleotide sequences attached to the 5’ end of PCR primers, have been developed which makes the MinION system cheaper than the MiSEQ for both influenza and Newcastle disease virus samples with costs of approximately $36 per sample. Specific primers for H5, H7, and H9 subtypes were developed that could be used with or without pan-influenza specific primers. A large part of the hemagglutinin gene can be amplified to allow for pathotype determination as well as provide enough sequence for molecular epidemiology. Because of the large amount of data produced, bioinformatics remains a bottleneck for analysis, and open source Galaxy software on a multicore server can be used with the MinION, similar to the MiSeq. However, efforts to rapidly analyze the data on the same laptop computer used to run the MinION sequencer are in progress. Because of the much lower cost of entry for this technology, more veterinary diagnostic labs are likely to begin using the technology for diagnostics of many pathogens.