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Evaluating methods for Avian avulavirus-1 whole genome sequencing
Saar Tal1, Meirav Ben Izhak2, Chaim Wachtel3
1The Poultry Health Laboratories, The Egg and Poultry Board, Israel.
Gene: X
|June 19, 2020
Summary
Whole genome sequencing of Avian avulavirus-1 (AAvV-1) using Ion Torrent kits is sufficient for many applications. For higher accuracy in avian paramyxovirus sequencing, Illumina NextSeq and Proton Torrent kits are recommended.
Area of Science:
- Virology
- Genomics
- Molecular Biology
Background:
- Avian avulavirus-1 (AAvV-1), formerly Newcastle Disease Virus, causes significant disease outbreaks in poultry and wild birds.
- Various whole genome sequencing methods exist for AAvV-1, including cloning, PCR-based approaches, and next-generation sequencing (NGS).
Purpose of the Study:
- To evaluate and compare the performance of different whole genome sequencing methods for Avian avulavirus-1.
- To identify the most accurate and efficient sequencing strategies for AAvV-1 surveillance and research.
Main Methods:
- Sequencing of 173 AAvV-1 field isolates and one vaccine strain using Ion Torrent (Proton and PGM) and Illumina (MiSeq and NextSeq) platforms.
- Comparison of target-specific primers (SP) and Sequence Independent Single Primer Amplification (SISPA) methods with standard NGS kits.
Main Results:
- SP and SISPA methods sequenced via Ion Torrent showed high error rates and truncated genomes.
- NGS platform kits consistently produced high sequence accuracy and near-complete genomes.
- High mutation rates were observed in AAvV-1 intergenic regions and within genes, exceeding those in the Fusion region.
Conclusions:
- Ion Torrent whole genome sequencing is adequate for routine AAvV-1 surveillance.
- Illumina NextSeq and Proton Torrent kits offer superior fidelity for AAvV-1 genomic studies requiring higher accuracy.
Keywords:
AAvV-1AAvV-1, Newcastle Disease virusMutationsNCBI, National Center for Biotechnology InformationNGSNGS, Next Generation SequencingNewcastle disease virusPGM, Personal Genome MachineSISPA, Sequence Independent Single Primer AmplificationSP, Specific primersSequencingWGSWGS, Whole Genome Sequence or sequencingnt, nucleotide
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