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Published on: July 27, 2018
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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
|September 17, 2021
Summary
Whole genome sequencing of Avian avulavirus-1 (AAvV-1) using Ion Torrent kits is sufficient for many applications. For higher accuracy, Illumina NextSeq and Proton Torrent kits are recommended for AAvV-1 surveillance.
Area of Science:
- Virology
- Genomics
- Molecular Biology
Background:
- Avian avulavirus-1 (AAvV-1), formerly Newcastle Disease Virus, causes significant disease in poultry and wild birds.
- Various whole genome sequencing methods exist for AAvV-1, including cloning, PCR, and next-generation sequencing (NGS).
Purpose of the Study:
- To evaluate the efficacy of different whole genome sequencing methods for Avian avulavirus-1 field isolates.
- To compare the accuracy and completeness of genomic data generated by various NGS platforms.
Main Methods:
- Sequencing of 173 AAvV-1 field isolates and one vaccine strain using Ion Torrent, Illumina MiSeq, and NextSeq platforms.
- Comparison of target-specific primers (SP) and Sequence Independent Single Primer Amplification (SISPA) with NGS kits.
Main Results:
- Ion Torrent sequencing with SP and SISPA resulted in 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 mutations in the Fusion region.
Conclusions:
- Whole genome sequencing using Ion Torrent kits is adequate for general AAvV-1 analysis.
- Illumina NextSeq and Proton Torrent sequencing kits offer superior fidelity for AAvV-1 whole genome sequencing when high accuracy is critical.
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