Evaluating methods for Avian avulavirus-1 whole genome sequencing

Saar Tal, Meirav Ben Izhak, Chaim Wachtel, Anat Wiseman, Tzipi Braun, Elinor Yechezkel, Einav Golan, Ruth Hadas, Adi Turjeman, Caroline Banet-Noach, Michal Bronstein, Avishai Lublin, Elyakum Berman, Ziv Raviv, Michael Pirak, Eyal Klement, Yoram Louzoun

Research output: Contribution to journalArticlepeer-review

2 Scopus citations

Abstract

Background: Avian avulavirus-1 (AAvV-1, previously Newcastle Disease Virus) is responsible for poultry and wild birds' disease outbreaks. Numerous whole genome sequencing methods were reported for this virus. These methods included cloning, specific primers amplification, shotgun PCR approaches, Sequence Independent Single Primer Amplification and next generation sequencing platform kits. Methods: Three methods were used to sequence 173 Israeli Avian avulavirus-1 field isolates and one vaccine strain (VH). The sequencing was performed on Proton and Ion Torrent Personal Genome Machine and to a lesser extent, Illumina MiSeq and NextSeq sequencers. Target specific primers (SP) and Sequence Independent Single Primer Amplification (SISPA) products sequenced via the Ion torrent sequencer had a high error rate and truncated genomes. All the next generation sequencing platform sequencing kits generated high sequence accuracy and near-complete genomic size. Results: A high level of mutations was observed in the intergenic regions between the avian avulavirus-1 genes. Within genes, multiple regions are more mutated than the Fusion region currently used for typing. Conclusions: Our findings suggest that the whole genome sequencing by the Ion torrent sequencing kit is sufficient. However, when higher fidelity is desired, the Illumina NextSeq and Proton torrent sequencing kits were found to be preferable.

Original languageEnglish
Article number100004
JournalGene: X
Volume1
DOIs
StatePublished - Feb 2019

Bibliographical note

Publisher Copyright:
© 2019

Keywords

  • AAvV-1
  • Mutations
  • NGS
  • Newcastle disease virus
  • Sequencing
  • WGS

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