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

doi:10.1016/j.gene.2019.100004

Evaluating methods for Avian avulavirus-1 whole genome sequencing

Gene X. 2019 Jan 9:1:100004. doi: 10.1016/j.gene.2019.100004. eCollection 2019 Feb.

Authors

Saar Tal¹, Meirav Ben Izhak², Chaim Wachtel³, Anat Wiseman^{1

4}, Tzipi Braun², Elinor Yechezkel¹, Einav Golan¹, Ruth Hadas⁵, Adi Turjeman⁶, Caroline Banet-Noach⁷, Michal Bronstein⁶, Avishai Lublin⁵, Elyakum Berman¹, Ziv Raviv⁴, Michael Pirak¹, Eyal Klement⁴, Yoram Louzoun⁸

Affiliations

¹ The Poultry Health Laboratories, The Egg and Poultry Board, Israel.
² Life Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel.
³ HyLabs NGS Services, Israel.
⁴ Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel.
⁵ Kimron Veterinary Institute, Division of Avian Diseases, Israel.
⁶ The Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.
⁷ Phibro Animal Health Corp. Ltd, Israel.
⁸ Department of Mathematics and Gonda Brain Research Center, Bar Ilan University, Israel.

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.

Keywords: AAvV-1; AAvV-1, Newcastle Disease virus; Mutations; NCBI, National Center for Biotechnology Information; NGS; NGS, Next Generation Sequencing; Newcastle disease virus; PGM, Personal Genome Machine; SISPA, Sequence Independent Single Primer Amplification; SP, Specific primers; Sequencing; WGS; WGS, Whole Genome Sequence or sequencing; nt, nucleotide.