Evaluating methods for Avian avulavirus-1 whole genome sequencing
| العنوان: | Evaluating methods for Avian avulavirus-1 whole genome sequencing |
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| المؤلفون: | Eyal Klement, Ziv Raviv, Tzipi Braun, Avishai Lublin, Elyakum Berman, Michael Pirak, Michal Bronstein, Elinor Yechezkel, Meirav Ben Izhak, Chaim Wachtel, Adi Turjeman, Yoram Louzoun, Caroline Banet-Noach, Einav Golan, Anat Wiseman, Saar Tal, Ruth Hadas |
| المصدر: | Gene: X, Vol 1, Iss, Pp-(2019) Gene: X |
| بيانات النشر: | Elsevier BV, 2019. |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | SP, Specific primers, nt, nucleotide, 0301 basic medicine, AAvV-1, Newcastle Disease virus, lcsh:QH426-470, NCBI, National Center for Biotechnology Information, Newcastle disease virus, Computational biology, Biology, Genome, Article, DNA sequencing, 03 medical and health sciences, 0302 clinical medicine, Genetics, Sequencing, Gene, AAvV-1, Whole genome sequencing, PGM, Personal Genome Machine, General Medicine, Ion semiconductor sequencing, biology.organism_classification, WGS, Whole Genome Sequence or sequencing, lcsh:Genetics, 030104 developmental biology, NGS, 030220 oncology & carcinogenesis, Avulavirus, SISPA, Sequence Independent Single Primer Amplification, Primer (molecular biology), NGS, Next Generation Sequencing, WGS, Mutations, Personal genomics |
| الوصف: | 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. Highlights • PCR amplification of the viral genome, results in partial genome sequences (72% and 98% respectively). • Primer based sequencing methods have 5 to 5.6 times more N reads compared to NGS platform sequencing kits, indicating poor sequence quality. • The Ion Torrent PGM sequencing results in sequencing 99% of the viral genome. • ProtonTorrent and Illumina Nextseq sequenced 99-100% of the viral genome, leading a to full genome sequence at high coverage. • The virus is mostly mutated within a host at intergenic regions. |
| تدمد: | 0378-1119 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4be478412fb0aa5141b7a0668b9fc4a9Test https://doi.org/10.1016/j.gene.2019.100004Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....4be478412fb0aa5141b7a0668b9fc4a9 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 03781119 |
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