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Evaluating methods for Avian avulavirus-1 whole genome sequencing

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...

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Autores principales: Tal, Saar, Ben Izhak, Meirav, Wachtel, Chaim, Wiseman, Anat, Braun, Tzipi, Yechezkel, Elinor, Golan, Einav, Hadas, Ruth, Turjeman, Adi, Banet-Noach, Caroline, Bronstein, Michal, Lublin, Avishai, Berman, Elyakum, Raviv, Ziv, Pirak, Michael, Klement, Eyal, Louzoun, Yoram
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285907/
https://www.ncbi.nlm.nih.gov/pubmed/32550541
http://dx.doi.org/10.1016/j.gene.2019.100004
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author Tal, Saar
Ben Izhak, Meirav
Wachtel, Chaim
Wiseman, Anat
Braun, Tzipi
Yechezkel, Elinor
Golan, Einav
Hadas, Ruth
Turjeman, Adi
Banet-Noach, Caroline
Bronstein, Michal
Lublin, Avishai
Berman, Elyakum
Raviv, Ziv
Pirak, Michael
Klement, Eyal
Louzoun, Yoram
author_facet Tal, Saar
Ben Izhak, Meirav
Wachtel, Chaim
Wiseman, Anat
Braun, Tzipi
Yechezkel, Elinor
Golan, Einav
Hadas, Ruth
Turjeman, Adi
Banet-Noach, Caroline
Bronstein, Michal
Lublin, Avishai
Berman, Elyakum
Raviv, Ziv
Pirak, Michael
Klement, Eyal
Louzoun, Yoram
author_sort Tal, Saar
collection PubMed
description 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.
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spelling pubmed-72859072020-06-16 Evaluating methods for Avian avulavirus-1 whole genome sequencing Tal, Saar Ben Izhak, Meirav Wachtel, Chaim Wiseman, Anat Braun, Tzipi Yechezkel, Elinor Golan, Einav Hadas, Ruth Turjeman, Adi Banet-Noach, Caroline Bronstein, Michal Lublin, Avishai Berman, Elyakum Raviv, Ziv Pirak, Michael Klement, Eyal Louzoun, Yoram Gene X Article 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. Elsevier 2019-01-09 /pmc/articles/PMC7285907/ /pubmed/32550541 http://dx.doi.org/10.1016/j.gene.2019.100004 Text en © 2019 Published by Elsevier B.V. http://creativecommons.org/licenses/by-nc-nd/4.0/ This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Article
Tal, Saar
Ben Izhak, Meirav
Wachtel, Chaim
Wiseman, Anat
Braun, Tzipi
Yechezkel, Elinor
Golan, Einav
Hadas, Ruth
Turjeman, Adi
Banet-Noach, Caroline
Bronstein, Michal
Lublin, Avishai
Berman, Elyakum
Raviv, Ziv
Pirak, Michael
Klement, Eyal
Louzoun, Yoram
Evaluating methods for Avian avulavirus-1 whole genome sequencing
title Evaluating methods for Avian avulavirus-1 whole genome sequencing
title_full Evaluating methods for Avian avulavirus-1 whole genome sequencing
title_fullStr Evaluating methods for Avian avulavirus-1 whole genome sequencing
title_full_unstemmed Evaluating methods for Avian avulavirus-1 whole genome sequencing
title_short Evaluating methods for Avian avulavirus-1 whole genome sequencing
title_sort evaluating methods for avian avulavirus-1 whole genome sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285907/
https://www.ncbi.nlm.nih.gov/pubmed/32550541
http://dx.doi.org/10.1016/j.gene.2019.100004
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