Cargando…
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...
Autores principales: | , , , , , , , , , , , , , , , , |
---|---|
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 |
_version_ | 1783544784807264256 |
---|---|
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. |
format | Online Article Text |
id | pubmed-7285907 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT talsaar evaluatingmethodsforavianavulavirus1wholegenomesequencing AT benizhakmeirav evaluatingmethodsforavianavulavirus1wholegenomesequencing AT wachtelchaim evaluatingmethodsforavianavulavirus1wholegenomesequencing AT wisemananat evaluatingmethodsforavianavulavirus1wholegenomesequencing AT brauntzipi evaluatingmethodsforavianavulavirus1wholegenomesequencing AT yechezkelelinor evaluatingmethodsforavianavulavirus1wholegenomesequencing AT golaneinav evaluatingmethodsforavianavulavirus1wholegenomesequencing AT hadasruth evaluatingmethodsforavianavulavirus1wholegenomesequencing AT turjemanadi evaluatingmethodsforavianavulavirus1wholegenomesequencing AT banetnoachcaroline evaluatingmethodsforavianavulavirus1wholegenomesequencing AT bronsteinmichal evaluatingmethodsforavianavulavirus1wholegenomesequencing AT lublinavishai evaluatingmethodsforavianavulavirus1wholegenomesequencing AT bermanelyakum evaluatingmethodsforavianavulavirus1wholegenomesequencing AT ravivziv evaluatingmethodsforavianavulavirus1wholegenomesequencing AT pirakmichael evaluatingmethodsforavianavulavirus1wholegenomesequencing AT klementeyal evaluatingmethodsforavianavulavirus1wholegenomesequencing AT louzounyoram evaluatingmethodsforavianavulavirus1wholegenomesequencing |