Evidence map›Paper›PMID 34530998›Full record

ArticleGene2019

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 and 7 more

Abstract read
PubMed Publisher
In one paragraph

Article in Gene, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors.

Saar TalThe Poultry Health Laboratories, The Egg and Poultry Board, Israel.
Meirav Ben IzhakLife Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel.
Chaim WachtelHyLabs NGS Services, Israel.
Anat WisemanThe Poultry Health Laboratories, The Egg and Poultry Board, Israel; Koret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel.
Tzipi BraunLife Science faculty and Gonda Brain Research Center, Bar Ilan University, Israel.
Elinor YechezkelThe Poultry Health Laboratories, The Egg and Poultry Board, Israel.
Einav GolanThe Poultry Health Laboratories, The Egg and Poultry Board, Israel.
Ruth HadasKimron Veterinary Institute, Division of Avian Diseases, Israel.
Adi TurjemanThe Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.
Caroline Banet-NoachPhibro Animal Health Corp. Ltd, Israel.
Michal BronsteinThe Center for Genomic Technologies, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.
Avishai LublinKimron Veterinary Institute, Division of Avian Diseases, Israel.
Elyakum BermanThe Poultry Health Laboratories, The Egg and Poultry Board, Israel.
Ziv RavivKoret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel.
Michael PirakThe Poultry Health Laboratories, The Egg and Poultry Board, Israel.
Eyal KlementKoret School of Veterinary Medicine, The Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Israel.
Yoram LouzounDepartment of Mathematics and Gonda Brain Research Center, Bar Ilan University, Israel. Electronic address: louzouy@math.biu.ac.il.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundAvian 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.

methodsThree 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.

resultsA 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.

conclusionsOur 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.

Indexed as

AAvV-1MutationsNewcastle disease virusNGSSequencingWGS

Identifiers

PMID34530998

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.