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Supplementary Information for: Sequence diversity and evolution of Infectious Bursal Disease Virus IBDV in Iraq

Citation

Abbas, Ali (2021), Supplementary Information for: Sequence diversity and evolution of Infectious Bursal Disease Virus IBDV in Iraq, Dryad, Dataset, https://doi.org/10.5061/dryad.s7h44j167

Abstract

Background and Aim: Infectious Bursal Disease (IBD) is a highly infectious disease which causes huge economic losses to the poultry industry due to the direct impact of the illness and indirect consequences such as decreasing the general immunity of the flock, leaving it naive to other diseases. In Iraq, IBD is highly prevalent despite vaccination programs, yet studies on sequence diversity of the causative virus are still rare.

Methods: A sample from Bursa of Fabricius from an IBD outbreak in a flock in the city of Najaf in Iraq was smeared on an FTA card. Amplicons of targeted regions in VP1 and VP2 genes were generated and sequenced. Sequences were then compared with other local and global sequences downloaded from GenBank repositories. Sequence alignment and DNA sequence analyses were achieved using MUSCLE, UGENE and MEGAx software. The molecular clock and sequence evolutionary analyses were applied using MEGAx tools.

Results: The strain sequenced in this study belongs to a very virulent Infectious Bursal Disease Virus (vvIBDV) as the DNA and phylogenetic analysis of VP1 and VP2 gene sequences showed a mutual clustering with similar sequences belonging to vvIBDV genogroup 3. Analyses of the hyper variable region of VP2 gene (hvVP2) of IBDV isolates from Iraq indicates a presence of sequence diversity. Interestingly, the two vaccine strains Ventri IBDV Plus and ABIC MB71 that showed the highest sequence similarity to the local isolates in the hvVP2 region are not used in vaccination routine against IBDV in Iraq.

Conclusion: Sequences of vvIBDV in Iraq are diverse. Remarkably, some of the available vaccine strains show high sequence similarity with local strains in Iraq; however, they are not included in the routine vaccination programs. Analysis of more samples involving more geographical regions is needed to draw a detailed map of antigenic diversity of IBDV in Iraq.


Please ensure that the sequence data has been uploaded to a structured repository, e.g. NCBI/ENA. Details can then be included in the data availability statement after the conclusion.

Please include details in the Software availability statement. I have added the format for you at the end of this paper.

Methods

Sample collection

A newly died bird from an outbreak of IBDV from a flock in An-Najaf province, was post-mortem examined and the enlarged Bursa of Fabricius was incised and examined.

RNA extraction

Bursa contents was sampled on (FTA) card (Whatman® FTA® card technology) with four sample areas per card containing cell wall lytic enzymes, protein denaturing agents and inhibit the nucleases effects on nucleic acids (Ali et al., 2017).

RNA samples on the FTA card were then sent to AniCon® Labor GmbH (Muehlenstraße 13a 49685 Hoeltinghausen, Germany), where the extraction of the IBDV RNA from FTA card was performed using Kylt® RNA/DNA Purification Kit according to the manufacturer’s protocol.

Multiple sequence alignment and sequence manipulation

The IBDV VP1 targeted region obtained in this study was aligned with other similar sequences downloaded from GenBank repositories using MUSCLE (Edgar and Edgar, 2004), alignments were manually edited, gaps removed and the percentage of pairwise sequence similarity matrices (Extended data were generated using the UGENE pipeline version 35.1 (Okonechnikov et al., 2012). This was also conducted for the hvVP2 nucleotide sequences.

Inferring the evolutionary history and time tree

The evolutionary history was obtained by the neighbour-joining (NJ) method (Saitou and Nei, 1987), with 1000 bootstrap replicates (Felsenstein, 1985), while the evolutionary pairwise distances (Extended data) were calculated by Maximum Composite Likelihood Method (MCL) using Tamura-Nei model ( Tamura and Nei, 1993).

Heuristic search of initial tree was obtained automatically by applying Neighbour-Joining and BioNJ to a matrix of pairwise distances (Extended data) estimated by the MCL method, then the topology was selected with superior log likelihood value.

For hvVP2 sequences of Iraq and vaccine strains, a time-tree to the NJ phylogenetic tree was inferred using the RelTime method (Tamura et al., 2012; Tamura, Tao and Kumar, 2018). The time-tree was estimated using 31 correction restraints and all ambiguous positions were removed for each sequence to give a final dataset of 309 sites. Molecular phylogenetic analysis was also performed using the maximum-likelihood method based on the Tamura-Nei model (Tamura and Nei, 1993).

All DNA sequence analyses and evolutionary inferences were performed using MEGAx software version 10.1.8 (Kumar et al., 2018) and the plotting of datasheets to the phylogenetic tree was achieved by iTOL web application (Letunic and Bork, 2019).

Usage Notes

This DATSETNAMEreadme.txt file was generated on 2021-03-13 by Ali Hadi Abbas


GENERAL INFORMATION

  1. Title of Dataset: Extended dataset of Sequence diversity and evolution of infectious bursal disease virus (IBDV) in Iraq
  2. Author Information
    1. Principal Investigator Contact Information
              Name: Ali Hadi Abbas
              Institution: Department of Microbiology, Faculty of Veterinary Medicine, University of Kufa, Iraq
              Address: University of Kufa, Najaf, Iraq
              Email: alih.abbas@uokufedu.iq
    2. Associate or Co-investigator Contact Information
              Name: Haider Ali AL saegh
              Institution: Department of Pathology and Poultry Diseases, Faculty of Veterinary Medicine, University of Kufa
              Address: University of Kufa, Najaf, Iraq
              Email: - haidera.alsaigh@uokufa.edu.iq
    3. Alternate Contact Information
              Name: Furkan Sabbar ALaraji
              Institution: Department of Pathology and Poultry Diseases, Faculty of Veterinary Medicine, University of Kufa
              Address: University of Kufa, Najaf, Iraq
              Email: furkans.alaraji@uokufa.edu.iq
  3. Date of data collection (single date, range, approximate date): 2019-01-07
  4. Geographic location of data collection: 32.0174395, 43648665, Najaf, Iraq.
  5. Information about funding sources that supported the collection of the data:
    The authors did not receive any funding to carry out this project.

SHARING/ACCESS INFORMATION

  1. Licenses/restrictions placed on the data: free access.
  2. Links to publications that cite or use the data:
  3. Links to other publicly accessible locations of the data:
    1. The new sequences isolated in this study, were deposited in GenBank repositories:
      1. GenBank: Infectious bursal disease virus isolate IqKufa 01 VP2 gene, partial cds. Accession number: MW020533.1. https://www.ncbnlm.nih.gov/nuccore/MW020533.1.
      2. GenBank: Infectious bursal disease virus isolate IqKufa 01 VP1 gene, partial cds. Accession number: MW020534.1. https://www.ncbi.nlm.nih.gov/nuccore/MW020534.1.
  4. Links/relationships to ancillary data sets:
  5. Was data derived from another source? Yes
    1. If yes, list source(s):
      1. Most of the data were retrieved from GenBank repositories, NCBI:
        1. https://www.ncbi.nlm.nih.gov/nuccore/?term=vp2%20infectious%20bursal%20disease
          2
        2. https://www.ncbi.nlm.nih.gov/nuccore/?term=vp1+infectious+bursal+disease

The extended data file (Table 1) contains the detailed information of GenBank accession numbers of sequences used in generating these data files.

  1. Recommended citation for this dataset:
    Please cite this dataset in relation to distribution of infectious burial disease in broiler chicken in Iraq.

DATA & FILE OVERVIEW

  1. File List:
    1. Table1_accesson_numbers_of_VP1_and_VP2_sequences_used_in_this_study. (GenBank accessions of VP1 and VP2 sequences used in this study.)
    2. TextFileToShow_connection_iTol_VP2. (Connections datasets allow the drawing of straight or curved lines between any two nodes in the tree. Width, colour, and opacity can be set for each line.)
    3. TextFileToShow_GRADIENT_iTol_VP2. (In gradient datasets, each ID is associated to a single numeric value which is converted to a coloured box based on the gradient defined.)
    4. IraqiVP2_pairwiseDistance.csv. (Pairwise distance of VP2 aligned region among strains isolated from Iraq).
      •    IBVD_VP1_NCBI_Hits_OurVP1.txt. (DNA sequences of all VP1 sequences used in this study).
    5. ABIC_and VentriVaccin_IraqV2_DNA_percentSimilrity_matrix.csv. (hvVP2 sequence similarity percentage of two vaccine strains compared to the Iraqi isolates).
    6. all_VP2_DNA_sequencesUsed.txt. (DNA sequences of all VP2 sequences used in this study).
  2. Relationship between files, if important:
    1. The row parental datasets are:
      1. IBVD_VP1_NCBI_Hits_OurVP1.txt.
      2. all_VP2_DNA_sequencesUsed.txt
        1. TextFileToShow_connection_iTol_VP2.
        2. TextFileToShow_GRADIENT_iTol_VP
        3. ABIC_and VentriVaccin_IraqV2_DNA_percentSimilrity_matrix.csv.
        4. TextFileToShow_GRADIENT_iTol_VP2.
        5. IraqiVP2_pairwiseDistance.csv.
  3. Additional related data collected that was not included in the current data package:
  4. Are there multiple versions of the dataset? no

METHODOLOGICAL INFORMATION

  1. Description of methods used for collection/generation of data:
    1. Main data used in this study were collected from GenBank repositories and accession numbers of entries are provided in extended data Table 1.
    2. The method used for identifying and genotyping-based classification carried out in this study, have been previously adopted by:
      1. doi: 10.1007/s00705-017-3500-4.
      2. https://patentimages.storage.googleapis.com/3d/e5/37/910756ed03cc58/WO2005017488A2.pdf
  2. Methods for processing the data:
    1. Multiple sequence alignment and sequence manipulation:
      1. The IBDV VP1 targeted region obtained in this study was aligned with other similar sequences downloaded from GenBank repositories using MUSCLE (Edgar and Edgar, 2004), alignments were manually edited, gaps were removed and the percentage of pairwise sequence similarity matrices (Extended data) were generated using the UGENE pipeline version 35.1 (Okonechnikov et al., 2012). This was also conducted for the hvVP2 nucleotide sequences.
    2. Inferring the evolutionary history and time tree:
      1. The evolutionary history was obtained by the neighbour-joining (NJ) method (Saitou and Nei, 1987), with 1000 bootstrap replicates (Felsenstein, 1985), while the evolutionary pairwise distances (Extended data) were calculated by Maximum Composite Likelihood Method (MCL) using Tamura-Nei model ( Tamura and Nei, 1993).
      2. Heuristic search of initial tree was obtained automatically by applying Neighbour-Joining and BioNJ to a matrix of pairwise distances (Extended data) estimated by the MCL method, then the topology was selected with superior log likelihood value.
      3. For hvVP2 sequences of Iraq and vaccine strains, a time-tree to the NJ phylogenetic tree was inferred using the RelTime method (Tamura et al., 2012; Tamura, Tao and Kumar, 2018). The time-tree was estimated using 31 correction restraints and all ambiguous positions were removed for each sequence to give a final dataset of 309 sites. Molecular phylogenetic analysis was also performed using the maximum-likelihood method based on the Tamura-Nei model (Tamura and Nei, 1993).
      4. All DNA sequence analyses and evolutionary inferences were performed using MEGAx software version 10.1.8 (Kumar et al., 2018) and the plotting of datasheets to the phylogenetic tree was achieved by iTOL web application (Letunic and Bork, 2019).
  3. Instrument- or software-specific information needed to interpret the data:
    1. UGENE software available from: http://ugene.net/download.html
      1. Source code available from: https://github.com/ugeneunipro/ugene/tree/master/src
      2. Archived source code at time of publication: version 35.1 (Okonechnikov et al., 2012).
    2. MEGAx software available from: https://www.megasoftware.net
      1. Source code available from: https://www.megasoftware.net/download_form.
      2. Archived source code at time of publication: version 10.1.8 (Kumar et al., 2018).
    3. iTOL web application software available from: https://itol.embl.de/itol.cgi
      1. Source code available from: https://github.com/albertyw/itolapi
      2. Archived source code at time of publication: version 5.0 ( Letunic and Bork, 2019).
  4. Standards and calibration information, if appropriate:
  5. Environmental/experimental conditions:
  6. Describe any quality-assurance procedures performed on the data:
    1. BLAST search on locally retrieved sequence to get the sequence relationship to globally, available sequences.
  7. People involved with sample collection, processing, analysis and/or submission:
    1. Haider Ali AL saegh and Furkan Sabbar ALaraji were involved in field trips and diagnosis of clinically, affected flocks and collection of Bursa of Fabricuos sample.
    2. ALli Hadi Abbas is responsible for sequence data submission and data analyses carried out in this study.

DATA-SPECIFIC INFORMATION FOR: [IraqiVP2_pairwiseDistance]

  1. Number of variables: 22
  2. Number of cases/rows: 22
  3. Variable List:
    1. Pairwise distance of VP2 aligned region among strains isolated from Iraqi. Including self comparison =0.
  4. Missing data codes:
  5. Specialised formats or other abbreviations used:
    1. Abbreviations used for variable are the sample name embedded in GenBank accessions.

DATA-SPECIFIC INFORMATION FOR: [ABIC_andVentriVaccin_IraqV2_DNA_percentSimilrity_matrix]

  1. Number of variables: 2
  2. Number of cases/rows: 16
  3. Variable List:
    hvVP2 sequence similarity percentage of two vaccine strains compared to all Iraqi isolates:

Sequence name

Percent of sequence similarity to KJ547670_Ventri_IBDV_Plus_vacc2014 vaccine

Percent of sequence similarity to AF457103_ABIC_MB71_vacc_2001 vaccine

IqKufa_Najaf2019  

 96%  

 96%

LC498531_Diyala2018  

 96%  

 96%

MF142534_422Iraq_2017  

 96%  

 96%

JX974583_Sulaim2012  

 96%  

 96%

MN464103_Diyala_2018  

 96%  

 96%

MN480452_Erbil2019  

 96%  

 96%

MH676061_Sulaim2018  

 97%  

 97%

MH676060_Sulaim2018  

 97%  

 96%

MH676059_Sulaim2018  

 97%  

 97%

JX974582_Sulaim2012  

 97%  

 96%

KC352669_kurdis2012  

 97%  

 96%

KC352668_kurdis2012  

 97%  

 96%

KC352659_kurdis2012  

 97%  

 96%

KC352660_kurdis2012  

 97%  

 96%

MF142535_423Iraq_2017  

 98%  

 98%

KC352666_kurdis2012  

 98%  

 98%

  1. Missing data codes:
  2. Specialised formats or other abbreviations used:
    1. Abbreviations used for variable are the sample name embedded in GenBank accessions.

The authors declared that no grants were involved in supporting this work.