Phylogenetic analysis of Infectious Bursal Disease viruses according to newly proposed model of classification into geno-groups

Khan, Rashid Ahmed; Habib, Md. Ahasan; Ali, Waqas; Shah, Muhammad Salah Ud Din; Ashraf, Asma; Tahir, Zahid Ali; Helal, Zeinab H.; Khan, Mazhar I.; Mahboob, Shahid; A-Al-Ghanim, Khalid; Al‐Misned, Fahad A.

doi:10.1016/j.jiph.2018.12.012

Cited by 15 publications

(12 citation statements)

References 49 publications

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“…The HVR of the VP2 gene was used for the construction of a phylogenetic tree using a proposed new IBDV classification (3,12). The evolutionary analyses were conducted using the maximum likelihood method and Kimura 2-parameter model (35), and the tree was constructed in MEGA-X (36) software following muscle alignment, and 1,000 bootstraps were applied.…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

“…The VP2 protein is an essential gene of the virus as it carries the protective antigen (9,10). It is the most widely studied gene, and has revealed the antigenic properties of IBDV (11)(12)(13). The VP2 protein is the major capsid protein of IBDV, containing major immunodominant epitopes, which are vital for inducing neutralizing antibodies against IBDV (9,14).…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity of Recent Infectious Bursal Disease Viruses Isolated From Vaccinated Poultry Flocks in Malaysia

et al. 2021

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Vaccination is an essential component in controlling infectious bursal disease (IBD), however, there is a lack of information on the genetic characteristics of a recent infectious bursal disease virus (IBDV) that was isolated from IBD vaccinated commercial flocks in Malaysia. The present study investigated 11 IBDV isolates that were isolated from commercial poultry farms. The isolates were detected using reverse transcription-polymerase chain reaction (RT-PCR) targeting the hypervariable region (HVR) of VP2. Based on the HVR sequences, five isolates (IBS536/2017, IBS624/2017, UPM766/2018, UPM1056/2018, and UPM1432/2019) were selected for whole-genome sequencing using the MiSeq platform. The nucleotide and amino acid (aa) sequences were compared with the previously characterized IBDV strains. Deduced aa sequences of VP2HVR revealed seven isolates with 94–99% aa identity to very virulent strains (genogroup 3), two isolates with 97–100% aa identity to variant strains (genogroup 2), and two strains with 100% identity to the vaccine strain (genogroup 1) of IBDV. The phylogenetic analysis also showed that the isolates formed clusters with the respective genogroups. The characteristic motifs 222T, 249K, 286I, and 318D are typical of the variant strain and were observed for UPM1219/2019 and UPM1432/2019. In comparison, very virulent residues such as 222A, 249Q, 286T, and 318G were found for the vvIBDV, except for the UPM1056/2018 strain with a A222T substitution. In addition, the isolate has aa substitutions such as D213N, G254D, S315T, S317R, and A321E that are not commonly found in previously reported vvIBDV strains. Unlike the other vvIBDVs characterized in this study, UPM766/2018 lacks the MLSL aa residues in VP5. The aa tripeptides 145/146/147 (TDN) of VP1 were conserved for the vvIBDV, while a different motif, NED, was observed for the Malaysian variant strain. The phylogenetic tree showed that the IBDV variant clustered with the American and Chinese variant viruses and are highly comparable to the novel Chinese variants, with 99.9% identity. Based on the sequences and phylogenetic analyses, this is the first identification of an IBDV variant being reported in Malaysia. Further research is required to determine the pathogenicity of the IBDV variant and the protective efficacy of the current IBD vaccines being used against the virus.

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Section: Phylogenetic Analysesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genetic Diversity of Recent Infectious Bursal Disease Viruses Isolated From Vaccinated Poultry Flocks in Malaysia

et al. 2021

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“…Such genetic modification is not uncommon: previous studies refer to similar genomic rearrangements in IBDV (Ibdv, Jackwood and Sommer-wagner, 2011;Michel and Jackwood, 2019). Other hvVP2 sequences from Iraq, especially those isolated from Kurdistan region (North of Iraq), showed a dispersal aggregation in the phylogenetic tree, suggesting genetic drift and possible mutations affected this protein coding region (Ali Khan et al, 2019). Despite this sequence variation between the results of the VP1 and hvVP2 phylogenetic analyses, both genic regions were clustered with vvIBDV isolates across the world, suggesting that our isolate is a vvIBDV strain.…”

Section: Discussionmentioning

confidence: 75%

Sequence diversity and evolution of infectious bursal disease virus in Iraq

2021

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Background: 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.

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“…In genogroup 4, the amino acid shared the common positions at 296F, 256V, 242V, 279N, and 289P. The sequence analysis showed the 92% similarity between the dIBDV and vaccinal strain of IBDV (Winterfield) that predicts the spread of these strains in Asian and non-Asian countries [ 24 ].…”

Section: Discussionmentioning

confidence: 99%

Molecular Characterization and Demographic Study on Infectious Bursal Disease Virus in Faisalabad District

et al. 2021

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The re-emergence of virulent strains of the Infectious Bursal Disease Virus (IBDV) leads to significant economic losses of poultry industry in Pakistan during last few years. This disease causes the infection of bursa, which leads to major immune losses. A total number of 30 samples from five IBD outbreaks during the period of 2019–20 were collected from different areas of Faisalabad district, Pakistan and assayed by targeting the IBD virus VP2 region through RT-PCR. Among all the outbreaks, almost 80% of poultry birds were found positive for the IBDV. The bursa tissues were collected from the infected birds and histopathological examination of samples revealed severe lymphocytic depletion, infiltration of inflammatory cells, and necrosis of the bursa of Fabricius (BF). Positive samples were subjected to re-isolation and molecular characterization of IBDV. The Pakistan IBDV genes were subjected to DNA sequencing to determine the virus nucleotide sequences. The sequences of 100 Serotype-I IBDVs showing nearest homology were compared and identified with the study sequence. The construction of the phylogenetic tree for nucleotide sequences was accomplished by the neighbor-joining method in MEGA-6 with reference strains. The VP2 segment reassortment of IBDVs carrying segment A were identified as one important type of circulating strains in Pakistan. The findings indicated the molecular features of the Pakistan IBDV strains playing a role in the evolution of new strains of the virus, which will contribute to the vaccine selection and effective prevention of the disease.

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Phylogenetic analysis of Infectious Bursal Disease viruses according to newly proposed model of classification into geno-groups

Cited by 15 publications

References 49 publications

Genetic Diversity of Recent Infectious Bursal Disease Viruses Isolated From Vaccinated Poultry Flocks in Malaysia

Genetic Diversity of Recent Infectious Bursal Disease Viruses Isolated From Vaccinated Poultry Flocks in Malaysia

Sequence diversity and evolution of infectious bursal disease virus in Iraq

Molecular Characterization and Demographic Study on Infectious Bursal Disease Virus in Faisalabad District

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