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Fulltext Molecular cloning of full-length haemagglutinin (H5HA) gene of highly pathogenic avian influenza virus (HPAI) H5N1

Mustapha Bala Abubakar, Aini Ideris, AbdulRahman Omar, Mohd Hair Bejo

Buletin Persatuan Genetik Malaysia, 2009;15(1):20-23.
MyJurnal

Avian Influenza viruses belonging to the Orthomyxoviridae family are enveloped viruses with segmented negative sense RNA genome surrounded by a helical symmetry capsid. Influenza viruses, especially the highly pathogenic avian influenza virus (HPAI) such as H5 or H7 subtype are the most important pathogens for the poultry industry in recent times. The haemagglutinin protein and neuraminidase, serves as the target for the immune response of the host. Due to recurrent genetic reassortments between avian and human influenza viruses, global pandemics may emerge and the naive human immunity could not withstand pressure by the novel hybrid virus. The emergence of genetic engineering technology provided the industry with new methods of manufacturing diagnostics tools and vaccines. After extraction of RNA from the cell culture of strain influenza A/Chicken/Malaysia/2004(H5N1) of AIV, the viral RNA was converted to cDNA by a specific primer. The cDNA was amplified by the polymerase chain reaction (PCR) and analyzed
by agarose gel electrophoresis. The intact PCR product of full length haemagglutinin gene was cloned in TO POTM TA Cloning vector. The full-length HA-encoding gene of H5N1 AIV was subcloned into a pPICZA vector. After successful ligation, the constructed plasmid was transformed into E.coli.Top10, Plasmid DNA from transformed bacteria was extracted in white colony and positive clones were confirmed by restriction digestion with Sacl and Not1 restriction enzymes, colony PCR screening and nucleotide sequencing. Construction of a recombinant pPICZA/H5HA plasmid containing the full length haemagglutinin gene was achieved as a first step
towards the expression in Pichia pastoris.
Fulltext Vaccines and vaccination against infectious bursal disease of chickens: prospects and challenges

Liew, Pit Sze, Nurulfiza Mat Isa, Omar Abdul Rahman, Aini Ideris, Mohd HAIRBEJO

The Pertanika Journal of Scholarly Research Reviews, 2016;2(2):23-39.
MyJurnal

Infectious bursal disease (IBD), also known as the Gumboro disease, has been a great
concern for poultry industry worldwide. The first outbreak of IBD due to very virulent (vv) IBD virus
(IBDV) infection in Malaysia was reported in 1991. The major economic impact of the disease is high
mortality and poor performance. The virus causes immunosuppression where if the infected chicken
recovered from the acute disease, they become more susceptible to infections of other pathogens and
fail to respond to vaccines. Therefore, prevention is important and vaccination has become the
principal control measure of IBDV infection in chickens. The conventional attenuated live and killed
vaccines are the most commonly used vaccines. With the advancement of knowledge and technology,
new generation of genetically-engineered vaccines like viral vector and immune complex vaccines
have been commercialised. Moreover, hatchery vaccination is becoming a common practise, in
addition to farm vaccination. Currently, the disease is considerably under controlled with the
introduction of vaccination. However, occasional field outbreaks are still commonly reported. The
demand for vaccines that could suit the field situation continues to exist. The endemicity of disease,
presence of challenge in the farm and maternally derived antibody in chicks are affecting the choice
vaccine as well as the vaccine development and vaccination strategies. In this review, advances made
in various vaccines that have been commercialised or under development, and challenges that they
face, are outlined. Furthermore, how the emergence of vvIBDV affect the progress of vaccine
development and influence its vaccination strategy are discussed.
Morphology comparison of swiftlet species from natural and man-made habitats in malaysia

Looi QH, Aini Ideris, Md Zuki bin Abu Bakar @ Zakaria, Abdul Rahman bin Omar

Sains Malaysiana, 2015;44:497-502.

In Malaysia, nests of Aerodramus fuciphagus (white-nest swiftlet) and Aerodramus maximus (black-nest swiftlet) are
harvested for commercial purposes, as one of the most valuable animal products. The taxonomy of a species is crucial,
as delineating species boundaries is fundamental to discover life’s diversity. However, swiftlet taxonomy has been
controversial, due to numerous undefined parameters. Although there are these limitations, morphological taxonomy
cannot be the unique approach for species identification and it is a valuable component in taxonomy studies. We have
undertaken a morphological approach to analyse community relationships among species of swiftlets. In this study, we
selected three different swiftlet species to generate two sets of comparisons: Within species and among different habitats.
This study found that A. fuciphagus from man-made habitats is generally larger in size compared to the natural habitat and
A. maximus is larger compared with A. fuciphagus. We postulate the difference in body size is due to dietary behaviour
and genetic variations of the swiftlets.
Immunochromatographic gold-based test strip for rapid detection of Infectious bursal disease virus antibodies

Nurulfiza I, Hair-Bejo M, Omar AR, Aini I

J Vet Diagn Invest, 2011 Mar;23(2):320-4.
PMID: 21398455

The immunochromatographic assay is an alternative method for simple and rapid detection of Infectious bursal disease virus (IBDV) in chickens using colloidal gold-antibody conjugate. The whole-virus antigen of IBDV (UPM04190 isolate) and the high-affinity polyclonal antibodies directed against IBDV were blotted onto nitrocellulose membranes for test and control lines, respectively. Evaluation of the strip was performed using serum samples from experimentally and naturally infected chickens. The results showed that the test strip was more sensitive than the commercial enzyme-linked immunosorbent assay (ELISA) because it could detect a dilution factor up to 120,000 (250 ELISA units) for positive samples. It was also specific, in that it detected IBDV antibodies and did not cross-react with antibodies to other chicken viruses. The method was rapid (2 min) in both clinical and field environments with samples needing only a minimum amount (50 µl) of blood to produce an acceptable detection signal. The pen-site test strip proved successful in monitoring the immune status of chickens against the IBDV infection.
Base usage and dinucleotide frequency of infectious bursal disease virus

Tan DY, Hair Bejo M, Aini I, Omar AR, Goh YM

Virus Genes, 2004 Jan;28(1):41-53.
PMID: 14739650

Base usage and dinucleotide frequency have been extensively studied in many eukaryotic organisms and bacteria, but not for viruses. In this paper, a comprehensive analysis of these aspects for infectious bursal disease virus (IBDV) was presented. The analysis of base usage indicated that all of the IBDV genes possess equivalent overall nucleotide distributions. However when the base usage at each codon positions was analysed by using cluster analysis, the VP5 open reading frame (ORF) formed a different cluster isolated from the other genes. The unusual base usage of VP5 ORF may indicate that the gene was originated by the virus "overprinting strategy", a strategy in which virus may create novel gene by utilizing the unused reading frames of its existing genes. Meanwhile, the GC content of the IBDV genes and the chicken's coding sequences was comparable; suggesting the virus imitation of the host to increase its translational efficiency. The analysis of dinucleotide frequency indicated that IBDV genome had dinucleotide bias: the frequencies of CpG and TpA were lower and the TpG was higher than the expected. Classical methylation pathway, a process where CpG converted to TpG, may explain the significant correlation between the CpG deficiency and TpG abundance. "Principal component analysis of the dinucleotide frequencies" (DF-PCA) was used to analyse the overall dinucleotide frequencies of IBDV genome. DF-PCA on the hypervariable region and polyprotein (VPX-VP4-VP3) gene showed that the very virulent IBDV (vvIBDV) was segregated from other strains; which meant vvIBDV had a unique dinucleotide pattern. In summary, the study of base usage and dinucleotide frequency had unravelled many overlooked genomic properties of the virus.
Fulltext TaqMan probe-based qPCR method for specific detection and quantification of fowl adenovirus 8b challenge from chickens inoculated with live attenuated or inactivated virus

Ugwu CC, Hair-Bejo M, Nurulfiza MI, Omar AR, Aini I

Open Vet J, 2023 Feb;13(2):171-178.
PMID: 37073244 DOI: 10.5455/OVJ.2023.v13.i2.4

BACKGROUND: Fowl adenovirus (FAdV) 8b and other serotypes cause inclusion body hepatitis (IBH) in chickens. Specific detection of aetiologic serotype in mixed infection and vaccine failure could be difficult.
AIM: The objective of this study was to develop a TaqMan probe-based qPCR method for the detection and quantification of the FAdV 8b challenge virus.
METHODS: Forty-eight broiler chickens inoculated with live attenuated or inactivated FAdV 8b strains at day 1 of age either with or without booster at day 14 post-inoculation were used. The chickens were challenged with a pathogenic strain of FAdV 8b at day 28 of age. Liver and cloacal swabs were collected on days 7 and 14 post-challenge. Primers and probes were designed, specificity confirmed, and used to carry out qPCR amplification.
RESULTS: The assay amplified the FAdV DNA challenge virus, but not that of the live attenuated virus. It could detect FAdV 8b DNA as low as 0.001 ng/µl in liver and cloacal swab samples. Copy numbers obtained indicate virus load and shedding.
CONCLUSIONS: It shows that a selective detection of FAdV 8b within serotype is possible. It can be useful for rapid detection and diagnosis of the disease, virus quantification and differentiation within species, determination of vaccination failure, and efficacy especially the virus load in the target organ and shedding.
Infectious bursal disease virus tissue tropism and pathogenesis of the infection in chickens by application of in situ PCR, immunoperoxase and HE staining

Hussein EA, Hair-Bejo M, Liew PS, Adamu L, Omar AR, Arshad SS, et al.

Microb Pathog, 2019 Apr;129:195-205.
PMID: 30738178 DOI: 10.1016/j.micpath.2019.01.049

Infectious bursal disease is one of an OIE list of notifiable diseases. Chicken is the only host that manifests clinical signs and its pathogenicity is correlated with the distribution of antigens in organs. This study was conducted to determine disease pathogenesis and virus tissue tropism by in situ PCR, immunoperoxidase staining (IPS), and HE staining. Twenty four chickens were infected with very virulent Infectious Bursal Disease Virus (vvIBDV). Fifteen chickens were kept as a control group. Infected chickens were sacrificed at hrs 2, 4, 6, 12, days 1, 2, 4, and 6 post-inoculation (pi). While, control chickens were euthanized on days 0, 1, 2, 4, and 6 pi. Different tissues were collected, fixed in 10% buffered formalin, and processed. At hr 2 pi, virus was detected in intestinal, junction of the proventriculus and gizzard, cecal tonsil, liver, kidney, and bursa of Fabricius. At hr 4 pi, virus reached spleen, and at hr 6 pi, it entered thymus. At hr 12 pi, virus concentration increased in positive tissues. The latest invaded tissue was muscle on day 1 pi. Secondary viraemia occurred during 12-24 h pi. In situ PCR was the most sensitive technique to highlight obscure points of infection in this study.
Velogenic newcastle disease virus tissue tropism and pathogenesis of infection in chickens by application of in situ PCR, immunoperoxase staining and HE staining

Hussein EA, Hair-Bejo M, Omar AR, Arshad SS, Hani H, Balakrishnan KN, et al.

Microb Pathog, 2019 Apr;129:213-223.
PMID: 30771470 DOI: 10.1016/j.micpath.2019.02.017

Limited deep studies are available in the field of early stages of pathogenesis of Newcastle disease virus (NDV) infection and tissue tropism of NDV. In this study, 24 specific pathogen free (SPF) chickens of white leghorn breed were infected with Newcastle disease (ND) by intranasal administration of 10⁵ 50% EID50/0.1 mL of velogenic NDV (vNDV). A second group of 15 chickens were kept as a control group. Chickens were monitored every day to record clinical signs. Infected chickens were euthanized by cervical dislocation at successive times, namely at hours (hrs) 2, 4, 6, 12, days 1, 2, 4, and 6 post-inoculation (pi). Whereas, control group chickens were euthanized on days 0, 1, 2, 4, and 6 pi. Tissues of brain, trachea, lung, caecal tonsil, liver, kidney, spleen, heart, proventriculus, intestine, and thymus were collected, fixed in 10% buffered formalin, embedded in paraffin, and sectioned. HS staining, immunoperoxidase staining (IPS) and in situ PCR were applied. It was concluded that at hr 2 pi, virus seemed to be inclined to trachea and respiratory tract. Meanwhile, it attacked caecal tonsils, intestine and bursa of Fabricus. While primary viraemia was ongoing, virus created footing in kidney and thymus. At hr 4 pi, proventriculus, liver, and spleen were attacked. However, at hr 6 pi, brain and heart were involved. Secondary viraemia probably started as early as hr 12 pi since all collected tissues were positive. Tissue tropism was determined in trachea, caecal tonsil, liver, bursa of Fabricius, intestine, proventriculus, lung, spleen, thymus, kidney, heart, and brain.
Fulltext Differential modulation of immune response and cytokine profiles in the bursae and spleen of chickens infected with very virulent infectious bursal disease virus

Rasoli M, Yeap SK, Tan SW, Roohani K, Kristeen-Teo YW, Alitheen NB, et al.

BMC Vet Res, 2015;11:75.
PMID: 25884204 DOI: 10.1186/s12917-015-0377-x

Very virulent infectious bursal disease virus (vvIBDV) induces immunosuppression and inflammation in young birds, which subsequently leads to high mortality. In addition, infectious bursal disease (IBD) is one of the leading causes of vaccine failure on farms. Therefore, understanding the immunopathogenesis of IBDV in both the spleen and the bursae could help effective vaccine development. However, previous studies only profiled the differential expression of a limited number of cytokines, in either the spleen or the bursae of Fabricius of IBDV-infected chickens. Thus, this study aims to evaluate the in vitro and in vivo immunoregulatory effects of vvIBDV infection on macrophage-like cells, spleen and bursae of Fabricius.
Fulltext Complete Genome Sequence of Rat Cytomegalovirus Strain ALL-03 (Malaysian Strain)

Balakrishnan KN, Abdullah AA, Camalxaman SN, Quah YW, Abba Y, Hani H, et al.

Genome Announc, 2015;3(3).
PMID: 26044413 DOI: 10.1128/genomeA.00451-15

The complete genome sequence of the ALL-03 strain of rat cytomegalovirus (RCMV) has been determined. The RCMV genome has a length of 197,958 bp and is arranged as a single unique sequence flanked by 504-bp terminal direct repeats. This strain is closely related to the English strain of RCMV in terms of genetic arrangement but differs slightly in size.