Seroprevalence and molecular characterisation of infectious bronchitis virus (IBV) in broiler farms in Sabah, Malaysia.

BACKGROUND: Infectious bronchitis virus (IBV) is classified as a highly contagious viral agent that causes acute respiratory, reproductive and renal system pathology in affected poultry farms. Molecular and serological investigations are crucial for the accurate diagnosis and management of IBV. OBJECTIVES: The purpose of this study was to determine the seroprevalence of IBV and to characterise the circulating IBV in poultry farms in Sabah Province, Malaysia. METHODS: To determine IBV antibodies, a total of 138 blood samples and 50 organ samples were collected from 10 commercial broiler flocks in 3 different farms by using the enzyme-linked immunosorbent assay (ELISA) (IDEXX Kit) and reverse transcription-polymerase chain reaction (RT-PCR) followed by sequencing. RESULTS: A total of 94.2% (130/138) of the samples were seropositive for IBV in the vaccinated flock, and 38% (52/138) of the birds was the IBV titre for infection. The selected seropositive samples for IBV were confirmed by RT-PCR, with 22% (11/50) being IBV positive amplified and sequenced by targeted highly conserved partial nucleocapsid (N) genes. Subsequently, phylogenetic analysis constructed using amplified sequences again exposed the presence of Connecticut, Massachusetts, and Chinese QX variants circulating in poultry farms in Sabah, Malaysia. CONCLUSIONS: The unexpectedly increasing mean titres in serology indicated that post infection of IBV and highly prevalent IBV in selected farms in this study. The sequencing and phylogenetic analysis revealed the presence of multiple IBV variants circulating in Malaysian chicken farms in Sabah, which further monitoring of genetic variation are needed to better understand the genetic diversity.

A transcriptomic (RNA-seq) analysis of Drosophila melanogaster adult testes overexpressing microRNA-2b-1.

MicroRNAs (miRNAs) are short non-coding single-stranded RNAs with approximately 22 nucleotides in length that negatively regulate the mRNA translation of a target gene. MiR-2b-1 belongs to the largest miR-2 family in Drosophila melanogaster with 8 members and this miRNA family is conserved in invertebrates. miRNAs play key roles in gene regulation, cell proliferation, cell death, cell differentiation and cell developmental homeostasis in multicellular organisms. Its role in various human diseases is continuously being studied. miRNAs also found out to be crucial in maintaining stem cell niche in D. melanogaster gonads. We have identified that ectopic overexpression of miR-2b-1 of D. melanogaster causes testicular bulging (a tumour like phenotype) in 3-5 days old adult flies. Hence, we have performed a transcriptomic (RNA-seq) analysis to understand the role of miR-2b-1 in the development, maintenance, and differentiation of D. melanogaster adult testis stem cells. Data are available from GEO (accession number GSE211399).

Seroprevalence of Zika Virus among Forest Fringe Communities in Peninsular Malaysia and Sabah: General Population-Based Study.

Zika virus (ZIKV) has had a history in Malaysia since its first isolation in 1966. However, it is believed that the immunity status among forest fringe communities has been underreported. We conducted cross-sectional surveillance of forest fringe communities from 10 Orang Asli villages and their peripheral communities in Perak, Pahang, and Sabah in Malaysia. A total of 706 samples were collected from 2019 to 2020 and screened for ZIKV exposure using an anti-ZIKV IgG ELISA kit. A neutralization assay against ZIKV was used to confirm the reactive samples. The seroprevalence results reported from the study of this population in Malaysia were 21.0% (n = 148, 95% CI, 0.183-0.273) after confirmation with a foci reduction neutralization test. The presence of neutralizing antibodies provides evidence that the studied forest fringe communities in Malaysia have been exposed to ZIKV. Multivariate analysis showed that those older than 44 years and those with an education below the university level had been exposed significantly to ZIKV. In addition, higher seropositivity rates to ZIKV were also reported among secondary school students from Bentong (Pahang) and residents from Segaliud (Sabah). No associations were identified between Zika seropositivity and gender, household size, house radius to the jungle, and income level. The presence of neutralizing antibodies against ZIKV among the study population might indicate that the causative pathogen had already circulated widely in forest fringe regions. Intervention for vector control, protection from mosquito bites, and awareness improvement should be encouraged in this population.

Data of knowledge towards Zika Virus infection in Sabah, Malaysia.

This dataset presents a cross-sectional survey and was conducted to assess the knowledge on Zika Virus infection among adults in Sabah. The data were collected from December 2019 to February 2021, 274 adults living in forest fringe communities were interviewed by trained personnel and have completed the distributed questionnaires. SPSS version 27.0 was used to analyzed the data. These data could serve as auxiliary information and/or research data for other researchers in Sabah. It could also serve as guide or reference data to other researchers outside Sabah who may be interested in carrying out similar research in other state.

Prevalence of Coronavirus Disease 2019 (COVID-19) in Different Clinical Stages before the National COVID-19 Vaccination Programme in Malaysia: A Systematic Review and Meta-Analysis.

More than 1.75 million COVID-19 infections and 16 thousand associated deaths have been reported in Malaysia. A meta-analysis on the prevalence of COVID-19 in different clinical stages before the National COVID-19 Vaccination Program in Malaysia is still lacking. To address this, the disease severity of a total of 215 admitted COVID-19 patients was initially recorded in the early phase of this study, and the data were later pooled into a meta-analysis with the aim of providing insight into the prevalence of COVID-19 in 5 different clinical stages during the outset of the COVID-19 pandemic in Malaysia. We have conducted a systematic literature search using PubMed, Web of Science, Scopus, ScienceDirect, and two preprint databases (bioRxiv and medRxiv) for relevant studies with specified inclusion and exclusion criteria. The quality assessment for the included studies was performed using the Newcastle-Ottawa Scale. The heterogeneity was examined with an I2 index and a Q-test. Funnel plots and Egger's tests were performed to determine publication bias in this meta-analysis. Overall, 5 studies with 6375 patients were included, and the pooled prevalence rates in this meta-analysis were calculated using a random-effect model. The highest prevalence of COVID-19 in Malaysia was observed in Stage 2 cases (32.0%), followed by Stage 1 (27.8%), Stage 3 (17.1%), Stage 4 (7.6%), and Stage 5 (3.4%). About two-thirds of the number of cases have at least one morbidity, with the highest percentage of hypertension (66.7%), obesity (55.5%), or diabetes mellitus (33.3%) in Stage 5 patients. In conclusion, this meta-analysis suggested a high prevalence of COVID-19 occurred in Stage 2. The prevalence rate in Stage 5 appeared to be the lowest among COVID-19 patients before implementing the vaccination program in Malaysia. These meta-analysis data are critically useful for designing screening and vaccination programs and improving disease management in the country.

Technical data on the inhibition properties of some medicinal plant extracts towards caseinolytic protease proteolytic subunit of Plasmodium knowlesi.

Proteolytic subunit of the caseinolytic protease system of Plasmodium knowlesi (Pk-ClpP; EC 3.4.21.92) is considered a viable target for antimalarial drug development to eradicate P. knowlesi malaria infection in Malaysia and Southeast Asian region. Inhibition of this system leads to a disruption in the protein homeostasis molecular machinery and therefore be lethal for the parasite. While plants are considered excellent sources of bioactive compounds exhibiting inhibition activity towards Pk-ClpP, many local medicinal plants remain unexplored. This article expands the data collected from the inhibition properties of the methanolic extract of Asystasia gangetica (Chinese Violet), Alstonia scholaris (Pulai Tree), Piper retrofractum (Javanese Long Pepper) and Smallanthus sonchifolius (Yacon) towards Pk-ClpP. These plants are widely found in Malaysia and Indonesia and have been traditionally used in various medical treatments. The present dataset showed that the extracts contained phenolic and flavonoid compounds in various concentrations, whereby S. sonchifolius was found to have the lowest content of phenolic and flavonoid contents, while A. gangetica and A. scholaris were statistically comparable, yet higher than P. retrofactum and S. sonchifolus. Further inhibition data assay towards Pk-ClpP revealed that A. gangetica, A. scholaris and P. retrofactum demonstrated remarkable inhibition activity with IC50 values of 39.06 ± 1.98, 48.92 ± 1.52, and 87.63 ± 3.55, respectively. However, the inhibition activity of these extracts was significantly lower than a serine protease inhibitor of phenylmethylsulfonyl fluoridenone (PMSF). Meanwhile, S. sonchifolus did not exhibit significant inhibition activity towards Pk-ClpP. In addition, Pk-ClpP was not inhibited by a cysteine protease inhibitor of E64.

Infectious Bronchitis Virus (Gammacoronavirus) in Poultry Farming: Vaccination, Immune Response and Measures for Mitigation.

Infectious bronchitis virus (IBV) poses significant financial and biosecurity challenges to the commercial poultry farming industry. IBV is the causative agent of multi-systemic infection in the respiratory, reproductive and renal systems, which is similar to the symptoms of various viral and bacterial diseases reported in chickens. The avian immune system manifests the ability to respond to subsequent exposure with an antigen by stimulating mucosal, humoral and cell-mediated immunity. However, the immune response against IBV presents a dilemma due to the similarities between the different serotypes that infect poultry. Currently, the live attenuated and killed vaccines are applied for the control of IBV infection; however, the continual emergence of IB variants with rapidly evolving genetic variants increases the risk of outbreaks in intensive poultry farms. This review aims to focus on IBV challenge-infection, route and delivery of vaccines and vaccine-induced immune responses to IBV. Various commercial vaccines currently have been developed against IBV protection for accurate evaluation depending on the local situation. This review also highlights and updates the limitations in controlling IBV infection in poultry with issues pertaining to antiviral therapy and good biosecurity practices, which may aid in establishing good biorisk management protocols for its control and which will, in turn, result in a reduction in economic losses attributed to IBV infection.

Factor Influences for Diagnosis and Vaccination of Avian Infectious Bronchitis Virus (Gammacoronavirus) in Chickens.

Infectious bronchitis virus (IBV) is a major economic problem in commercial chicken farms with acute multiple-system infection, especially in respiratory and urogenital systems. A live-attenuated and killed vaccine is currently immunized to control IBV infection; however, repeated outbreaks occur in both unvaccinated and vaccinated birds due to the choice of inadequate vaccine candidates and continuous emergence of novel infectious bronchitis (IB) variants and failure of vaccination. However, similar clinical signs were shown in different respiratory diseases that are essential to improving the diagnostic assay to detect IBV infections. Various risk factors involved in the failure of IB vaccination, such as various routes of application of vaccination, the interval between vaccinations, and challenge with various possible immunosuppression of birds are reviewed. The review article also highlights and updates factors affecting the diagnosis of IBV disease in the poultry industry with differential diagnosis to find the nature of infections compared with non-IBV diseases. Therefore, it is essential to monitor the common reasons for failed IBV vaccinations with preventive action, and proper diagnostic facilities for identifying the infective stage, leading to earlier control and reduced economic losses from IBV disease.

Highly Active Cellulose-Supported Poly(hydroxamic acid)-Cu(II) Complex for Ullmann Etherification.

Highly active natural pandanus-extracted cellulose-supported poly(hydroxamic acid)-Cu(II) complex 4 was synthesized. The surface of pandanus cellulose was modified through graft copolymerization using purified methyl acrylate as a monomer. Then, copolymer methyl acrylate was converted into a bidentate chelating ligand poly(hydroxamic acid) via a Loosen rearrangement in the presence of an aqueous solution of hydroxylamine. Finally, copper species were incorporated into poly(hydroxamic acid) via the adsorption process. Cu(II) complex 4 was fully characterized by Fourier transform infrared (FTIR), field emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray (EDX), transmission electron microscopy (TEM), inductively coupled plasma optical emission spectrometry (ICP-OES), thermogravimetric analysis (TGA), X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) analyses. The cellulose-supported Cu(II) complex 4 was successfully applied (0.005 mol %) to the Ullmann etherification of aryl, benzyl halides, and phenacyl bromide with a number of aromatic phenols to provide the corresponding ethers with excellent yield [benzyl halide (70-99%); aryl halide (20-90%)]. Cu(II) complex 4 showed high stability and was easily recovered from the reaction mixture. It could be reused up to seven times without loss of its original catalytic activity. Therefore, Cu(II) complex 4 can be commercially utilized for the preparation of various ethers, and this synthetic technique could be a part in the synthesis of natural products and medicinal compounds.

Bacterial community diversity in the rhizosphere of nickel hyperaccumulator plant species from Borneo Island (Malaysia).

The Island of Borneo is a major biodiversity hotspot, and in the Malaysian state of Sabah, ultramafic soils are extensive and home to more than 31 endemic nickel hyperaccumulator plants. The aim of this study was to characterize the structure and the diversity of the rhizosphere bacterial communities of several of these nickel hyperaccumulator plants and factors that affect these bacterial communities in Sabah. The most abundant phyla were Proteobacteria, Acidobacteria and Actinobacteria. At family level, Burkholderiaceae and Xanthobacteraceae (Proteobacteria phylum) were the most abundant families in the hyperaccumulator rhizospheres. Redundancy analysis based on soil chemical analyses and relative abundances of the major bacterial phyla showed that abiotic factors of the studied sites drove the bacterial diversity. For all R. aff. bengalensis rhizosphere soil samples, irrespective of studied site, the bacterial diversity was similar. Moreover, the Saprospiraceae family showed a high representativeness in the R. aff. bengalensis rhizosphere soils and was linked with the nickel availability in soils. The ability of R. aff. bengalensis to concentrate nickel in its rhizosphere appears to be the major factor driving the rhizobacterial community diversity unlike for other hyperaccumulator species.

Isolation site influences virulence phenotype of serotype 14 Streptococcus pneumoniae strains belonging to multilocus sequence type 15.

Streptococcus pneumoniae is a diverse species causing invasive as well as localized infections that result in massive global morbidity and mortality. Strains vary markedly in pathogenic potential, but the molecular basis is obscured by the diversity and plasticity of the pneumococcal genome. We have previously reported that S. pneumoniae serotype 3 isolates belonging to the same multilocus sequence type (MLST) differed markedly in in vitro and in vivo phenotypes, in accordance with the clinical site of isolation, suggesting stable niche adaptation within a clonal lineage. In the present study, we have extended our analysis to serotype 14 clinical isolates from cases of sepsis or otitis media that belong to the same MLST (ST15). In a murine intranasal challenge model, five ST15 isolates (three from blood and two from ears) colonized the nasopharynx to similar extents. However, blood and ear isolates exhibited significant differences in bacterial loads in other host niches (lungs, ear, and brain) at both 24 and 72 h postchallenge. In spite of these differences, blood and ear isolates were present in the lungs at similar levels at 6 h postchallenge, suggesting that early immune responses may underpin the distinct virulence phenotypes. Transcriptional analysis of lung tissue from mice infected for 6 h with blood isolates versus ear isolates revealed 8 differentially expressed genes. Two of these were exclusively expressed in response to infection with the ear isolate. These results suggest a link between the differential capacities to elicit early innate immune responses and the distinct virulence phenotypes of clonally related S. pneumoniae strains.

Site of isolation determines biofilm formation and virulence phenotypes of Streptococcus pneumoniae serotype 3 clinical isolates.

Streptococcus pneumoniae is a diverse species causing invasive as well as localized infections that result in massive global morbidity and mortality. Strains vary markedly in pathogenic potential, but the molecular basis is obscured by the diversity and plasticity of the pneumococcal genome. In the present study, S. pneumoniae serotype 3 blood (n = 12) or ear (n = 13) isolates were multilocus sequence typed (MLST) and assessed for biofilm formation and virulence phenotype. Blood and ear isolates exhibited similar MLST distributions but differed markedly in phenotype. Blood isolates formed robust biofilms only at pH 7.4, which were enhanced in Fe(III)-supplemented medium. Conversely, ear isolates formed biofilms only at pH 6.8, and Fe(III) was inhibitory. Biofilm formation paralleled luxS expression and genetic competence. In a mouse intranasal challenge model, blood isolates did not stably colonize the nasopharynx but spread to the blood; none spread to the ear. Ear isolates colonized the nasopharynx at higher levels and also spread to the ear compartment in a significant proportion of animals; none caused bacteremia. Thus, pneumococci of the same serotype and MLST exhibit distinct phenotypes in accordance with clinical site of isolation, indicative of stable niche adaptation within a clonal lineage.