Benji Brayan Ilagan Silva

National Pingtung University of Science and Technology

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Kuo‐Pin Chuang

National Pingtung University of Science and Technology

Huai-Ying Huang

Tajen University

Jaymee R. Encabo

University of the Philippines Los Baños

Andrew D. Montecillo

University of the Philippines Los Baños

Jen‐Pin Chuang

National Cheng Kung University

Yu‐Chang Tyan

Kaohsiung Medical University

Susan A. Sedano

University of the Philippines Los Baños

Freddiewebb B. Signabon

University of the Philippines Los Baños

Ronilo Jose D. Flores

University of the Philippines Los Baños

Hoàng Văn Minh

Hanoi University

Cooperative Institutions

University of the Philippines Los Baños

National Pingtung University of Science and Technology

National Cheng Kung University

Mapúa University

Kaohsiung Medical University

Chang Gung Memorial Hospital

Osaka University

Chung Yuan Christian University

Kaohsiung Medical University Chung-Ho Memorial Hospital

National Health Research Institutes

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Retrospective detection and whole genome sequencing identify the first local case of Pigeon Rotavirus A infection in Taiwan from 2018

Scientific Reports (2025)

Benji Brayan Ilagan Silva Michael Louie R. Urzo Andrew D. Montecillo Jaymee R. Encabo Jen‐Pin Chuang

Abstract In 2018, pigeon Rotavirus A G18P[17] was identified in Australia as the causative agent of a disease outbreak presenting as vomiting and diarrhea, reminiscent of the young pigeon disease syndrome. This virus has subsequently been detected in several other countries, including Belgium, Denmark, Germany, Great Britain, Poland, and the United States. This study was conducted to determine the presence of pigeon Rotavirus A among archived samples collected in Taiwan, and to subsequently characterize the whole genome of a local isolate. Two hundred twenty-five pigeon liver samples collected from 2018 to 2023 were tested for the presence of pigeon rotavirus A RNA using PCR. A sample from 2018 tested positive, and the successful rescue of infective virions was achieved. The first coding-complete genome of this virus from Taiwan was successfully sequenced, revealing that isolate NPUST-001 belongs to genotype G18P[17]-I4-R4-C4-M4-A4-T4-N4-E19-H4. To date, this is the earliest known rotavirus A isolate with this exact genotype constellation recovered from a domestic pigeon sample in the Asian region. Phylogenetic analysis of the VP6 segment showed that isolate NPUST-001 belongs to a distinct lineage of pigeon Rotavirus A which comprises of several other strains reported from mainland China and the USA. Although no recent cases were detected, active surveillance for rotaviral infection among suspected cases is recommended to gather more information on the epidemiology of this virus locally.

Molecular Epidemiology

10.1038/s41598-025-87271-6

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Epidemiology and genetic diversity of Streptococcus suis in smallhold swine farms in the Philippines

Scientific Reports (2023)

Susan A. Sedano Mary Grace Concepcion T. Cantalejo Christine Grace Angela R. Lapitan Angelo Miguel Elijah S. de Guzman Jennielyn T. Consignado

This study aimed to determine the presence and characteristics of locally circulating strains of Streptococcus suis, the most important streptococcal pathogen in swine. Oral swab samples were collected from pigs from 664 representative smallhold farms across nine provinces in the Philippines. Isolates were identified and characterized using PCR assays. The study revealed an isolation rate of 15.8% (105/664, 95% CI: 13.0-18.6) among the sampled farms. Two hundred sixty-nine (269) S. suis isolates were recovered from 119 unique samples. Serotype 31 was the most prevalent (50/269, 95% CI: 13.9-23.2) among the other serotypes identified: 5, 6, 8, 9, 10, 11, 15, 16, 17, 21, 27, 28, and 29. The detection of the three 'classical' S. suis virulence-associated genes showed that 90.7% (244/269, 95% CI: 87.2-94.2) were mrp-/epf-/sly-. Multilocus sequence typing (MLST) analysis further revealed 70 novel sequence types (STs). Notably, several local isolates belonging to these novel STs formed clonal complexes (CC) with S. suis strains recovered from Spain and USA, which are major pork-exporting countries to the Philippines. This study functionally marks the national baseline knowledge of S. suis in Philippines.

Streptococcus suis

Multilocus sequence typing

Molecular Epidemiology

10.1038/s41598-023-48406-9

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Genetic Diversity of Domestic Cat Hepadnavirus in Southern Taiwan

Viruses (2023)

Benji Brayan Ilagan Silva Jinyang Chen B. Villanueva Zi-Ying Lu Hua-Zhen Hsing

Domestic cat hepadnavirus (DCH) is an infectious disease associated with chronic hepatitis in cats, which suggests a similarity with hepatitis B virus infections in humans. Since its first identification in Australia in 2018, DCH has been reported in several countries with varying prevalence rates, but its presence in Taiwan has yet to be investigated. In this study, we aimed to identify the presence and genetic diversity of DCH infections in Taiwan. Among the 71 samples tested, eight (11.27%) were positive for DCH. Of these positive cases, three cats had elevated levels of alanine transaminase (ALT) and aspartate transaminase (AST), suggesting an association between DCH infection and chronic hepatitis. Four DCH-positive samples were also tested for feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) coinfection. One sample (25%) was positive for FIV, whereas there was no positive sample for FeLV (0%). In addition, we performed whole genome sequencing on six samples to determine the viral genome sequences. Phylogenetic analyses identified a distinct lineage compared with previously reported sequences. This study highlights the importance of continuous surveillance of DCH and further research to elucidate the pathophysiology and transmission route of DCH.

Feline leukemia virus

10.3390/v15102128

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Immunogenicity and Protective Activity of Pigeon Circovirus Recombinant Capsid Protein Virus-Like Particles (PiCV rCap-VLPs) in Pigeons (Columba livia) Experimentally Infected with PiCV

Vaccines (2021)

Huai-Ying Huang Benji Brayan Ilagan Silva Shen-Pang Tsai Ching‐Yi Tsai Yu‐Chang Tyan

Pigeon circovirus (PiCV) is the most recurrent virus diagnosed in pigeons and is among the major causative agents of young pigeon disease syndrome (YPDS). Due to the lack of an established laboratory protocol for PiCV cultivation, development of prophylaxis is hampered. Alternatively, virus-like particles (VLPs), which closely resemble native viruses but lack the viral genetic material, can be generated using a wide range of expression systems and are shown to have strong immunogenicity. Therefore, the use of VLPs provides a promising prospect for vaccine development. In this study, transfected human embryonic kidney (HEK-293) cells, a mammalian expression system, were used to express the PiCV capsid protein (Cap), which is a major component of PiCV and believed to contain antibody epitopes, to obtain self-assembled VLPs. The VLPs were observed to have a spherical morphology with diameters ranging from 12 to 26 nm. Subcutaneous immunization of pigeons with 100 µg PiCV rCap-VLPs supplemented with water-in-oil-in-water (W/O/W) adjuvant induced specific antibodies against PiCV. Observations of the cytokine expression and T-cell proliferation levels in spleen samples showed significantly higher T-cell proliferation and IFN- γ expression in pigeons immunized with VLPs compared to the controls (p < 0.05). Experimentally infected pigeons that were vaccinated with VLPs also showed no detectable viral titer. The results of the current study demonstrated the potential use of PiCV rCap-VLPs as an effective vaccine candidate against PiCV.

Circovirus

10.3390/vaccines9020098

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Politics as an Abiotic Component: Educational Perspectives in Environmental Management and Educational Sustainability in the Philippines

51st BIOTA Annual National Convention and Scientific Sessions (2016)

Shaunnah Ysabel Villareal Cledera Benji Brayan Ilagan Silva

This is an exploratory study on the perspectives in teaching ecological sustainability (ES) and environmental management (EM) in the Philippines. Ecology, the scientific branch focused on the study of interactions between and among biotic and abiotic components of the environment, has been historically more inclined to focus on (1) the “natural order of things” as undisturbed by humans, and (2) the rehabilitation of this “natural order.” Working on the premise that within the hierarchical and nested model, ecosystem interactions are complex and constantly evolving, this paper reasserts the constant reassessment and reconstruction of the concept of “natural order” by considering politics as an abiotic component of an ecosystem. The curricula of five CHED Centers of Excellence in Biology for 2014 were used as initial basis for analysis of ES and EM educational perspectives. Are the existing courses contextualized within the dominant and contending socio-political perspectives on ES and EM? Content analysis was applied to the curricula of the five universities to valuate their ES and EM components in the context of socio-politics. This study seeks to evaluate the critical approaches of the scientific community in the academe as an articulation of their effort to cross the divide between the life sciences and political system, and to actively engage the issue of sustainable development. This paper claims that, based on the curricula analyzed, the ES and EM education in the Philippines is insufficient in its attempt to consider politics as a factor which cannot be divorced with the issue of ecological awareness and the current global trends in ES and EM discourse.

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Lytic phages display protective effects against soft rot-causing Pectobacterium sp.

Biocontrol Science and Technology (2022)

Aeron Jade S. Parena Benji Brayan Ilagan Silva Rae Mark L. Mercado Adelbert Adrian A. Sendon Freddiewebb B. Signabon

Soft rot caused by Pectobacterium sp. is responsible for significant losses in vegetable production worldwide. Methods for the effective control of soft rot are limited and primarily based on good agricultural practices. The use of bacteriophages as biocontrol agents appears to be a promising alternative to combat phytopathogens. In this study, we investigated the efficacy of lytic phages recovered from symptomatic cabbage tissues and environmental samples against soft rot caused by Pectobacterium carotovorum subsp. carotovorum. Three bacteriophage isolates, designated as vB_PcaP-A3, vB_PcaM-D1, and vB_PcaM-J3, were observed to effectively lyse P. carotovorum subsp. carotovorum. Phage vB_PcaP-A3 exhibited virion morphology similar to the members of the podovirus group, while phages vB_PcaM-D1 and vB_PcaM-J3 showed myovirus morphology based on transmission electron microscopy. The optimal multiplicity of infection (MOI) differed greatly among the three phages. All three phages survived incubations at 30, 40 and 50 °C and pH conditions ranging from 3.0 to 9.0, but were all inactivated at 60°C and at pH 12. Both monophage and cocktail preparations were effective in inhibiting the growth of P. carotovorum subsp. carotovorum in the in vitro challenge tests. In the potato slice assays, while treatment with cocktail preparations completely inhibited the development of soft rot in tissue slices, monophage treatments not only resulted in a significant reduction of tissue maceration in slices, but also showed protective effect against soft rot in tubers. Overall, these results demonstrate the efficacy of phages vB_PcaP-A3, vB_PcaM-D1, and vB_PcaM-J3 for the biocontrol of soft rot caused by P. carotovorum subsp. carotovorum.

Pectobacterium carotovorum

Lytic cycle

Pectobacterium

10.1080/09583157.2022.2122403

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Development and Validation of KASP Assays for the Genotyping of Racing Performance-Associated Single Nucleotide Polymorphisms in Pigeons

Genes (2021)

Ching-Chi Chang Benji Brayan Ilagan Silva Huai-Ying Huang Ching‐Yi Tsai Ronilo Jose D. Flores

Pigeon racing’s recent upturn in popularity can be attributed in part to the huge prize money involved in these competitions. As such, methods to select pigeons with desirable genetic characteristics for racing or for selective breeding have also been gaining more interest. Polymerase chain reaction—restriction fragment length polymorphism (PCR-RFLP) for genotyping-specific genes is one of the most commonly used molecular techniques, which can be costly, laborious and time consuming. The present study reports the development of an alternative genotyping method that employs Kompetitive Allele Specific Polymerase Chain Reaction (KASP) technology with specifically designed primers to detect previously reported racing performance-associated polymorphisms within the LDHA, MTYCB, and DRD4 genes. To validate, KASP assays and PCR-RFLP assays results from 107 samples genotyped for each of the genes were compared and the results showed perfect (100%) agreement of both methods. The developed KASP assays present an alternative rapid, reliable, and cost-effective method to identify polymorphisms in pigeons.

Variants of PCR

10.3390/genes12091383

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Pigeon Circovirus over Three Decades of Research: Bibliometrics, Scoping Review, and Perspectives

Viruses (2022)

Benji Brayan Ilagan Silva Michael Louie R. Urzo Jaymee R. Encabo Alea Maurice Simbulan Allen Jerard D. Lunaria

The pigeon circovirus (PiCV), first described in the literature in the early 1990s, is considered one of the most important infectious agents affecting pigeon health. Thirty years after its discovery, the current review has employed bibliometric strategies to map the entire accessible PiCV-related research corpus with the aim of understanding its present research landscape, particularly in consideration of its historical context. Subsequently, developments, current knowledge, and important updates were provided. Additionally, this review also provides a textual analysis examining the relationship between PiCV and the young pigeon disease syndrome (YPDS), as described and propagated in the literature. Our examination revealed that usages of the term 'YPDS' in the literature are characterizations that are diverse in range, and neither standard nor equivalent. Guided by our understanding of the PiCV research corpus, a conceptualization of PiCV diseases was also presented in this review. Proposed definitions and diagnostic criteria for PiCV subclinical infection (PiCV-SI) and PiCV systemic disease (PiCV-SD) were also provided. Lastly, knowledge gaps and open research questions relevant to future PiCV-related studies were identified and discussed.

Circovirus

Subclinical infection

10.3390/v14071498

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Genetic diversity of domestic cat hepadnavirus in Taiwan

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Benji Brayan Ilagan Silva Jinyang Chen B. Villanueva Zi-Ying Lu Hsing-Hua Zhen

Abstract Domestic cat hepadnavirus (DCH) is an infectious disease associated with chronic hepatitis in cats, suggesting a similarity with hepatitis B virus infection in humans. Since its first identification in Australia in 2018, DCH has been reported in several countries with varying prevalence rates, but its prevalence in Taiwan has not yet been investigated. Here, we aimed to identify the presence and prevalence of DCH infections in Taiwan. Among 71 samples tested, eight (11.27%) were positive for DCH. Of these positive cases, three cats had elevated levels of alanine transaminase (ALT) and aspartate transaminase (AST), suggesting an association between DCH infection and chronic hepatitis. Four DCH-positive samples were also tested for feline immunodeficiency virus (FIV) and feline leukemia virus (FeLV) co-infection, one (25%) was positive for FIV while none for FeLV (0%). In addition, we performed whole genome sequencing of six samples to determine the viral genome sequences. Phylogenetic analyses identified a distinct lineage compared with previously reported sequences. Considering the recent findings suggesting the potential risk of DCH for interspecies or zoonotic transmission, this study suggests the importance of continuous surveillance of DCH and further research to elucidate the pathophysiology and transmission route of DCH.

Feline leukemia virus

Feline immunodeficiency virus

10.1101/2023.09.29.560097

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TRICHODERMA-INDUCED SYSTEMIC RESISTANCE AGAINST THE SCALE INSECT (UNASPIS MABILIS LIT & BARBECHO) IN LANZONES (LANSIUM DOMESTICUM CORR.)

The Journal Agriculture and Forestry (2019)

Benji Brayan Ilagan Silva Charina Gracia Banaay Kevin C. Salamanez

Unaspis mabilis infestations have been causing huge economic losses to the lanzones industry in the Philippines since 2009.This study, therefore, seeks to determine the use of Trichoderma as myco-biocontrol agent to increase lanzones (Lansium domesticum) defense and resistance against this insect.Two experiments were designed to test for the protective and rescuing capacity of Trichoderma inoculation against the insect pest.For both experiments, leaf area, leaf count, scale insect populations and densities were observed over time.Additionally, to assess the phytochemical response of the plants, the concentrations of jasmonic acid, salicylic acid, total phenol content, and total flavonoid content were also measured in the rescuing capacity experiment.Results indicated that the plants inoculated with Trichoderma were performing better, showing lower populations and slower growth rate of the insect, than the uninoculated plants for both the protective and rescuing capacity experiments.Phytochemical analysis revealed the presence of tannins, phlobatannins, flavonoids, steroids, glycosides, and alkaloids in the leaves of L. domesticum.Total phenols and flavonoids showed decreasing concentrations as the infestation progressed, while the concentrations of jasmonic acid and salicylic acid in scaleinsect-infested plants were found to be influenced by the inoculation of the plants with Trichoderma.

Scale insect

Trichoderma

10.17707/agricultforest.65.2.05

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