Biobanking of vector-borne viruses in the Philippines: basic principles, best practices, and challenges

Abstract

Vector-borne diseases remain a public health burden in the Philippines. Evidence-based strategies are being explored to control and eradicate these diseases. This study aims to outline a procedural framework for biobanking vector-borne viruses and identify best practices and challenges associated with the process. This study includes data from a biobanking initiative titled, “Molecular Profiles and Biobanking of Vector-borne Viruses in Selected Hospitals in Luzon.” Two partner sites were included in this study, and all samples collected were stored at the VRV Biobank. Standard operating procedures (SOPs) were prepared for sample collection to viral detection, characterization, and storage. The VRV Biobank houses serum aliquots, nucleic acid extracts, infected culture fluid and their associated data from 182 recruited participants. Key strengths of the implementation include adherence to protocols, integration of quality control strategies, frequent updating of SOPs, training biobank personnel, transparency during recruitment, effective coordination between partner sites, and characterization of banked samples. However, challenges in ethical compliance, procedural variations across partner sites, limited local training programs, procurement issues, and biobank staffing were identified. This study highlights best practices and challenges in biobanking and addresses gaps in the practice by developing a comprehensive framework informed by practical insights gained during actual implementation. This foundational biobank report represents the first documented effort to establish a curated virus biobank in the Philippines.

Supplementary Information

The online version contains supplementary material available at 10.1038/s41598-026-43667-6.

Introduction

In the Philippines, vector-borne diseases pose a major public health challenge. Tropical conditions, rapid urbanization, and high population density contribute to an environment conducive to the spread of arboviruses like Dengue, Chikungunya, Zika, and Japanese encephalitis^1–3. Dengue is particularly burdensome, with hundreds of thousands of cases reported annually and recurring large-scale outbreaks. In 2019, the Philippines recorded the highest number of dengue cases globally, accounting for 437,563 cases and 1,689 deaths attributed to dengue infection^4–6. Between January and November 16, 2024, the Department of Health (DOH) reported a total of 340,860 dengue cases—an 81% increase compared to the same period in the previous year⁶. Despite efforts focused on vector control and public awareness, the periodic return of these diseases highlights deficiencies in long-term surveillance, diagnostic innovation, and preparedness for new viral threats.

The epidemiology and evolution of vector-borne viruses and their hosts are increasingly understood through advances in molecular diagnostics and genomics^7–9. With such advancements, various molecular approaches have enabled the development of tools against vector-borne viruses¹⁰. This progress relies significantly on the availability of high-quality, well-preserved biological samples and their associated data. Consequently, biobanking—the structured collection, processing, storage, and governance of biological materials¹¹—has become a critical infrastructure for biomedical research and public health preparedness¹². The establishment of these facilities paves the way for translational research and innovations¹³, including drug and vaccine development¹⁴, improving diagnostic and therapeutic services¹⁵, and widespread sharing of genomic and health-related data^14,16. Furthermore, the spread of SARS-CoV-2 during the Coronavirus disease 2019 (COVID-19) pandemic underlined the importance of pandemic-preparedness among health systems around the globe. These biorepository facilities played a central role in the handling of viral specimens and disseminating laboratory knowledge across health units and diagnostic institutions¹⁷.

Despite its growing global importance, biobanking remains underdeveloped in many low- and middle-income countries (LMICs), including the Philippines. While efforts are underway to establish national biorepositories, the collection and storage of vector-borne viruses—particularly those derived from human clinical samples—remain fragmented and poorly standardized¹⁴. Virus biobanks are not an entirely new concept to the global scientific community, as virus biobank networks such as the European Virus Archive (EVA) have been around since 2008, which has gained more widespread importance due to the COVID-19 pandemic¹⁸. However, some barriers exist, including limited biosafety infrastructure, ethical and regulatory complexities, the absence of harmonized protocols, and a lack of coordinated policy support^13,14. Moreover, biobanking of potentially high-risk pathogens requires strict adherence to biosecurity, chain-of-custody procedures, and ethical consent protocols to ensure the safe and equitable use of biospecimens, especially in LMICs^19,20.

To address these gaps, this study aims to develop a procedural framework and foundational biobank report for the biobanking of human-derived vector-borne viruses in the Philippines, with future applications in health research and public health response. Specifically, the study will outline basic biobanking principles as they apply to arboviral pathogens, identify technical and institutional challenges, and propose standard operating procedures for ethical sample collection, virus isolation and long-term storage. By defining a locally applicable framework aligned with international best practices, this study presents a foundational biobank report on a virus biobank aimed to capacitate local and international research. At this foundational stage, the success of the VRV biobank is defined by the establishment of operational procedures and the usability of samples in research. The VRV biobank acts as a vital research resource by processing, organizing, characterizing, and maintaining specimens and its associated data.

Methods

Project description and sites

This study includes data and information from the project titled, “Molecular Profiles and Biobanking of Vector-borne Viruses in Selected Hospitals in Luzon”, funded by the Department of Science and Technology (DOST) monitored by the DOST-Philippine Council for Health Research and Development (DOST-PCHRD). This is the second of three projects under the Vector-borne and Respiratory Viruses Biobanking program (VRV Biobanking), a program which aims to establish a curated national virus biobank under the Virology and Vaccine Research Program (VRP) of the DOST.

The project partnered with selected DOH hospitals in Luzon for sample collection. The Luzon group of islands is the most populated of the three island groups of the Philippines. and is composed of 8 regions, which includes the National Capital Region (NCR). The partner hospitals were selected based on their health research capacity, including the presence of established institutional research ethics committees and substantial experience in implementing health research studies.

Partner site 1 is Baguio General Hospital and Medical Center (BGHMC), a tertiary government hospital with a 1500-bed capacity, located in Baguio City in the Cordillera Administrative Region (CAR). Partner site 2, Rizal Medical Center (RMC), is a 500-bed capacity government hospital located in Pasig City, NCR (Fig. 1). In early 2024 data, CAR and NCR reported 90,119 and 24,232 dengue cases, respectively^21,22.

Fig. 1.

Geographic locations of partner site 1 (BGHMC, Baguio City) and partner site 2 (RMC, Pasig City) and the Biobank site (VRV biobank, Taguig City) as mapped in the Philippines. Images from https://commons.wikimedia.org/.

The Biobank Site is located at a heightened-containment laboratory located at DOST-Industrial Technology Development Institute (DOST-ITDI), DOST Compound, General Santos Avenue, Bicutan, Taguig City (Fig. 1). The distances from the biobank site for partner sites 1 and 2 are 263 km and 13.5 km, respectively.

Preparation of SOP

Standard operating procedures (SOPs) were drafted by the project team to ensure consistent, efficient and accurate execution of the biobanking processes. These guidelines were based on available literature, and aligned with local and internationally-accepted standards on biosafety, biosecurity and biobanking. The SOPs on patient recruitment, sample collection and transportation were based on general phlebotomy guidelines, several journals on the transport of biological materials, and the World Health Organization (WHO) laboratory safety manual²³. SOPs on laboratory processes and biobanking were based on the package inserts of reagent kits, manuals on handling biological samples by the WHO and National Research Council (United States of America), the recommendations of the International Society for Biological and Environmental Repositories (ISBER), the NSW Health Statewide Biobank, and product information from American Type Culture Collection (ATCC).

SOPs also include the definition of roles and responsibilities of the personnel involved in the biobanking processes. During the project implementation period, particularly in running the biobank, the project staff functioned as laboratory custodians and biobank managers.

The drafted SOPs were reviewed and approved by the project and program leaders, as well as the co-investigators, and subsequently validated by the project team to ensure that the expected and defined outcomes are met. All SOPs are updated as needed, and subsequent validations and reviews were done by the project personnel to ensure alignment with changing local regulations and continuous process improvement. Printed copies of the latest versions of the SOPs are available in the VRV Biobank for quick access by the laboratory and biobank personnel.

Partnership management and ethics considerations

To proceed with patient enrollment, the DOST-ITDI, as the project’s implementing agency, established partnerships with the partner sites through a clinical research agreement (CRA). The CRA outlines the legal aspects of implementation at the partner sites and defines the roles, obligations, and responsibilities of the involved parties. The document also details the purpose of the agreement, financial terms, legal and ethical compliance of both parties, data ownership, publication rights, confidentiality, and the terms for study amendments and termination of the partnership. During this period, the project team also partnered with physicians or medical consultants from each site, designating them as project collaborators and site investigators. They are responsible for carrying out the functions of the partner sites, as outlined in the CRA, and facilitating communication between the project team and the partner hospitals.

Following this, the project obtained ethics clearance from the Single Joint Research Ethics Board (SJREB) and was assigned the protocol code SJREB-2024-22. The SJREB is an institution organized under the DOH that conducts joint reviews of multi-site research studies for implementation across hospitals funded and supervised by the agency. Obtaining ethics clearance from the SJREB is a prerequisite for initiating project implementation in the partner DOH hospitals. This clearance, the study protocol, signed copies of the CRA, and application forms were then submitted to the institutional ethics boards.

After obtaining board approvals, the project team conducted pre-implementation meetings at the partner sites with the project collaborators. These meetings were held to allow proper endorsements with the involved medical doctors and allied healthcare personnel, and to proactively identify and address potential issues that may arise during the actual participant enrollment procedures.

The study was conducted in accordance with the Declaration of Helsinki. All procedures—including participant enrollment, collection, analysis, and storage of samples and data—were performed in strict compliance with the rules and regulations established by all approving and monitoring bodies overseeing the implementation of the study. Relevant biobanking, biosafety, and biosecurity guidelines from ISBER and the WHO were also integrated into the conduct of biobanking processes.

Participant enrollment

Participant enrollment was conducted in the emergency room (ER) and the outpatient department (OPD) clinics of the partner hospitals. The project staff coordinated closely with collaborators and attending physicians during the recruitment and consent process, ensuring that appropriate measures were implemented to prevent any disruptions or interruptions to the delivery of patient care. However, since the study recruitment process was not institutionalized in the partner sites, not all eligible patients were referred automatically. Participant recruitment relied solely on those who were screened and referred by the site collaborators and partner medical doctors in the partner sites. As part of the original project proposal, the target size of sample collection was 182 enrolled patients using quota sampling.

The inclusion criteria for the study include individuals aged 19–60 years old presenting with acute febrile illness or systemic viral infection symptoms such as headache, rashes, and body or muscle pain within the first 5 days of initial presentation. Pregnant women, as well as patients diagnosed with terminal comorbid disease, COVID-19, tuberculosis, or other risk group 3 pathogens, are automatically excluded from participation in the study. Only participants referred by either the site collaborators or partner medical doctors who matched the inclusion criteria and provided consent were included in the study.

Consent was obtained through an informed consent form, signed by both the patient and the project staff. Prior to obtaining consent, the project staff explained key information about the study, with emphasis on the voluntary nature of their participation. In addition, the participants are also requested to affirm their consent by checking a specific tick box stating, “Yes, I am allowing my samples to be tested and stored indefinitely for future use” if they agree. A copy of the signed consent form and executive summary of the study, including contact details of project personnel, were provided to the patient after the screening process. Participants who were unwilling to sign the consent form were excluded. Associated clinical and laboratory data were collected among consenting individuals only, using a case report form (CRF). The CRF was used to gather demographic information (age, sex and address), patient history (preliminary diagnosis, onset of illness, signs and symptoms, relevant past medical history), physical examination findings (blood pressure, body weight, respiratory rate, pulse rate, oxygen saturation and body temperature), and laboratory results (complete blood count or CBC , dengue nonstructural protein 1 (NS1), and dengue immunoglobulin M and G (IgM and IgG) rapid tests) from consenting patients.

Anonymity was maintained by assigning a unique identification code to the CRF and its associated data entries. These codes do not contain any personal identifiers and were used solely to organize participants according to the date and time of their enrollment in the study.

Sample collection

Blood samples were drawn from patients who met the inclusion criteria and provided consent. A total of 4–8 mL of blood was collected from each patient by the project staff and placed in clot activator tubes (yellow-top). For the patient’s convenience and to avoid multiple blood draws, samples for other laboratory tests, requested by the attending physician were also extracted. 

Similar to the CRF, the tubes were labeled only with the same identification code. This code serves as the basis for identifying all laboratory outputs and products resulting from the sample. Fully clotted samples were then centrifuged in the clinical laboratories of the partner sites to separate the serum from the cellular components.

For samples collected in partner site 1, the centrifuged samples were temporarily stored in an ultra-low temperature feezer at − 80 °C before transporting to the biobank site. On the other hand, all centrifuged samples in partner site 2 are immediately transported to the biobank site.

The project staff maintains an updated master list of recruited participants, anonymized through their identification numbers, in a password-protected storage system. This is done to monitor the progress of patient recruitment and ensure consistency within the project team.

Sample transportation

Collected samples were transported within 24 h to the biobank site in a triple packaging system under cold-chain storage conditions (Fig. 2). The collection tubes were wrapped in interleaving tissue papers and placed in a zip-lock biohazard bag. The tubes were then secured in a rack to prevent movement during transport and promptly transferred to an icebox containing frozen gel packs to maintain a temperature of 2–8 °C. The outer container or icebox is labeled with a biohazard symbol, the address of the biobank site and contact numbers of the project staff to facilitate retrieval upon loss. The project staff personally transports the samples from the partner sites to the biobank site in DOST-ITDI to ensure security and adherence to institutional logistical protocols.

Fig. 2.

Triple packaging system.

Upon receipt at the biobank site, tube labels are cross-checked against the master list for verification and subsequently processed for aliquoting. Improperly labelled samples, samples with insufficient volume (less than 4 mL), samples with transport delays of more than 72 h and incomplete documents are rejected and are discarded according to procedure. This entire process was accompanied by proper endorsement and documentation through the use of a logbook.

Sample processing and data management

Four aliquots of the serum samples were prepared for biobanking and other laboratory downstream analyses. The first aliquot is for nucleic acid extraction (160 μL), while the second is for cell culture (50 μL). The remaining 750 µL aliquots of serum samples were processed for biobanking and placed in properly-labeled 2 mL cryovials. All aliquots were stored in an ultra-low temperature freezer at – 80 °C until further processing or use. (Fig. 3). Isolation and purification of viral RNA from the collected samples were performed using commercially-available nucleic acid extraction kits.

Fig. 3.

Preparation of aliquots from collected serum samples. Images from https://bioart.niaid.nih.gov/.

All pertinent laboratory information gathered throughout the process, as well as an updated inventory of banked samples, is stored in a secure storage system functioning as a Laboratory Information Management System (LIMS), which is accessible only to authorized members of the project team.

Data entries in the case report forms are likewise consolidated and organized in a master data sheet, maintained and may be accessed only by the project staff. All documents containing identifying information from the participants, including signed informed consent forms and accomplished case report forms, are stored in a safety vault in the VRV Biobanking office at DOST-ITDI. The vault is part of a storage drawer made out of robust steel material and protected by a combination dial and a set of keys, with authorized members of the project team serving as its custodians.

Virus detection and culture

Viral RNA was extracted using the QIAamp^® Viral RNA kit (Qiagen, Germany). Sample lysis was done by mixing 140 μL of serum sample to the Buffer AVE + carrier RNA with Buffer AL solution and was incubated at room temperature for 10 min. Ethanol (96–100%) was added to the lysed sample and was mixed by vortexing and then transferring the solution to spin columns. Washing was performed using the wash buffers (Buffer AW1 and AW2). Elution was performed by carefully dispensing 60 μL of the elution buffer (Buffer AE) to the column membrane, incubating the buffer and sample for about 1 min and then centrifuging at 6000 × g (14, 000 rpm) for 1 min. Quality of viral RNA was determined by running the samples in 2% agarose gel. Viral RNA quantity was measured using a Nanodrop spectrophotometer (Thermo Fisher Scientific, USA).

Viral detection and amplification of the isolates was performed using VIASURE ZDC Multiplex RT-PCR Assay kit (Cartest Biotec, Spain) according to manufacturer’s procedure, to detect the presence of Dengue (DENV), Chikungunya (CHIKV), and Zika (ZIKV) viruses. Briefly, 15 µL rehydration buffer was added to the PCR wells of the strips to rehydrate the PCR buffer and primers. Around 10 ng/µL of DNA template was used for reverse transcription and amplification using the following one-step PCR conditions: 1 cycle of reverse transcription at 45 °C for 15 min, 1 cycle of initial denaturation at 95 °C for 2 min, 45 cycles of denaturation at 95 °C for 10 s including annealing and extension at 60 °C for 50 s.

As per the manufacturer’s Instructions for Use (IFU), samples were classified as positive if they exhibited a characteristic sigmoidal amplification curve with a cycle threshold (Ct) value of < 40, provided that the internal control yielded a valid amplification signal in the corresponding channel (FAM for DENV, ROX for CHIKV, and Cy5 for ZIKV).

Viral inoculation and propagation were performed using cell lines available from culture collections. A mosquito cell line, C6/36 Aedes albopictus cells, was inoculated with PCR-positive serum samples. The infected culture fluid (ICF) was then harvested on days 7 and 14. The harvested ICF was then aliquoted into two (2) 1.5 mL microcentrifuge tubes for processing (160 μL for nucleic acid extraction, and 340 μL for plaque titration assay) and two (2) 2 mL cryogenic vials for banking at − 80 °C in ultra-low temperature freezers. The ICF aliquot stored for nucleic acid processing was subjected to extraction and end-point PCR to confirm presence of inoculated virus in the mosquito cell line. 

For the characterization of the virus, viral infectivity assay, analysis of structural morphology, sequencing and mutation analysis will be performed. Once completed, the results and details of these assays should be available as an associated data of the biobanked samples.

Biobanking

Serum samples, nucleic acid extracts, and infected culture fluid (ICF) in cryogenic vials were labelled with identification codes and banked in ultra-low temperature freezers at − 80 °C for long-term preservation. The project team maintains an inventory of the banked viral samples to facilitate their curation and retrieval.

Specimen and document disposal

All biological samples in the VRV biobank identified for disposal are segregated according to the point of receipt or generation, as referenced in the biobank inventory. The samples are handled within a biosafety cabinet and placed inside an autoclavable bag. These are then autoclaved at a temperature of 121 °C for at least 15 min. Decontaminated samples are transferred to a leak-proof plastic container labeled with a biohazard symbol, material information and date of decontamination. The wastes are then placed in a clearly identified area in the laboratory for pending final disposal, and endorsed to a third-party waste treatment facility, followed by disposal in a sanitary landfill. These procedures are done following general biosafety and environmental guidelines from the Department of Environment and Natural Resources (DENR) for infectious waste disposal, in order to minimize risks to both personnel and environment²⁴.

In the event of participant withdrawal, facility closure or termination of operations, the VRV biobank project team shall collect all appropriate documents from storage and will be destroyed using a paper shredder. All associated data and related laboratory information would also be deleted from the master sheet and LIMS.

The project team maintains detailed records of sample and document disposal, from the point of identification, type of disposal method used, dates and time of disposal and witness signatures.

Results

Patient demographics and arbovirus detection in biobanked samples

A total of 182 participants from the two partner sites were enrolled in the study, comprising 161 from partner site 1 and 21 from partner site 2. The mean age of participants was 31.5 years (standard deviation: 10.5), with ages ranging from 19 to 60 years (Table 1). Females made up the majority of participants, with 113 individuals (62.1%), while males accounted for 69 individuals (37.9%) (Table 2). In addition, all 182 participants presented with fever, while other commonly reported signs and symptoms included headache (56.6%), joint pain (36.8%), fatigue (32.4%), and nausea (26.4%). These signs and symptoms were observed either alone or in combinations.

Table 1.

Participant demographic data distribution (age).

Statistic	Age (years)
Mean	31.5
Minimum	19
Maximum	60

Table 2.

Participant demographic data distribution (sex).

Sex	Number (n)	Percentage (% = n/N × 100)
Male	69	37.9
Female	113	62.1
Total (N)	182	100

Figure 4 illustrates the participant recruitment for the duration of 10 months, starting on September 16, 2024, and concluding on July 17, 2025. The average number of recruited participants from both partner sites per month is 17.

Fig. 4.

Monthly participant recruitment.

Serum samples were collected from 182 participants. All samples were accepted for data analysis and sample processing following validation and cross-checking against the study’s inclusion and exclusion criteria, and verification of obtained consent from participating individuals.

Table 3 shows the distribution of stored samples in the VRV biobank. For each serum sample collected from the 182 participants, 2 serum aliquots were stored, resulting in a total of 364 serum aliquots intended for ongoing and future research activities. Designated 160 μL aliquots were not kept for storage but for viral RNA extraction, resulting in 182 aliquots of viral RNA stored (Fig. 3). The RNA extracts were tested for Multiplex qRT-PCR assay for DENV, CHIKV and ZIKV. Out of 182 viral RNA extracts, 50 tested positive for the presence of arboviruses. These samples were subsequently subjected to viral inoculation and culture. Two aliquots were obtained from each harvested culture fluid, resulting in 100 banked vials.

Table 3.

Distribution of biobanked samples.

	Number of biobanked samples (in aliquots)
Serum	364
Extracted RNA	182
Infected Culture Fluid (ICF)	100
Total	646

Table 4 shows the results of the multiplex qRT-PCR assay. A total of 50 samples (27.5%) tested positive for at least one of the four viruses by qRT-PCR. Among these, 47 (25.8%) tested positive for DENV, 1 (0.6%) tested positive for CHIKV and 2 (1.1%) for ZIKV. The remaining 132 (72.5%) tested negative for the four viruses.

Table 4.

qRT-PCR assay results.

RT-qPCR assay result	Frequency (n = number of participants)	Percentage (% = n/N × 100)
Dengue (DENV)	47	25.8
Chikungunya (CHIKV)	1	0.6
Zika (ZIKV)	2	1.1
Negative	132	72.5
Total (N)	182	100

From the hospital procedures, the project team recorded information of dengue detection by DENV Rapid Diagnostic Tests (RDTs). In the Philippines, performing RDTs for DENV, CHIKV and ZIKV are not routinely part of hospital procedures, as dengue diagnosis and management is still largely dependent on clinical presentation⁴⁴. DENV RDTs include dengue NS1 and Dengue Duo (IgM and IgG)—test indicators of laboratory confirmed dengue in addition to a positive qRT-PCR result for dengue.

Table 5 summarizes the qRT-PCR data and the hospital’s DENV RDT results. Twenty-five (13.7%) of those biobanked samples were positive for the presence of DENV by both qRT-PCR and DENV RDT. Nine samples (4.9%) tested negative in DENV RDT were found to be positive by qRT-PCR for the presence of one of the three arboviruses (2 ZIKV; 7 DENV). Furthermore, 16 samples (8.8%) from cases of probable dengue (no DENV RDT data available) tested positive for the presence of DENV or CHIKV by qRT-PCR (1 CHIKV; 15 DENV).

Table 5.

qRT-PCR results and clinical/laboratory dengue parameters.

qRT-PCR result (DENV, CHIKV, ZIKV)	Laboratory-confirmed dengue		Probable dengue**	Total
	Positive for dengue RDTs*	Negative for dengue RDTs*
Positive***	25 (13.7%)	9 (4.9%)	16 (8.8%)	50
Negative	31 (17.0%)	18 (9.9%)	83 (45.6%)	132
			Total	182

Dengue RDTs* = Dengue NS1 or Dengue Duo (IgM and IgG) tests performed in the partner sites.

Probable dengue** = a patient living in or history of travel to endemic areas with fever and two or more of the following: nausea, vomiting, rash, aches and pains, tourniquet test positive, leukopenia, or any other warning signs²⁵.

POSITIVE*** = qRT-PCR Results with Ct value < 40.

Thirty-one biobanked samples (17.0%) that have associated positive DENV RDT results were negative for the presence of any of the arboviruses by qRT-PCR, while 18 samples (9.9%) had coinciding negative qRT-PCR and DENV RDT results. The remaining 83 samples (45.6%), considered probable cases of dengue based on clinical presentation alone, tested negative for qRT-PCR.

Discussion

Participant and sample distribution

Notably, more patients were recruited from partner site 1 than from partner site 2 (161 vs. 21, respectively). However, this does not reflect the statistical distribution of dengue cases in these cities. As previously mentioned, participant recruitment for research is often not institutionalized, hence the manner of referring patients for study participation entirely depends on the willingness and capacity of site collaborators to identify and refer eligible patients. Inclusion to the study is also influenced by the patient’s decision to participate. This is one limiting factor in biobanks since only representative specimens are collected and may not reflect the frequency of disease. To add, in the Philippines, hospitals as sample source sites will only have general research ethical procedures in place, while their own research structure is limited or sometimes non-existing. This poses a challenge in establishing disease-focused biobanks where the source of the specimens (mainly hospitals) is a different facility that is governed by various institutions and located far from the biobank. For cases similar to the VRV biobank and its partner sites, it is recommended that study participation be strongly incorporated into hospital procedures. From this perspective, it may be more advantageous for the hospitals to establish their own disease-focused biobanks to ensure procedural efficiency. At the same time, hospital-based biobanks are encouraged to promote specimen and data accessibility. Moreover, hospital leaders, local researchers, funding agencies, and policymakers in the Philippines are encouraged to collaborate in harmonizing guidelines and strengthening policies on biobanking for health research in the country.

In this report, it is also noticeable that the recruitment numbers peaked during the monsoon months (September to December), particularly in October 2024, when 37 participants were enrolled in the study. Dengue infection is endemic in the country⁴⁴, however, an increase in the number of cases is always observed during the monsoon months. This is due to the presence of the ideal breeding and living conditions for mosquitoes brought by the increased rainfall during the monsoon months⁴⁵. Interestingly, the participant recruitment data show the consistent presence of dengue cases even outside the rainy season throughout the 10-month duration of the recruitment process. This may suggest the persistent presence of dengue and arboviral diseases in the vicinity of the partner sites.

Looking at the multiplex qRT-PCR results and DENV RDTs results from the partner sites (Table 5), the qRT-PCR assay detected 50 samples that were positive for at least one of the arboviruses. Interestingly, only 25 of these were also detected as DENV-positive by DENV RDTs. Nine samples that tested negative for DENV by DENV RDTs were subsequently found to be positive for either ZIKV or DENV by qRT-PCR. Among these 9, two were positive for ZIKV and seven were positive for DENV. Furthermore, out of the 16 probable dengue cases with no available DENV RDT data, 15 samples tested positive for DENV and 1 for CHIKV, as shown in the qRT-PCR results (Tables 4 and 5). These findings demonstrate that qRT-PCR was able to detect the presence of arboviruses in collected serum samples that were not previously detected by DENV RDTs. As DENV, CHIKV and ZIKV RDTs are not routinely performed in hospitals, the qRT-PCR assay can also serve as an important tool to detect arboviral infections. It is particularly valuable for differentiating among the three arboviruses, as clinical management and treatment may vary. This capability is particularly critical for the detection of ZIKV among pregnant women.

It is also noteworthy to look into the samples that tested positive for DENV by DENV RDT but were negative in the results of the qRT-PCR. This is a known occurrence in the diagnosis of dengue and can be caused by several factors related to the timing of the tests or potential cross-reactivity²⁶. qRT-PCR tests detect the virus’s genetic material and are most effective during the early acute phase of illness (typically the first 5–7 days) when viral loads are highest. After this window, the viral load decreases, and the RT-PCR is more likely to yield a false negative result⁴⁷. The study results show however, that 18 samples have coinciding negative detection of DENV (both by DENV RDT and qRT-PCR). Eighty-three patients who have probable dengue (no DENV RDT available) were tested negative for the presence of arboviruses by qRT-PCR.

In the context of biobanking and health research, it is important to consider sample associated data in experimentation and analysis. For the VRV biobank, the results of qRT-PCR and other sample-associated data (e.g. DENV RDT, symptoms, presence of warning signs, other viral characterization, etc.) will guide researchers to understand which samples are best for their research projects. For future arbovirus biobanking initiatives, it is recommended to consider inclusion of the DENV RDT testing in all recruited patients. This will ensure laboratory confirmation of dengue, rather than relying solely on clinical information, especially since arbovirus RDTs are not routine procedures in hospitals.

Best practices in establishing a vector-borne virus biobank

The implementation of this biobanking initiative for human-derived vector-borne viruses in the Philippines generated several critical insights and best practices which can be useful to future efforts in establishing sustainable biobanking systems for infectious disease research, especially that national efforts remain fragmented¹³. Standard operating procedures were drafted by the project team which are consistent with international biobanking and biospecimen management guidelines, including those from the ISBER and the WHO. The standardization of procedures forms the foundation of quality management in biobanks, primarily ensuring that the stored biological samples are of the highest quality and comply with modern health research standards^27,28. The project SOPs served as a guide and manual for the project staff in performing routine patient recruitment, sample collection, transportation and various laboratory tasks, forming a procedural framework for the biobanking process of human-derived arboviruses (Figs. 5 and 6).

Fig. 5.

Diagrammatic procedural framework for participant enrollment, sample collection and transportation for biobanking.

Fig. 6.

Diagrammatic procedural framework for the laboratory processes and biobanking.

In addition, there was a series of consultations on the SOPs with project co-investigators and process validations by the project staff to reflect the actual work setting in the biobank site laboratory and partner sites. Quality control was embedded within the biobanking system through a mechanism for periodic SOP updating. Updates were performed based on operational experience and routine internal reviews, ensuring that the SOPs remained responsive to field conditions and evolving research standards. This dynamic updating process forms a critical element of continuous quality improvement and risk mitigation. Importantly, the same staff involved in participant recruitment and sample processing were also engaged in the development and contextualization of SOPs. This bottom-up approach allowed for procedural adaptability, ensuring that protocols were not only scientifically robust but also feasible, given the logistical realities of local health settings.

Maximizing sample integrity requires adherence to established SOPs and properly trained staff²⁹. The staff of the project was able to attend a one-day introductory course on biobanking facilitated by the Philippine Genome Center’s Biobanking Core Facility (PGC-BCF). After which, the staff also attended a writeshop to look into the SOPs developed by the VRV Biobank. The introductory course and biobank writeshop were made to tailorfit the needs of the VRV Biobank. In addition to this, all field and laboratory personnel were trained in Good Clinical Practice (GCP), Good Laboratory Practices (GLP) and Biorisk management. This included instruction on ethical recruitment, biosafety, documentation, and sample handling. Such training enhances the credibility and reproducibility of downstream analyses using biobanked samples. To support the limited training and education in biobanking in the Philippines, the training on GCP and GLP has significantly provided the project staff the needed knowledge in executing biobanking activities. In biomedical research, it is emphasized that irrespective of place and purpose of scientific work, GLP quality standard should be implemented³⁰. The VRV Biobank handles virology samples, requiring stringent containment protocols within its laboratories. Since biobanks serve both research and clinical purposes, the need for GCP is also deemed relevant. Research and diagnostic laboratories globally adhere to safety guidelines and procedures established by various regulatory authorities³¹.

While the collection of samples defined by a set of criteria contributes to the successful establishment of biobanks, it is also important that rejection criteria should be in place as well. A clearly defined sample rejection protocol was instituted to ensure that only high-quality and properly collected biospecimens were admitted to the biobank. Criteria for rejection included compromised labeling, insufficient volume, hemolyzed samples, improper storage conditions during transport, or lack of completed documentation. This protocol is essential in maintaining the integrity of the biobank and ensuring data validity for future research.

The SOPs are categorized into General, Technical, and Equipment SOPs. These definitions and the categorization of the SOPs are operational, project-specific and tailored to the functionalities of the VRV Biobank.

• General SOPs outline the definitions and implementations of other SOPs and describe fundamental aspects of laboratory and biobank operations, including accessibility, biosafety, biosecurity and waste management.

• Technical SOPs detail the steps involved in carrying out recurring processes or tasks which may also include measures to mitigate difficulties or setbacks that may be encountered. In addition, these documents also outline the roles and responsibilities of the personnel responsible for performing the tasks.

• Equipment SOPs detail the handling, operation, and maintenance of individual machines and laboratory apparatuses.

All project files, including the SOPs, master lists of participants and associated data collected from each step of the process, are stored in a password-protected storage, which functions as a Laboratory Information Management System (LIMS) that is accessible only to authorized members of the project team.

Efficient coordination between partner collection sites and the biobank site was a key strength of this project. This was attributed to the pre-existing orientation of participating institutions toward collaborative health research and the proactive commitment of project leaders and project staff. Regular communication, shared documentation systems, and coordinated workflows contributed to ensuring standardization across sites. The submission coordination was matched with continuous engagement with the partner site’s Research Ethics Committees (RECs). Immediate implementation followed after securing the Clinical Research Agreement (CRA) which ensured clarity in institutional roles and data/sample sharing protocols.

Clinical field collection teams reported high levels of participant receptiveness to research inclusion, which may reflect increasing public awareness of the value of health research or, alternatively, the strength of recruitment approaches used by trained staff. This receptiveness is an encouraging factor for future longitudinal or multi-site studies requiring biobanking components. All participants were provided with informed consent forms translated into three languages—English, Filipino, and Ilocano—and accompanied by proper explanation. The consent form included a clearly worded clause indicating their agreement to allow future use of their samples for health research, such as “Yes, I am allowing my samples to be tested and stored indefinitely for future use.” This transparency not only upholds ethical standards but also strengthens participant trust and the long-term utility of stored biospecimens.

For participant enrollment, it has proven best to maintain good rapport and coordination with the attending physicians and hospital personnel in the partner sites. This ensured that the standard of care was rendered for all the participants and allowed the inclusion and exclusion criteria to be considered during the screening process. In addition, close collaboration between the project team and attending physicians helped establish trust and increased confidence among potential study participants. This positive influence on patient recruitment could be due to the general tendency of patients to trust medical practitioners, particularly in the context of recruitment conducted within tertiary health care facilities, such as the partner sites involved in this study¹⁴.

To support biobanking efforts of a country, the acceptability of the general public towards its activities is essential. To date, the Philippines has a record of only a total of 21 publications utilizing samples from biobanks¹⁴. Unfortunately, this data does not include projects that utilized biobanks but remained unpublished, or those published but failed to report the sample source as “biobanks” or “biobanked samples”. This warrants more initiatives to ensure proper orientation of researchers on biobanks and increased trust of the general public to biobanking activities towards translational medicine. For example, the collection of breast cancer tissues at the St. Luke’s Medical Center’s Human Cancer Biobank has supported a study on the BRCA1 and BRCA2 screening in Filipinos³². This led to the optimization of BRCA testing in their institution. The University of the Philippines-Diliman utilized banked serum samples of adults having pre-existing immunity against Human adenovirus type 5 (HAdV-5). This study suggested that vaccination programs should consider the implementation of vaccination techniques, such as a prime-boost regimen or addition of booster doses, to circumvent potential negative effects of pre-existing immunity in the efficacy of HAdV-5 vector vaccines³³. Similarly, the biobanked samples at PGH were used to explore infectious disease genomics, contributing to rapid responses to emerging health threats such as COVID-19³⁴.

The VRV Biobank tested samples for the presence of arboviruses by qRT-PCR. All positive samples were further inoculated and cultured. The results of qRT-PCR and other sample-associated data will guide researchers in identifying samples that best suit their research interests. In biobanking, the associated data are as valuable as the banked specimens⁴⁶. Therefore, similar initiatives should ensure the availability of additional information for each specimen. For the VRV Biobank, the characterization of the virus, viral infectivity assay, analysis of structural morphology, sequencing and mutation analysis are ongoing.

Figure 7 shows the actual biobanked samples of the VRV biobank stored in ultra-low temperature freezers for long-term preservation.

Fig. 7.

Photographs of biobanked samples of the VRV Biobank in cryovials stored at − 80 °C.

Challenges in establishing a vector-borne virus biobank

Compliance with ethical regulations was facilitated through effective coordination with partner institutions, enabling the efficient processing of requirements. Site collaborators played a crucial role in maintaining continuous communication with the institutional ethics committees and other hospital departments involved in the sampling procedures. However, in this study, the ethics review process took a considerable amount of time due to various factors, including a shortage of experts to review the biobanking aspects outlined in the protocol. This highlights the limited resources of biobanking expertise in the country which can streamline such initiatives. Multi-site reviews requiring more hands-on and effective coordination across partner sites and the SJREB, further contributed to the delays in securing ethics clearance. It is therefore necessary for project investigators to allocate more than the ample amount of time towards getting an ethics approval. Consequently, the team missed the opportunity to capture samples during the peak of the southwest monsoon season in the Philippines (July to August 2024). This period is critical, as transmission of vector-borne viruses is typically at its highest in the country³⁵ and Dengue cases in Baguio City and the rest of Benguet province, locale for partner site 1, were reaching record levels³⁶.

In terms of specimen transport, defining the role and responsibilities of the dedicated project staff has proven beneficial to achieving optimal results. This is in addition to building the capacity of the project staff through in-house training in transporting biological materials and multiple validations of the SOPs on specimen transportation. A recurring difficulty noted by the project team came from procedural differences between the two partner sites. Samples collected at partner site 1 required temporary storage and experienced longer transport times due to the site’s significantly farther distance from the biobank site, compared to those collected at partner site 2. Traveling from partner site 1 to the biobank site takes approximately 5–7 h, while the transit time from partner site 2 to the biobank site is typically recorded as 45 min to 1 h. Despite these variations in travel duration between the two sites, the quality and acceptability of the samples for the downstream laboratory processes remains satisfactory, as determined by the laboratory staff. The samples must meet the following criteria: sufficient sample volume (at least 2 mL of separated serum), absence of hemolysis, complete label (identification code) and transported within 24 h under cold-chain storage conditions (2–8 °C). This approach could potentially serve as a good basis for developing protocols for transporting blood samples from distant sites for biobanking purposes.

One significant challenge encountered during the implementation of the biobanking project was the lack of locally available training and education programs specific to biobanking practices. While international online courses exist, they often require dedicated time— one factor that limited the participation of the VRV Biobank project, since most of its staff are assigned to do the collection and virus characterization processes. To add, budget allocation for formal training was not initially factored into the project design, reflecting a broader gap in institutional awareness of biobanking as a specialized field requiring capacity building. This constraint hindered the ability to fully equip staff with the technical and ethical competencies necessary for high-quality biobank operations. The project personnel’s experience highlights a need to develop and institutionalize local training programs and certification pathways that are accessible, contextually relevant, and sustainable to support the growing role of biobanking in Philippine health research.

Procurement issues, including a strict bidding process and delays in the delivery of laboratory equipment and supplies, also posed challenges during project implementation. These factors led to setbacks in the performance of biobanking and laboratory activities, which in turn delayed the achievement of some target goals of the study. This may be due in part to the novelty of the Republic Act No. 12009 or the ‘New Government Procurement Act,’ whose stipulations and implementing rules and regulations are still being navigated by government agencies, such as the DOST. Suppliers have also noted that delays in securing clearance from the Bureau of Customs resulted in postponed delivery dates. The Cancer Phenome Biobank in the University of the Philippines—Philippine General Hospital (UP-PGH) cited a similar experience in procurement, where the purchase of certain equipment took an entire year, compounding pre-existing challenges related to its establishment and physical infrastructure¹³.

Another key challenge was the absence of dedicated personnel assigned specifically to manage and oversee the biobanking component of the project implementation. Although staff were available and able to execute the basic procedures related to sample collection, documentation, and storage, the lack of a focused biobank team, such as a designated biobank staff, manager, custodian, or technical officer, limited the project’s capacity for continuous improvement, innovation, and strategic development of the biobanking system. Without personnel solely responsible for overseeing quality assurance, data integration, and long-term sustainability planning, biobanking activities remained functional but static. This experience emphasizes the need of future biobanking initiatives to include dedicated roles within project teams to ensure not only the proper execution of core processes, but also the growth, optimization, and integration of biobanking into national and global research infrastructure.

Conclusion

The European Commission Joint Research Center (EC-JRC) enumerates the following as general feature of biobanks: (a) collection and storage of biological materials combined with medical, epidemiological data, (b) dynamic development of the biobanks—continuous collection in a long-term prospect, (c) association with an ongoing research project, (d) application of specimens’ anonymization for the donors’ privacy sake; and (e) implementation of governance standards and procedures^37,38. All of which are fulfilled by the VRV Biobanking project. Best practice guidelines from international organizations such as ISBER, WHO–IARC, and OECD have significantly advanced biobanking^39,40.

While human-derived sample biobanks frequently utilize helpful standards regarding tissue use, comprehensive guidelines and references for virus biobanking appear limited, both domestically and internationally. This scarcity hinders standardization and harmonization efforts. This report therefore highlights the importance of establishing a virus biobank in LMICs, coupled with complete SOPs aiding its efficient operation and intent to share data and resources. The SOP on participant enrolment which includes gathering of clinical and demographic data, has ensured the availability of not only the biological specimen but also associated demographic and clinical data. The SOPs on specimen collection, transportation, processing and data management as well as virus detection and culture will ensure that sample-observed biological changes will accurately reflect the true phenomena rather than variations due to processing or sampling⁴¹.

The VRV Biobank, has a total of 182 recruited participants, 182 collected serum samples which resulted in a total of 364 serum aliquots, 182 nucleic acid, and 100 infected culture fluid samples stored in its facility. To date, the VRV biobank is the first documented framework established for collecting, storing, processing, and biobanking vector-borne viruses for future health research applications in the Philippines. While the project team is aware of biobanking efforts from various R&D groups, there has been limited information about their procedures and collection. These other biobanks also have limited accessibility and specimen/data sharing protocols. The VRV biobank, on the other hand, is publicly funded and will be maintained by the DOST-ITDI, a national center focused on developing R&D technologies that are aligned to improve quality healthcare and life. This will therefore ensure long-term accessibility for the stored samples. Funding the biobank through the national funds has guaranteed that the resources will be used to support both local and international health research initiatives. The present report will disseminate information about the VRV biobank to local and international researchers, policy makers and funding agencies. Currently, the DOST-PCHRD, is drafting the national guidelines on biobanks for health research to ensure that all DOST-funded biobanking resources are accessible, including the VRV biobank.

With the intent of the Philippine government to establish the Virology and Vaccine Institute of the Philippines (VIP) made public on 22 May 2020⁴², developed into a national bill⁴³, and later on signed into a law through the VIP Act (Republic Act 12290), there is a call for a more structured framework in establishing a biobank or network of biobanks for virology research. The VRV Biobank could allow sharing of genomic and health-related data and provide high-quality specimens for health researchers in the future. Two local research projects are utilizing the biobanked samples, focusing on dengue diagnostic tools and understanding mechanistic processes of dengue in relation to other diseases. Moreover, to date, this initiative has opened opportunities for collaborations and further studies with foreign institutions.

This report enumerates challenges in the establishment and operations of a virus biobank with the intent to deliver helpful information not only to researchers but also to other players of health research in the Philippines (hospital management, policy makers and funding agencies). It has also identified best practices from experiential observations to guide the developing biobank ecosystem of the Philippines. The VRV biobank offers a structured framework and shared resources to capacitate health research projects aimed to combat novel, vector-borne illnesses.

Author contributions

Conceptualization, M.T.A.D., A.Y.C.L.A., and K.J.A.C.C.; methodology, J.R.R.S., N.C.S., C.J.G.C.B., J.C.M.D.L., and L.E.B.B.; validation, L.K.D.C., N.C.S., A.Y.C.L.A., and K.J.A.C.C.; resources, M.T.A.D., A.Y.C.L.A., and K.J.A.C.C.; data curation, L.K.D.C., N.C.S., A.Y.C.L.A., and K.J.A.C.C.; writing—original draft preparation, L.K.D.C., and J.R.R.S.; writing—review and editing, M.T.A.D., N.C.S., A.Y.C.L.A., and K.J.A.C.C.; visualization, J.R.R.S., N.C.S., C.J.G.C.B., J.C.M.D.L., and L.E.B.B.; supervision, M.T.A.D., L.K.D.C., N.C.S., A.Y.C.L.A., and K.J.A.C.C.; project administration, J.C.M.D.L., C.J.G.C.B., A.Y.C.L.A., K.J.A.C.C. and M.T.A.D.; funding acquisition, M.T.A.D., A.Y.C.L.A., and K.J.A.C.C. All authors have read and agreed to the published version of the manuscript.

Funding

This study includes data and information from the project titled, “Molecular Profiles and Biobanking of Vector-borne Viruses in Selected Hospitals in Luzon”, funded by the DOST and monitored by the DOST-PCHRD.

Data availability

Additional data that support the findings of this study are available on reasonable request from the corresponding authors. The project’s participant recruitment documents (informed consent and data collection forms) are attached to this article as supplemental files.

Declarations

Competing interests

The authors declare no competing interests.

Ethics approval and consent to participate

The study was conducted in accordance with the Declaration of Helsinki, and collection of patient samples was approved by the SJREB and was assigned the protocol code SJREB-2024-22. The institutional ethics boards of both participating institutions, BGHMC and RMC, reviewed the study and approved its implementation in their respective sites. Written consent was obtained from each participant after they received an executive summary of the study from the project staff. In addition, all participants voluntarily provided a separate written consent allowing the VRV biobank to store their samples for testing and future use. The collected samples and all resulting products are labelled with an identification code that does not contain any personal identifiers. All associated data obtained from participants are stored in a password-protected Laboratory Information Management System, accessible only to authorized members of the project team.