UPLB vs. COVID-19: Curbing the pandemic through science

While most Filipinos find solace in their homes to keep themselves safe and sound from the COVID-19 strain, many men and women in the Philippines and across the world remain vulnerable to infection. A lack of access to quality healthcare and the necessary tools to provide adequate testing, as well as general governmental mismanagement would be the likeliest reasons as to why this is.

However, since the pandemic has swooped the world, departments of the University of the Philippines Los Baños (UPLB) have lent their talents and resources to aid communities in adjusting to the times. While donation drives provided most necessities, from food to medicine, and while various school programs helped stranded UPLB dormers make their way back to their homes, possible salvation came in another form: science.

Knowledge is power

To ensure an efficient and holistic process, the Office of the Chancellor formed Task Force Laban ng Bayan Kontra COVID-19 (LB Kontra COVID-19), which comprises five distinct committees fulfilling different tasks. Vice-Chancellor for Research and Extension Rex Demafelis serves as the overall head of the initiative.

On the matter of information, the Knowledge Management Committee— headed by College of Agriculture and Food Science’s (CAFS) Institute for Plant Breeding (IPB) researcher and Plant Pathology Laboratory head Dr. Mark Angelo Balendres—takes charge in securing and presenting all forms of pandemic-related information to the public.

Other departments have made the effort to work on information initiatives independent from the task force.

With education being harder to access in the time of COVID-19, the College of Human Ecology’s Department of Human and Family Development Studies (CHE-DHFDS) saw the need for education. Thus, “Tsikiting Stories” (“tsikiting” being a rough translation of “chiquitin,” the Spanish for children) told educational stories that the values of various safety measures during the pandemic, including, among other topics, social distancing.

The brainchild of DHFDS professors Raphael M. Ferrer and Nephtaly Joel B. Botor, the project saw light last 2019’s The Symposium on the Child and the Family, when a single-volume compilation of the work was shown. With a large roster of artists, writers, and editors collaborating on the project, Tsikiting Stories gained further attention during the Taal Volcanic eruption, which helped children cope with the situation.

The Committee for Research and Development, headed by CAFS Institute of Weed Science, Entomology, and Pathology faculty member Dr. Filomena Sta. Cruz. They are charged with researching more efficient means to achieve mass-testing, such as methods in replicating more enzymes needed for test kits to fulfill their function.

“Doing the math,” as UPLB calls it in a press release is another objective for the committee, with calculating projections proven to be very much essential in understanding how the COVID-19 pandemic works. The UP COVID-19 Pandemic Response Team is assembled to do just that, computing for models that explain how scenarios would play-out during this event while providing recommendations to mitigate the possible damages from these scenarios. 

“In this COVID-19 pandemic, the quantitative sciences can offer insights on what happened in the past and connect it to the present, and if we can, forecast what lies ahead. From data analysis to mathematical modeling, we can formulate strategies to hinder the spread of SARS-COV-2 in our community.“

Dr. Jomar Fajardo Rabajante
College of Arts and Sciences – Institute of Mathematical Sciences and Physics (CAS-IMSP)

The models that they have created discuss how the disease is transmitted in various scenarios, including among medical frontliners and their patients, in working sectors, and in mass gatherings. 

The latter model was researched by the team’s main media man Dr. Jomar Fajardo Rabajante, a member of the UPLB’s College of Arts and Sciences – Institute of Mathematical Sciences and Physics (CAS-IMSP). Dr. Rabajante’s experience in the fields of data analysis and applied mathematics among others made him an integral member. On the importance of their work, Dr. Rabajante explained that “in this COVID-19 pandemic, the quantitative sciences can offer insights on what happened in the past and connect it to the present, and if we can, forecast what lies ahead. From data analysis to mathematical modeling, we can formulate strategies to hinder the spread of SARS-COV-2 in our community.”

Outside of calculations, the UP COVID-19 Pandemic Response Team also teamed up with the UPLB Biomathematics Initiative to create a website that helps people to choose their jobs. The website, simply called “Job Risk Profiling” does exactly what one would expect: provide analytics for occupation, including the income and the risk percentage. One could make use of the Freeloaded Calculator to calculate from the thousand options of occupation available, and the Open Calculator, for unlisted jobs.

They also made the “Workplace Outbreak Simulator.” With the use of Microsoft Excel, users would be able to calculate the likelihood of an outbreak taking place in the workplace, by analyzing data such as office population and safety measures implemented.

Tools of the trade

Outside of data gathering and presentation, UPLB departments have taken this time to craft items that would ensure that medical frontliners would be safe while on the job.

The  Committee for Technology and Facility Innovation, headed by College of Engineering and Agro-Industrial Technology (CEAT) dean Dr. Arnold Elepaño, focuses on technological initiatives, and to provide more medical equipment. In-turn, it comprises of three subcommittees:

• Clinical Technology Development, which focuses on manufacturing medical equipment, among which are medical ventilators and intubation tubes.
• Facility Development and Operation, which oversees the construction of all medical facilities, including mortality, quarantine, and waste management areas, and the application of safety protocols such as thermal imaging.
• Supply Chain Management, which works on managing the resources for the laboratories and the test samples, while also monitoring patients, as well as the contact tracing process through the use of the UP-Philippine General Hospital (PGH) database.

Under this committee, CAS-IMSP made use of their Fabrication Laboratory (FabLab) to manufacture personal protective equipment (PPEs), which are then given to physicians working within campus grounds, and those within nearby communities and institutions such as the HealthServ Los Banos Medical Center and the University’s Housing Office, Police Force, and Health Service. Operational since March 27, 2020, the FabLab has crafted and distributed 3D-printed face shields that prevent aerosol droplets from coming into contact with their faces, and easier-to-use laser-cut ear guards.

This committee also produces replaceable ventilator parts such as venturi valves, splitters (to aid multiple patients at the same time), caps (to sheet splitters), and Intubation boxes for decontaminating intubation tubes.

A joint collaboration between UPLB and the TAU ALPHA fraternity led to the creation of the “WeHealAsOne Hundred Test Booths Project.” Under this, 100 swabbing booths designed for non-contact testing would be manufactured and distributed to recipients in-need, residing within the northern and southern Luzon areas.

Designed by CEAT’s Industrial Engineering Department faculty member Mark Anthony Baldoz, who explained that the booths are made from acrylic, stainless steel, and polycarbonate resources, it included three sections. The first involves physicians interviewing with the patient, and recording the needed data. The second has another physician performing the test, with the use of built-in black gloves that would hold the swabs. The third, unmanned, would serve as the storage for the collected samples.

They are also working on a program that would help patients keep track of results gathered from before, during, and after testing, while collaborating with sponsors to keep the data for the future testing facility. With an increase in orders, the project is now planning on producing more booths, covering about 64 municipalities across 21 provinces.

Testing, testing 

Perhaps the most important objective that the whole task force had to work on was solving the mass-testing issue.

Collaborating with fellow UPLB alumni Chato and Jason So, and Dr. Cesar Nadala, Dr. Lourdes Nadala credited local research for paving the way for SAMBA II kit’s development, which allows patients to be tested for any possible trace of COVID-19, even for asymptomatic individuals under 90 minutes. “Sharing of locally generated information was key in expediting the development of the diagnostic test for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) detection,” she said.

A Facebook post from Brian Galagnara showed that in UPLB, agricultural scientist and Philippine Genome Center affiliate Dr. Antonio C. Laurena is heading a project that involves developing a new method of DNA analysis that would be achieved through an improved testing kit. Known as the “loop-mediated isothermal amplification” (LAMP), this measure hoped to make mass-testing more possible by not having to rely on more expensive laboratory equipment and would allow even inexperienced users to detect the strain even on asymptomatic individuals. 

Galagnara stated that the team is working entirely for free, and in the 3.5 required months of development, he invited interested people to donate to the team in the hopes of raising a total P3.85 million for the project to be approved by the Food and Drug Association (FDA). “Also, a vaccine will take 18-24 months to reach us. Until then, continuous testing is vital to mitigate or suppress the spread of the disease and to reopen our economy. Therefore, the need for various innovations in mass testing is an ever-growing requirement.”

Meanwhile, UPLB alumnus Catharine Aquino-Fournier aided in the development of yet another, swifter type of testing kit. Working in with her colleagues in the Functional Genomic Center Zurich (FGCZ) of the University of Zurich and the Swiss Federal Institute 

of Technology, they were able to develop HiDRA-seq, which would only require saliva or anything that does not require one’s genetic sample, in addition to the devices having built-in contact tracers.

Although there is a 10% margin of error, the device’s ability to be able to analyze to about a hundred thousand samples, as well as its contract tracing could ease mass testing woes.

And now to mass testing

Two remaining committees are assigned to take part in UPLB’s most ambitious move in the pandemic: the retrofitting of BIOTECH’s Immunology Laboratory into a COVID-19 Molecular Diagnostic Laboratory, which itself was finally realized with its accreditation last June 30, 2020.

To ensure biosafety and security, biosafety cabinets, and closed-circuit televisions (CCTVs) are placed.

Overall, the project is overseen by the Committee on Establishment of the UPLB COVID-19 Testing Center, headed by UHS director Dr. Jessie Imelda Foronda-Walde, and would serve as the inspecting body in ensuring that the facility would gain the Department of Health’s (DOH) Stage 2 validation. Building guidelines from DOH and the World Health Organization (WHO) with regards to receiving, testing, and storing areas are also given to them for strict compliance.

Upon its completion, the facility would be able to make use of the current go-to testing method, the real-time reverse transcription-polymerase chain reaction (RT-PCR)-based testing. Through this, a swab would be inserted into the individual’s nose or throat, and from the samples, the DNA strands would be replicated and differentiated from one another to detect the virus. Results are usually expected around 24 hours or more. 

Meanwhile, the Protocol Establishment Committee, headed by BIOTECH research assistant professor Dr. Severina Exconde, would be the one to formulate safety and management guidelines as approved by the Research Institute for Tropical Medicine (RITM) for the facilities to use.

To ensure that the facility personnel would be knowledgeable about the necessary processes, staff members, consisting of professional laboratorians and volunteers, participated in training programs. Among them were two programs from the University of the Philippines Manila’s (UPM) National Institutes of Health (NIH). One was an online course covering biosafety measures and biorisk management among other topics. This is then followed by a course on how to execute the RT-PCR-based testing, which is also done in collaboration with UP Diliman’s (UPD) the National Institute of Molecular Biology and Biotechnology (NIMBB). [P]