UP's Pride and Glory
by Janessa Villota (PGC Mindanao)
More than a year after the first reported case in Wuhan, People's Republic of China, the SARS-CoV-2 virus has created a pandemic across the globe that is unprecedented in human history. As a local response to the global pandemic, the Philippine Genome Center Mindanao (PGC Mindanao) has partnered with Accessible Genomics, the University of Glasgow, and COVID-19 laboratories in Mindanao to engage in a research project that will investigate the dynamics of the SARS-CoV-2 spread in selected hospitals and communities in the region. Viral RNA collected from COVID-19 patients in some laboratories and hospitals in Mindanao will be sequenced by PGC Mindanao using the MinION, a portable genetic sequencer donated by Accessible Genomics, which will also serve as a learning experience for the Center as it prepares to expand its omics facility and services. Results from the sequencing will be used solely for research to aid local hospitals and communities in COVID-19 prevention and control.
Accessiblegenomics.org is a volunteer, open science initiative formed by scientists from across the globe. It aims to use the recent advances in sequencing technology to capacitate laboratories in the developing world for genomic surveillance of pathogens and documenting the experience to develop a deployment manual for other laboratories. The organization has received funding and support from Just One Giant Lab, GISAID, and New England Biolabs, Inc.
Accessible Genomics has recently partnered with the University of Glasgow and PGC Mindanao for the pilot deployment of the handheld MinION sequencer by Oxford Nanopore Technologies in the southern Philippines. This handheld sequencing machine costs less than a premium smartphone, making it easily accessible to laboratories. The University of Glasgow will provide technical assistance to the team on the Minion sequence workflow, database management, and data analysis. The collaboration primarily aims to establish a learning experience on on-site next-generation sequencing, which can be transferred to other research initiatives in Mindanao such as in agriculture and biodiversity. It also provides additional training for PGC Mindanao personnel on next-generation sequencing workflows as the Center prepares to engage more partners and support for the establishment of its sequencing laboratory.
Oxford Nanopore MinION.
The Oxford Nanopore MinION is a portable sequencer and has the lowest instrument cost among all sequencing platforms with a 97.5 to >99.3% raw read accuracy (Oxford Nanopore Technologies, 2021). The technology has demonstrated its utility for sequencing biological entities, from the simple nano-sized viruses to complex plants and animals, generating sequence information that is sufficient to provide comprehensive insights into the underlying genome architecture. It has also been validated to produce SARS-CoV-2 consensus sequences with the same accuracy as other sequencing platforms (Bull et al., 2020 and Charre et al., 2020). Its low start-up cost is an advantage for research laboratories that are just establishing their own sequencing projects.
Actual sequencing in PGC Diliman using Illumina NextSeq 550
While this pilot project in sequencing takes off, the Department of Health (DOH), the University of the Philippines - Philippine Genome Center (UP-PGC), and the University of the Philippines - National Institutes of Health (UP-NIH) have an ongoing bio-surveillance program to detect SARS-CoV-2 variants in the Philippines.
PGC Diliman uses Illumina NovaSeq 6000 for its 750 weekly sequencing output and NextSeq550 for the 350 sample runs. These high throughput sequencing equipment capable of 3,000 Gb and 120 Gb sequencing outputs, respectively, require high capital expenditure for equipment acquisition and consequently high startup and annual maintenance costs. They are suited for large-scale surveillance which is conducted by health agencies in order to inform and guide public health authorities.
Illumina NextSeq550 in PGC Diliman
Global genomic surveillance of SARS-CoV-2 is used to monitor the characteristics and movements of the virus, including the emergence of new variants that may spread more easily, cause more severe disease, or may escape from immune recognition. Such information can help guide authorities and researchers to improve public health measures and medical interventions for COVID-19. The genomic surveillance in the Philippines has identified Variants of Concern (VOCs) in the country such as Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.2). The Beta variant was the first reported in Mindanao and was detected in March of this year from one (1) patient in Northern Mindanao (DOH, 2021). A cluster of six (6) cases of the highly transmissible Delta variant was also reported in Northern Mindanao with all the specimens collected on June 28.
Currently, plans are underway to fast-track the expansion of genomic surveillance in the main regions of the country through the Department of Health and Department of Science and Technology, as well as other efforts by both the government and private sectors in the country.
PGC Mindanao was launched in 2019 as a satellite facility of PGC in Diliman and hosted by the University of the Philippines Mindanao to open the doors for Mindanaoans to explore opportunities, issues, and challenges relevant to the region. It was established through seed funding worth P40 million of state of the art equipment from the Department of Science and Technology-Philippine Council for Health Research and Development (DOST-PCHRD).
PGC Mindanao is a DOST-supported facility and is one of its major partners in forwarding omics research in Mindanao. The Center has been actively engaged with Mindanao-based agencies, institutions, and communities in its vision to deliver locally relevant solutions through science.
Department of Health (2021, March 21). Continuing Biosurveillance detects additional B.1.1.7 and B.1.351 CASES and P.1 variant case [Press release]. Retrieved from https://doh.gov.ph/doh-press-release/CONTINUING-BIOSURVEILLANCE-DETECTS-ADDITIONAL-B-1-1-7-AND-B-1-351-CASES-AND-P-1-VARIANT-CASE
Charre, C., Ginevra, C., Sabatier, M., Regue, H., Destras, G., Brun, S., Burfin, G., Scholtes, C., Morfin, F., Valette, M., Lina, B., Bal, A., & Josette, L. (2020). Evaluation of NGS-based approaches for SARS-CoV2 whole genome characterisation. Virus Evolution, (6)2, 1-8. https://orcid.org/0000-0002-5597-094X
Bull, R., Adikari, T., Ferguson, J., Hammond, J., Stevanovski, I., Beukers, A., Naing, Z., Yeang, M., Verich, A., Gamaarachchi, H., Wook Kim, K., Luciani, F., Stelzer-Braid, S., Eden, JS., Rawlinson, W., van Hal, S., & Deveson, I. (2020). Nature Communication, 11(6272), 1-8. https://doi.org/10.1038/s41467-020-20075-6
Oxford Nanopore Technologies. (2021 May). Accuracy. Retrieved from https://nanoporetech.com/accuracy?fbclid=IwAR13szqfEoN9zrAoxxiL_Syh4FuegnKlUXioP7cexoVKGRfDtyqvjYqbyW4
MANILA, Philippines – The University of the Philippines - Diliman (UPD) is still the most popular university in the Philippines, according to the 2021 Ranking of Philippine Universities, a non-academic result revealing online popularity as released recently by UniRank (formerly 4 International Colleges & Universities or 4icu.org), an international higher education search engine and directory reviewing accredited institutions in the world.
The University of the Philippines Mindanao is #25 in its ranking. (https://www.4icu.org/ph/)
NOTE: According to the Commission on Higher Education (CHED), there are 2,393 total Higher Education Institutions (HEIs) in 2019, including satellite campuses of State Universities and Colleges.
Read the UP Mindanao Chancellor's May 2021 Report to the President's Advisory Council: https://bit.ly/2WHqLAp
Written by Celeste Ann Castillo Llaneta
The University of the Philippines (UP) celebrates its 113th founding anniversary on 18 June 2021 and its second during the COVID-19 pandemic.
As with last year’s celebration, UP’s 17 campuses are still closed. In addition, the country remains under quarantine to contain the spread of the viral disease that shut the world down in 2020. However, the faculty, students, staff, alumni, and other members of the UP community continue to commemorate UP’s annual milestones with a sense of nostalgia and longing for life in the University’s verdant campuses again, a sense of pride in UP’s continuing achievements through this extraordinary period in its history, and hope for a University of the Philippines for the future in a post-COVID world.
113 years of excellence
The country’s premier state university was founded on June 18, 1908, through Act No. 1870 of the Philippine Assembly, with the mandate to give “advanced instruction in literature, philosophy, the sciences and arts, and to give professional and technical training” to every qualified student regardless of “age, sex, nationality, religious belief, and political affiliation.”
Over the past 113 years, the University evolved from being the pinnacle of the American-established educational system to a “University for the Filipino” as envisioned by its first president, Murray Simpson Bartlett. It weathered through World Wars and the recovery effort, periods of political unrest and the subsequent declaration of Martial Law in 1972, the end of a dictator’s reign and the return to democracy, and the transition into a digital world racing toward the Fourth Industrial Revolution. [Click here for a more detailed history of UP.]
In 2008, UP celebrated its first centennial. The Republic Act No. 9500 was also signed this year, establishing UP as the country’s national university. By the year 2017, when former UP College of Law Dean Danilo L. Concepcion took the reins as UP President, UP had grown into a massive University System consisting of eight constituent universities located in 21 campuses throughout the Philippine archipelago.
UP in the “new normal”
Then in 2020, UP confronted its biggest crisis since the Second World War as the world grappled with a hundred-year pandemic. The University met this new challenge head-on, harnessing its considerable knowledge resources to aid the members of its academic community, the government, and the country’s citizens. UP scientists and engineers have created locally produced, accurate, and affordable COVID-19 test kits, personal protective equipment, sanitation facilities, and much-needed sanitation chemicals. UP social scientists and researchers have mapped the progression of the disease through the country, creating databases and generating research that would inform policy and decision-making on the national and local levels. UP artists and musicians have shared works that inspire, give hope, and pay tribute to the country’s heroes. UP students, alumni, administrators, and residents have come together to help the UP community survive the viral outbreak and the quarantine. And UP’s doctors, nurses, and healthcare providers through the UP Philippine General Hospital once again heroically serve those in need despite the risks to life and well-being.
UP has been moving non-stop since then. The run-up to its 113th anniversary has been marked with shifts, breakthroughs, progress, and a selfless commitment to serve the people throughout the pandemic. UP held fast not only against the pandemic but against threats to its academic freedom as well. Even in the face of a fire that hit the third floor of the UP Philippine General Hospital, the country’s premier COVID-19 referral center, UP medical and administrative personnel responded with courage and discipline, thus preventing any loss of life and earning for several staff members conferment of the Order of Lapu-Lapu for their extraordinary acts of service and exceptional contributions to the country.
Shift to remote learning
By the time the first semester of Academic Year 2020-2021 began, UP had made the necessary preparations to shift to fully remote teaching and learning, with guidance from the UP Open University and its wealth of resources that help guide academic institutions in making the shift. To take on the admittedly tricky challenge of shifting abruptly from traditional classroom learning, UP crafted its Academic Roadmap for AY 2020-2021 along with three operational principles: 1) to protect the UP community from the pandemic; 2) to sustain the continuity of instruction and learning; and, 3) to consider equity concerns in all plans.
Some measures UP were: subscribing to a Zoom account for webinars that can accommodate up to 3,000 participants; purchasing the learning management system, Canvas, and continuing upgrade UP’s own LMS; acquiring software to support remote work, teaching, and learning; and procuring additional library resource subscriptions and library information systems. In addition, UP faculty prepared course packs that are made available online and offline, with physical course packs produced and delivered to students via courier or through the various campuses at no cost to students.
To help support UP students from vulnerable households who were at the risk of dropping out because they lacked the means to continue their studies via remote learning, UP launched the Kaagapay sa Pag-aaral ng Iskolar ng Bayan fundraising campaign to help provide these students with the gadgets and connectivity they needed. UP also provided device and connectivity support for faculty and staff who are working from home. To help care for and support the students’ mental health and well-being during this exceptionally trying period, UP also created and is currently strengthening its Mental Health and Wellness Network across the UP System to provide psychosocial support and services to UP students and facilitate referrals for treatment and other interventions.
Breakthroughs, honors, and expansion
Despite the pandemic, UP scientists and researchers continued to produce cutting-edge research and make history-defining discoveries. Just to name a few: In March 2021, Dr. Deo Florence L. Onda of the UP Marine Science Institute became the first and only Filipino and one of the first two human beings to make the first crewed descent into Emden Deep, the third deepest point on Earth. In the next month, a team of researchers, including UP archaeologists Dr. Janine Ochoa and Dr. Armand Mijares, discovered fossil remains of three extinct giant cloud rat species in northern Luzon. And UP scientists and engineers continued to work with the Philippine Space Agency to create breakthroughs in the country’s space program, such as the successful launch of the nano-satellite Maya-2 and the planned launch of the Multispectral Unit for Land Assessment or MULA satellite.
The University also set in motion its plans to expand the UP Visayas campus in the province of Antique to more effectively implement its continuing education programs. The UP Manila has similarly signed a Memorandum of Agreement to establish a UP School of Health Sciences extension campus in Tarlac. In UP Mindanao, discussions are ongoing for a proposed city hospital on campus, in line with its Mindanao Health Initiative.
In recognition of their outstanding lifetime achievements and valuable contribution to the University and the country, two former UP presidents—National Scientist Emil Q. Javier and Alfredo E. Pascual—and Amb. Edgardo Espiritu and retired Supreme Court Justice Antonio T. Carpio were conferred honorary degrees by the University.
UP para sa bayan
Fulfilling its mandate and role as the country’s national university, UP continued to do its utmost to aid the national and local governments and serve the people during the COVID-19 pandemic. The UP Manila, the UP National Institutes of Health, and the UP College of Medicine share their knowledge, expertise, and experience in treating and managing COVID-19 through the ongoing weekly webinar series, “Stop COVID Deaths,” produced by TVUP. These webinars, a valuable source of scientifically and medically accurate COVID-19 information, are available to the public via TVUP’s YouTube channel.
The Philippine Genome Center and the UP Manila National Institutes of Health also detect and track the different SARS-CoV-2 variants spreading throughout the country through genomic biosurveillance. At the same time, the UP-PGC’s two satellite facilities based in UP Visayas and UP Mindanao train local health professionals in rRT-PCR testing and helped set up laboratories in their regions. The PGC Visayas and Mindanao also monitoring their respective areas for other pathogens that might pose a threat to health and food security.
UP Los Baños (UPLB) opened the COVID-19 Molecular Diagnostics Laboratory to serve as a subnational testing center for Laguna and nearby provinces. Both UPLB and UP Diliman have offered their Copeland Gymnasium and College of Human Kinetics gymnasium, respectively, as COVID-19 vaccination centers for the UP community and nearby municipalities.
UP constituent units continue to produce free, educational webinars for the public, live-streamed on their respective social media sites and YouTube channels. UP has also supported and promoted the establishment of community pantries, which have become symbols of the Filipino’ bayanihan spirit since it was pioneered by entrepreneur and UP College of Fine Arts alumna Ms. Ana Patricia Non.
These and much more are UP’s achievements in just a year since its anniversary celebration last year. As the national university turns 113, the UP community and the country continue to look forward to the new heights UP will reach as a University of the Future, moving firmly into the “next normal” of a post-COVID-19 world.