College of Science and Mathematics

UP Mindanao hosts RESBAKuna

Written by Rene Estremera. Posted in News

UP Mindanao facilitated the COVID-19 vaccination of 2,023 government personnel from  June 30 to July 20, 2021 as a cooperating agency for the local RESBAKuna program organized by the Davao City Health Office and the Association of Regional Executives of National Agencies-Region XI (ARENA-XI).

The cooperating agencies were led by the Department of Science and Technology-Region XI (DOST-XI) headed by Regional Director Anthony Sales who is the current president of ARENA-XI. Doctors, auxiliary medical personnel, and personnel from various national government agencies served as volunteers in various capacities from the registration to post-vaccination. City Health personnel delivered the vaccines and carried out disinfection at the end of each day.    

The RESBAKuna sessions were undertaken in time for the June 2021 vaccine roll-out for members of the A4 sector composed of frontline personnel in essential sectors, including government employees, as determined by the Department of Health and the national Inter-Agency Task Force for Communicable Diseases. 

UP Mindanao served as a cooperating agency for RESBAKuna as part of its mandate as a public service university and as an advocate of science in support of public policy. The UP Mindanao vaccination team was constituted by Chancellor Prof. Larry Digal with Assoc. Prof. Lyre Anni Murao as the Focal Person and Site Supervisor and supported by Vice Chancellor for Administration Assoc. Prof. Karen Joyce Cayamanda as Overall Site Coordinator. 

The vaccination was held in the building atrium and the university provided its adjoining classrooms, facilities, audio-visual equipment, computer units, and beds. Personnel services were also provided for data encoding, counseling, vaccine administration, security and maintenance. The science laboratory provided a refrigerator for vaccine storage under the supervision of Assoc. Prof. Aleyla de Cadiz as Cold Chain Manager. A number of UP Mindanao graduates extended their services as medical interns for the post-vaccination monitoring and assessment.



RESBAKuna in UP Mindanao on July 29-30, 2021 provided 770 persons with their second vaccine doses. The 770 persons on July 29-30 were composed of 383 essential workers mostly in government service, ten adults with co-morbidities, and two senior citizens.

Over the two days, there were no recorded Adverse Events Following Immunization (AEFI), no recorded refusals, or spoilage of vaccines.

RESBAKuna in UP Mindanao was co-organized with the City Health Office and the Association of Regional Executives of National Agencies (ARENA)-Region XI and was held in the UP Mindanao administration building, with personnel and logistical support provided by the university to augment the ARENA team of volunteers. 

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In the following weeks, UP Mindanao will continue to serve as a vaccination site from July 28 onward for the government personnel who are scheduled to receive their second dose of vaccines. 

 In the photos (clockwise from top left): View of the UP Mindanao Administration Building Atrium during the RESBAKuna vaccination day; Trained volunteers administer the vaccines; UP Mindanao graduates serve as medical doctors in the post-vaccination monitoring and assessment; Vaccinated personnel have their picture taken in the RESBAKuna photo wall.

PGC Mindanao embarks on collaborative SARS-COV-2 study

Written by Rene Estremera. Posted in News

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. 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. 

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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. 

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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

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.

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.

Oxford Nanopore Technologies. (2021 May). Accuracy. Retrieved from

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