Chancellor’s Report to the President’s Advisory Council

MINDANAO COVID-19 SITUATIONER

The COVID-19 Tracker (https://ncovtracker.doh.gov.ph) had the following data for the six Mindanao regions as of 30 September 2021: 

• 330,645 total cases since the start of the pandemic 

• 19,719 active cases 

• 5,526 deaths since the start of the pandemic 

The quarantine status of Davao City’s quarantine status was lowered to the more relaxed General Community Quarantine on 06-30 September 2021, from the “General Community Quarantine with Heightened Restrictions” in effect starting July to August 2021. 

CONTRIBUTE TO NATIONAL DEVELOPMENT

COVID-19 Initiatives & Collaboration

In September 2021, the UP Mindanao Multi-Purpose Gym and the Faculty and Staff Housing Building completed their 17th month of use as COVID-19 Isolation Facilities of the Davao City government. The memorandum of agreement was extended for another three months beginning 20 July 2021. 

The Philippine Genome Center (PGC) Mindanao provided SARS-COV-2/ COVID-19 Diagnostics Training to six (6) medical personnel of Kidapawan City Molecular Lab on 29-30 September 2021, as part of the continuing UP TRAINS Program to assist the Department of Health.

PGC Main in UP Diliman provided Next Generation Sequencing (NGS) equipment and manpower to PGC-Visayas and PGC-Mindanao to further expand their capacity for genomically-informed biosurveillance in the country.

In September 2021, PGC Mindanao prepared to procure equipment and consumables for the project, “Enhancing National Pandemic Preparedness and Response in the Philippines Through Genomic Biosurveillance: Utilizing the UP PGC Network in Luzon, Visayas, and Mindanao,” funded by the Department of Budget and Management. Also, PGC Mindanao received a donation of OT-2 Liquid Handler Labware from Opentrons and Bacillus subtilis protein secretion toolkit from Stanford University.

“Molding Learners into Leaders:” Knowledge Creation and Public Service; Promote Access and Diversity

Towards  producing competent and ethical graduates

The BS Architecture program again witnessed a 100%-passing performance by its graduates in the August 2021 Architects Licensure Exam, adding to its roster eight new licensed architects:

• Antonrey Catabas, BSA 2018
• Kenneth Dolero, BSA 2018
• Yna Corazon Espinosa, BSA 2018
• Nezcel Federizo, BSA 2018
• Kate Gallofin, BSA 2018
• Emman Militar, BSA 2019
• JC Waldo Serquiña, BSA 2019
• Duane Soliva, BSA 2018

Image for bulletin above: https://drive.google.com/file/d/1PZB6q6gDVesd9QzKDWySWZAqI3d6jFOu/view?usp=sharing(CREDIT: Graphic courtesy of UAPSA)

The Koro Kantahanay chorale’s video recording of “Kayo Mungay Daun,” a tribal song, was played in the Convocation. Two video predictions were given their premiere screenings: 

• UP Mindanao 2021 Campus Tour video (short version), produced by the UP Mindanao Virtual Tour Committee and the BACMA Sibya Media Production Unit (https://youtu.be/cXI_rcSdXpQ) 
• “Mensahe,” a short film of a student undergoing remote learning, by BA Communication and Media Arts student Jeneva Pauline Zulueta (https://youtu.be/HNDuMid-w64).

Read more: https://drive.google.com/file/d/1-mJyKkon80Pe_6Tp6xoVc3GtQBLrJ-PW/view?usp=sharing

The University of the Philippines Mindanao (UPMin), in collaboration with the London School of Hygiene and Tropical Medicine (LSHTM), UK, has successfully completed the One Health Omics Project, a week-long free online bioinformatics workshop from October 11-16, 2021. Out of 124 applicants, only 40 were shortlisted to participate in the workshop composed of faculty members, clinicians, and researchers from different regions in Mindanao. In the opening ceremony, Dr. Aleyla De Cadiz, Project Leader of One Health Omics, said that the workshop serves to capacitate Filipino researchers in Mindanao on omics technology in the surveillance, management, and control of infections in a One Health setting. 

“We want to expose Mindanaoan researchers to bioinformatics tools and techniques which can be helpful in their research focus and future research endeavors in the region,” she said.

Bioinformatics is a combination of biology and information technology that allows researchers to use a computer to further examine and understand the characteristics of an organism or a microbe through its genome, such as the SARS-CoV-2 virus responsible for the COVID-19 disease. 

Today, bioinformatics algorithms made it possible to quickly assemble the genome sequence of the coronavirus which helped scientists to quickly develop diagnostic test kits and give an immediate head start in vaccine development.

The bioinformatics workshop was facilitated by Dr. Jody Phelan, Julian Libiseller-Egger, Daniel Ward, Anton Spadar, and Paula Josefina Gómez González, bioinformatics experts from LSHTM, all members of Professor Taane Clark’s team.

Dr. Phelan, one of the lead trainers expressed his willingness to help and assist the participants beyond the workshop activity. He encouraged the young Filipino researchers to keep on doing the materials in their own time. Dr. Phelan also looks forward to conducting face-to-face training soon. “I would love to meet everyone face-to-face so let us hope that the situation improves and that we can travel.”

The workshop proved to be very challenging to the participants given that bioinformatics is a new learning field in health research, but they were grateful to have been introduced to its concepts and applications. 

“The workshop gave us the technical experience and knowledge in handling datasets in different omics approaches. This will be very useful to a researcher like me who is interested in doing omics approach studies,” said Vanessa Joy Diamante, a researcher at the Philippine Genome Center (PGC) Mindanao.

Joseph Mari Querequincia, a registered pharmacist and faculty member of San Pedro College Davao, said he was grateful to have been included in this training course.

“The workshop allowed me to warrant a skill for Bioinformatics in which I could utilize for future academic and research undertakings related to pharmacogenomics and drug discovery,” said Querequincia.

Meanwhile, Dr. Jonah Adtoon, an Internal Medicine Specialist at the Department of Health (DOH) XI declared her willingness to be involved in more clinical research projects in the omics field for disease investigation and patient management.

Professor of Genomics and Global Health in LSHTM and the lead United Kingdom (UK) coordinator Prof. Taane Clark said that the skills learned during the workshop will allow the participants to apply big data methods to genomics questions and investigations.

"Bioinformatics and genomics techniques, as well as conducting related molecular investigations, are important skills for the participants to become genomics and genomic epidemiological experts and will contribute to improving the health of the Philippines population. Some of the trainees in our previous workshops are now trainers in bioinformatics, and it is very exciting and personally rewarding to be part of capacity building and strengthening in genomics, and contribute to ongoing Philippines-UK biomedical collaborations," he said.

In her message, PGC Mindanao Program Director Dr. Lyre Anni Murao recalled the first workshop conducted by LSHTM at PGC in Diliman and its influence on the establishment of PGC in Mindanao.

“The workshop played a pivotal role in establishing our facility, because without a background on omics we wouldn’t be able to take PGC Mindanao to where it is right now, so thank you very much for sharing your skills and expertise,” she said.

The workshop was made possible through the PGC Mindanao team of Dr. Lyre Anni Murao, Dr. Joel Hassan Tolentino, Dr. Ritchie Mae Gamot, Dr. Giovanna Fae Oguis, Ms. Ediflor Yanong, Mr. Jan Divina, Mr. Polo Gaite, Ms. Marian Luayon, Ms. Janessa Villota, and Mr. Ruben Enad, Jr.

The One Health Omics Project was funded by DOST-Newton Agham Researcher Links Workshop grant from the British Council in partnership with London School of Hygiene and Tropical Medicine (LSHTM) and supported by the Department of Science and Technology (DOST) - Philippine Council for Health Research and Development (PCHRD). The workshop is also co-sponsored by the Philippine Genome Center (PGC) Mindanao.

The LSHTM will be having its second run of Online Bioinformatics Workshop on November 22-25, 2021 which will focus on Infectious Diseases. This will be participated by 30 participants from the Philippines and 30 participants from the UK. 

#     (By JANESSA V.VILLOTA, Information Officer I, Philippine Genome Center Mindanao)

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.

References:

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