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