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De-centralising genomic surveillance

This case study demonstrates how regional labs can play a pivotal role in genomic surveillance efforts.
© COG-Train

To address this pressing challenges of centralised genomic surveillance, the Philippines Department of Health (DOH) with its established surveillance network was utilized to leverage in the crafting of additional genomic surveillance for SARS-COV-2 led by the Research Institute for Tropical Medicine (RITM) in collaboration with various Sub-national Laboratories (SNLs); the Epidemiology Bureau (DOH-EB); the Regional Epidemiology and Surveillance Units (RESUs) and its surveillance units within the DOH; and strong support from the University of Glasgow (UOG) with funding from the UKRI GECO-COMP. This project dubbed the GECO PH Project (https://www.geco-seqlab.org/) is deemed to be a landmark catalyst to empower local laboratories to perform their own genomic surveillance using state-of-the-art real-time Nanopore whole genome sequencing technology (e.g. MinION, GridION). This initiative has boosted the sequencing capacity of the Philippines for genomic surveillance, particularly for COVID-19.

The Genomic Epidemiology of COVID in the Philippines (GECO PH) project has operationalized genomic surveillance and informed responses across the Philippines to embed large-scale real-time sequencing capacity at the national reference laboratory (RITM) and builds local sequencing capacity at (Sub-national Laboratories) SNLs for national, regional, and local-scale responses in the Philippines. The research will further enable the evaluation of control measures across settings, from infection controls to prevent hospital-acquired infections, lockdowns to interrupt community transmission, and quarantining and movement restrictions to contain introductions, whilst increasing our understanding of SARS-CoV-2 transmission and control.

Ensuring sample and data ownership

Due to the intricate natures, functions, and relationships of each stakeholder within the healthcare system in the Philippines, the RITM as the national reference laboratory for emerging and re-emerging infectious diseases of the Department of Health (DOH), forged agreements with the SNLs, Epidemiology Bureau (DOH-EB), and the University of Glasgow (UOG) to formalize and ensure the roles and responsibilities of each stakeholder are clear, distinct, and avoid overlap with each other. Embedded within the agreements is the participation of the SNLs in a consortium which facilitates the sharing and cooperation within the context of research and investigation of SARS-CoV-2 sequences and associated data. Moreover, it underpins the upholding of scientific etiquette, by acknowledging the originating laboratories providing the specimens, and the submitting laboratories generating sequence and other metadata, ensuring fair exploitation of results derived from the data, and promoting collaboration among researchers on the basis of open sharing of data and respect for all rights and interests.

To guarantee the success of the GECO PH surveillance through the consortium, the project undertook the following key steps and activities:

Ethical Clearance

The research project obtained approval from the Single Joint Research Ethics Board of the DOH and various local ethical boards of the RITM and SNLs, a vital part of the framework of crafting the biosurveillance of SARS-COV-2 in the country.

Advocacy

Advocacy is critical to the roll-out of the surveillance project and its sustainability and future integration into the surveillance program of the DOH, the principal health agency in the Philippines responsible for the regulation of various healthcare providers including the SNLs and DOH-EB for the provision of health services, particularly in the ongoing pandemic. A policy issuance from DOH ensured support for the capacity building of RITM and more particularly the SNLs to carry out their own sequencing activities. Moreover, a series of meaningful meetings were conducted to formalize the consortium’s objectives and goals.

Consequently, a laboratory needs assessment was conducted to identify gaps, propose solutions and ensure the readiness of the SNLs for rapid sequencing. The needs assessment includes evaluation of facilities (space for workstation and equipment, Wi-Fi access, sample storage, etc.), logistics (supplies and sample transport), biosafety (PPEs, disinfection/sterilization procedures, waste disposal, etc.), equipment, staff (knowledge and skills), metadata (electronic and paper records, kinds of data collected, etc.), and policy environment for genomic research and surveillance.

Coordination

To facilitate close coordination within the consortium, regular meetings using various social media platforms such as Viber chat groups and Slack channels are employed for rapid updates, planning, queries and dissemination of information and guidance.

Training

Capacity building to perform rapid sequencing hallmarks the crafting of the consortium. There is a great fervour among the SNLs to acquire knowledge, skills and technology to sequence the genome of pathogens particularly SARS-COV-2. Briefly, the training comprised of lectures and demonstrations videos; and practical/hands-on sessions. Practical sessions include primarily cDNA preparation, multiplex PCR, library preparation, sequencing, data retrieval from Mk1C and basic bioinformatics and RedCAP exercises.

© COG-Train
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