RITM strengthens its sequencing capacity
Photo caption: Dr. Luke William Meredith from the University of Cambridge demonstrates the loading of a Nanopore flow cell to RITM laboratory staff.

Laboratory personnel from the Research Institute for Tropical Medicine (RITM) successfully passed the training on next-generation sequencing (NGS) hosted by the World Health Organization (WHO) at RITM from September 19-23, 2022.

Eight (8) RITM laboratory personnel – three (3) from the Molecular Biology Laboratory (MBL) and five (5) from the Philippine National Influenza Center (PNIC) underwent the 5-day training to increase the technical capacity of RITM staff in performing NGS of respiratory pathogens such as Influenza and Respiratory Syncytial Virus (RSV).

Dr. Luke William Meredith from the University of Cambridge led the hands-on experience on processing nucleic acid from preparation to sequencing using two (2) commonly used NGS platforms – Illumina MiSeq and Oxford Nanopore Technology GridION.

These technologies will enable the advanced tracking of changes within viruses that are among the diseases for global and local surveillance such as Severe Acute Respiratory Infection (SARI), Influenza-like Illness (ILI) and RSV.

“Following this training, we will be able to generate data and define the local epidemiology of Influenza. The patterns of circulation can help us during our outbreak and pandemic preparedness response,” said RITM Virology Department Head Dr. Mayan Lumandas on the need for this learning intervention.

According to Dr. Meredith, sequencing-based surveillance adds key information that allows for faster and more targeted information about the pathogen to be obtained.

In comparison to Sanger sequencing that only sequences a single DNA fragment, NGS sequences millions of fragments simultaneously per run – sequencing hundreds to thousands of genes at one time. NGS offers ultra-high throughput, scalability, and speed.

Using NGS for respiratory pathogens is one of the strategies to strengthen the surveillance activities of RITM-PNIC. Surveillance together with diagnostic testing are the two complementary testing strategies for preventing and controlling outbreaks.

In line with this, the five (5) subnational laboratories under RITM-PNIC namely, the Baguio General Hospital and Medical Center (BGHMC), the San Lazaro Hospital (SLH), the Lung Center of the Philippines (LCP), the Vicente Sotto Memorial Medical Center (VSMMC), and the Southern Philippines Medical Center (SPMC) will also undergo the training in Davao from September 26-30, 2022.

The NGS sequencing data will serve as a vital component in the characterization of human seasonal viruses and zoonotic viruses that can potentially cause disease outbreaks. These data will also be used in the development of vaccines by the Global Influenza Surveillance and Response System (GISRS).

The timely and rapid provision of accurate sequence data shared through publicly accessible databases also directly contributes to the global efforts against Influenza and other respiratory viruses.

“With the advent of the various SARS-CoV-2 subvariants, the Monkeypox virus, and multiple emerging and reemerging infectious diseases (EREIDs), building capacity for sequencing is more relevant than ever. So, we hope that this capacity-building will boost our efforts nationwide via surveillance network in the Philippines,” said RITM Molecular Biology Laboratory Head Dr. Timothy Dizon.

RITM houses PNIC that supports the country’s influenza surveillance by providing continuous, timely, and accurate laboratory results; manpower and technical expertise in responding to influenza outbreaks; and, policy recommendations for influenza prevention and control in the Philippines.

by Allenor Enciso, Communication and Engagement Office