The Research Institute for Tropical Medicine (RITM) hosted a site visit for the experts from the Centre for Pathogen Genomics of the Peter Doherty Institute for Infection and Immunity (Doherty Institute) last February 14, 2023.
According to Doherty Institute Microbiological Diagnostic Unit Public Health Laboratory Director Prof. Ben Howden, their team was tapped by the World Health Organization to support the Department of Health Epidemiology Bureau towards the establishment of a Philippine Genomic Surveillance Consortium.
“The establishment of a Philippine Genomic Consortium under the leadership of the Department of Health will foster better and greater contribution to science by the different member units leading to a systematic correlation between genome sequencing and clinical outcomes,” said RITM OIC-Director Atty/Dr. Ana Liza H. Duran.
The visit aimed to gather an understanding of RITM’s infrastructure and capacity for pathogen genomics through collaborative discussion on how genomics has been implemented in the Institute’s laboratories. RITM Molecular Biology Laboratory (MBL) Head Dr. Timothy John Dizon discussed the Institute’s genomics capacity primarily talking on behalf of MBL – RITM’s core facility for sequencing and bioinformatics.
Currently, MBL operates two (2) laboratory suites for polymerase chain reaction (PCR) and one (1) general post-PCR laboratory suite. These laboratories house first, second, and third generation sequencing platforms such as the ABI 3500 Genetic Analyzer, Illumina MiSeq, Oxford Nanopore Tech GridIon, Oxford Nanopore Tech Mk1c, and Oxford Nanopore Tech MinIon.
The Bioinformatics Team and Data Management Team of MBL perform targeted regional-based sequencing and targeted whole genome sequencing through different activities, but with reagent supply and manpower as limiting factors.
“Even before the pandemic, RITM has been active in sequencing through research.” said Dr. Dizon as he explained how MBL’s sequencing activities has expanded to include surveillance and investigation activities as well.
Apart from research purposes, MBL runs sequencing for surveillance activities of influenza-like illness (ILI), severe acute respiratory infection (SARI), tuberculosis (TB) drug resistance, and HIV drug resistance. Sequencing also enabled MBL to confirm the first detected case of Influenza A(H1) and MERS-CoV; conduct metagenomics of Monkeypox; and investigate diseases of unknown etiology such as the capillaria philippinensis infection in Davao.
“The expertise built from this foundation allowed us to translate sequencing technologies to public health response,” explained Dr. Dizon.
Dr. Dizon also highlighted the sequencing activities carried out by the different laboratories in the Institute – the Antimicrobial Resistance and Surveillance Reference Laboratory (ARSRL) on genomic studies on antimicrobial resistance; the Special Pathogens Laboratory (SPL) on genomic epidemiology of rabies; the National TB Reference Laboratory (NTRL) on genomic drug resistance of TB; and the Virology Department on wastewater environmental surveillance and ILI-SARI expansion.
The five (5) national reference laboratories (NRLs) of RITM engage in genomic sequencing – MBL, ARSRL, SPL, NTRL, and Virology will actively participate in the activities of the project and provide necessary information to Doherty Institute towards the development of strategies and governance structures for the consortium.
“The integration of genomics into our present healthcare system is progress that will benefit the Filipino people,” said Atty/Dr. Ana Liza H. Duran.
by Allenor Enciso