Nationwide genomic biosurveillance
The routine genomic biosurveillance for SARS-CoV-2 in the Philippines through the Philippine Genome Center (PGC), in coordination with the Department of Health (DOH) – Epidemiology Bureau and the Inter-Agency Task Force (IATF) Task Force on COVID-19 Variants began during the last week of December 2020 with the confirmation of VoC (Variant of Concern) B.1.1.7 (“UK variant” or WHO labeled “Alpha” variant) in samples from returning residents. This was followed by the detection of B.1.351 (“South African Variant” or “Beta” variant) and P.1 (“Brazilian Variant” or “Gamma” variant) in the country’s main urban centers. In addition to this, a variant unique to those reported thus far in the GlSAID database was identified in local samples and designated “P.3”, which was later designated as the “theta” variant following the WHO classification scheme for variants of interest (VOI).
Phylogenetic analysis of historical samples submitted to the Philippine Genome Center points towards the origin and circulation of this variant in the Philippine population as far back as October 2020, which raised concerns regarding the implications of this variant on vaccination efforts due to the expression of the documented antibody escape mutation E484K. This was amidst growing concerns regarding repeat infections on top of reports of emerging Variants of Concern (VoC) circulating both locally and globally.
IGSP beginnings
The Immunogenomic Surveillance Program for COVID-19 (IGSP) was established to characterize the clinical presentation and progression of COVID-19 cases based on the VoCs thus identified. This is crucial in documenting the long-term effects of previous exposure to the different VoCs in light of reports of prolonged symptoms post-infection called “long COVID-19”, as well as subsequent infections from more recently identified VoCs. With the identification of the “Philippine variant” P.3, it was imperative for the country to actively document cases of this variant both clinically and genomically to inform both local and international policy efforts directed towards not only monitoring these unique variants, but also evaluating any long-term sequelae and subsequent susceptibility to future SARS-CoV-2 infections. The main objectives of the IGSP include documenting the clinical course of Theta cases concerning WHO-designated VoCs; assessing the serological status of Theta about VoCs, and profiling and comparing the long-term sequelae among individuals infected with Theta and VoCs.
The program was conducted in collaboration with the Department of Health-Epidemiology Bureau (DOH-EB) using a retrospective-prospective cohort design. Participants were recruited from the NCR, Region III, Region IV-A, Region VI, and VII which represent the main geographic locations from which P.3 was identified throughout its propagation. Implementation sites during the study are the UP System Philippine Genome Center (PGC), Vicente Sotto Memorial Medical Center (VSMMC), Teresita L. Jalandoni Provincial Hospital (TLJPH), and West Visayas State University Medical Center (WVSUMC).
Project Leader:
Cynthia P. Saloma, PhD
Project Site Investigator:
Marc Edsel C. Ayes, MD
Implementing Agency:
UP System – Philippine Genome Center (PGC)
Y3 (2023-2024)
IGSP Core Research Team
Paolo S. Taracatac – Science Research Specialist I
Meryl Rose Q. Asa – Science Research Specialist I
Jenny Rose C. Manuel – Project Development Officer I
Jasmin V. Lee – Science Research Assistant
Juverlyn Joy D. Panagdato – Science Research Assistant
Visayas Site Investigators:
Ruby O. Rusia-Uy, MD
Dolores Rommela T. Ruiz, MD
Aretha Ann C. Gacutan-Liwag, MD
Y1 (2021-2022)
IGSP Core Research Team
Maricris M. Macasinag – Science Research Specialist I
Meryl Rose Q. Asa – Science Research Specialist I
Katrina T. Tagasa – Project Development Officer I
Emily G. Padul – Science Research Assistant
Elaiza Camille T. Pigao – Science Research Assistant
Jhassiy B. Layacan – Science Research Assistant
Visayas Site Investigators:
Ruby O. Rusia-Uy, MD
Dolores Rommela T. Ruiz, MD
Aretha Ann C. Gacutan-Liwag, MD
Y2 (2022-2023)
IGSP Core Research Team
Maricris M. Macasinag – Science Research Specialist I
Meryl Rose Q. Asa – Science Research Specialist I
Danica Abigail B. Velasco – Project Development Officer I
Paulin Shean L. Garcia -Science Research Assistant
Jasmin V. Lee -Science Research Assistant
Visayas Site Investigators:
Ruby O. Rusia-Uy, MD
Dolores Rommela T. Ruiz, MD
Aretha Ann C. Gacutan-Liwag, MD
Program updates
The IGSP 1 program, with IGSP 2 and 3 conducted a program review on August 8, 2024 (In photos above), to discuss updates, problems encountered, accomplishments, and plans as it nears completion.
As of October 2, 2024, the IGSP 1 program proponents published an open access article titled: Long-term COVID-19 Sequelae by Theta and SARS-CoV-2 Variants in a Philippine Cohort, authored by Dr. Cynthia P. Saloma, Dr. Marc Edsel C. Ayes, Paolo S. Taracatac, and Meryl Rose Q. Asa, published in Frontiers in Medicine under the Infectious Diseases: Pathogenesis and Therapy section.
The study was conducted as a longitudinal observational study involving four regions, Metro Manila, CALABARZON, Western Visayas, and Central Visayas, which represent the main epicenters of the pandemic with the highest probability of encountering a P.3 variant based on existing identification of case variants.
