The Philippines is expanding its genomic surveillance efforts as domestic and international mobility continues to rise, bringing heightened risk for respiratory and enteric virus transmission. Public-health agencies are reinforcing systems that monitor influenza, respiratory syncytial virus (RSV), COVID-19, and the enteroviruses that cause hand–foot–and–mouth disease (HFMD), amid a significant increase in cases nationwide.
Increasing Mobility Brings Renewed Public-Health Challenges
Travel volumes have steadily returned to near pre-pandemic levels. According to the Manila International Airport Authority (MIAA), the Ninoy Aquino International Airport (NAIA) handled 3.81 million passengers in November 2023—about 97 percent of its November 2019 traffic. By the first nine months of 2025, NAIA had processed 38.88 million passengers, reflecting robust recovery in both domestic and international travel.
Public-health experts note that higher mobility increases the likelihood of viral transmission in crowded airports, terminals, transport hubs, and urban centers. This underscores why genomic monitoring—first widely deployed for COVID-19—has become a critical tool for detecting emerging viral threats early.
HFMD Surge Increases Need for Enterovirus Monitoring
Beyond respiratory viruses, the Philippines has recorded a significant rise in hand–foot–and–mouth disease (HFMD). As of August 2025, the Department of Health (DOH) registered 37,368 HFMD cases—a seven-fold increase from the same period in 2024.
The sudden rise, heavily affecting daycare centers, young children, and households, highlights the need to strengthen surveillance of enteroviruses. Experts emphasize that genomic data can help determine whether more virulent strains—such as Enterovirus A71 (EV-A71) or Coxsackievirus A16—are circulating. Such strains have caused more severe outbreaks in various parts of Asia.
However, as of the latest publicly available information, routine genomic characterization of HFMD pathogens in the Philippines remains limited. Health authorities and research institutions continue to advocate expanding enterovirus sequencing as part of a multi-pathogen bio surveillance strategy.
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The State of Genomic Capacity in the Philippines
The Philippine Genome Center (PGC), under the University of the Philippines, serves as the country’s main hub for viral genomic sequencing. Established well before the pandemic and expanded during it, PGC and its satellite facilities—including PGC Visayas in Iloilo—have conducted regular sequencing runs for SARS-CoV-2.
The decentralization of sequencing capacity, particularly to regional centers, reduces delays in transporting samples from provinces and strengthens responsiveness to outbreaks outside Metro Manila.
While various academic and private laboratories have upgraded their molecular diagnostic capacity, public records do not confirm the establishment of entirely new government-designated national sequencing centers specifically for respiratory or HFMD surveillance in 2025. Instead, the focus has shifted toward sustaining and expanding existing infrastructure built during the pandemic.
Why Multi-Pathogen Sequencing Matters
Influenza
The Philippines remains part of global influenza surveillance systems such as the Global Influenza Surveillance and Response System (GISRS). Sentinel sites continue to collect samples from patients with influenza-like illness (ILI) and severe acute respiratory infection (SARI), some of which undergo genomic analysis. Sequencing helps detect antigenic drift, lineage changes, and emerging strains that could influence vaccine formulation and public-health advisories.
RSV
A 2024–2025 pilot program by the Research Institute for Tropical Medicine (RITM) identified RSV as one of the leading causes of severe respiratory illness among children under two years old. While diagnostics have expanded, routine whole-genome sequencing of RSV is still limited. Scaling this capacity is important for understanding transmission patterns and predicting seasonal outbreaks.
COVID-19
The country continues to detect SARS-CoV-2 subvariants through routine sequencing. For instance, the Omicron subvariant JN.1 was identified in late 2023, and additional reports in 2024 confirmed detection of other globally circulating subvariants, including those from the so-called “FLiRT” family. As of mid-2025, DOH reports noted no new variant of concern demonstrating increased severity, and vaccines continued to offer strong protection against severe disease.
Enteroviruses (HFMD)
The limited genomic surveillance of HFMD-causing enteroviruses remains a key gap. Experts emphasize expanding molecular typing to determine whether more severe strains are responsible for rising cases.
What Strengthened Genomic Surveillance Requires
Experts outline several priorities to sustain and improve the country’s sequencing capacity:
- Institutionalize multi-pathogen genome sequencing.
Facilities like PGC and RITM must receive long-term support to sequence not only SARS-CoV-2 but also influenza, RSV, and enteroviruses. - Improve specimen logistics and data systems.
Efficient transport of samples, especially from remote provinces, is essential. Strengthening data-sharing protocols ensures that sequencing results quickly reach decision-makers. - Scale up training and workforce development.
More bioinformaticians, epidemiologists, and laboratory technicians are needed to maintain a robust surveillance network. - Increase transparency.
Regularly publishing surveillance bulletins summarizing sequencing data would help inform clinicians, local governments, and the public. - Integrate genomic findings into public-health action.
Sequencing data should guide vaccination strategies, outbreak response, travel advisories, and risk communication—especially during periods of heavy mobility.
A Quiet but Crucial Shield
As more Filipinos travel for reunions, work, tourism, and daily commuting, the risk of importing or spreading viral infections remains ever-present. Strong genomic surveillance—much of it happening behind the scenes—provides early warning signals that help prevent small outbreaks from becoming larger crises.
Thanks to the infrastructure developed during the pandemic and continued efforts by PGC, RITM, sentinel hospitals, and regional laboratories, the Philippines retains the capacity to detect new viral strains and respond with scientific precision. Yet experts warn that this system requires sustained investment. Genomic surveillance often operates quietly, but its ability to detect the unexpected makes it one of the most essential public-health tools today.
Photo by Bernd 📷 Dittrich on Unsplash
