On 2–11 July 2025 Indonesia’s three national polio laboratories and the Ministry of Health (MoH) joined a World Health Organization (WHO)-supported Whole Genome Sequencing (WGS) workshop in Bandung, West Java Province, marking a major step forward in the country’s ability to detect, track and respond to polioviruses.
Led by experts from the United Kingdom’s Medicines and Healthcare Products Regulatory Agency – a Global Specialized Laboratory under the Global Polio Laboratory Network (GPLN) – the training provided hands-on instruction in sequencing the complete poliovirus genome. The WGS workshop came just weeks after Indonesia achieved a significant milestone: the successful interruption of poliovirus circulation, confirmed by the third Outbreak Response Assessment (OBRA-3) in June 2025.
Between November 2022 and July 2024, Indonesia confirmed 15 polio cases across nine provinces. In response, MoH, with WHO and UNICEF support, delivered more than 60 million doses of novel oral polio vaccine type 2 (nOPV2) nationwide and strengthened acute flaccid paralysis (AFP) surveillance, with the outbreak’s formal closure now keenly anticipated.
The 10-day WGS workshop – hosted by the National Polio Laboratory in Bandung – brought together 12 participants from national polio laboratories in Jakarta, Bandung and Surabaya, alongside MoH officials. Training covered the complete workflow, from RNA extraction and semi-nested PCR amplification, to nanopore sequencing, bioinformatics analysis and interpretation, with strong emphasis on quality control.
Crucially, the workshop introduced WGS as an enhancement to the GPLN’s standard diagnostic process, which involves virus isolation, Reverse Transcriptase PCR and partial genome analysis via Sanger sequencing. While effective, Sanger sequencing examines only part of the genome. WGS sequences the entire genome, enabling more precise mutation detection, stronger case linkage and clearer mapping of transmission chains. This is critical for identifying virus origins, guiding targeted immunization and strengthening outbreak containment.
“WGS is not only a laboratory tool but an integral part of disease surveillance,” said Dr. Darmawali Handoko, Head of the National Health Biology Laboratory, MoH. “Genomic changes alone can determine whether a situation escalates, with regional and global implications. This is why building WGS capacity is indispensable, especially as we move into the eradication and elimination phases of diseases.”
Laboratory technicians prepare poliovirus samples for WGS. Credit: WHO/Joshua Harmani
While OBRA-3 confirmed that polio transmission had been interrupted in Indonesia, it also made recommendations to sustain progress, particularly in high-risk areas like Papua, which borders Papua New Guinea. Maintaining high-quality AFP surveillance, improving routine immunization, addressing vaccine hesitancy and introducing the hexavalent vaccine in Papua remain priorities.
“By embedding WGS into routine polio surveillance, Indonesia can act faster and with greater accuracy when polioviruses are detected, reducing the risk of further spread and protecting children from lifelong paralysis,” said Dr Stephen Chacko, Team Lead, Communicable Diseases at WHO Indonesia. “This capacity not only safeguards Indonesia’s polio-free status but also supports the global effort to eradicate the disease.”
The trained laboratory technicians will now apply WGS to select poliovirus isolates, embedding this technology within the national polio surveillance framework. Working with MoH, GPLN and other partners, WHO will continue to support these efforts, ensuring that Indonesia remains ready to detect, investigate and respond to any future threat.
Written by Joshua Harmani, National Professional Officer (VPD Surveillance), WHO Indonesia; Tina Kusumaningrum, National Professional Officer (Laboratories), WHO Indonesia; and Mindo Nainggolan (National Coordinator of Polio Outbreak Response and Measles Rubella Elimination), WHO Indonesia