PAHO and CDC strengthen regional capacities for influenza genomic surveillance through an international bioinformatics workshop

Santiago, Chile, April 28, 2026 (PAHO) - From April 13 to 17, 2026, professionals from National Influenza Centers (NICs) in Chile, Guatemala, Mexico, Panama, Paraguay, and Peru participated in the International Workshop on Bioinformatics for Influenza Genomic Surveillance. The workshop was jointly organized by the WHO Collaborating Center for Surveillance, Epidemiology and Control of Influenza at the United States Centers for Disease Control and Prevention (CDC), the American Association of Public Health Laboratories (APHL), and the Pan American Health Organization (PAHO).

This initiative contributes to strengthening bioinformatics capacities in the Region and expanding the autonomy of NICs to generate, analyze, and share genomic data on influenza viruses promptly. To advance this objective, the workshop focused on strengthening technical capacities for the analysis and interpretation of next-generation sequencing (NGS) data, oriented toward public health decision-making.

Over five intensive days, participants combined theoretical and practical sessions that enabled them to acquire and consolidate competencies in operating systems, command-line use, genome assembly, sequence alignment, phylogenetic analysis, and genomic epidemiology. They were also trained in the use of the bioinformatics tool MIRA, developed by CDC, for assembling respiratory virus genomes from raw sequencing data, facilitating their timely analysis for surveillance purposes.

The training addressed the full cycle of influenza genomic surveillance, including the generation of reports on circulating subtypes and clades, the automation of genomic data processing, and the timely submission of high-quality sequences to global platforms such as GISAID. These capacities are essential to support decision-making processes on influenza vaccine composition, monitor the circulation of subclades, assess antiviral susceptibility, and detect emerging zoonotic influenza viruses or those with pandemic potential. In operational terms, this type of analysis makes it possible to identify changes in circulating viruses and provide timely evidence for public health decision-making at national and regional levels.

As part of the workshop activities, participants, together with representatives from CDC and PAHO, conducted a technical visit to the Institute of Public Health of Chile (ISP), where they toured the Molecular Genetics Reference Laboratory and the National Influenza Center. This activity made it possible to observe the installed capacities in the host country in operation and to strengthen technical exchange among national and regional teams, including experiences on the implementation of genomic surveillance in real-world contexts.

In addition to serving as a WHO Collaborating Center, CDC acts as a sequencing reference laboratory for PAHOGen/RESVIGEN, the regional genomic surveillance network led by PAHO. PAHO reaffirms its commitment to the sustained strengthening of regional capacities in genomic surveillance for influenza and other respiratory diseases, promoting technical cooperation and networking to advance more resilient surveillance systems and greater health security in the Region of the Americas.

Materials and resources from the CDC-developed workshop are publicly available on the event website: https://cdcgov.github.io/id-bioifx-workshop/