In a globally unprecedented event for polar science and virology, a team of researchers from the University of Chile and the Chilean Antarctic Institute (INACH) has, for the first time, successfully sequenced the complete genomes of the highly pathogenic avian influenza virus (H5N1) found in Antarctic birds.
This discovery, the first direct genetic analysis of this dangerous virus variant, was recently published in the journal Emerging Infectious Diseases, a publication of the U.S. Centers for Disease Control and Prevention (CDC). The achievement marks a milestone in health monitoring on the Antarctic continent.
The study was made possible thanks to samples collected during a mass die, off of Antarctic skuas (Stercorarius antarcticus) that occurred in the 2024 austral summer on James Ross Island, as part of the LX Antarctic Scientific Expedition (ECA 60) organized by INACH. The research was led by Dr. Marcelo González Aravena, researcher at INACH’s Scientific Department, together with Dr. Víctor Neira, professor at the Faculty of Veterinary and Animal Sciences, University of Chile.
“This is the first time the H5N1 virus has been sequenced and genetically characterized in Antarctic birds, allowing us to understand its behavior in an extreme, pristine, and particularly vulnerable ecosystem,” said Neira, who is also the article’s lead author.
The samples were first processed on site and later sequenced in Santiago using state-of-the-art portable equipment. With Oxford Nanopore’s MinION technology, the team succeeded in sequencing six complete viral genomes, all belonging to clade 2.3.4.4b, the same clade responsible for mass die-offs among wild birds, marine mammals, and even humans on multiple continents.
The phylogenetic analysis revealed a high genetic similarity to viruses detected in gulls and sea lions on the South Georgia Islands, confirming a viral migration route from South America to Antarctica.
“This research positions Chile as a leader in genomic surveillance of emerging viruses in polar regions,” said González. “At INACH, we are committed to Antarctic science that not only observes but also responds to global threats within the world’s most fragile ecosystem, one governed by the Antarctic Treaty System, and that contributes to decision-making with data validated in this international forum.”
The genetic analysis identified mutations associated with antiviral resistance and virulence, although no mammalian, adaptive mutations have been detected so far.
The research also involved experts from international centers, including Dr. Rafael Medina from the Emory University Center of Excellence for Influenza Research and Response (USA), who emphasized the pioneering nature of sequencing in such a challenging environment. “Early access to genetic data is key to anticipating the risks of new viral adaptations. This kind of field-based surveillance represents the future of global epidemiology,” said Medina.
Beyond its scientific value, the study demonstrates that with accessible technology, technical training, and international collaboration, it is possible to generate critical knowledge even in the world’s most remote locations. Using portable platforms and efficient methods, the team achieved complete sequencing with moderate costs and high accuracy.
The researchers warn that, given the persistence of the virus in the region during the 2024–2025 season, it will be essential to strengthen surveillance of various species, including penguins, sea lions, and seabirds, and to monitor potential genetic recombination events between Antarctic and South American strains that could lead to new viral lineages.
“Sequencing this virus in Antarctica is not only a technical achievement, it’s also a warning sign and an example that high-impact science for planetary protection can emerge from the Global South,” Neira concluded.
Report from the Chilean Antarctic Institute (INACH)