Detection and phylogenetic analysis of highly pathogenic A/H5N1 avian influenza clade 2.3.4.4b virus in Chile, 2022

Abstract

Highly pathogenic avian influenza (HPAI) A/H5N1 viruses continue to pose a significant threat to animal and human health worldwide. In late 2022, the first confirmed case of HPAI A/H5N1 infection in wild birds in Chile near the Chilean-Peruvian border was reported. Active surveillance by our group in the adyacent Lluta river estuary revealed an increase in A/H5N1 prevalence coinciding with the arrival of migratory birds from the Northern Hemisphere. Genomic analysis of A/H5N1-positive samples demonstrated a close genetic relationship to strains detected in Peru during the same period, which originated from A/H5N1 viruses causing outbreaks in North America. Notably, we identified genetic mutations that did not correlate with known enhanced transmission or binding traits to mammalian receptors. In summary, this study provides valuable genomic insights into the A/H5N1 Clade 2.3.4.4b viruses in wild birds in Chile, emphasizing the need for enhanced surveillance and response strategies to mitigate the threat posed by these highly pathogenic avian influenza viruses in South America.

Keywords: Avian influenza; Chile; HPAI; South America; phylogenetic analysis; wild birds.

Figure 1.

Maximum likelihood phylogeny of the HA genes of H5N1 viruses detected in Chile, 2022. A/H5Nx phylogeny of all H5 clades and 2.3.4.4b clade viruses containing Chilean A/H5N1 viruses and closest relatives. Chilean viruses are highlighted in bold red indicated by a red arrow. H5 clade 2.3.4.4a-g are indicated by coloured shading. Candidate vaccine viruses and their associated H5 clade numbering is shown in bold.