Highly pathogenic avian influenza A (H5N1) virus outbreak in Peru in 2022-2023

Abstract

Background: An epizootic of highly pathogenic avian influenza A (H5N1) has spread worldwide since 2022. Even though this virus has been extensively studied for many decades, little is known about its evolution in South America.

Methods: Here, we describe the sequencing and characterization of 13 H5N1 genomes collected from wild birds, poultry, and wild mammals in Peru during the genomic surveillance of this outbreak.

Results: The samples belonged to the highly pathogenic avian influenza (H5N1) 2.3.4.4b clade. Chilean and Peruvian samples clustered in the same group and therefore share a common ancestor. An analysis of the hemagglutinin and neuraminidase genes detected new mutations, some dependent upon the host type.

Conclusions: The genomic surveillance of highly pathogenic avian influenza is necessary to promote the One Health policy and to overcome the new problems entailed by climate change, which may alter the habitats of resident and migratory birds.

Keywords: 2022–2023 outbreak; Avian influenza A; Clade 2.3.4.4b; H5N1; HPAI; Sequencing.

Graphical abstract

Fig. 1

Graphical representation of the avian flu (H5N1) outbreak in Peru in 2022–2023 compiled by the National Center for Epidemiology, Disease Prevention, and Control of Peru until August 28, 2023. (A) Number of H5N1-subtype-positive cases is shown by region as a blue gradient, where the different types and frequencies of hosts (poultry and wild birds, dolphin, lion, sea lion) are represented in a circular graph at the edge of each region. There was a wide distribution of positive cases in wild birds and poultry across almost all Peruvian regions, and in sea lions in southern Peru. Specific positive cases were observed in other mammals, such as a dolphin and lion, in the regions of Piura and Junín, respectively. Each type of host is represented in black figures. Asterisks (*) on the map indicate the places of collection of the sequenced sample. (B) Global view of dead animals in Peru as a gray gradient. The frequencies of different types of animals (avian/mammalian) and environments at the collecting sites (beach, island, pna) are depicted in a circular graph. pna: protected natural area. Data were compiled by Agrorural, SERFOR, SENASA, and SERNANP.

Fig. 2

Phylogenetic tree of H5N1 subtype influenza virus hemagglutinin (A) and neuraminidase (B) genes collected during the 2022–2023 outbreak in Peru. Data were downloaded from GISAID up to September 4, 2023. The final figure was obtained with Figtree. Samples sequenced by the INS in Peru are highlighted in bold and colored red. The reference sequence used to root the phylogenetic tree was A/goose/Guangdong/1/1996 (available in the NCBI database under the accession numbers NC_007362.1 and NC_007361.1); the reference is not shown in the figure. The clade containing the Peruvian samples is shaded in orange. Samples from other countries are colored as follows: Ecuador (blue), Colombia (purple), Venezuela (turquoise), and Mexico (green). Samples from Chile, the USA, and other countries are not highlighted. Pictorial representations of each host is shown in the figure. New mutations are highlighted on the appropriate branch.