Circulation of highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b in highly diverse wild bird species from Peru

Abstract Highly pathogenic avian Influenza virus (HPAIV) has emerged in unprecedented records in recent years. Despite the large reports of cases in Asia, Europe, and North America, little is known about its circulation in South America. Here, we describe the isolation, and whole genome characterization of HPAIV obtained from sampling 26 wild bird species in Peru, representing one of the largest studies in our region. Out of 147 samples analyzed, 20 were positive for detection of avian influenza virus using a qRT-PCR-based assay. Following inoculation into embryonated chicken eggs, fourteen viral isolates were obtained from which six isolates were selected for genome characterization, based on their host relevance. Our results identified the presence of HPAIV H5N1 subtype. Phylogenetic analysis revealed that these isolates correspond to the clade 2.3.4.4b, sharing a common ancestor with North American isolates and forming a novel subclade along with isolates from Chile. Altogether, changes at the amino acid levels compared to their closest relatives indicates the virus is evolving locally, highlighting the need for constant genomic surveillance. This data evidence the chances for spillover events increases as the virus spreads into large populations of immunologically naïve avian species and adding conditions for cross species transmission.