Phylodynamics of avian influenza A(H5N1) viruses from outbreaks in Brazil

Abstract

Our study identified strains of the A/H5N1 virus in analyzed samples of subsistence poultry, wild birds, and mammals, belonging to clade 2.3.4.4b, genotype B3.2, with very high genetic similarity to strains from Chile, Uruguay, and Argentina. This suggests a migratory route for wild birds across the Pacific, explaining the phylogenetic relatedness. The Brazilian samples displayed similarity to strains that had already been previously detected in South America. Phylogeographic analysis suggests transmission of US viruses from Europe and Asia, co-circulating with other lineages in the American continent. As mutations can influence virulence and host specificity, genomic surveillance is essential to detect those changes, especially in critical regions, such as hot spots in the HA, NA, and PB2 sequences. Mutations in the PB2 gene (D701N and Q591K) associated with adaptation and transmission in mammals were detected suggesting a potential zoonotic risk. Nonetheless, resistance to neuraminidase inhibitors (NAIs) was not identified, however, continued surveillance is crucial to detect potential resistance. Our study also mapped the spread of the virus in the Southern hemisphere, identifying possible entry routes and highlighting the importance of surveillance to prevent outbreaks and protect both human and animal populations.

Keywords: Complete genetic characterization, Phylodynamics, Point mutations; Highly pathogenic avian influenza virus; Outbreaks.

Fig. 1

Phylogenetic analysis of highly pathogenic avian influenza A(H5N1) from wild birds, poultry, and mammals, Brazil. Maximum-likelihood method was used for phylogeny of hemagglutinin H5 sequences from avian influenza viruses in IQ-TREE multicore v.1.6.12. Phylogenetic tree was generated with Geneious Prime® 2024.0.3 software and edited with iTOL tool (https://itol.embl.de/). Sequences were aligned by using the MAFFT program in the Geneious Prime® 2024.0.3 software and editor for the same software. We used the best-fitted evolutionary model based on BIC = Bayesian Information Content models; robustness of tree topology was assessed with 1000 bootstrap replicates Green color indicate clustering of strains from Brazil and sequences from this study; “LDDV” indicates the sequences from this study. Non–goose/Guangdong lineage virus strains from Eurasia were outgroups. A, B and C shares a most recent common ancestor with viral lineages of Chile, Uruguay, and Argentina (2022–2024). With 82–92% bootstrap support values, confirming its closest phylogenetic relatedness with the sequences from South American.

Fig. 1

Phylogenetic analysis of highly pathogenic avian influenza A(H5N1) from wild birds, poultry, and mammals, Brazil. Maximum-likelihood method was used for phylogeny of hemagglutinin H5 sequences from avian influenza viruses in IQ-TREE multicore v.1.6.12. Phylogenetic tree was generated with Geneious Prime® 2024.0.3 software and edited with iTOL tool (https://itol.embl.de/). Sequences were aligned by using the MAFFT program in the Geneious Prime® 2024.0.3 software and editor for the same software. We used the best-fitted evolutionary model based on BIC = Bayesian Information Content models; robustness of tree topology was assessed with 1000 bootstrap replicates Green color indicate clustering of strains from Brazil and sequences from this study; “LDDV” indicates the sequences from this study. Non–goose/Guangdong lineage virus strains from Eurasia were outgroups. A, B and C shares a most recent common ancestor with viral lineages of Chile, Uruguay, and Argentina (2022–2024). With 82–92% bootstrap support values, confirming its closest phylogenetic relatedness with the sequences from South American.

Fig. 2

Left: Spatial representation of the possible dissemination routes of H5N1 using the 250 closely related sequences to the Brazilian variant using the Beast 2.0 and SPREAD software. Right: Distribution among Brazilian states of bird and mammal species with NGS analysis.