Phylogenetic Analysis of H5N1 Genomes

In addition to the virus sequences obtained from foxes and wild birds in the Netherlands in this study, the top five BLAST results for related sequences in Eurasia were included in the phylogenetic analysis. These H5N1 genome sequences were downloaded from the GISAID database (26 (link)). A phylogenetic analysis of the complete genome sequences was performed for each genome segment separately, aligning the virus sequences using MAFFT v7.475 (27 (link)) and reconstructing the phylogeny using a maximum likelihood (ML) analysis with IQ-TREE software v2.0.3 and 1,000 bootstrap replicates (28 (link)). The ML tree was visualized using the R package ggtree (29 (link)). The GISAID sequences used in the phylogenetic analysis are listed in Table S5, in which we acknowledge all of the contributors to the GISAID database.

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Bordes L., Vreman S., Heutink R., Roose M., Venema S., Pritz-Verschuren S.B., Rijks J.M., Gonzales J.L., Germeraad E.A., Engelsma M, & Beerens N. (2023). Highly Pathogenic Avian Influenza H5N1 Virus Infections in Wild Red Foxes (Vulpes vulpes) Show Neurotropism and Adaptive Virus Mutations. Microbiology Spectrum, 11(1), e02867-22.

Publication 2023

Birds Genome H5n1 Tree Virus

Corresponding Organization : Wageningen University & Research

Other organizations : Utrecht University

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Variable analysis

independent variables

Virus sequences obtained from foxes and wild birds in the Netherlands
Top five BLAST results for related sequences in Eurasia

dependent variables

Phylogenetic analysis of the complete genome sequences for each genome segment

control variables

Control variables not explicitly mentioned

controls

Positive control: None mentioned
Negative control: None mentioned

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