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. 2022 Nov 22;14(12):2601. doi: 10.3390/v14122601

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© 2022 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Maximum-likelihood phylogenetic tree of the HA gene segment. As per the key, H5N1 sequences detected in Botswana between July and September 2021 are highlighted in orange, Eurasian H5N1 sequences detected during 2020 and 2021 are highlighted in blue, and H5N1 sequences detected in Africa between December 2020 and December 2021 are highlighted in purple. Relationships among the Eurasian and African 2020/21 H5 HPAIV strains were inferred by adding the novel sequence data from Botswana to that available on GISAID Epiflu on 25 February 2022. The sequences were then filtered to include only Influenza A virus subtype H5N1 and are rooted to A/Goose/Guangdong/1/1996_|H5N1|_1996-01-01. In September 2022, further H5N1 sequences were added from GISAID for Burkina Faso and from GENBANK for Benin and Lesotho. Sequences were aligned using MAFFT v7.407 and phylogenetic tree inferred using Miyawaki with ultrafast bootstrap node support. Trees were visualised in FigTree v1.4.4.