High pathogenicity avian influenza (HPAI) H5N1 virus detected in brown Skua using portable laboratory while at sea in Antarctica

Abstract

We report the draft genome sequence of a high pathogenicity avian influenza (HPAI) H5N1 clade 2.3.4.4b virus found in a brown skua (Stercorarius antarcticus) on Torgersen Island, which was detected and sequenced in situ using a portable laboratory while in Antarctica.

Keywords: 48 hours; Antarctica; H5N1; HPAI; brown skua; gene sequencing; genome analysis; portable laboratory; rapid tests.

Fig 1

Phylogenetic analysis of a H5N1 HPAI sample taken from a Brown skua on Torgersen Island (red) compared with other publicly available H5N1 clade 2.3.4.4b HPAI genomes from the surrounding Antarctic islands. Reference H5N1 clade 2.3.4.4b HPAI genomes were downloaded from GISAID, followed by extraction of the HA segment for phylogenetic analysis. Alignments were produced using MAFFT v7.490. Evolutionary history was inferred by using the maximum likelihood method and Tamura-Nei model. The tree with the highest log likelihood (−2,808.97) is shown. The percentage of 500 trees in which the associated taxa clustered together is shown next to the branches. Initial trees for the heuristic search were obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise distances estimated using the Tamura-Nei model and then selecting the topology with a superior log likelihood value. The tree is drawn to scale. This analysis involved 22 nucleotide sequences. There were a total of 1,777 positions in the final data set. Bootstrap values below 70 were removed from the final tree. Evolutionary analyses were conducted in MEGA11 (5).