Preliminary genomic analysis of H5N1 HPAIV from South Georgia
Brown skuas (Stercorarius antarcticus) on South Georgia confirmed positive for H5N1 High Pathogenicity Avian Influenza Virus (HPAIV).
13 November 2023
Suspected avian influenza cases on South Georgia
In October 2023, the National and International (WOAH/FAO) Reference Laboratory for Avian Influenza at the Animal and Plant Health Agency (APHA) in the United Kingdom received samples from staff at the British Antarctic Survey (BAS) based on Bird Island, South Georgia due to suspicion of avian influenza in brown skuas (Stercorarius antarcticus).
Brown skuas (Stercorarius antarcticus) forage within the colonies of other seabirds on South Georgia. Photo credit: A. Corbett-Kuiper.
Laboratory confirmation of H5N1 HPAIV
The samples received at APHA were collected from 3 birds and all were confirmed to be positive for H5N1 high pathogenicity avian influenza virus (HPAIV).
Viral genome sequencing was undertaken, and three genomes were produced which shared 99.86-100% nucleotide identity to each other across all 8 influenza virus gene segments.
Phylogenetic assessment
These sequences were subjected to phylogenetic assessment which demonstrated that the sequences from Bird Island clustered with sequences from South America, particularly Uruguay, Peru and Chile. Analysis of the Bird Island sequences using the USDA H5N1 genotyping tool, GenoFLU, found all 3 sequences were of the B3.2 genotype; a reassortant of the original Eurasian H5N1 that incurred into North America in late 2021, and local North American avian influenza viruses.
Comparison with South American sequences
A review of the publicly available full genome sequences from South America found that the B3.2 genotype was predominant in the region.
The sequences obtained from samples collected on South Georgia have been made available through the GISAID EpiFlu platform (https://gisaid.org) under the following accession numbers: EPI_ISL_18439562, EPI_ISL_18439563 and EPI_ISL_18439564.
Ongoing investigations and collaboration
Further analyses of the sequences from Bird Island are underway and APHA are continuing to work closely with BAS and the Government of South Georgia and the South Sandwich Islands.