Yi-Mo Deng

Despite Antarctica’s geographic isolation, the first incursion of high pathogenicity avian influenza (HPAI) H5N1 was detected in the 2023/24 austral summer. Surveillance for HPAI H5N1 in Antarctica remains patchy due to logistical, financial, and infrastructure challenges, with many suspected cases remaining unconfirmed, and few viral genomes sequences available to date. Through the 2024/25 austral summer we undertook five sampling expeditions to the South Shetland Islands and Antarctic Peninsula facilitated by cruise ships/operators. Across more than 500 faecal environmental samples collected from apparently healthy penguins and marine mammals, we found no detectable evidence of HPAI H5N1. However, HPAI H5N1 was detected in all but one of the skua carcasses sampled, which, in most cases, were found within meters of penguin sub-colonies. All HPAI H5N1 viral genomes sequences from skuas on the Antarctic Peninsula fell within a single lineage, which included those genomes from skuas sampled in the 2024/25 season from the South Shetland Islands. Genomes were in a different clade to those from the Antarctic Peninsula collected in the 2023/24 austral summer. Our results confirm although the prevalence may be low, HPAI H5N1 is established in Antarctica, emphasizing the need for ongoing surveillance to monitor and mitigate threats to wildlife, even in the planet’s most isolated regions.

Background: Genomic surveillance of human seasonal influenza viruses is an essential component of the Global Influenza Surveillance and Response system (GISRS) and informs the recommendations for the seasonal influenza vaccine composition. Phylogenetic analysis of viral genome sequences is used to identify groups of viruses sharing potential antigenic change, and computational models are used to predict which viral variants are likely to circulate at high levels in upcoming seasons. To facilitate discussion and reporting of genetic diversity, as well as to communicate antigen recommendations, up‐to‐date and sufficiently granular definitions of genetic clades are important. Methods: We implemented a nomenclature system for Segments 4 (haemagglutinin) and 6 (neuraminidase) of human Influenza A(H3N2), A(H1N1)pdm09, and Influenza B that dynamically adapts to the diversity of circulating viruses. New subclades were proposed by a clade suggestion algorithm based on criteria including (i) the number of sequences in the group, (ii) the distance from the direct parent clade, and (iii) the weighted number of amino acid substitutions on the branch leading to the common ancestor of the subclade. Results: Algorithmic clade proposals were reviewed and assigned a systematic hierarchical label consisting of a leading letter, followed by numbers (e.g., G.1.3). Names are kept short by aliasing that is collapsing prefixes into unique letters. Subclade definitions are shared openly to promote adoption and tool development. Nextclade is supporting this new nomenclature, and it is being used routinely by the GISRS network. Conclusions: With increasing genomic surveillance, the need for up‐to‐date classification schemes is growing and we hope that the current dynamic proposal will adapt to growing data volumes and aid in simplifying the interpretation of these data.

In Australia and New Zealand, late outbreaks of an A(H3N2) variant virus termed subclade K extended the 2025 influenza season. Subclade K viruses were genetically and antigenically distinct from the 2025 vaccine A(H3N2) strain A/Croatia/10136RV/2023 (H3N2)-like virus and previously circulating subclade J viruses. Subclade K viruses have since been detected in over 34 countries and appear to have spread globally, except in South America. It is thus likely that they will further expand during the northern hemisphere winter 2025/26 season.

Background: Genomic surveillance of human seasonal influenza viruses is an essential component of the Global Influenza Surveillance and Response system (GISRS) and informs the recommendations for the seasonal influenza vaccine composition. Phylogenetic analysis of viral genome sequences is used to identify groups of viruses sharing potential antigenic change and computational models are used to predict which viral variants are likely to circulate at high levels in upcoming seasons. To facilitate discussion and reporting of genetic diversity, as well as to communicate antigen recommendations, up-to-date and sufficiently granular definitions of genetic clades are important. Methods: A nomenclature system for segments 4 (haemagglutinin) and 6 (neuraminidase) of human A(H3N2), A(H1N1)pdm09, and influenza B. Results: We devised a clade suggestion algorithm that proposes new subclades based on criteria including (i) the number of sequences in the group, (ii) the divergence from the directly ancestral clade, and (iii) the number and quality of amino acid substitutions on the branch leading to the common ancestor of the subclade. Algorithmic clade proposals were reviewed and assigned a systematic hierarchical label consisting of a leading letter, followed by numbers (e.g., G.1.3). Names are kept short by aliasing, that is collapsing prefixes into unique letters. Subclade definitions are shared openly to promote adoption and tool development. Nextclade is supporting this new nomenclature and it is being used routinely by the GISRS network. Conclusions: With increasing genomic surveillance, the need for up-to-date classification schemes is growing and we hope that the current dynamic proposal will adapt to growing data volumes and aid in simplifying the interpretation of these data.

Background: Vaccine effectiveness (VE) estimates provide important post‐marketing assessment of how well seasonal influenza vaccines prevent medically attended influenza disease. We present VE estimates for primary care in Australia for the 2017–2019 seasons.Methods: The study used a test‐negative design. Influenza VE was estimated from adjusted logistic regression models comparing the odds of vaccination among influenza‐test‐positive cases and test‐negative non‐cases. Estimates were made overall and separately by influenza type, subtype, lineage and clade and stratified by age group. Antigenic similarity of influenza viruses to vaccine strains was assessed using the haemagglutination inhibition assay, and phylogenetic analysis was performed on sequenced viruses.Results: The study included 2879, 1973 and 3371 general practice patients with swabs collected during 2017, 2018 and 2019 respectively. Influenza A(H3N2) was predominant in 2017 and 2019, while influenza A(H1N1)pdm09 predominated in 2018. VE was estimated at 37% (95% CI 22, 48) for the 2017 season, 53% (95% CI 33, 67) for 2018 and 50% (95% CI 40, 58) for 2019. In general, estimates were higher against A(H1N1)pdm09 and influenza B viruses and lower against A(H3N2) viruses. Across the three seasons, antigenic data identified a greater proportion of A(H1N1)pdm09 and influenza B viruses than A(H3N2) viruses as antigenically similar to the cell‐propagated reference viruses. VE estimates by clade generally indicated higher VE among viruses in the same clade as the vaccine viruses.Conclusions: Influenza VE varied across influenza seasons and by influenza type/subtype. Given the ongoing evolution of circulating influenza viruses, vaccine improvements are needed, especially for influenza A(H3N2).

Influenza virus–specific tissue-resident memory (Trm) CD8 ⁺ T cells located along the respiratory tract provide cross-strain protection against a breadth of influenza viruses. We show that immunization with a single-cycle influenza virus vaccine candidate (S-FLU) results in the deposition of influenza virus nucleoprotein (NP)–specific CD8 ⁺ Trm along the respiratory tract that were more cross-reactive against viral variants and less likely to drive the development of cytotoxic T lymphocyte (CTL) escape mutants, as compared to the lung memory NP-specific CD8 ⁺ T cell pool established following influenza infection. This immune profile was linked to the limited inflammatory response evoked by S-FLU vaccination, which increased TCR repertoire diversity within the memory CD8 ⁺ T cell compartment. Cumulatively, this work shows that S-FLU vaccination evokes a clonally diverse, cross-reactive memory CD8 ⁺ T cell pool, which protects against severe disease without driving the virus to rapidly evolve and escape, and thus represents an attractive vaccine for use against rapidly mutating influenza viruses.

We report in-concert dynamics of 18 key immune parameters, related to clinical, genetic and virological factors, in patients hospitalized with influenza across different severity levels. Influenza disease was associated with correlated increases in IL6/IL-8/MIP-1α/β cytokines and lower antibody responses. Robust activation of circulating T follicular helper cells (cTfhs) correlated with peak antibody-secreting cells (ASC) and influenza heamaglutinin-specific memory B-cell numbers, which phenotypically differed from vaccination-induced B-cell responses. Influenza-specific CD8 ⁺ /CD4 ⁺ T-cells increased early in disease and remained activated during patient recovery. Here, we describe the broadest to-date immune cellular networks underlying recovery from influenza infection, highly relevant to other infectious diseases.